Single Nucleotide Polymorphisms and Insertion–Deletions for Genetic Markers andAnchoring the Maize Fingerprint Contig Physical Map

I. Vroh Bi,* M. D. McMullen, H. Sanchez-Villeda, S. Schroeder, J. Gardiner,M. Polacco, C. Soderlund, R. Wing, Z. Fang, and E. H. Coe, Jr.

ABSTRACTSingle nucleotide polymorphisms (SNPs) and insertion–deletions

(InDels) are becoming important genetic markers for major cropspecies. In this study we demonstrate their utility for locating finger-print contigs (FPCs) to the genetic map. To derive SNP and InDelmarkers, we amplified genomic regions corresponding to 3000 unigenesacross 12 maize (Zea mays L.) lines, of which 194 unigenes (6.4%)showed size polymorphism InDels between B73 and Mo17 on agarosegels. The analysis of these InDels in 83 diverse inbred lines showedthat InDels are often multiallelic markers in maize. Single nucleotidepolymorphism discovery conducted on 592 unigenes revealed that44% of the unigenes contained B73/Mo17 SNPs, while 8% showedno sequence variation among the 12 inbred lines. On average, SNPsand InDels occurred every 73 and 309 bp, respectively. Multiple SNPswithin unigenes led to a SNP haplotype genetic diversity of 0.61 amonginbreds. The unigenes were previously assigned to maize FPCs byovergo hybridization. From this set of unigenes, 311 (133 SNP and178 InDel) loci were mapped on the intermated B73 3 Mo17 (IBM)high-resolution mapping population. These markers provided un-ambiguous anchoring of 129 FPCs and orientation for 30 contigs. TheFPC anchored map of maize will be useful for map-based cloning, forgenome sequencing efforts in maize, and for comparative genomicsin grasses. The amplification primers for all mapped InDel and SNPloci, the diversity information for SNPs and InDels, and the corre-sponding overgoes to anchor bacterial artificial chromosome (BAC)contigs are provided as genetic resources.

MAIZE, one of the most important crops in the world,is a diploid species with an estimated haploid ge-

nome size of 2500 Mb, and a high level of sequence com-plexity due to the abundance of multiple families of re-petitive elements (SanMiguel et al., 1996; Myers et al.,2001). Knowledge of the maize genome will allow theimprovement of desired traits by refining gene isolationand molecular breeding strategies. Molecular markersprovide a means to estimate diversity, to assess geneticrelationships, and to map genes underlying important

agronomic traits in crop species. The utility of DNAmarkers for determining relationships and genetic simi-larity in maize was reported for DNA markers such asrestriction fragment length polymorphism (RFLP) andfor simple sequence repeat (SSR) (Taramino and Tin-gey, 1996; Smith et al., 1997; Senior et al., 1998; Bernardoet al., 2000, Romero-Severson et al., 2001).

Sequence variants of SNPs and/or InDels are themarkers of choice for genotyping and mapping becauseof their abundance and amenability to high-throughputscreening. Furthermore, SNPs and InDels can contrib-ute directly to a phenotype (Thornsberry et al., 2001) orthey can associate with a phenotype as a result of linkagedisequilibrium (Daly et al., 2001). Despite the extensiveuse of SNPs to study human genetic disorders, there havebeen fewer extensive surveys of SNPs in plants (Tenail-lon et al., 2001). Previous studies inmaize indicated, how-ever, that SNPs and InDels occur at a relatively highfrequency in maize genes (Rafalski, 2002; Bhattramakkiet al., 2002; Batley et al., 2003a), and in flanking regionsof maize microsatellites (Matsuoka et al., 2002; Mogget al., 2002; Batley et al., 2003b). Single nucleotide poly-morphism discovery projects routinely identify InDelpolymorphisms that can be used as diagnostic or map-ping tools by analyzing size polymorphisms of polymer-ase chain reaction (PCR) products on agarose gel, as wellas SNPs that can be mapped by a number of assay sys-tems (Kwok 2000).

Integrated genetic and physical genome maps are es-sential for map-based cloning, comparative genomics,and as templates for genome sequencing efforts. A pri-mary goal of the Maize Mapping Project (MMP) is todevelop an integrated genetic and physical map of maizeto enable the cloning of maize genes controlling pheno-types and crop productivity. Positioning genes to chro-mosomal location is important for establishing correla-tion with phenotype, thus facilitating our understandingof biochemical pathways and biological mechanismscontrolling agronomically important traits (Davis et al.,1999; Matthews et al., 2001). The MMP has assembleda high-resolution genetic map for the intermated B73 3Mo17 (IBM) population (Lee et al., 2002) consisting of»1000 RFLP, and »1000 SSR markers (MaizeGDB,www.maizegdb.org, verified 4 Aug. 2005). Many of theRFLPs and SSRs were generated from EST sequences(Davis et al., 1999; Sharopova et al., 2002), and there-fore, directly mark the position of candidate genes for

I. Vroh Bi, Inst. for Genomic Diversity, Cornell Univ., Ithaca, NY14853; M.D. McMullen, M. Polacco, and E.H. Coe, Jr., AgronomyDep., Plant Sciences Unit, Univ. of Missouri, Columbia, MO, andUSDA-ARS Plant Genetics Research Unit, Columbia, MO 65211;H. Sanchez-Villeda, S. Schroeder, and Z. Fang, AgronomyDep., PlantSciences Unit, Univ. of Missouri, Columbia, MO 65211; J. Gardiner,BIO5 Inst., Univ. of Arizona, Tucson, AZ 85721; C. Soderlund, Ari-zona Genomics Computational Lab., Univ. of Arizona, Tucson, AZ85721; R. Wing, Arizona Genomics Inst., Univ. of Arizona, Tucson,AZ 85721. Research was performed at the University of Missouri,Columbia, and was funded by NSF Grant DBI# 9872655 to the Univer-sity of Missouri. Received 6 Dec. 2004. *Corresponding author (biv2@cornell.edu).

Published in Crop Sci. 46:12–21 (2006).Genomics, Molecular Genetics & Biotechnologydoi:10.2135/cropsci2004.0706ª Crop Science Society of America677 S. Segoe Rd., Madison, WI 53711 USA

Abbreviations: BAC, bacterial artificial chromosome; cM, centimorgan;FPC, fingerprint contig; InDel, insertion–deletion polymorphism;MMP, Maize Mapping Project; PCR, polymerase chain reaction; PIC,polymorphic information content; RFLP, restriction fragment lengthpolymorphism; SNP, single nucleotide polymorphism; SSR, simplesequence repeat.

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phenotypes and traits. The parents of the IBM popula-tion, B73 and Mo17, represent the two major heteroticgroups of U.S. maize germplasm, namely Stiff Stalk(B73) and non-Stiff Stalk (Mo17). The IBM population(Lee et al., 2002) includes 302 recombinant inbred linesthat underwent four generations of random mating atthe F2 stage. The combination of a large number of linesand the map expansion due to the randommating gener-ations result in a genetic map resource with approxi-mately 17 times the resolving power of the prior maizemap standard (Coe et al., 2002).

To develop the resources for physical mapping, threeBAC librairies representing approximately 27-fold ge-nome coverage were constructed from the inbred lineB73.HindIII fingerprinting of all three libraries and con-tig assembly using FPC software (Soderlund et al., 2000)are being performed at the University of Arizona (Coneet al., 2002; www.genome.arizona.edu/fpc/maize, veri-fied 4 Aug. 2005). The IBM markers have been hybrid-ized to the fingerprinted BACs and the BAC-markerassociations have been entered into FPC. This anchorsand orders contigs based on the genetic information,hence, providing an integrated genetic and physical map.

Recently, .10 600 maize unigenes were used as thesequence source for overgo probes that were hybridizedto high-density BAC filters (Gardiner et al., 2004).These probes identified BACs corresponding to .9300unigenes. The mapping strategy adopted by the MMP in-cluded, in silico correspondence, BAC pooling to anchormapped markers, and the use of SNPs/InDels as a com-plementary tool to anchor unmapped unigenes has beenoutlined previously (Cone et al., 2002). Although a num-ber of the FPCs containing overgo hybridizations werelocated on the genetic map by sequence similarity of theunigene sequences to RFLPor SSR loci on the IBMmap,or by the BAC pooling strategy (Yim et al., 2002), themajority of the unigenes www.agron.missouri.edu/files_dl/MMP/Cornsensus/) are currentlywithout a geneticmapposition. To speed integration of the maize genetic andphysical maps we have undertaken a mapping approachto place unigenes that contain B73/Mo17 polymorphismon the IBM genetic map through SNPs or InDels, therebyanchoring the corresponding contigs.

The goals of the present research are (i) to analyzethe utility of InDels identified within the MMP and ad-dress how these InDels can serve as general geneticmarkers for the maize research community; (ii) to con-duct physical mapping of unigenes using SNPs and In-Dels to anchor BAC contigs to the genetic map; and(iii) to disseminate the maize SNP and InDel resourcesto the scientific community.

MATERIALS AND METHODS

Plant Materials

The genomic DNA from 12 inbred lines was used for SNPand InDel discovery. Among the 12 lines, B73 and Mo17 arethe parents of the IBM population (Lee et al., 2002). Four ofthe lines, Tx303, CO159, T218, and GT119, are the parentsof two additional SSR mapping populations (Sharopova et al.,2002). The lines NC7A, Mp708, and Tx501 were chosen to fur-

ther broaden the germplasm examined. The line W22R-scm2was included because of its extensive use by many maizegeneticists. Illinois High Oil (IHO) and Illinois Low Oil (ILO)were added as part of a collaboration project on applicationto agronomic trait analysis. The SNPs and InDels that werepolymorphic between B73 and Mo17 were genotyped in 286individuals of the IBM population (Lee et al., 2002, Sharopovaet al., 2002). Eighty-three maize inbred lines that representmuch of the diversity inmaize (Remingtonet al., 2001)wereusedto assess InDel diversity (Supplemental Table 1). The origin andthe composition of the 83 lines are described at http://www.maizegenetics.net/germplasm/lines.htm (verified 4 Aug. 2005).

Amplification of Genomic DNAand Sequence Analysis

The unigene set www.agron.missouri.edu/files_dl/MMP/Cornsensus/, verified 4 Aug. 2005) was generated at DuPontusing publicly available maize ESTs to seed their proprietaryEST collection (Cone et al., 2002, Gardiner et al., 2004). The39-untranslated regions (39-UTR) of unigenes were targetedto design PCR primers that amplify about 300 to 500 bp, usingPrimer3 (Whitehead Institute, Cambridge, MA). All PCR re-actions were performed using a PTC-225 thermocycler fromMJ Research (Watertown, MA). The following touchdownPCR program was used to amplify all the unigenes in the sameconditions: 10 cycles of 1 min at 948C, 1 min at 658C with218Cincrement per cycle, and 90 sec at 728C, followed by 35 cyclesof 1 min at 948C, 1 min at 558C, and 90 sec at 728C. The PCRamplification of unigenes was confirmed on 2% SFR agarosegels (Amresco, Solon, OH) stained by ethidium bromide.

Large InDels, visible on a 2% SFR agarose gel (Amresco,Solon, OH) between B73 and Mo17, were further analyzedto assess the polymorphic information content (PIC) of eachInDel in the 83 inbred lines listed in Supplemental Table 1.The PIC values were calculated using the formula PIC 5 1 2Oi51 to n 3 fi2, where fi is the frequency of the ith allele, andn is the number of alleles (Smith et al., 1997).

Loci polymorphic due to InDels detectable on agarose gelsbetween B73 and Mo17 during primary screening were PCR-amplified in 286 individuals of the IBM population, and geno-types were visually determined directly from agarose gels.Primers that did not reveal InDels between B73 andMo17 andgave consistent, single product amplification in all 12 lines wereadvanced to the sequencing phase for SNP and short InDeldiscovery. Nucleotide diversity parameter p (Tajima 1983) andhaplotype diversity were analyzed using the DnaSP program(Rozas et al., 2003).

Identification of Sequence Variantsand Data Management

A single PCR fragment per unigene was sequenced on bothstrands. Only SNPs that occurred in at least two of the 12 inbredlines were considered for mapping to minimize sequencingerrors and PCR artifacts. Sequence variants were highlightedas described in Fig. 1, and SNP interrogation primers weretypically designed with a 50–618C annealing temperature usingthe Oligo Analyzer (v. 2.0, IDT, San Jose, CA). Oligonucleo-tide primers were synthesized by MWG Biotech, Inc. (HighPoint, NC).

Bioinformatics routines developed to process data in theSNP project required integration of existing programs withcustom PERL and Visual Basic scripts for sequence alignmentand quality evaluation, automated detection of sequence vari-ants and their position in the sequence, and generation ofmapping files (Fig. 1). The SNP discovery and mapping pipe-

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13VROH BI ET AL.: MAIZE FINGERPRINT CONTIG PHYSICAL MAPANCHORING

line was integrated into the Laboratory Information Manage-ment System (LIMS) of theMMP (Sanchez-Villeda et al., 2003).

Multiplex Single Nucleotide Polymorphism AssaysThe approach for determination of SNP genotypes has seven

steps: (i) separate PCR amplification of each unigene, (ii)pooling of up to six different unigene PCR products for simul-taneous detection of sequence variants, (iii) exonuclease andphosphatase digestion, (iv) multiplex SNP primer extensionreaction, (v) second phosphatase digestion, (vi) resolving la-beled interrogation primers on anABI PRISM 3700 Sequencer,and (vii) analysis of data with GeneScan and Genotyper soft-ware (Applied Biosystems, Forster City, CA). Sequence vari-ants detected by sequence alignment were first validated inthe parental lines B73 and Mo17 before determining genotypesin the IBM population following the manufacturer’s protocolfor the SNaPshot Kit (Applied Biosystems, Forster City, CA).The multiplex SNP extension consisted of a 0.5-mL aliquot ofthe enzyme-treated mix per individual SNP and the extensionproducts were resolved on an ABI PRISM 3700 Sequencer(Applied Biosystems, Forster City, CA).

Linkage MappingGenotypes for loci exhibiting SNPs and/or InDels between

B73 and Mo17 were determined for 286 individuals of theIBM population. Linkage mapping was conducted using Map-maker/EXP version 3.0b (Lander et al., 1987) on a UNIX plat-form. The SNP and the InDel loci were integrated into aframework IBM map consisting of 247 RFLP and SSR loci.Markers were assigned to chromosomes with a minimum LODscore of 15 using the assign command. The SNP and InDelloci were ordered on the chromosomes with the build (LOD 3)and place (LOD 2) commands. Map distances were calculatedusing the Haldane mapping function.

RESULTSOptimization of Single Nucleotide

Polymorphism ReactionsAt the beginning of the genotyping process, it was nec-

essary to optimize reaction conditions and determine

the number of SNPs per multiplex reaction. The DNAof 286 individuals of the mapping population was ar-rayed into three 96-well plates. After PCR amplification,plates of different unigenes of a given multiplex groupwere bulked into final plates for enzyme treatment be-fore use in SNP reactions. In a six-plex reaction, thisresults in avoiding enzyme treatment for 15 plates permultiplex reaction. For the number of SNPs per multi-plex reactions, we tested three- to eight-plex. Underour conditions, we found that the maximum numberof amplicons per multiplex reaction to achieve a goodresolution of SNP peaks on an ABI 3700 capillary se-quencer was six. In this case, the maximum volume ofmultiplex reaction analyzed on the ABI 3700 was 3 mLto keep the background noise at the minimum level.To assess the accuracy of the genotyping and mappingprocess, the genotype determination process was re-peated at three different SNPs, in two different multi-plex reactions for three unigenes; AY110160 on chromo-some 1, AY110063 on chromosome 5, and AY109644on chromosome 7. For each unigene, both SNPs mappedto the same genetic location.

Maize SNPs and InDels as Genetic MarkersGenomic regions corresponding to 3000 unigenes were

screened by PCR amplification across 12 maize lines.Of these unigenes, 194 (6.4%) showed size polymor-phism on agarose gels between B73 and Mo17 due toInDels, herein called large InDels, as opposed to short-length InDels that were present in sequences but didnot result in visually obvious size polymorphism on 2%SFR (Amresco, Solon, OH) agarose gels. Accounting forlarge and short InDels resulted to an average of oneInDel every 309 bp. Since the first objective of this re-search was to anchor the maize FPCs, unigenes showinglarge InDels between B73 andMo17were not sequenced.

Fig. 1. Pipeline for polymerase chain reaction amplification of unigenes, sequencing, and data processing for genotyping and mapping singlenucleotide polymorphisms and insertion–deletion loci.

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Rather, they were genetically mapped by agarose gelscreening of 286 individuals of the IBM population.

We conducted SNP discovery on the first set of 592unigenes sequenced in the project. The analysis showedthat 260 unigenes (44%) contained B73/Mo17 SNPs,while 8%of the unigenes did not show any polymorphismamong the 12 inbred lines. On average, 5.5 sequencevariants occurred per unigene, with SNPs and InDelsoccurring every 73 bp and 309 bp, respectively. A pre-vious study in maize found a frequency of one SNPevery 70 bp, and one InDel every 160 bp (Rafalski et al.,2001). To assess the utility of SNPs as genetic markers,more detailed analysis was conducted on 470 unigeneshaving aligned sequence longer than 200 nucleotidesacross the 12 lines. The genetic diversity (p, the averagepairwise difference) assessed in all the 470 unigene align-ments varied from 0 to 0.016, with an average of 0.009.Individual SNP are almost always biallelic, leading to atheoretical maximum genetic diversity level of a singleSNPmarker of 0.5.However, when combinations of SNPspresent in the 470 unigenes were used to derive allelehaplotypes the genetic diversity range from 0 to 1, with anaverage of 0.61. This range of SNP haplotype diversitycompares favorably with the genetic diversity of RFLPand SSR markers, and demonstrates that SNPs can behighly informative across maize germplasm when ana-lyzed and used at the haplotype level. Unigenes withthree haplotypes were the most frequent, with everyclass from 1 to 12 represented (Fig. 2).

To assess the discriminatory power of InDels as mo-lecular markers, 173 of the 194 large InDels identifiedbetween B73 and Mo17 were PCR-amplified in 83 di-verse inbred lines (Supplemental Table 1). Figure 3 showsan example of PCR amplification in unigene AY104252

in a set of these inbred lines. The 173 markers detecteda total of 539 alleles among the 83 inbred lines. Thenumber of alleles per unigene varied from 2 to 6 withthe three-allele class (39.8%) as the largest (Table 1).These results showed that InDels are often multiallelicmarkers in maize. The PIC values for these InDel mark-ers for the 173 unigenes ranged from 0.04 to 0.76, withan average value of 0.47 (Fig. 4). For assessment of SSRsin the same germplasm, one SSR was chosen per chro-mosome and tested against the 83 inbred lines. Thenumber of SSR alleles varied from 2 to 5 and PIC valuesranged from 0.22 to 0.73, with a mean of 0.54, onlyslightly higher than that of the large InDel markers.Information on allele number, PIC values, overgo iden-tification, and sequence of PCR primers are given inSupplemental Table 2 for each InDel marker.

Genotyping of SNPs and InDelsin the IBM Population

Using one SNP interrogation primer per unigene, wetested 260 unigenes on B73 and Mo17, the parental linesof our IBM mapping population, to validate the SNPs.The B73 and Mo17 genotypes for 246 (95%) SNPs werein concordance with the SNPs predicted by the sequenc-ing data. Among the validated SNPs, 133 were used todetermine genotypes in 286 individuals of the IBM popu-lation by multiplex primer extension assays. The geno-types of 178 unigenes displaying large InDels betweenB73 and Mo17 were scored also on the IBM populationby direct size polymorphism on 2% SFR (Amresco,Solon, OH) agarose gels. Therefore, a total of 311 unigeneloci (represented by 178 InDel and 133 SNP markers)were derived for placement on the IBM genetic map viathe LIMS (Sanchez-Villeda et al., 2003) by automateddata processing and mapping.

Anchoring FPCs on the IBM Genetic MapThe 311 maize unigenes genotyped in this study were

mapped relative to a framework of 247 genetic markers

Fig. 2. Distribution of single nucleotide polymorphism haplotypeclass among 470 maize unigenes analyzed for sequence diversity.

Fig. 3. Profile of a B73/Mo17 insertion–deletion marker in 2% SFR(Amresco, Solon, OH) agarose gel for unigene AY104252 showingthree alleles in diverse inbreds of maize.

Fig. 4. Distribution of polymorphic information content values for173insertion–deletion markers tested in 83 diverse inbreds of maize.

Table 1. Distribution of allele class for 173 InDel markers testedin 83 diverse inbreds of maize.

Allele class No. of InDels Frequency

%2 47 27.13 69 39.84 42 24.25 11 6.36 4 2.3

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evenly distributed across the 10 maize chromosomes, thustotaling 558 markers (Fig. 5). The genetic map spans 5630centimorgans (cM), with the number of mapped unigenesranging from21on chromosome9 to 54 on chromosome1.

The mapped unigenes were evaluated to determinewhich might serve to anchor contigs to the genetic map.The 311 unigenes mapped in this study provided unam-biguous anchoring of 129 contigs by association withovergo probes used for BAC hybridization (Fig. 5). Theunigenes that did not provide unambiguous contig as-signment resulted from overgo hybridizations that eitherfailed to identify a contig, or identified multiple contigs(underlinedmarkers in Fig. 5). Themultiple contigs iden-tified by a single overgo may represent duplicate generegions, or contigs that should be merged during manualediting. In 33 cases, two or more adjacent unigenesidentified a single contig (Fig. 5), allowing 30 contigs tobe oriented relative to the genetic map. The remainingthree contigs correspond to off-framemarkers, and there-fore await the precise placement of theses unigenes fororientation. These results allowed a physical-to-geneticratio to be calculated for 33 regions distributed through-out the 10 chromosomes, from one contig on chromo-some 5 and chromosome 9, to seven contigs on chromo-some 4. The genetic-to-physical distance varied from23.1 to 1143 kb cM21, where the physical distance is mea-sured in the FPC metric CB (consensus band) units,which is approximately 4096 bases per CB. Thus, genetic-to-physical distance showed a variation of almost twoorders of magnitude. It is worth noting that the geneticmap of IBM is expanded nearly fourfold relative to astandard genetic map (Coe et al., 2002; Sharopova et al.,2002); therefore, these size estimates would be expectedto be about four times greater on a standard genetic map.

The amplification primers for all mapped InDel andSNP loci and the interrogation primers for SNP loci areprovided in Supplemental Table 3.

DISCUSSIONIn this study SNP discovery was performed on 592

genes across 12 maize inbred lines. The results confirmthose of earlier reports (Tenaillon et al., 2001; Rafalskiet al., 2001; Batley et al., 2003a) that both SNP andInDel frequency in maize is very high (one SNP every73 bp and one InDel every 309 bp). This level of poly-morphism is greater than other crop species examinedto date such as rice (Oryza sativaL.) (one SNPper 268 bp;Shen et al., 2004) and soybean [Glycine max (L.) Merr.](one SNP per 328 bp; Zhu et al., 2003). Although onlya single »300 sequence alignment for each gene was ob-tained, 92% exhibited sequence polymorphism, indicat-ing that an SNP strategy will permit genetic mappingof essentially any maize gene of interest. Although themaize genome contains many duplicate genes and genefamilies, these did not present a major problem in geno-typing assays because the same primers were used forthe amplification of genotyping fragments as used in theinitial sequencing. Primer sets that amplified multiplegenes were detected by the presence of multiple frag-ments in screening before sequencing or near identical

paralogs were identified by the presence of heterozy-gous bases within inbred lines. Primer sets yielding eitherof these problems are excluded from use in SNP geno-typing assays.

The integration of genetic and physical maps, which isdone by locating the FPCs on the genetic map, is a com-plex task in eukaryotic genomes such as maize. Throughthe use of SNPs and InDels as complementary tools toBAC pooling and in silico anchoring in the MMP, wehave placed 311 unigenes of maize onto the IBM geneticmap, among which 293 unigenes (94%) are assigned byovergo hybridization to one or more contigs. Of theseunigenes, 167 (54%) correspond with overgo probes thathybridized to fingerprinted BACs, providing unambigu-ous locations for the corresponding FPCs on the geneticmap of maize. Contigs associated with the remaining126 unigenes were directed toward the manual editingpipeline for anchoring. Only 18 unigenes (6%) failed toidentify contigs, probably because of the failure of overgohybridization. These results clearly demonstrate the powerof SNP and InDel analysis to provide genetic markersfor maize genetic and physical map integration. The studyfurther shows that in addition to the traditional BAC-endsequencing, SNPs and InDels can be used to orient contigsor to confirm contig orientation on a transcript map.

Thirty-three contigs, anchored by two or more uni-genes each, provided the relationship between physicaland genetic distance at the anchored points for all 10maize chromosomes. The present results show that thegenetic to physical distance in maize varies more thanan order of magnitude. That 311 markers identified 33pairs of linked markers within the »1600 contigs as ofJune 2004 suggests that much of the recombination inmaize may occur in small physical regions. This agreeswith results from studies on recombination rates withinthe bronze1 (Dooner, 1986), anthocyaninless1 (Brownand Sundaresan, 1991), and waxy1 (Okagaki and Weil,1997) loci. Because the IBM population underwent suc-cessive rounds of intermating, differences in recombina-tion rates between regions should be magnified as eachregion accumulated recombination events in each gen-eration. Thus, a more nonuniform distribution of recom-bination is expected for the IBM map than for standard,one-generation maps (Sharopova et al., 2002). The an-choring and ordering of more contigs will give us a com-prehensive comparison between the genetic and the phys-ical map distances in maize.

The unambiguous anchoring of FPCs to the IBM ge-netic map is the main focus of our SNP project. We con-tinue to sequence and map unigenes through SNPs andInDels with the objective of mapping 1000 unigenes tothe IBM genetic map. The maize FPC map has now ad-vanced to the state that we can focus our sequencing andSNP mapping efforts solely on unigenes that identifysingle contigs. This will allow all mapped loci to serveas contig anchor points. These data are being integratedinto an iMap for public display www.maizemap.org, veri-fied 4 Aug. 2005). In addition to the detailed informa-tion on the SNPs and InDels provided in Supplemental

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Fig. 5. Integrated genetic and physical map of the intermated B73 3 Mo17 (IBM) population based on single nucleotide polymorphisms (SNPs)and insertion–deletion (InDel) markers with the fingerprint contigs of June 2004. The types of markers (SNP or InDel) used to map the uni-genes are given in Supplemental Table 3. Bars are bacterial artificial chromosome (BAC) contigs detected by two or more adjacent markers.The BAC contigs associated to unigenes are noted (ctg#). Unigenes that detected several BAC contigs are underlined. Off-frame markersare in italic, and markers that are not listed in Supplemental Table 3 are the framework markers used to assign SNP and InDel markers tomaize chromosomes.

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Tables 2 and 3, a SNP database identifier was in- cludedin the bioinformatic resources of the MMP http://www.maizemap.org/cgi-bin/SNPDataDisplay/SNPData4.cgi,verified 4 Aug. 2005). Such resources are significantaids to map-based cloning of genes with agronomic orbiological significance, to marker-assisted selection, togenome sequencing, to understanding of genome struc-ture and functions, and to comparative genomics in thegrass family.

ACKNOWLEDGMENTS

This research was supported by NSF grant DBI# 9872655.The authors would like to thank Bertrand Lemieux, Universityof Delaware, for DNA of the IHO and ILO lines. Names ofproducts are necessary to report factually on available data:however, the parties neither guarantee nor warrant the stan-dard of the product, nor imply approval of the product to theexclusion of others that may also be suitable. We thank KarenCone and Georgia Davis for shared genome mapping andLinda Schultz and Ngozi Duru for technical assistance.

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21VROH BI ET AL.: MAIZE FINGERPRINT CONTIG PHYSICAL MAPANCHORING

Supplemental Table 1. Origin of the 83 diverse inbreds of maizeassayed for 173 insertion–deletion polymorphism markers.

Inbred Origin based subpopulation

B73 U.S. and Northern Stiff38–11 U.S. and Northern non-StiffA272 semitropical inbredsA441–5 semitropical inbredsA554 U.S. and Northern non-StiffA6 semitropical inbredsA619 U.S. and Northern non-StiffA632 U.S. and Northern StiffB103 semitropical inbredsB104 U.S. and Northern StiffB14A U.S. and Northern StiffB37 U.S. and Northern StiffB68 U.S. and Northern StiffB84 U.S. and Northern StiffB97 U.S. and Northern non-StiffCI187 U.S. and Northern non-StiffCM105 U.S. and Northern StiffCM174 U.S. and Northern StiffCML247 semitropical inbredsCML333 semitropical inbredsCML91 semitropical inbredsCMV3 U.S. and Northern non-StiffD940Y semitropical inbredsEP1 U.S. and Northern non-StiffF2834T semitropical inbredsF44 U.S. and Northern non-StiffF7 U.S. and Northern non-StiffGT112 U.S. and Northern non-StiffH95 U.S. and Northern non-StiffH99 U.S. and Northern non-StiffHP301 U.S. and Northern non-StiffI137TN semitropical inbredsI29 U.S. and Northern non-StiffIA2132 U.S. and Northern non-StiffIDS28 U.S. and Northern non-StiffIL101 U.S. and Northern non-StiffIL14H U.S. and Northern non-StiffIL677A U.S. and Northern non-StiffK55 U.S. and Northern non-StiffKUI11 semitropical inbredsKUI2007 semitropical inbredsKUI21 semitropical inbredsKUI3 semitropical inbredsKUI43 semitropical inbredsKUI44 semitropical inbredsKY21 U.S. and Northern non-StiffM162W semitropical inbredsM37W semitropical inbredsMo17 U.S. and Northern non-StiffMO24W U.S. and Northern non-StiffMS153 U.S. and Northern StiffN7A US and MixedN192 U.S. and Northern StiffN28HT U.S. and Northern StiffNC250 U.S. and Northern StiffNC260 U.S. and Northern non-StiffNC296 semitropical inbredsNC298 semitropical inbredsNC300 semitropical inbredsNC304 semitropical inbredsNC320 U.S. and Northern non-StiffNC338 semitropical inbredsNC348 semitropical inbredsNC350 semitropical inbredsNC352 semitropical inbredsND246 U.S. and Northern non-StiffP39 U.S. and Northern non-StiffPA91 U.S. and Northern non-StiffSC213R semitropical inbredsSC55 U.S. and Northern non-StiffSG18 U.S. and Northern non-StiffT232 U.S. and Northern non-StiffT8 U.S. and Northern non-StiffTX601 U.S. and Northern non-StiffTZI10 semitropical inbredsTZI18 semitropical inbredsTZI8 semitropical inbredsU267Y semitropical inbredsW117HT U.S. and Northern non-StiffW153R U.S. and Northern non-StiffW182B U.S. and Northern non-StiffW64A U.S. and Northern non-StiffWF9 U.S. and Northern non-Stiff

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Supplemental Table 2. Allele number, polymorphic information content (PIC) values, and sequence of polymerase chain reactionprimers for 173 B73/Mo17 insertion-deletion polymorphismmarkers derived from 173maize unigenes, and displaying size polymorphismon 2% SFR agarose gel among 83 diverse inbreds of maize. Accession numbers were sorted by ascending order. Overgo names usedto view contigs and hybridized bacterial artificial chromosomes in WebFPC http://www.genome.arizona.edu/fpc/WebAGCoL/maize/WebFPC/, verified 2 Aug. 2005).

Accession OvergoNo. ofalleles PIC Forward primer Reverse primer

AI665421 si605011A07 2 0.47 GTGAAGGTCTTCCACCACGTATTC GATTCTTCGGGCTGATAGTACCCTAI691686 si606023F08 4 0.37 AGTCCCGACATCATTGTGACTTTT GAGGCTGGAGTATTCTTTGGCTTTAI737346 si606039C09 4 0.51 ACAGAATAGCTGTGATAGGCACCC GCAATTCGATACCAAGATCATTCCAI737983 si606044D05 3 0.57 ATCAGATGTTACCGGTTTTGATGC CATGTCTAAAGGTTGGAGGGAGACAI745823 si605077F08 2 0.30 GTCGAATTCTATGGGAACTCGTCA CTGCTGCTTCGTCCCTGATGAI745852 si605074C02 3 0.42 AAGTCCTCAGGAATGGTCAGTGTC TTTGGGAGCTGCTAGGATTATCAAAI770873 si606059F03 3 0.53 GGTGGGTTGGGTTTGACTACTATG GAAGAAGAACCGCAGTACAAGGACAI812156 si605086B11 3 0.49 CCTTGGTACACTACCTGCTCCAGT CAGCATCTTGAGTGCTTACCCATTAI901738 si618009H12 3 0.41 GCATCCCATATTCCCATTGACTAA CCATGGAAGTGGGAGATGCTACAI920617 si618016E09 4 0.65 TTCTTCCACCTCTACTAGGCACCA TGTTCAAAGAATGAACATGATGCGAI987507 si614054G01 4 0.65 AACCACTTGAATTAACACCACGAAA GAGATGCGAGAAGGGAAGTCAATAAW171800 si618050D08 4 0.60 CTTGTGCATAAGGACGGTGGT TTGGTGGTATATTGACGATGGTTGAW179494 si618046E03 4 0.41 ACCTCATCTACCTTGCTCATCAGG TAGCCCTAAAGCAATGCATCAGTAAW215946 si687046G05 3 0.26 GCCTCTGTAGGATGGATGTGATCT TATGGGCATTGTTACCCCTTGTAGAW225120 si687024F01 2 0.58 TAAAATTCTTTTCTCCCAGGCAAC CAAGGTATATCCAAAGATCCAGGACAW257883 si687063E06 3 0.54 CTTGTGGTTGTTTCTCCTGATGTG CAAGCATATACAGCTTCTGCTCCCAW267377 si829001F06 2 0.48 GGGATCTACGTACCCCAAGCTTTA CGCTGTCTCCTAAAGAAAACTACACAGAW313301 si660023C07 3 0.27 GGCATTATCCGTAGACAGCTTCAT GTCGTCTGATGGGTCCTCCAAW400087 si707051B04 2 0.37 AAGACCAGAGAGAGCCTGCAGTTA ACATATAGTTGAATCCGCAGCTCAAY103770 PCO100327 3 0.51 ATCCGTCTTACCCTTATCCCAAAA GCGCATTTCTAGTTTTTAGCAACGAY103806 PCO111734 2 0.27 AAGAGGTGAACATTGGTGCTAAGG TTTTTAAGCGCAACTCCAGATGATAY103821 PCO084551 2 0.49 GGAGTTGGGTTTTGCCTCCTATAC GATAAGCATGCAACAACTTCCAGAAY103844 PCO132874 3 0.58 CATACTGAAGGGAACGGACGAC TGCAACTGAGTTCAGAACAGTAAGCAY103848 PCO061754 4 0.59 ATCTGCCTTATCCTCACCTTCCTC CAAGCAACCAACCCAGTACTACAAAY104017 PCO119482 2 0.46 GGAGATTGCCCACATGTACAAGAC GAACATTAACCAAAGAGCACCGACAY104079 PCO134626 2 0.33 AGGCAGTACAGAAGAGGAGCAAGA AGGGAGTACATCGCAAGTAACAGCAY104214 PCO099155 2 0.45 CTGTAATACAATGCGTGCGCTAAG GCCAGCAAGATCATAATCTCCATCAY104252 PCO110637 6 0.29 ATTGCATTAACCATTGATTCCTGG CAAACCACTCCAAACTACATGGGTAY104289 PCO114336 5 0.67 CTGTTGGAAATAAACCTGCCATTC TCGCCTAACCTAGACCAACATCATAY104360 PCO094248 3 0.52 CTTTGGATCCTGCCTATGCACTAC TCATCAGGACACACAATGTTACGAAY104386 PCO096835 3 0.61 CGAGTTCGACACCAGCTACATCT GACGAGCGTAGTGCAAGATGATTAAY104465 PCO087457 2 0.49 CTCCCTCAACACACTTCTCAGGAT TATGAGAATGGCAGTCGAAAAACCAY104511 PCO117256 2 0.46 CTCCCTTCTCAAACATCAGGAAGA TCGTCGACTCAAACTTTATTCCAAAY104566 PCO130617 2 0.42 GATTCTGACAGTTTCCGTCAACCT GGACAACCCGCATCAAACATAAY104742 PCO152525 4 0.40 GGCATGATCTGAAGAAGTTTTTGG AGACGTCCGAACATCTGTCATGTAAY104775 PCO061308 4 0.64 GCATTTCCTGGTGGTGAAGTTATC AAGCTCTTGAACCGCATTAAGGATAY104784 PCO129009 5 0.77 GAGAAGAAGACTAACGGCACGAAA GTGCGTCTGGTACACAACACAAGAY104923 PCO144363 4 0.67 TGTTTTGCTTCATGACATGTGTGT GCTTCACAGACCAAATTCAATGTTTAY104976 PCO136133 4 0.65 GAGAGAACGGTGTTCTTTGACGAC CGACAGGGATGAGCTATACAAACCAY105029 PCO082331 3 0.59 ATCAAGGCCTAGGTCAGAACTGTG TTTCTGGGACGGAGTACATACCATAY105069 PCO099796 4 0.60 GCCACTGTTGCTTTCATACTTGTG AACCAGTGGCAAATATCCGATAAAAY105176 PCO111982 4 0.60 AGCACACTGATGCACTAATGAAGG AACATCAGAAACCACCTACCAGGAAY105303 PCO075489 3 0.26 CTCCTCATCTGGGTCACCATCT CAAGCATGAGATAAACTGGATGGAAY105347 PCO089398 5 0.72 GTGGCCAACTATATCCAGAAGACG ACAGATTAAAGCCAAACAAACCGAAY105457 PCO149506 4 0.66 AATGCAGGAAATACAAAGAAGGCA CCATTCAACTTGGAGAACATAAAAGGAY105480 PCO116288 5 0.63 TATCCCTAGGCTGAAGACTGTTGC CGAGGAAACAAACAGGCTCTAAAAAY105589 PCO140163 3 0.58 CTCAGCATTGTAGGCTCGTCAATA AGACAATGTCAACTTGGTTTCTCGAY105728 PCO142478 4 0.41 AAAGGCCTTGAGAAGACAGGAGAT GTACATCAGTTGCATAGGGTCCGTAY105761 PCO136937 3 0.33 TTCACACTGATTTTGAAAGGGGTT ACAAGCCATACAATTGTGCATGTTAY105785 PCO107575 5 0.52 AAGCAGAATTCAAGGTGGTAGCAG GCAACCAAACAGGATCTAGGTGAGAY105849 PCO098078 6 0.61 GAAGGGTTCATTTGATGCTGAAAA TATTACAGGTGTCCCTCGGTTGTGAY105910 PCO106969 3 0.09 TACAGAGGTTACCCACGAGGATTT CGGAGTAAGACTCAAAAGCAACAGAY105915 PCO131593 4 0.69 GTGCATCAAGTTCTCTCATCCCTT TCCACTCTAAACATCTCTCTGAGGCAY105971 PCO076386 4 0.69 AACCTCACCTTGTGGACTTCTGAC CCATACCACATTTGATTATTGCCAAY106040 PCO125510 3 0.56 AGCGACACTTTCTCCAGTTACCAC GTAACCTCCTTTGATGTAGTCGGCAY106088 PCO099462 3 0.53 CGGAGACCGGTAGAGGAAATTAAG TTTTTGCGAGACATAAAGTGGTAGTGAY106230 PCO119904 3 0.40 CACATGGTACAAGGAGAACAGGTG AAGTTCTCGCAGTGGTCTTGTTTCAY106269 PCO138212 4 0.69 CCAATTACACCACCGAGATCTACC AACCGCTTAAACAGCACGATTAGTAY106323 PCO084517 3 0.35 CGAGAACACAGGGAAATCTGAAGT TCCTGCAATAAACTTGTGTAATGTGTGAY106398 PCO135705 4 0.38 GCTTTCCAGAACATAAATTGGTGG TGGTAACAGTCGTCAAGTACCACACAY106414 PCO109372 3 0.59 TGTGACACACCAGCAAGTCCTAAT TATGAGGTCACATCTGCTATGGCTAY106472 PCO062666 5 0.67 CCACACATAAAACACAGACCCAGA TTTTGACACACAAAGCAGCAAGATAY106487 PCO060271 3 0.40 CCTGATCGAGCTCAGGAGGAT AGTATTCTGGCAAATTCCCCATCTAY106517 PCO071075 3 0.58 CAGCATGTTCAGTCCAAGTGCTAC CCCCTTCAATTACATTACATGACTGCAY106538 PCO145991 2 0.15 ATGTTGCAACCTGAGCTCTTTACC AGGAGGCCAATTTCATTTGTTTTTAY106592 PCO063726 4 0.57 ATTTTGATGGGAAACAGTCCTTGA CCAAATCCTAAAGACACTGCCATCAY106606 PCO135617 6 0.75 AGACGATAGCATTGGATCCTCTTG GCATCCCTGCTTAAAGAGTCCATAAY106635 PCO086427 4 0.34 CTAGCTAGGGCTGCCCGTGT GTGCAAGCCGGGAAACAATACAY106712 PCO129934 2 0.43 CCTTCGTGCTCAGGTACTACGTCT GCGTTACAAATATGACATTACAAAACCAAY106733 PCO107634 3 0.55 ATACCTGCTGGGTTCTTAGAAGGG CAGCCTCGATGAATAGGAACAAGTAY106736 PCO074335 3 0.61 GACAAGCAGGATGAGAGGAAGAAG GCACAGTCTTAAATTGCACACCACAY106822 PCO104784 3 0.42 GAAGACCCAGATGATCTCACTGCT GTACAAATCGATTGACAGTGGCAGAY106902 PCO068526 4 0.30 TGCTATGACAAATGAATGAGCGTT GACATGTTTTGCGCTTGAAGAAATAY106921 PCO069699 4 0.34 AGTTCCTCAACGAAGAATCCACTG AACAGACGGTCGCTTAATCTTCTGAY106948 PCO141323 3 0.60 CCAGGATGCTTCCTTCAGTACAGT TCCATATATACACATGGGCAACTGAAY107140 PCO079694 2 0.50 GGAAGGAAAACTTCTCCCCCTAGT TTCCCTGCTGTAAAATATCTGGTTGAY107207 PCO128140 4 0.65 AGATCATCCACAGAGGAGACCATC AAGCAGATGCGCATATCAATGAGAY107218 PCO140184 3 0.59 ACTACGAATCCAGCGACAAGAAAG ACCTCATTTATCAGGCTGAAAGCAAY107240 PCO146525 3 0.50 GGGAACTGGATCATTCTAGTCGTG CTTCTCCTGCTCCTACTCCTGCTAY107256 PCO118908 3 0.58 GGAAGTTGGTATGGTTCCTGGAC ATACGTCGCAACCAATATACGGTCAY107363 PCO107756 3 0.52 AAGAGATGACGCCGTGAGAACTAC GAGGATGTGTTTTGCTGGATTCTTAY107559 PCO061815 4 0.62 TGTTGTAAGAAGCATCCTGTTCCC ATCGCGATGCACTGGTTCTGAY107622 PCO102097 4 0.58 ATTTCATTTTTCTTCCCCCTCTTG ATGGATCAAACGGATCTTTAAGCAAY107726 PCO062847 3 0.33 ATGCAGATGCAGTGTGAGATGTTT GGATCATATGGGATTTCCTGTTCA

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Accession OvergoNo. ofalleles PIC Forward primer Reverse primer

AY107797 PCO101826 4 0.53 AAGTGCTTGATTTCGTTACTGCCT TTTTTGAGACCTTGGAATGTTTGTTAY107822 PCO087182 5 0.71 CAGTTGCAATCTTAGGGTACGAGG CACAATCCAAAATGTTTTACATCCGAY107847 PCO116807 3 0.66 GAGAAGACCCACTACTCAGGGACC AATACACAGATCGAGGGAGCAGAGAY108004 PCO068796 3 0.59 CGTTCTAAAATATCCGGTCTGCAT CTAGATCAGATCATGTTTGCACCCAY108039 PCO102751 3 0.62 GGTGTTACTGGACTACGGTTGAGG TTAATTCACACAGTGCATGGACAAAY108049 PCO078116 3 0.63 GCAGAGAGCATAGGTGATCGTTTT CTGCAGTGAGTTTAACAAGACCGAAY108063 PCO143084 6 0.76 CATAGCGCAGTTGATGTGTGATGT GATTTTTACACCAAGCGACAGGAAAY108084 PCO147505 3 0.59 TAAATGCCATGCTGAAGATTTCCT TCCAAATGTAAGCTAAGTGTGGTTCAAY108090 PCO099415 2 0.41 AGCTGGTTCCTACTTTGGCTCTTT TTACCTACTGAGCGAATGGTAGCCAY108096 PCO136722 3 0.33 CGAGGAGAAGAAGCCTTACATTGA TCATTCATGTAGCAACGATAACGGAY108243 PCO134814 2 0.44 GAGATGGCAAGAATGATAGCCTGT AAAGAGCAAAAACAGAGAGGGAGGAY108476 PCO126344 2 0.31 CGGATTTCACTCTTAGGTTGAGGA CCACGTTCTCATCTGGGTTAAAAGAY108514 PCO088312 5 0.51 CTCTGTTCTTGTTTCCAACGGACT AGGAGCTTGGCTCTCTTGAAACTCAY108625 PCO087393 2 0.45 CAAACTGTTGATCTGGGTGTTGAG TGGCAGTTGACACTACAGAAAATCAAY108650 PCO072650 4 0.06 AGTCGCAGAGCCACAGGTTC AACATGGAACAGAGGCAGACGTAAY108778 PCO075654 3 0.49 ACTGGGCCACTATGAGATTGTAGG ACATTTTGCACGCAAATAGATCCTAY108804 PCO063114 2 0.50 GGTGTGACAAATTTCAGCAGTACG TTTTTATCAGCAAACAAGCAGCAGAY108849 PCO091677 4 0.68 AATCCGCTTTCCTAGCTCTAATCG GAACAGCCTTATGTTCTTCTCGGAAY108914 PCO102879 3 0.10 AGCAAAGAAGCCAAAGAGCAACT TCTGCAGTCTGCTGTTCTTCAAGTAY109550 CL135_2 3 0.33 CTTCGATGCAGTGTTCTCAGTTGT AGCATTCGGCACAATTTTGTACTTAY109570 CL1864_2 2 0.21 CTCCTTGATCATCTCGAAATAGGG GTGATCACTGATTTCTGGTCATGGAY109575 CL1708_1 4 0.37 CTACATCAAGGACGACAGCAAGAC TTGATGGACATACTAACCAACCCCAY109592 CL34788_1 2 0.48 AACACTTGCCAATGACCAATCTTT TCTAACCTTGTCAGCCTCAAATCCAY109606 CL4591_1 2 0.40 ACAACAGACTCTGACAGCTTGCAC GATTCATTCTTCCGGGTTGTACTGAY109645 CL4356_2 3 0.42 AGCATCATCTTTGAGGTTACCAGC CTGCGTTTCTTCTCCTGTTCATCAY109668 CL6375_1 4 0.51 GATGTTTGCTGGTTTGTCTCTCCT TTAACAGCTTTTGCGACGGATAATAY109687 CL45878_1 3 0.48 TATAGCATCATTGCCATCACGTTC GAGAGAAGAGAAGCACCGCAACAY109698 CL4149_1 2 0.47 ACGAGCATCACGAGAAGAAGG AAACACACGTAAATTCACATTATTCAGAAY109699 CL7702_2 3 0.46 CAAGGTTTCTTATACCATGCGAGG CAGCCAATCTGATCGAAAAGTTCTAY109722 CL2887_1 2 0.09 TGCAAAAGAATTGGTTGTAAATGG AGGCAGTATTCAAAGGCATTTCTGAY109730 CL2227_3 3 0.58 GTTGGAAGTCCGGAGACTGGAT GCAAACATAGGTCCCAAATGGTAAAY109816 CL0_-2 4 0.42 CCTAGTGATCATGAATTTCCTCGG GGAATTGCTTATTTGCAGCATACCAY109828 CL16525_1 4 0.39 GTACCTCTCGACCAGGTCCTTGA CAATTTAAAGCAGCAACGACGGAY109835 CL587_1 3 0.62 TTGATATCTTTTCTCTTGGGGCAG AACCTTAACACAACAGCAGCAACAAY109853 CL2096_2 3 0.60 GTAGAGCAAGGCCTGTGAATGG TCAGAAGCAGTTCAATCACACACAAY109859 CL21031_1 2 0.15 ACGCTAAAGACAAGCAACCAAAAG CCATGTTCAAGTGTTCAACTGGTCAY109873 CL6571_1 3 0.29 GCTTATGGAGATGTTATGCCAAGG GAAGGGAATATTAACACGGCTGCTAY109996 CL2349_1 4 0.55 ACTCCAGTTTAGGCACTGATTCCA CAGTAGAGAATTGCGCACACCAGAY110132 CL40355_1 3 0.19 TCATCAAAGATAGGTTTTCGCCAT CTTTCAGACCTGAAGAAGGGATGAAY110167 CL14540_1 2 0.37 CGACATCTAGATCAATCCAAGCAA ACTCGCTTCGACTCCGACAGAY110191 CL21485_1 3 0.05 GTAGAGCGTGTAGTCCGTCACCTT AATCCTCCTCCTCCAGCCACAY110231 CL852_1 2 0.46 GAATAAGTCGTACTCCGGCACAGT CCATCTAGATCTCGTGCTACCGATAY110296 CL11152_1 2 0.50 GCGTGCTGAGACTTACCTGGTATT AACGCAGCATAATCTGGAAATTCAAY110313 CL16676_1 4 0.58 CAGAGGGATGTGTTGCAGGTG ACCCACCCTCGTCTGTTATGGAY110330 CL946_1 2 0.28 GCAACGACGACTTACCAAGAGTTC CTCATGCGACAGTAGGTAGGAAGCAY110374 CL34066_1 2 0.04 AACACTGTCCGTTCCAGATCATTT GGTTGCTATAGACAAGCACTGCACAY110382 CL32455_1 2 0.39 AAATTCATCACGCTGATTTGGTTT CAAGGCTGATAATATCTGGGCATCAY110439 CL194_1 5 0.36 CAGGCGCTCCATATATAAACTTCG GCCATGAAATCAGTCTTGAGGTGTAY110539 CL13530_1 3 0.39 CAGCCAAATAACTGATCTGCAATG ATTCTTTGGTAGCAGCAGGTCTTGAY110567 CL7839_1 4 0.59 GAAGTGTGTGATGTGTCAGACGTG TAGAAGACACATGAAGCAGCCAACAY110812 CL13054_1 2 0.48 ACACTCAAATCCCTCCAATCCATA TTGCTGCGTCTTGATGATCTGTATAY110825 CL16923_1 3 0.44 TTTCAGGTATTGTGTTGTCGTGCT ATAACATCCGAGTCAGAGGAGCAGAY110872 CL65845_1 2 0.20 ACTCAATTAGGACAAGTGCAGCCT ACGCTCATACTGGCATACCTCACTAY110873 CL10452_1 2 0.07 TCAATCGATGGTCAGAGTAGGTGA ATTTAACAAGGTGAGGCTGTTGGAAY110906 CL14503_1 3 0.50 GCAACGTCACTTCAACAGATTGTC CAAACAATGAGGCAGAAGTATGGAAY110949 CL12681_1 2 0.51 TGACTGTTGCTGAGCCTGTTACC GTTTCACTGACTCGAGGGTTCGAY110983 CL778_1 4 0.65 GCTAAGGCAGCACAAATGAATCTT ACCTTAGACCGTCTTCGGCGAY110989 CL5869_1 3 0.59 GGTTTGCATTTCAGTATCGTAGCC AGGAATGACGTATGGATTCTCTCGAY111044 CL38592_1 2 0.50 CGCTATGAACTCATGGAGAAAACC CTGGAGATCGACCAGTGCGTAY111071 CL51477_1 2 0.38 AAGCCCACCTGATGATACATGACT TATTAGGGCTGATGGAGCTATTGGAY111073 CL39692_1 2 0.46 TTCCAAGAGACATTACACGCAGAA CTCATCCATCATAACTGTCCACCCAY111125 CL6928_1 4 0.53 GGTCAACGTCGGGAAGAACAC CGGGTGGCTTTTGAATGTAAATCTAY111142 CL9565_1 3 0.67 AGTAGATCATGCATCCATCGTCAG TCAAGGAAGGTGAAACCATTAGGAAY111153 CL12437_1 3 0.29 CCCTTTCGGTAGAATCAAGGATCT AGCCAAGGCAGAAAGTCCAATATCAY111178 CL5772_1 3 0.39 CAAGGATCGTCACCTTCAACTC CCCATAGTCCATACATACATGAAAGAAY111236 CL31103_1 4 0.64 TGCTTGTTTTGTTGCTGATCCTAA CTTCTCAAGGCCGAGCAGACAY111239 CL24605_1 4 0.54 CAGGCAAGCTGCTAGAACTTTAGG TCCAGTCGTCTCAACTAGTGTTGCAY111254 CL29988_-2 2 0.21 GGAACTAGCCATCTAGTTTGCGTT GAAATGAACATATTAGGCGAAGCGAY111434 CL58207_1 3 0.55 AACAAGATCAGATCGGCGAAGTAG CTTCCCCATAAATGCAATCCATAAAY111480 CL34114_1 2 0.48 GGCTTCAAGGATGCTTCATACAGT AGATATGGGGTCTTCAAAATAGTGACAAY111507 CL7343_1 3 0.60 TGGTTGTTGGTAGCACTAACTGGA CAGAGGGAGTATAAACGTTAGCTTCAAAY111629 CL9311_1 2 0.42 CTAGTATTCGAGGAACTGAGCGGA CGTTGTCAGAAGAAATGCAGATTGAY111680 CL11621_2 3 0.58 TACCACATTCAGGTATTCGGGTTC TAAGCCAAAGATCTTGAGGGGAAGAY111767 CL62610_1 3 0.58 GATCAACGTCAAGGATACGTGCTC TTAGCTAGCGACCGTGGTACTCATAY111819 CL21419_1 3 0.57 GCAGTAGAACCCGATCAGAAAGAA ATATGTCAACTCTCCCCTTATGCGAY111834 CL67476_1 5 0.68 CATTACACACGTAGGCATCAAACC TGTGAGATGACGAGGATGAGACAAY111865 CL16874_1 3 0.56 TCCTCAGGATGGTCAGGTACAAG ACCGACACTTGGTTGATGAGAGATAY111936 CL22280_1 4 0.67 GTCTCTGCATCGGCATCATAATC TTGGTTTACCGAATCTCACCTCATAY112073 CL6800_1 2 0.50 AGATTGCTAGCTTTATTCCGGTCC GACCATCTGGAGGAGTACAGCAGAY112075 CL52019_1 4 0.67 AATGCTGACTTGTAGAGGGTGGAG GCTTGGTATGAGGAGGCAGAAAATAY112092 CL14065_1 5 0.58 GTGAATAGCTTCAGTTCTGCGTGA GTCTCCTCAGCTTGACTCTGGCAY112127 CL11712_1 3 0.52 ATCAAGCACCTGAAATGCTACACA GTTTTAAGCAGTGGGTTCATGTCCAY112131 CL12768_1 3 0.44 TCGTCCTCCGCTTGTTACTATCTC CAGCTTTACGCAACTACAGAAGCAAY112354 CL34571_2 2 0.45 TTTCCCCACCAATACAAACATCTC ATCATCAGCGTCCTGAAAATGTGTAY112405 CL10251_1 2 0.41 GATCAGCTCACGTGCAATAACATC ACCTTTGTGCTATAGTGGGAGGTGAY112466 CL10221_1 2 0.49 TTGAAGTTCTTGTAGAAGTCCGCC GGCATATGGAGTACAAGGTTGAGCAY112581 CL11475_1 3 0.43 TGGGTATGTTACAATTCCTGCAAA AGGATGAAGAAGCTGTTATGGCTGBE056994 si945036H05 3 0.58 AGGACTACAAGGATAAGCTGGCG CTATCTCCTTGGAGACCCTGGAGTBE639338 si946021A07 2 0.43 AGCTGGAGAAGCTGCGTAAGACTA ATTGCAATGGCTTTGTATGCAG

Supplemental Table 2. Continued.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Supp

lemen

talTa

ble3.

Unige

nesmap

pedby

sing

lenu

cleo

tidepo

lymorph

isms(SNPs)

orinsertion-

deletio

npo

lymorph

isms(InD

els)

toan

chor

bacterialartificialchromosom

e(B

AC)

contigson

maize

chromosom

esan

dtheircorrespo

ndingpo

lymerasechainreactio

nan

dSN

Pinterrog

ationprim

ers.

Unige

nesarelistedin

map

positio

norde

rfrom

shortto

long

arm

ofmaize

chromosom

es.Overgo

names

can

beused

toview

contigsan

dhy

bridized

BACsin

Web

FPC

http://www.gen

ome.arizon

a.ed

u/fpc/Web

AGCoL

/maize/W

ebFPC/,

verifie

d2Aug

.20

05).

Chrs

Accession

Overgo

Typ

eFo

rwardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

Chr1

AY110314

CL24410_–1

SNP

TCATCCTTTTGCAACCACTACTCA

GCATA

GATTGGGTTACCAGTTGGA

ATCACCATGAAGCAAGCA

AY110401

CL809_1

SNP

TGCACCTGCTCCACAAGTA

CAG

CGTA

ACGTGTCATTATGTTCTCCG

GTCAATGTTGACGGCGGT

AY108650

PCO072650

InDel

AGTCGCAGAGCCACAGGTTC

AACATGGAACAGAGGCAGACGTA

–AY103844

PCO132874

InDel

catactgaagggaacggacgac

tgcaactgagttcagaacagtaagc

–AY107207

PCO128140

InDel

agatcatccacagaggagaccatc

aagcagatgcgcatatcaatgag

–AY109929

CL4401_1

SNP

TCAAACTGTCTGAAGATCCCAATG

TTGACTGCTGAACCACGATTA

GAA

AAAAAATCGGCGTCTCTACT

AY110052

CL33106_1

SNP

TTGTTTACGAGGATGTTGAGCTTG

GAACAACAACTGCGAGATGGC

AAAAAATATCGCCGTGCCCGA

AY110028

CL302_1

SNP

GAAAACAATCAGGGAAGAGGAAGG

GTTCACAGCACCAGCATTTGTTAC

AAAATCAGATCGCATTGAACACACT

AY106592

CL14065_1

InDel

attttgatgggaaacagtccttga

ccaaatcctaaagacactgccatc

–AY106736

PCO116807

InDel

GACAAGCAGGATGAGAGGAAGAAG

GCACAGTCTTAAATTGCACACCAC

–AY110640

CL833_1

SNP

ACAAATTCTACAGACACGGGAGGA

AATTGCGCTTCGAATA

GACTGAAC

AAAAAATAGAGTTA

GACACTCAGAC

AY110632

CL5778_1

SNP

ATCAAGACCAAGGTGCTCGTCT

GCACACCTTCTGAATCCTTCAAGT

CCAAGGTCCACTTCACCGC

AY110393

CL5132_1

SNP

ATA

TTCATCGTCGTCGTCAAGCTG

GACCCTCCAAGATCGGACCTC

CTACAAGTTGCAAACCATGGAAAT

AW400087

si707051B04

InDel

AAGACCAGAGAGAGCCTGCAGTTA

ACATA

TAGTTGAATCCGCAGCTCA

–AY108090

CL62610_1

InDel

agctggttcctactttggctcttt

ttacctactgagcgaatggtagcc

–AY110330

CL946_1

InDel

GCAACGACGACTTACCAAGAGTTC

CTCATGCGACAGTAGGTAGGAAGC

–AY110241

CL8900_1

SNP

AACATCACCAGGTTCAGCTTCTTC

TTCGGAAATA

TCCGCACTAAAAGA

AAAAGGTTGACTCTCTTTTACATCC

AY112354

CL34571_2

InDel

TTTCCCCACCAATACAAACATCTC

ATCATCAGCGTCCTGAAAATGTGT

–AY106088

PCO099462

InDel

cggagaccggtagaggaaattaag

tttttgcgagacataaagtggtagtg

–AY109646

CL1599_-1

SNP

GGGGACGACACTGATA

CTACTGCT

TTA

ACAACAACGGTTGGACACTTG

AAAAGTGGTGACCACGACGACAG

AY111680

CL11621_2

InDel

TACCACATTCAGGTATTCGGGTTC

TAAGCCAAAGATCTTGAGGGGAAG

–AY109678

CL18174_1

SNP

CGGACCAGACAATATTCCAAGTTC

CTTTCCCAAATA

ATTCGTGGTCAA

AAAAAAAAATTCAGGTACATGACGGAGACATC

AY110396

CL18635_1

SNP

AACCATACAGTA

CAGGAGGGTCCA

CAAAGGTTGGATATCCCAAGTGAA

CAAAATGCTTCGAAGCAAGCC

AI855190

si603009F08

SNP

AGATGTCCAGGTACTTGAGCCG

GAGCCTGTGGCTGGAGAAGAT

AAAAAACCTCACCGAGCTGCC

AY112092

CL14065_1

InDel

GTGAATA

GCTTCAGTTCTGCGTGA

GTCTCCTCAGCTTGACTCTGGC

–AY109499

CL2801_1

SNP

GTTCTTTCCGTCGATGTATCCCT

GCTA

TGCAGAGCCTCCTCGT

AAAAAAAAAAATA

GCGGTTGATTGCAGATTG

AY110566

CL45690_1

SNP

ATCAGGTTGATTTCACAGCAGTTG

CAGCTCAATCATCGAATTCTTGC

AAAAAAAAGATGGCTGCTCTCCAGGTA

AY110296

CL11152_1

InDel

GCGTGCTGAGACTTACCTGGTATT

AACGCAGCATA

ATCTGGAAATTCA

–AY104360

PCO094248

InDel

GATGGAATAGCTGGCATCCATA

AG

ACAGCTGAGGTAAGCACAAAGTGA

–AY111153

CL12437_1

InDel

CCCTTTCGGTAGAATCAAGGATCT

AGCCAAGGCAGAAAGTCCAATA

TC

–AY107847

PCO116807

InDel

gagaagacccactactcagggacc

aatacacagatcgagggagcagag

–AY111834

CL67476_1

InDel

CATTACACACGTA

GGCATCAAACC

TGTGAGATGACGAGGATGAGACA

–AY110356

CL22447_1

SNP

GCAGTGGCCATTCTCGTAGTA

TTT

AGTCTAGGAAACACTTGGGAAGCA

GTCTTGACGAACCACCACT

AY110191

CL21485_1

InDel

GTAGAGCGTGTAGTCCGTCACCTT

AATCCTCCTCCTCCAGCCAC

–AY110159

CL11942_1

SNP

AGAAAGAGGGGAGCATA

TAAACCG

TCACGTGATCTGAAGTA

CCCATA

CA

TTCTGCATCACTGGGGAGAC

AY110313

CL31053_1

InDel

TGTGAACATCTTGAGCTTCTTTGC

CGACATTGGATA

CACTGAGGAAGA

–AY110349

CL11942_1

SNP

AGAAAGAGGGGAGCATA

TAAACCG

TCACGTGATCTGAAGTA

CCCATA

CA

AAAAAATTTTCGTATTGAATTGGTTGCAAG

AY109506

CL7587_1

InDel

GCTCTACTCCAACCTCAAGGACAC

AAACATA

GTCATCGGCAGGACAGT

–AY110452

CL23944_1

SNP

GTCGAGGATTACTCTCCCTCCTGT

CATCGCAACAACAGGATCATAGG

CACCGGATGCCAAGCTGTT

AI665421

si605011A07

InDel

GTGAAGGTCTTCCACCACGTATTC

GATTCTTCGGGCTGATAGTACCCT

–AY110019

CL471_1

SNP

GTATGGGAACTGGCAATAATGTGG

GAAACTGGGGCTAATA

GCAAGCTC

AAAAAAAAAAAAAAAGAATCAAGGGTTCTAAGTACAAAAC

AY108625

PCO087393

InDel

CAAACTGTTGATCTGGGTGTTGAG

TGGCAGTTGACACTACAGAAAATCA

–AY111936

CL22280_1

InDel

GTCTCTGCATCGGCATCATA

ATC

TTGGTTTACCGAATCTCACCTCAT

–BE639426

si946033A04

SNP

AGGTACTCGTCGGAAGATTCTTTG

CTCCCTCCTGACCACCTCACT

ATTTATCTGATCATA

TGAGGTATTGCCATTT

AY108136

PCO095183

InDel

ACTCCTGACATTCCTGAGATGGAG

GCAAATGTTTGCCCTAAGTGTGTC

–AY109834

CL7866_1

SNP

TACAGTTTGCAGGAGCAAGACAAG

ATTTCAGGTCCTTCATTCCATTTG

AAAAACAAATTCCGCACAGCTGAATCAATA

AY108778

PCO075654

InDel

ACTGGGCCACTATGAGATTGTAGG

ACATTTTGCACGCAAATAGATCCT

–AY110426

CL31361_-2

SNP

GAGATGCCGTAGACAGTA

ACAGCC

AACTACATCAACGGCAACGTGTC

AGGACAGCTGAACCGTATGATGATTGA

AY110479

CL16056_1

SNP

GGGCTAGACTGCTGAAGGTAACAA

ATTCCAAGTATCAGTGCCGAACTC

CAAAATCAAGAAGAATCTAATCATCAGCTAA

AY106606

PCO135617

InDel

agacgatagcattggatcctcttg

gcatccctgcttaaagagtccata

–AY110160

CL7400_1

SNP

ACACCTCTTTGACGAACCTCTGTC

CAAGGACCTCATCCATGGTTTC

AAAAAAAAAAAATGGAACTTAATGAGGTGCTTTA

AY111767

CL62610_1

InDel

gatcaacgtcaaggatacgtgctc

ttagctagcgaccgtggtactcat

–AY110983

CL778_1

InDel

GCTAAGGCAGCACAAATGAATCTT

ACCTTA

GACCGTCTTCGGCG

–AY109916

CL11745_1

SNP

GTTATCAAGAGGCTGAAAGTGGGA

GTGTCTGATTCTGTGGTGGCTATG

GAGCATACACCACCTTTA

G

Con

tinue

dne

xtpa

ge.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Chrs

Accession

Overgo

Type

Forw

ardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

Chr2

AY108849

PCO091677

InDel

AATCCGCTTTCCTAGCTCTAATCG

GAACAGCCTTATGTTCTTCTCGGA

–AY109692

CL301_1

SNP

ACAGAAGTATGCCATGGGCTAGAA

GCTCACTGGAACGTCTTTCTTTCA

TGGTCCTCAAAAGTCCATTCATA

CTTG

AY109603

CL18778_1

SNP

AGCCTGTCCTTCGTTACTGACATC

CATCTTGTGGGTTTGGTGCAG

AAAAAAAAAAATA

ATGCTCCTCCACATCCTGC

BE640649

si945021E10

SNP

CGGTA

TGTCTCATTTCCTATTGCC

AGCAACAGGCTCTGGTGTTATCTC

AAAAAAAACCGGTGAGGTTCACTAGTCATTA

AY109516

CL5703_1

InDel

TGTCGTTTACGGTTACTGGTCCTT

ATTCCATGCATTCATCCTGACAC

–AY112075

CL52019_1

InDel

AATGCTGACTTGTAGAGGGTGGAG

GCTTGGTATGAGGAGGCAGAAAAT

–AY112131

CL12768_1

InDel

TCGTCCTCCGCTTGTTACTATCTC

CAGCTTTACGCAACTACAGAAGCA

–AY106040

PCO125510

InDel

AGCGACACTTTCTCCAGTTACCAC

GTAACCTCCTTTGATGTAGTCGGC

–AI745852

si605074C02

InDel

aagtcctcaggaatggtcagtgtc

tttgggagctgctaggattatcaa

–AI920398

si603020H12

SNP

CTGCTTTCATCCATCACAATTCAC

CTTCAAGGAGATA

AGGGAGCGACT

AAAAAAAAAAAAAAAGATCACGTTAAGAGAAACAAA

AY104214

PCO099155

InDel

CTGTAATA

CAATGCGTGCGCTAAG

GCCAGCAAGATCATA

ATCTCCATC

–AI691686

si606023F08

InDel

AGTCCCGACATCATTGTGACTTTT

GAGGCTGGAGTATTCTTTGGCTTT

–AY110266

CL17243_1

SNP

CCCTCTTGAAACTAATA

CTGCCGA

GTCAAAGAGGTGATCACAGTGGTG

TTTGCAAGGTAGAAATTACATA

ATC

AY106712

PCO129934

InDel

CCTTCGTGCTCAGGTACTACGTCT

GCGTTACAAATA

TGACATTACAAAACCA

–AY103590

PCO098412

InDel

ggtcgatttgcttctgagttgttt

tgttctatgtgtgttttcctgtgga

–AY107218

PCO140184

InDel

actacgaatccagcgacaagaaag

acctcatttatcaggctgaaagca

–AY111434

CL58207_1

InDel

aacaagatcagatcggcgaagtag

cttccccataaatgcaatccataa

–AY112466

CL10221_1

InDel

TTGAAGTTCTTGTAGAAGTCCGCC

GGCATATGGAGTACAAGGTTGAGC

–AY110485

CL1980_2

SNP

CAAGATTGAGACTGAGCTGACCAA

AAGCCTAATA

GGGTGAGTTGGAGC

TGCACCACAAACCCCTTTTCAG

AY104386

PCO096835

InDel

cgagttcgacaccagctacatct

gacgagcgtagtgcaagatgatta

–AY109687

CL45878_1

InDel

TATA

GCATCATTGCCATCACGTTC

GAGAGAAGAGAAGCACCGCAAC

–AW681281

si707094H09

SNP

CAACCATA

CAAGTTTCCTCTCGCT

ATGACGAATTTGCAGATCATTGTG

AAAAAAATGCAGTATTTATTTCGTAT

AY110336

CL54827_1

SNP

TGACAAGTTTATCTGACGGAGGCT

GGAATTATTCAAATTGCGCAGAG

AATTCATCCATCGGGCTCTCAGAAA

AY105915

PCO131593

InDel

GTGCATCAAGTTCTCTCATCCCTT

TCCACTCTAAACATCTCTCTGAGGC

–AY109981

CL18929_1

SNP

CTTGCTGCATCTCTCACATCAAGT

TCTCCTTTATGCAGTTCACCAACA

CAGAGTACTACTTCTCTAGGTATTC

AY108804

PCO063114

InDel

GGTGTGACAAATTTCAGCAGTA

CG

TTTTTATCAGCAAACAAGCAGCAG

–AY110410

CL7336_1

SNP

GGTCTGTAGTGACACGCTGAAGAA

TGTTATTATA

CGCAACATGCGGTC

ACGCGCCTCTTCTTCGGT

AY109722

CL2887_1

InDel

TGCAAAAGAATTGGTTGTAAATGG

AGGCAGTATTCAAAGGCATTTCTG

–AY109917

CL13558_2

SNP

ACTGGGAGTGTGCTAAATGAGGTT

GGCGATGTTGGAGAAACACTATTC

AAAAAACCATGCTCTTCCTGCGACTA

AY109583

CL18551_1

SNP

TCAAAGTCTGATTCACGAGAGCAC

CCACCTTACAAATCTCTTGCTGCT

TGGATCTTTGTTTGCAAGATGGGC

AI668346

si605031A07

SNP

CAGCCCTTATTTCATTTCCATCAG

TGATGGTAGATTTGCCAAAATTCA

AGGTGGCCTCTTATCATC

AY109645

CL4356_2

InDel

AGCATCATCTTTGAGGTTACCAGC

CTGCGTTTCTTCTCCTGTTCATC

–AY107622

PCO102097

InDel

atttcatttttcttccccctcttg

atggatcaaacggatctttaagca

–AY109575

CL1708_1

InDel

CTACATCAAGGACGACAGCAAGAC

TTGATGGACATA

CTAACCAACCCC

–AY109592

CL34788_1

InDel

AACACTTGCCAATGACCAATCTTT

TCTAACCTTGTCAGCCTCAAATCC

–AY110467

CL42453_1

SNP

GATCTTCCAATCTGGCTGTTCATT

AAGTTCTACGTCATTGGTGGGAAA

AAAAACCCCAGCCATGAACTGATGTA

TAAY111236

CL31103_1

InDel

TGCTTGTTTTGTTGCTGATCCTA

ACTTCTCAAGGCCGAGCAGAC

–AY109586

CL860_-1

SNP

TAAAACTTTCGTGGGGTTACCCTT

CATTCAATCGTTGTTTGCATTCTC

CAAATCTCGATGACAGAAACAAACG

Chr3

AY109549

CL1501_1

SNP

AACTCAACGTCCTCTTCATCAACC

CCATACAGTCCTGCAATTCTTGG

TCCCTGTTTGTTAGTAATGCTGTTTT

AY107363

PCO107756

InDel

AAGAGATGACGCCGTGAGAACTAC

GAGGATGTGTTTTGCTGGATTCTT

–AY109870

CL2099_1

SNP

AGGAACTGATCCAGAAAGCTGCTA

AAGCATATTACACCGTATCGGAGG

AAAAGCAGCAGGTGGCGGA

AY110403

CL5194_1

SNP

CGCTGATGCCTGTTAATA

GTGAAG

ATGCAACCGGAAATATGTACTTGA

CCTTCCGTCCACTGCACAT

AY108004

PCO068796

InDel

CGTTCTA

AAATA

TCCGGTCTGCAT

CTAGATCAGATCATGTTTGCACCC

–AY106948

PCO141323

InDel

ccaggatgcttccttcagtacagt

tccatatatacacatgggcaactga

–AY110151

CL4217_1

SNP

AGGCATGTA

GGAATTGACCGAATA

TTACATCGTAAACAACCAGACCGA

AAACAGCACCAACAAAGATCATCAAA

AY110297

CL25043_1

SNP

CCACCGTACATA

GAAACAGTGTCG

CTGTTATCTGCCATA

AAAGGAGCG

CTCGTACAGAGGACTCAGCTC

AI714716

si606017F01

SNP

ATCCTAATGCTCACCACCGTAGAC

AAAACAAAGCTGGAGGCGACTT

ATTATTCATGTTGGTGAGAATTAGTGGTAG

AY110352

CL12989_2

SNP

CATA

TCACGCACACTACCACAACA

TTCTGGAACTACCGAAGAAGATCG

AAAAAAAAGATGAAGCTCAAGAAACAATACATG

AY112215

CL7356_1

InDel

CAGGCAAGCTGCTAGAACTTTAGG

TCCAGTCGTCTCAACTAGTGTTGC

–AY111507

CL7343_1

InDel

TGGTTGTTGGTAGCACTAACTGGA

CAGAGGGAGTATA

AACGTTAGCTTCAA

–AY111541

CL56108_1

InDel

TGCTTCCAATTCCAACCAGTA

GAT

CGGCACGAGTGTAAATCTGGTAAT

–AW179494

si618046E03

InDel

ACCTCATCTACCTTGCTCATCAGG

TAGCCCTAAAGCAATGCATCAGTA

–AY106230

PCO119904

InDel

CACATGGTACAAGGAGAACAGGTG

AAGTTCTCGCAGTGGTCTTGTTTC

–AY111296

CL62634_1

InDel

TGAACACCTTCTCTTCGAGGTACG

GCTGTAGGAATTCGGCACGAG

–AI770873

si606059F03

InDel

GGTGGGTTGGGTTTGACTACTATG

GAAGAAGAACCGCAGTA

CAAGGAC

–BE639846

si946038G12

SNP

CTCCTACATCCTCGCTACGGC

AGAATCACCAACCTCTCAGCACTT

GTCTTACTGCACTGATGGG

AY105347

PCO089398

InDel

gtggccaactatatccagaagacg

acagattaaagccaaacaaaccga

–

Supp

lemen

talTab

le3.

Con

tinue

d.

Con

tinue

dne

xtpa

ge.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Chrs

Accession

Overgo

Type

Forw

ardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

AY110055

CL10277_1

SNP

TTTGGAACCCTGCATTATA

CACCT

GAAACAGCAGTGCAATA

CCACAAC

CCAAGTAGGATA

CACCTGTCG

AY110812

CL13054_1

InDel

acactcaaatccctccaatccata

ttgctgcgtcttgatgatctgtat

–AY111125

CL6928_1

InDel

GGTCAACGTCGGGAAGAACAC

CGGGTGGCTTTTGAATGTAAATCT

–AI770795

si606058D10

SNP

TGCCTGGGCTTATAATA

CCATCAT

GGAACTTCCCGGTGCTACTAGATT

AAAAAAAAAAAAAAAAAAAAAGGTCAAGTTGTTAGCTTTG

AI920617

si618016E09

InDel

TTCTTCCACCTCTACTAGGCACCA

TGTTCAAAGAATGAACATGATGCG

–AI745823

si605077F08

InDel

GTCGAATTCTA

TGGGAACTCGTCA

CTGCTGCTTCGTCCCTGATG

–AY107303

PCO142509

InDel

TCAAGGATTACTCCAGCTA

CGTGA

GCACGAGCTAGTCTCGAGTTTTT

–AY104511

PCO117256

InDel

CTCCCTTCTCAAACATCAGGAAGA

TCGTCGACTCAAACTTTATTCCAA

–AY105849

PCO098078

InDel

GAAGGGTTCATTTGATGCTGAAAA

TATTACAGGTGTCCCTCGGTTGTG

–AY109934

CL64932_1

SNP

CGTA

CAACTTCACCATCAGCATGT

CAGGTCCCGTTCTCGAAGTG

AAAAAAACCATCAACGACCTGGAGC

BE639338

si946021A07

InDel

GGAACTAGCCATCTAGTTTGCGTT

GAAATGAACATA

TTAGGCGAAGCG

–AY111254

CL29988_–2

InDel

GGAACTAGCCATCTAGTTTGCGTT

GAAATGAACATA

TTAGGCGAAGCG

–AY110567

CL7839_1

InDel

GAAGTGTGTGATGTGTCAGACGTG

TAGAAGACACATGAAGCAGCCAAC

–Chr4

AY109715

CL333_1

SNP

GTTA

TCAGCGACTGATGAATGTGG

CAAAGTTTTATGATTTGAAACGGGA

AAAATA

TGTGGGGCTAAGTCCGGT

AY107692

PCO146629

InDel

caaagttcattgaatcggtgaaaa

ctgaaacttatttgctcacctatgatct

–AY110398

CL736_1

SNP

CGATGGTTGTTGCTTTCAGTGTAG

ATTTGTAAACATGGTTGGCGTTTC

TGTATCACTCATGTTAGTTTGTTAAAAA

AY110253

CL871_1

SNP

TACTGGATCCTCAAGAACTCCTGG

AAAGGTCATGTTCTTTGCATTCGT

AAAAAAAAAAAAAAAAAAAACACAAATCTTCAGATA

AAGC

AY110573

CL1596_1

SNP

AGATGCTCAACAGAATGTCCATGA

ATAGCGTGTTTTACATGAGGACCC

TGCTCACACCCATGATGTTACC

AY110290

CL17864_1

SNP

ACGATTGCTCAGCAGCTCTAATCT

GGGATCAGTGTACGGGTCAAATA

CGAATA

GAAAGTTAGTCAACAACTTAAAAAA

AY110872

CL65845_1

InDel

actcaattaggacaagtgcagcct

acgctcatactggcatacctcact

–AY110562

CL26590_1

SNP

GCTA

CTATTGACACGAACGAGGGT

AGATGTA

CAAGCTTGGCAAGAAGC

AAAAAAAGAGACGAGTACGGCCAC

AY110355

CL11612_1

SNP

GGAGGCAAGTTGATGGTTCTTATG

TCGCTGTTCTCTGAACAAGCAAT

TGTTCAACTGGTGGAGCCACA

AY110310

CL4235_1

SNP

GGCTGTCCACGGTCAAGAAC

CAACCCAATAATGCTTCATCCTGT

ACTGCAGGACGGCAAGATCAT

AY108440

PCO119336

InDel

gatcatctccccattgttcttgtc

catattctatggaacactgcacgg

–AY109534

CL50733_1

SNP

GCCTGCAGATGGCTACTGAACTAT

TTGTGGATGGAAAGCATGTA

ATGA

GGGCTTCCTCGCCTGATGAATTT

AY110185

CL32627_1

SNP

TTTCAGGATAATGGCCTTGTAGGA

GGCGTTCAGAATATAAGCCAGATG

GGCATTCTTGGTATTCTGAAAAAA

AY104784

CL32627_1

InDel

gagaagaagactaacggcacgaaa

gtgcgtctggtacacaacacaag

–AY112127

CL11712_1

InDel

ATCAAGCACCTGAAATGCTACACA

GTTTTAAGCAGTGGGTTCATGTCC

–AY110631

CL19053_1

SNP

CCTGACAAGGTCCTCTGGTAGCTC

TCATGAACTTCCTCGAAGAGAACG

AAAAAAAAATACCTGCGCTCAGAAACAAG

AY108096

PCO136722

InDel

CGAGGAGAAGAAGCCTTACATTGA

TCATTCATGTA

GCAACGATA

ACGG

–AY105971

PCO076386

InDel

AACCTCACCTTGTGGACTTCTGAC

CCATACCACATTTGATTATTGCCA

–AY110989

CL5869_1

InDel

GGTTTGCATTTCAGTA

TCGTAGCC

AGGAATGACGTA

TGGATTCTCTCG

–AY109980

CL10245_1

SNP

GAGAAATATGGCCTGGTAGTGGTG

CAGTCCTTTCCAAACAGTCAGAGC

GTTGATGAAAAACAACTCTTAGATA

AAY110949

CL12681_1

InDel

TGACTGTTGCTGAGCCTGTTACC

GTTTCACTGACTCGAGGGTTCG

–AY110170

CL65658_1

SNP

CATCTCAACTAGCCGTGAAGGAAG

GGTCGCCTCCACCTCAGACT

AAAAAAAAAAAATCTCACAGGTACCTA

TCCTT

AY106822

PCO104784

InDel

gaagacccagatgatctcactgct

gtacaaatcgattgacagtggcag

–AY109933

CL27530_1

SNP

AAGGACCAAAACCGTTCTCTTCTC

GAAGGAGAGGTGGGTACAACAAGA

TACTGACCTAGAAAGGTGGCTCCT

AY109730

CL2227_

3InDel

gttggaagtccggagactggat

gcaaacataggtcccaaatggtaa

AY110064

CL27003_1

SNP

TAGACGTTATAGGAGCCCCTCCAG

CGTA

GGAAACCAACCCTTTCTTG

AAATGCGTA

GCTCATTCTTGTGG

AY110231

CL852_1

InDel

GAATA

AGTCGTACTCCGGCACAGT

CCATCTAGATCTCGTGCTACCGAT

–AY108514

PCO088312

InDel

CTCTGTTCTTGTTTCCAACGGACT

AGGAGCTTGGCTCTCTTGAAACTC

–BE997321

si947017G02

InDel

AGCCTCAATCTCAGAAGAAGAGCA

CCGATCTATCAATGTGTTTGTGGA

–AY106414

PCO109372

InDel

tgtgacacaccagcaagtcctaat

tatgaggtcacatctgctatggct

–AY109668

CL6375_1

InDel

GATGTTTGCTGGTTTGTCTCTCCTT

TTAACAGCTTTTGCGACGGATA

A–

AY109859

CL6375_1

InDel

ACGCTAAAGACAAGCAACCAAAAG

CCATGTTCAAGTGTTCAACTGGTC

–AY109611

CL37807_1

SNP

CTACCGCCATACTCCTGTACGTCT

TGACAAGGCAAAGCACAAATTTTA

GGACAGTACAGATGTTCATCAGGA

Chr5

AI676903

si605046E08

SNP

CGCTTGTCAGTCTAATA

CGCCTCT

GTCCAAGGCCTGATGTCAATA

ATC

AAAAAAACATGGATCTGCAGGATTC

AY110625

CL1125_2

SNP

AAAGGTTGAGTTGCTTGGTGAGAC

CCCACTAATATCAACTCGGCAAAG

AACCATTACACCACTCCCATGTTCC

AY109758

CL1976_1

SNP

CACATCTACTTCTGCGGTTTGAAG

ACTGCCAAAAGCAACTGCAC

TCGATTCAATTTCAATCATGTGTTTGTCTCC

AY111819

CL21419_1

InDel

gcagtagaacccgatcagaaagaa

atatgtcaactctccccttatgcg

–AY106472

PCO062666

InDel

ccacacataaaacacagacccaga

ttttgacacacaaagcagcaagat

–AY109733

CL5075_1

SNP

AGGGTTTCTGTTTAGGCAGTTTCC

ACGTGAAACGATGAAATTGAACCT

GGATGAGACTTAATTCTGGTTTGACTC

AY106398

PCO135705

InDel

GCTTTCCAGAACATAAATTGGTGG

TGGTAACAGTCGTCAAGTACCACAC

–AY111142

CL9565_1

InDel

AGTA

GATCATGCATCCATCGTCAG

TCAAGGAAGGTGAAACCATTAGGA

–AY109606

CL4591_1

InDel

ACAACAGACTCTGACAGCTTGCAC

GATTCATTCTTCCGGGTTGTACTG

–AY109995

CL9999_1

SNP

CTTTCCTTCGTAGCCTGTGCTAAA

CCAGATGACCGTGTTGAGTATGAG

AAAAAAAAAAAAAAAAGCATATCACATTTAGGCCC

AY104079

PCO134626

InDel

AGGCAGTA

CAGAAGAGGAGCAAGA

AGGGAGTA

CATCGCAAGTAACAGC

–

Supp

lemen

talTab

le3.

Con

tinue

d.

Con

tinue

dne

xtpa

ge.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Chrs

Accession

Overgo

Type

Forw

ardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

BE639933

si946044B06

SNP

GTA

CAGACATA

CGAGGGGCACAG

CACGAGGTTAGTTGGTTCTGTGTG

TGACAACCTTCTGCACAT

AY110906

CL14503_1

InDel

GCAACGTCACTTCAACAGATTGTC

CAAACAATGAGGCAGAAGTATGGA

–AY105029

PCO082331

InDel

ATCAAGGCCTAGGTCAGAACTGTG

TTTCTGGGACGGAGTACATA

CCAT

–AY105906

PCO103687

InDel

accctgtctacttcttgacgaacg

agacagacagacagacaccaggaa

–AY109532

CL1742_1

SNP

GGACTATTTGGTGGATTTAGCAGG

CGAAAACTCTA

TGTTTAATTGACACCT

AAAAAAAAGCTGCGTTGTCCTCTCTATATA

TAY109682

CL2492_–1

SNP

GCTGTTCATGTACCAGAGCTTTCA

AGATGGATGTACAGAGCTCAGGCT

AATGGATCCGGACGGGGCTC

AY106487

PCO060271

InDel

GCTTTCCAGAACATAAATTGGTGG

TGGTAACAGTCGTCAAGTACCACAC

–AY108049

PCO078116

InDel

CCTGATCGAGCTCAGGAGGAT

AGTATTCTGGCAAATTCCCCATCT

–AY112581

CL11475_1

InDel

GCAGAGAGCATA

GGTGATCGTTTT

CTGCAGTGAGTTTAACAAGACCGA

–AY105069

PCO099796

InDel

TGGGTATGTTA

CAATTCCTGCAAA

AGGATGAAGAAGCTGTTATGGCTG

–AY110825

CL16923_1

InDel

gccactgttgctttcatacttgtg

aaccagtggcaaatatccgataaa

–AY110063

CL863_1

SNP

TTTCAGGTATTGTGTTGTCGTGCT

ATAACATCCGAGTCAGAGGAGCAG

AAAAAAAAAAAAAATGGATGCATCGAGTGAGTC

AY109938

CL19962_1

SNP

GACACACAAGTTGCGATCCATTAG

CGATCAAGCTTTTGCCATTCTCTA

AAAGGGAACTCTTGCTCA

AY105176

PCO111982

InDel

agcacactgatgcactaatgaagg

aacatcagaaaccacctaccagga

–AY110369

CL10716_1

SNP

CAGATGTAAGCACAGGTGATCTGG

GGTAGAAGGGTCTTGGAGTGGAGT

AAAATCTTCAGTA

CTATGGTTAGCATTGGTA

X64446

siX64446

InDel

CTCAAGGTGTGGTACGTGGTCAG

GGCCATGGCACCAGCTAGTA

T–

AY110413

CL8857_1

SNP

ATCAACACAGTCCTTGTGGAAACA

ATATGCTGTTGCCTTCCCTGATTA

ACGCAGTACGTCTATCTTGAATTTTTA

GTT

AY110182

CL16596_1

SNP

TGGTCGAACCTTCTTGGCTTACTA

GGGTCTTGGCCTTTTAGAATTCAC

AAAAGAAGTTTGCAGAACAGGC

AY105910

PCO106969

InDel

TACAGAGGTTACCCACGAGGATTT

CGGAGTAAGACTCAAAAGCAACAG

–AW065811

si614062B02b

InDel

TGGTCTCGATGTTA

ACCGTACTGA

GGCAAATA

AGTATTCCCCTCCATC

–Chr6

AY106921

PCO069699

InDel

AGTTCCTCAACGAAGAATCCACTG

AACAGACGGTCGCTTAATCTTCTG

AY110100

CL1035_1

SNP

ACTAGCAGACTGAACTCTTCGTGGA

ATCAAATCAAAGGAAGCCCACAG

GTGTGTTTTAAAGCTTGATGCTATA

TAATA

AY110213

CL1225_1

SNP

GATCACGTGGTCATTGACAAGAAG

GTA

ACTTCGGTCAACCTCTACCCC

AAAAAAAAAAAAAAACCTCATA

CATGGTGG

AY104775

PCO061308

InDel

GCATTTCCTGGTGGTGAAGTTA

TC

AAGCTCTTGAACCGCATTAAGGAT

–AY111964

CL9771_1

InDel

ATGGTACATGCATCACCTGAGAAA

CCCCTTCTCTGTTCATGGTTAATG

–AY105303

PCO075489

InDel

ctcctcatctgggtcaccatct

caagcatgagataaactggatgga

–AI737983

si606044D05

InDel

ATCAGATGTTA

CCGGTTTTGATGC

CATGTCTAAAGGTTGGAGGGAGAC

–AY104742

PCO152525

InDel

ggcatgatctgaagaagtttttgg

agacgtccgaacatctgtcatgta

–AY107240

PCO146525

InDel

GGGAACTGGATCATTCTAGTCGTG

CTTCTCCTGCTCCTACTCCTGCT

–AI665560

si605012H03

SNP

GAGCACTAGGATGGACGATTGC

GTTCTTCAGGAATTATCAAGGGGC

AATTTAATA

TATA

CTTTGGCAAGAACTGAGA

AY110542

CL4202_1

SNP

ATGTA

CATGGTGTCGCAGAACG

TCTA

TCTATCGCCATCGAGCAAT

AAAAAAATGGTGCGGGCCGAC

AY110435

CL57831_1

SNP

GGTGCACCTTCTTGACGAGG

ACGGCACAAAGATA

ATGGGCTAC

AATTCAACAGCACAGTCGTTGG

AY108243

PCO134814

InDel

gagatggcaagaatgatagcctgt

aaagagcaaaaacagagagggagg

–AY110260

CL26716_1

SNP

GCTTCCTGGTAAGGTTTGCTGATA

GAGAATTGGCTTTTGGAACATTTG

AAAAAAAAATCAACCGTCCCATTTCATTGTTAA

AY109873

CL6571_1

InDel

GCTTATGGAGATGTTA

TGCCAAGG

GAAGGGAATA

TTAACACGGCTGCT

–AY110873

CL10452_1

InDel

TCAATCGATGGTCAGAGTAGGTGA

ATTTAACAAGGTGAGGCTGTTGGA

–AY110050

CL392_1

SNP

CTTCCTGACAGGTACATCGACCAT

GTA

ACTGTTGTTCCGGCGACAC

AAAAAAAGATCTGGGCCTATA

GAGATG

AI737346

si606039C09

InDel

ACAGAATA

GCTGTGATAGGCACCC

GCAATTCGATACCAAGATCATTCC

–AY112405

CL10251_1

InDel

GATCAGCTCACGTGCAATAACATC

ACCTTTGTGCTATA

GTGGGAGGTG

–AY104923

PCO144363

InDel

TGTTTTGCTTCATGACATGTGTGT

GCTTCACAGACCAAATTCAATGTTT

–AY105728

PCO142478

InDel

AAAGGCCTTGAGAAGACAGGAGAT

GTA

CATCAGTTGCATA

GGGTCCGT

–AY110400

CL15423_2

SNP

ATGAAGAGCTGGATTCAAGATTGG

CGAGTTGAGTTCAGTTCCTAAGGG

CAATGAATGTGTTGGCTGTTGGGT

AY104289

PCO114336

InDel

CTGTTGGAAATA

AACCTGCCATTC

TCGCCTA

ACCTA

GACCAACATCAT

–AY109797

CL10211_1

SNP

CTGGTA

AATTGGTAGGGCAACTGA

CCTCCCACGACCTCTTCGTC

AAATGCCAAAGAAGTGGGGCAATGT

AY109996

CL2349_1

InDel

ACTCCAGTTTAGGCACTGATTCCA

CAGTA

GAGAATTGCGCACACCAG

–AY106902

PCO068526

InDel

TGCTATGACAAATGAATGAGCGTT

GACATGTTTTGCGCTTGAAGAAAT

–Chr7

BE056994

si945036H05

InDel

aggactacaaggataagctggcg

ctatctccttggagaccctggagt

–AY104465

PCO087457

InDel

CTCCCTCAACACACTTCTCAGGAT

TATGAGAATGGCAGTCGAAAAACC

–AY108063

PCO143084

InDel

CATA

GCGCAGTTGATGTGTGATGT

GATTTTTACACCAAGCGACAGGAA

–AW308691

si618080H02

SNP

GCAGTTGTTAGCAAGAGGGAACTC

AATGAAACTGTCAAAGGAGGATGC

TGTCTTCTTCGCGACTTCACC

AY109536

CL5684_1

SNP

CTCTA

AGACGAGCTGCTGAAAAGG

TGAAAAGAGAAAGGAGCTGACCAA

AAAAAAAAATGTCTATGCACCCACAA

AY105589

PCO140163

InDel

CTCAGCATTGTAGGCTCGTCAATA

AGACAATGTCAACTTGGTTTCTCG

–AY110473

CL10705_–2

SNP

ATA

GGGTCTCACTCTCATGGCAAG

CGAAGTTCATATCTTCGGGAATTG

CCTTCTCCGTCTGCCAGC

AY110576

CL21448_1

SNP

TGCTCCAGACTGACAACTCAATTC

TACATTACAAACATGGCAGCTGGT

AATCCTTATA

TTTGGGACTAAACTTGT

AY112356

CL4745_2

InDel

taccccatacattttcctcgctaa

ttcacaaaggctctgttgagattg

–AY109809

CL29132_1

SNP

TTTAGAACTTCTGGTTTTGCTCCG

GTGATTCTGAGGAAGATAGCCAGC

CAACTGATGCTGAGATA

CCCTGAACAA

AY105254

PCO115023

InDel

agtttgcaaatctgctcaagatcc

ttgagttcggagtcaggggtaac

–

Supp

lemen

talTa

ble3.

Con

tinue

d

Con

tinue

dne

xtpa

ge.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Chrs

Accession

Overgo

Type

Forw

ardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

AY109968

CL376_1

SNP

ACAGCACTCTTCGCCTACAATTTC

TCATGCTACCAAAGAAAAGCTGAA

AAAAACAGTTGTTCAGTTTGTCCATACA

AY110374

CL34066_1

InDel

AACACTGTCCGTTCCAGATCATTT

GGTTGCTATA

GACAAGCACTGCAC

–AY106517

PCO071075

InDel

cagcatgttcagtccaagtgctac

ccccttcaattacattacatgactgc

–AI987507

si614054G01

InDel

AACCACTTGAATTA

ACACCACGAAA

GAGATGCGAGAAGGGAAGTCAATA

–AY107797

PCO101826

InDel

AAGTGCTTGATTTCGTTACTGCCT

TTTTTGAGACCTTGGAATGTTTGTT

–AY109644

CL12102_–1

SNP

GTAGGCGGTCTTCTGACTTTCGTA

ACAAGGGAGAGAGCTGCCATC

AAAAAAAATCGCGAAGGGGACTCC

AY108039

PCO102751

InDel

ggtgttactggactacggttgagg

ttaattcacacagtgcatggacaa

–AY110023

CL41684_1

SNP

TGACCTGAGCTTTTAGGGTGACTC

CACAATTA

CTATCGACTCTCACGGTC

AAAAAAAAAAAAAAAAAAAATA

TGGTTTCATCCACCTTGA

AY110439

CL194_1

InDel

CAGGCGCTCCATA

TATAAACTTCG

GCCATGAAATCAGTCTTGAGGTGT

–AW267377

si829001F06

InDel

GGGATCTA

CGTACCCCAAGCTTTA

CGCTGTCTCCTAAAGAAAACTACACAG

–AY104976

PCO136133

InDel

gagagaacggtgttctttgacgac

cgacagggatgagctatacaaacc

–AY103848

PCO061754

InDel

atctgccttatcctcaccttcctc

caagcaaccaacccagtactacaa

–AY109703

CL4455_1

SNP

CTACACTAGGGGTGCAGGTGAGAT

TCCAATCTCCAAGAGTCTTTTA

TTCAA

GTTA

TTCTCAGGCACCCTTCTTGCC

Chr8

AY111865

CL16874_1

InDel

TCCTCAGGATGGTCAGGTACAAG

ACCGACACTTGGTTGATGAGAGAT

–AY109699

CL7702_2

InDel

CAAGGTTTCTTATACCATGCGAGG

CAGCCAATCTGATCGAAAAGTTCT

–AY111073

CL39692_1

InDel

ttccaagagacattacacgcagaa

ctcatccatcataactgtccaccc

–AY111071

CL51477_1

InDel

aagcccacctgatgatacatgact

tattagggctgatggagctattgg

–AY106269

PCO138212

InDel

CCAATTACACCACCGAGATCTACC

AACCGCTTA

AACAGCACGATTAGT

–AW244963

si687017E04

SNP

AY110450

CL27631_2

SNP

ATGGGTATGTA

CAGGTACAGGGCT

GCATA

CTGTTTGAGTCCAGCTGTT

AAAATGACACATGCAGGTTCAATGCTA

AY103821

PCO084551

InDel

GGAGTTGGGTTTTGCCTCCTATA

CGATA

AGCATGCAACAACTTCCAGA

–AY109740

CL2942_1

SNP

TTGATCAGGATTCGTGTCTATCCA

GGACAGCACATA

AACCTTGAAATATG

TTTGTTGGTGACTTGTTTCTTATGA

AY105457

PCO149506

InDel

AATGCAGGAAATA

CAAAGAAGGCA

CCATTCAACTTGGAGAACATA

AAAGG

–AY110032

CL34676_1

SNP

CCTTCTTGATCTATTCCCTGCTGA

AAACATA

CCCAATATACCTCCCGC

AAAAAAAAAAATGGCTGTTGTAAAAGAGAGAA

AY109626

CL1397_1

SNP

GATTACAGAGCACAAGTTCGGACA

GTGACCATGAACAGCTTGTCGTT

AAAAAATTTCAGTTTCTCACCTGAAGGAAAAGAAAG

AY108084

PCO147505

InDel

TAAATGCCATGCTGAAGATTTCCT

TCCAAATGTA

AGCTA

AGTGTGGTTCA

–AY110056

CL10675_1

SNP

GTACTCTCCCTTGTTGTAGGGCAA

TGGCGTGTCTACCTCTGAAATACA

AAAGTTTTGAGCACCTGTATC

AY104017

PCO119482

InDel

GGAGATTGCCCACATGTA

CAAGAC

GAACATTAACCAAAGAGCACCGAC

–AY104566

PCO130617

InDel

GATTCTGACAGTTTCCGTCAACCT

GGACAACCCGCATCAAACATA

–AY10

9883

CL42

920_

1SN

PTCTCTTCTTGGTTTCAAGGTCCAC

TCCATGCTCCAGTGCTACGATA

AAAAAACTTTCTTATCGGTGCCCC

AY107140

PCO079694

InDel

ggaaggaaaacttctccccctagt

ttccctgctgtaaaatatctggttg

–AY111629

CL9311_1

InDel

ctagtattcgaggaactgagcgga

cgttgtcagaagaaatgcagattg

–AY110569

CL10335_2

SNP

TTTAGCAAGCGAACATGTCTGAAG

GTGGTGTGCGTATCAAGAAGCAT

TTAAGAATGTA

CTGTAGTTAAAACTGGAGAA

AY110539

CL13530_1

InDel

CAGCCAAATA

ACTGATCTGCAATG

ATTCTTTGGTAGCAGCAGGTCTTG

–AY109593

CL7515_1

SNP

GCCAAGAATGATA

CCAAAACGAAG

CTGTCAATGCAGGCTTATGATGTC

AAAAAAAGAGTA

TGAGGATTATCATGTGGGCAT

AY110053

CL2103_2

SNP

ATCCTCCTTGGGTTTACTCTCTCG

CAAGCTCACCAAGATGTCGGA

AAAAAAAAAAAACAATCCCTTCAATCTGGCG

AY110127

CL4812_1

SNP

GCAGTAACCTTTGTAGGCGACAGT

TCAATA

GCGAAGCATTCAGTTCAG

AAAAGAATGTA

ATTATGCAATGTAACTGTATGC

AY103806

PCO111734

InDel

AAGAGGTGAACATTGGTGCTAAGG

TTTTTAAGCGCAACTCCAGATGAT

–AY109853

CL2096_2

InDel

GTAGAGCAAGGCCTGTGAATGG

TCAGAAGCAGTTCAATCACACACA

–Chr9

AY104252

PCO110637

InDel

ATTGCATTAACCATTGATTCCTGG

CAAACCACTCCAAACTACATGGGT

–AY109531

CL1198_1

SNP

CCTGCCAAGAACTGGGAGAAC

CACCGAACAGCAGGGATTATTTAC

AAAAGCGCGAGATCAGGGG

AY109570

CL1864_2

InDel

CTCCTTGATCATCTCGAAATA

GGG

GTGATCACTGATTTCTGGTCATGG

–AY107559

PCO061815

InDel

TGTTGTAAGAAGCATCCTGTTCCC

ATCGCGATGCACTGGTTCTG

–AY109816

CL0_–2

InDel

GCCATA

TTTCTTTACGACGACGAC

CTTTTAGTA

TGCGCCTAGCATTGG

–AI812156

si605086B11

InDel

CCTTGGTACACTACCTGCTCCAGT

CAGCATCTTGAGTGCTTA

CCCATT

–AY103770

PCO100327

InDel

ATCCGTCTTACCCTTATCCCAAAA

GCGCATTTCTAGTTTTTAGCAACG

–AW257883

si687063E06

InDel

CTTGTGGTTGTTTCTCCTGATGTG

CAAGCATA

TACAGCTTCTGCTCCC

–AY109764

CL5759_1

SNP

GCTTCTACGTTCTCCCAGATGC

TTATTACAATGCATAGCTCCCACG

TCTTGGTTAGATTTTGCCTTCCCATTCTGTT

AY110217

CL9357_1

SNP

CCCACCCGTTGTTTATA

ACTCTGT

ACCAGGGCAAGATCAAATCTGTTA

AAAAAAAAAATGGTTGAGGAAAGAAAGA

AY109792

CL22067_1

SNP

GACTTGCACCTTTTCAGAACGAAC

CCAGGGCAAGAATA

ACTACAACCA

TCTTGTACATCTTTCACAACGGTG

AW215946

si687046G05

InDel

gcctctgtaggatggatgtgatct

tatgggcattgttaccccttgtag

AY109550

CL135_2

InDel

CTTCGATGCAGTGTTCTCAGTTGT

AGCATTCGGCACAATTTTGTACTT

AY110141

CL39723_1

SNP

AACCAGAGAACTGCTGTTGATTCC

AAGAGTCCAGGAACTTCAATGCAA

ATGAAATGGCCATACATGGCAGAGTA

AY109819

CL3318_1

SNP

GATGAAGCCTAAGCAAGAGGTGAA

CTTCTTTGCAGCCTCGTTAAACAT

AAATTTGGATTTACAGTTCATTGTTGTCCTTCT

AY109543

CL854_1

SNP

ACATGAATCCAAGGTGGAACCTAA

TTGTGTCTACTGTCAAATCCTGGC

CTTGAAACTCTCCCACGCTCAC

AY110382

CL32455_1

InDel

AAATTCATCACGCTGATTTGGTTT

CAAGGCTGATA

ATA

TCTGGGCATC

–AY106323

PCO084517

InDel

CGAGAACACAGGGAAATCTGAAGT

TCCTGCAATA

AACTTGTGTAATGTGTG

–

Supp

lemen

talTa

ble3.

Con

tinue

d

Con

tinue

dne

xtpa

ge.

Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.

Chrs

Accession

Overgo

Typ

eFo

rwardprim

erReverse

prim

erSN

Pinterrog

ationprim

er

AY106075

PCO127444

InDel

ttcatcaaccagaggaagaggaac

gcgtccggacaaactatgctatac

–AI901738

si618009H12

InDel

GCATCCCATATTCCCATTGACTAA

CCATGGAAGTGGGAGATGCTAC

–AW216329

si687049E06

SNP

CTTGAACCATGCTAAGCTTCATCC

ATCGGTTTTGCGAAGTA

CAAAAGA

AATTAACCCTCAAGAGACTTCATA

TTGAA

Chr10

AY110060

CL35548_1

SNP

TAGAAAATGGATGACCATCCCAAG

TCAGAAGGCACAGGTCTATGAACA

ACTACCTTCAGAACGAAAGC

AW330564

si707029B01

SNP

CGCACTATGAGTCGGCTGAAC

CCACTTGGTA

CTACACACGCATTC

GTGTGTTTTTAGTTTA

TTATTGTGCTA

AW225120

si687024F01

InDel

GGGAATGTA

TAGTTTCTGGGCTGA

ACACCAATAAAGCGAGTCAAGGAA

–AY110360

CL2011_1

SNP

TATTTTAAGTTCGGCCTTTCATGC

AAGGATA

CAAGCGAAAGAATGCTG

AAATTTCCTGGTTACAATTTATCTT

AI795367

si605011H02

SNP

GCATGGATCATAATGTTCTCCACA

GAGGGTGGATA

CTTGACTGCTGAT

TCGTGAAGCTTCAACATGGCGAATA

AY109994

CL768_1

SNP

GACGATCTGTCTGTTTCACGAAGA

TATGACTTGCCACAAAAGCAATTC

GAGGGCAAAGGCAGACAGA

AY107726

PCO062847

InDel

ATGCAGATGCAGTGTGAGATGTTT

GGATCATA

TGGGATTTCCTGTTCA

–AY105746

PCO099975

InDel

TTCACACTGATTTTGAAAGGGGTT

ACAAGCCATA

CAATTGTGCATGTT

–AY110411

CL242_1

SNP

ACTCTACTCCTCGCGTCAATGTTC

ACAACGAGATA

ATTCTGGAGCGAG

AAAGAGAGATCGCGGACTGGG

AY110248

CL4753_–2

SNP

TGTCCTGTTCTCCATTTGTTGTGT

CATTGCTAAACACTGGGTCAGTTG

AAAAAAAAAAAAAAATA

GGGCTGGGGGCA

AY112073

CL6800_1

InDel

AGATTGCTAGCTTTATTCCGGTCC

GACCATCTGGAGGAGTACAGCAG

–AY111178

CL5772_1

InDel

CAAGGATCGTCACCTTCAACTC

CCCATA

GTCCATA

CATACATGAAAGA

–AY110514

CL948_1

SNP

AAGAATGCTGAACCAAGAGTTTCG

CCCAAACTCCAAACTCAATTCAAA

GCTTGTAACATTCCCTAATTAATGTAAATTTATG

AY109584

CL2436_1

SNP

GAGGAGAACAAACTGCTCATA

GGC

TCCTTCCTACGGTA

TCTCAGAAAACT

AAAAAAACACTAGCCAAACTGTCA

AY109920

CL36143_1

SNP

ATCCAGTGATCCCCTAAAATCCTC

CATA

CTTTTGGATGACAGTGGTGC

AAAAACAAAAGGTTAAGGATTCCGAGCT

AY109876

CL1675_1

SNP

GTGCAACGTTCTGCTTCCTTTACT

TGGAATGGGAGACGTGTCTTTAATA

AAAAAAAAAAAATA

ATGCCATCGTACAAGAATGGATG

AY106635

PCO086427

InDel

CTAGCTA

GGGCTGCCCGTGT

GTGCAAGCCGGGAAACAATA

C–

AY110365

CL38215_1

SNP

GCGATGCCACTACAGCTA

CAACTA

ACTCTA

TGGCAAGACCCATTCAAG

AAAAAAACACTGCACCAACACCTG

AY109698

CL4149_1

InDel

ACGAGCATCACGAGAAGAAGG

AAACACACGTAAATTCACATTATTCAA

–AY108476

PCO126344

InDel

CGGATTTCACTCTTAGGTTGAGGA

CCACGTTCTCATCTGGGTTAAAAG

–AY110634

CL3121_1

SNP

TACTACAACAGGCTAAGGGCGGTA

CAGGACGTGCCCTCAAAGAC

AAAGCACCTGCAGCTTCATGTT

AY106733

PCO107634

InDel

ATA

CCTGCTGGGTTCTTAGAAGGG

CAGCCTCGATGAATA

GGAACAAGT

–AY107822

PCO087182

InDel

CAGTTGCAATCTTA

GGGTACGAGG

CACAATCCAAAATGTTTTACATCCG

–AY110167

CL14540_1

InDel

CGACATCTAGATCAATCCAAGCAA

ACTCGCTTCGACTCCGACAG

–AY110016

CL16508_1

SNP

GGCTCATCTGGAACGAATA

CAAAT

CCAAATCCCTGAGCTCCAAAG

ATGGCACCATA

TGCCGATG

AY109829

CL35744_1

SNP

TGACATA

GCTCGTCCAACTGTAGC

ATGCTGCTATTGGTCTTCTTCTGG

CCAATA

GTATGCCTCACGATAATCATCAAA

Supp

lemen

talTab

le3.

Con

tinue

d.Reproducedfrom

CropScience.PublishedbyCropScienceSociety

ofAmerica.Allcopyrights

reserved.