SAMEER KHANALDEPARTMENT OF CROP AND SOIL SCIENCES

THE UNIVERSITY OF GEORGIA

DEVELOPMENT OF AN A-GENOME DIPLOID MODEL FOR COMPARATIVE GENOMICS IN

PEANUT AND OTHER LEGUMES

BACKGROUND

OBJECTIVES SUMMARY

IMPORTANCE OF PEANUT

Among food legumes, second in national and global economic importance

United States World

Crop AreaHarvested

(ha)

Production(Mg)

AreaHarvested

(ha)

Production(Mg)

Soybean 28,842,260 82,820,048 91,386,621 209,531,558

Peanut 650,340 2,112,700 25,217,201 36,492,147

Source: compiled from faostat.fao.org

PEANUT PRODUCTION CONSTRAINTS

Abiotic Constraints

Drought

High Temperaturewww.gapeanuts.com/news/2006/092906.asp

southeastfarmpress.com/news/091106-peanut-markets/

www.washingtonpost.com/wp-dyn/content/article/2006/07/29/AR2006072900414_pf.html

Abiotic Constraints

Drought

High Temperature

Biotic Constraints

Diseases

Insect-Pests

PEANUT PRODUCTION CONSTRAINTS

Source: Diseases compiled from plantpathology.tamu.edu/Texlab/Fiber/Peanuts/atlas-toc.html

edis.ifas.ufl.edu/IN176

Third most important source of vegetable protein

Among food legumes, second in national and global economic importance

IMPORTANCE OF PEANUT

Fourth most important source of vegetable oil

Twelfth most important food crop in the world

Source: ICRISAT (www.icrisat.org) and the UN-FAO

PEANUT IMPROVEMENT CONSTRAINTS

• POLYPLOIDY (YOUNG ET AL., 1996)

• AUTOGAMY (HALWARD ET AL., 1991)

• NARROW GENETIC BASE (KNAUFT & GORBET, 1989)

AA BBX

AB

AABB

PARENTS:

INTERSPECIFIC HYBRIDIZATION

F1 HYBRID:

SPONTANEOUS CHROMOSOME DOUBLING

ALLOTETRAPLOID

PEANUT :

LOW GENETIC VARIABILITY

PEANUT IMPROVEMENT CONSTRAINTS

LACK OF SOURCES OF RESISTANCE TO SEVERAL ABIOTIC/BIOTIC STRESSES IN CULTIVATED PEANUT

Source: peanut.tamu.edu/peanut_photos.htm

PEANUT IMPROVEMENT CONSTRAINTS

DIFFICULT TO INTROGRESS RESISTANCE GENES FROM DIPLOID WILD SPECIES

WARRANTS COMPLEX CROSSES OR GENETIC TRANSFORMATION

LAGGING IN GENOMIC RESOURCES AND APPLICATION OF MOLECULAR BREEDING SOLUTIONS TO THE PERTINENT PROBLEMS

Source: peanut.tamu.edu/peanut_photos.htm

REALIZATIONS

- A CONSENSUS MAP FOR ARACHIS

- MAPPING PHENOTYPIC AND QUANTITATIVE TRAIT LOCI (QTLs)

- MARKERS LINKED TO THE GENES OF INTEREST FOR MARKER ASSISTED SELECTION (MAS)

CROP IMPROVEMENT THROUGH MOLECULAR BREEDING TECHNIQUES REQUIRE:

OBJECTIVES

INCREASING THE FREQUENCY OF HIGH-THROUGHPUT DNA MARKERS IN THE A-GENOME

FIRST OBJECTIVE

GOALA MICROSATELLITE-ENRICHED LINKAGE MAP FOR A-GENOME

MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME

- DIPLOID RFLP MAP PRODUCED FROM AN INTERSPECIFIC (A. duranensis x A. stenosperma) HYBRID (HALWARD ET AL., 1993)

- TETRAPLOID RFLP MAP PRODUCED FROM HYBRID BETWEEN A. hypogaea AND A ‘SYNTHETIC’ AMPHIDIPLOID [A. batizocoi x A. diogoi)] (BUROW ET AL., 2002)

- RECENTLY FIRST MICROSATELLITE-BASED MAP IS PUBLISHED IN Arachis (MORETZSOHN ET AL., 2005).

LINKAGE MAPPING IN DIFFERENT PEANUT SPECIES

MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME

MICROSATELLITES OR SIMPLE SEQUENCE REPEATS (SSRs) ARE MULTIPLE REPEATING UNITS OF 1 TO 4 BASE PAIRS EXAMPLE: (A)5, (AT)7, (CGG)9, (ACGG)6

- SCREENING SEQUENCES FROM GENOMIC LIBRARY- SCREENING SSR ENRICHED LIBRARY- SCREENING EST SEQUENCES

- SCREENING OF SSRs AGAINST DIFFERENT GENOTYPES

SSR DEFINITION

SSR DEVELOPMENT

POLYMORPHISM DETECTION

MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME

- 720 MARKERS SCREENED AMONG 18 ELITE AND 14 EXOTIC GERMPLAM ACCESSIONS

- 556 SSR MARKERS FOUND POLYMORPHIC

- 336 (60.4%) WERE POLYMORPHIC IN (A. Kuhlmanii x A. diogoi)

- 82 OUT OF 336 HAVE ALREADY BEEN MAPPED (MORETZSOHN ET AL., 2005)

Source: Ma (Communication)

SCREENING AVAILABLE SSR MARKERS FOR POLYMORPHISMS

MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME

-MAPPING POPULATION OF A. kuhlmanii X A. diogoi-GENOTYPING 82 PREVIOUSLY MAPPED AND 254 PREVIOUSLY UNMAPPED SSR MARKER LOCI

-THREE FOLD INCREASE IN THE DENSITY OF DNA MARKER LOCI IN THE A-GENOME

RESEARCH OVERVIEW FOR THE FIRST OBJECTIVE

OBJECTIVES

GENETIC MAPPING OF NUCLEOTIDE BINDING SITE – LEUCINE RICH REPEATS (NBS-LRR) REGISTANCE GENE CANDIDATE (RGC) LOCI

SECOND OBJECTIVE

GOALMAPPING OF 100-150 NBS-LRR RGCs

GENETIC MAPPING OF NBS-LRR RGC LOCI

- GROUPED INTO SEVERAL FAMILIES - MOST R-GENE PROTEINS CHARACTERIZED BY NUCLEOTIDE

BINDING SITE LEUCINE RICH REPEATS - 150 NBS-LRR-ENCODING GENES IN Arabidopsis thaliana AND

>400 IN Oryza sativa

Source: McHale et al. 2006

NBS LRR

TIR/CCN C

RESISTANCE GENES IN PLANTS

GENETIC MAPPING OF NBS-LRR RGC LOCI

INDEL AND SSCP MARKERS BEING DEVELOPED

NBS-LRR TEMPLETES: BERTIOLI ET AL. (2004), YUSKEL ET AL. (2005), COOK ET AL. (UNPUBLISHED DATA)

SCREENING: 58 NBS-LRR TEMPLETES SCREENED SO FAR

EIGHT CULTIVATED PEANUT (AABB) : HIGHLY MONOMORPHIC

FOUR DIPLOID GENOTYPES: HIGHLY POLYMORPHIC

RGC7

RGC4

RGC8

DU

R25

DU

R35

BA

T6

BA

T8

HY

P-G

TC-9

HY

P-A

100

HY

P-A

EQ

-2

HY

P-P

RV

-1H

YP

-TifrunnerH

YP

-HIR

-3H

YP

-GTC

-20H

YP

-FST-3

DUR BAT

- AFLP-BASED MAPPING OF RESISTANCE TO APHID VECTOR (HERSELMAN ET AL., 2004)- THREE SMALL MAP SETS WITH MARKERS FOR ROOT KNOT NEMATOD RESISTANCE (JESUBATHAM AND BUROW, 2006)

RESISTANT GENE MAPPING IN PEANUT

MARKERS USED FOR MAPPING NBS-LRR RGC LOCI

GENETIC MAPPING OF NBS-LRR RGC LOCI

- MAPPING NBS-LRR RGC LOCI IN MAPPING POPULATION OF A. kuhlmanii x A. diogoi F2 PROGENY

-SCREEN AND MAP AVAILABLE INDEL AND SSCP MARKERS FOR 50 NBS-LRR GENES

-DEVELOP, SCREEN AND MAP ADDITIONAL MARKERS FOR 50-150 ADDITIONAL NBS-LRR GENES

RESEARCH OVERVIEW FOR THE SECOND OBJECTIVE

OBJECTIVES

IDENTIFY NBS-LRR ALLELES INTROGRESSED FROM WILD DIPLOID INTO CULTIVATED TETRAPLOID LINES

THIRD OBJECTIVE

GOALIDENTIFY AND CHARACTERIZE SEVERAL NBS-LRR GENES

Line P.I. Number Background Reference  PI 262141 A. cardenasii Donor    PI 261942 A. hypogaea Parent    PI 261943 A. hypogaea Parent  GP-NC WS 1 PI 564844 Wild Introgression Line (WIL) Stalker and Beute (1993)GP-NC WS 2 PI 564845 WIL Stalker and Beute (1993)GP-NC WS 3 PI 564846 WIL Stalker and Beute (1993)GP-NC WS 4 PI 564847 WIL Stalker and Beute (1993)TXAG-6 PI 565287 WIL Simpson et al. (1993)TXAG-7 PI 565288 WIL Simpson et al. (1993)ICGV 86699 PI 591815 (A. batizocoi/A. duranensis)//NC 2 Reddy et al. (1996)ICGV 87165 PI 594923 WIL Moss et al. (1997)ICGV SM 86715 PI 598133 WIL Moss et al. (1998)COAN PI 610452 WIL Simpson and Starr (2001)GP-NC WS 5 PI 619169 WIL Stalker et al. (2002a)GP-NC WS 6 PI 619170 WIL Stalker et al. (2002a)GP-NC WS 7 PI 619171 WIL Stalker and Lynch (2002)GP-NC WS 8 PI 619172 WIL Stalker and Lynch (2002)GP-NC WS 9 PI 619173 WIL Stalker and Lynch (2002)GP-NC WS 10 PI 619174 WIL Stalker and Lynch (2002)GP-NC WS 11 PI 619175 (NC 6//NC Ac 3033)/GP-NC WS 1 Stalker et al. (2002b)GP-NC WS 12 PI 619176 (NC 6//NC Ac 3033)/GP-NC WS 1 Stalker et al. (2002b)GP-NC WS 13 PI 619177 (NC 5//PI 270806)/GP-NC WS 4 Stalker et al. (2002b)GP-NC WS 14 PI 619178 WIL Stalker et al. (2002b)GP-NC WS 15 PI 619179 WIL Stalker et al. (2002b)NR 0817 PI 639266 AT-108/GP-NC WS 5 Anderson et a. (2006)NR 0812 PI 639267 AT-108/GP-NC WS 5 Anderson et a. (2006)N96076L PI 641950 N90004/GP-NC WS 13 Isleib et al. (2006)

IDENTIFICATION AND CHARACTERIZATION OF NBS-LRR GENES

IDENTIFICATION AND CHARACTERIZATION OF NBS-LRR GENES

-SCREENING AVAILABLE LINES FOR R-GENE INTROGRESSION

-IDENTIFYING INTROGRESSED NBS-LRR ALLELES

- CHARACTERIZING NOVEL NBS-LRR ALLELES

RESEARCH OVERVIEW FOR THE THIRD OBJECTIVE

SUMMARY

• WILD RELATIVES OF CULTIVATED PEANUT ARE THE SOURCES OF NOVEL RESISTANCE GENES

• MOLECULAR BREEDING TOOLS FACILITATE TO TRANSFER USEFUL GENES FROM WILD DIPLOID TO CULTIVATED PEANUT SPECIES

• SSR-ENRICHED LINKAGE MAP WILL BE DEVELOPED FOR AA-GENOME DIPLOID MODEL

• MORE THAN 100 NBS-LRR RGC LOCI WILL BE MAPPED WITH SSCP AND INDEL MARKERS

• WILD INTROGRESSION LINES WILL BE SCREENED TO IDENTIFY NBS-LRR ALLELE

END OF THE PRESENTATION

THANK YOU