the oryza map alignment project (omap): a new resource for comparative genome studies within oryza

15.1 Introduction............................................................................................395 15.2 Development of the OMAP BAC Library Resource .............................397 15.3 Development of Wild Species FPC/STC Physical Maps.......................399

15.3.1 BAC End Sequencing.....................................................................399 15.3.2 BAC Fingerprinting........................................................................399 15.3.3 Analysis of Structural Variation Between O. sativa and the

3 AA Genome OMAP Accessions.................................................401 15.4 Summary, Conclusions, and Future Research........................................404 References......................................................................................................407

15.1 Introduction

Rice (Oryza sativa L.) is the most important human food crop in the world. The agronomic importance of rice, its shared evolutionary history with ma-jor cereal crops, and small genome size have led to the generation of a high-quality finished genome sequence by the International Rice Genome

Rod A. Wing , HyeRan Kim1, Jose Luis Goicoechea1, Yeisoo Yu1, Dave Kudrna1, Andrea Zuccolo1, Jetty Siva S. Ammiraju1, Meizhong Luo1, Will Nelson2, Jianxin Ma3, Phillip SanMiguel3, Bonnie Hurwitz4, Doreen Ware4, Darshan Brar5, David Mackill5, Cari Soderlund2, Lincoln Stein4 and Scott Jackson3

1Arizona Genomics Institute, University of Arizona, Tucson, AZ 85721, USA; 2Arizona Genomics Computational Laboratory, University of Arizona, Tucson, AZ 85721, USA; 3Department of Agronomy and Genomics Core Facility, Purdue University, West Lafayette, IN 47903, USA; 4Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; 5International Rice Research Institute, Los Baños, Laguna, Philippines

15 The Oryza Map Alignment Project (OMAP): A New Resource for Comparative Genome Studies Within Oryza

Reviewed by John M. Watson and Evans Lagudah

1

396 Rod A. Wing et al.

sequence now serves as a unifying research platform for a complete func-tional characterization of the rice genome. Such an analysis will investi-gate the rice transcriptome, proteome, and metabolome, with the goal of understanding the biological function of all 35,000 to 40,000 rice genes and applying that information to improve rice production and quality. This comprehensive analysis will utilize a variety of techniques and resources from expression and genome tiling arrays to collections of tagged mutant populations developed in elite cultivars grown around the world.

Comparative genomics between the cereal genomes and within the genus Oryza will also play a critical role in our understanding of the rice genome (Ahn et al. 1993; Ahn and Tanksley 1993; Bennetzen and Ma 2003; Han and Xue 2003; Huang and Kochert 1994; Jena et al. 1994; Ma and Bennetzen 2004). By comparing genome organization, genes, and in-tergenic regions between cereal species, one can identify regions of the genome that are highly conserved or rapidly evolving. Such regions are expected to yield key insights into genome evolution, speciation, and do-mestication. The study of conserved noncoding sequences (CNSs) between cereal genomes will also increase our ability to understand and isolate regulatory elements required for precise developmental and temporal gene expression (Kaplinsky et al. 2002).

The genus Oryza is composed of two cultivated (O. sativa and O. gla-berrima) and 21 wild species (Khush 1997; Vaughan et al. 2003). Based on recent phylogenetic data, Ge et al. (1999) proposed that Porteresia coarctata should be included in the genus as the 24th Oryza species. Culti-vated rice is classified as an AA genome diploid and has 6 wild AA ge-nome relatives. The remaining 15 wild species are classified into 9 other genome types that include both diploid and tetraploid species. Figure 15.1 shows a proposed phylogenetic tree of the genus Oryza as described by Ge et al. (1999) based on the analysis of two nuclear genes and one chloro-plast gene. The wild rice species offer a largely untapped resource of agri-culturally important genes that have the potential to solve many of the problems in rice production that we face today, such as yield, drought, and salt tolerance as well as disease and insect resistance.

To better understand the wild species of rice and take advantage of the IRGSP genome sequence, we have embarked on an ambitious comparative genomics program entitled the Oryza Map Alignment Project (OMAP). The long-term objective of OMAP is to create a genome-level closed experimen-tal system for the genus Oryza that can be used as a research platform to study evolution, development, genome organization, polyploidy, domestica-tion, gene regulatory networks, and crop improvement. The specific objectivesof OMAP are to (1) construct deep-coverage large-insert bacterial artificial

Sequencing Project (2005). The highly accurate and public IRGSP

15 The Oryza Map Alignment Project (OMAP) 397

GGJJHHJJHHFFHHKKKKDD(EE)CCDDCCBBCCBBAA

O. barthii, O. glaberrima, O. longistaminata, O. nivara, O. sativa, O. rufipogonO. punctataO. minuta, O. punctataO. eichingeri, O. officinalis, O. rhizomatisO. alta, O. grandiglumus, O. latifoliaO. australiensisO. ?O. schlechteriO. brachyanthaO. ?O. longiglumis, O. ridleyiO. ?O. granulata, O. meyeriana

Fig. 15.1. Phylogenetic tree of the genus Oryza. (Modified from Ge et al. 1999)

chromosome (BAC) libraries from 11 wild and 1 cultivated African Oryza species (O. glaberrima); (2) fingerprint and end-sequence clones from all 12 BAC libraries; (3) construct physical maps for all 12 Oryza species and align them to the IRGSP genome sequence; and (4) perform a detailed re-construction of rice chromosomes 1, 3, and 10 across all 12 Oryza species (Wing et al. 2005).

This chapter presents our current progress for OMAP and some early glimpses into the results we are finding.

15.2 Development of the OMAP BAC Library Resource

Wild rice accessions were obtained from (1) the International Rice Re-search Institute (IRRI) Los Baños, Philippines; (2) the National Insti-tute of Genetics, Mishima, Japan; and (3) Cornell University, Ithaca, New York (Table 15.1). The major criteria for the selection of these wild rice accessions were that each one was robust and that sufficient seed was available for distribution to the community, and that each contained poten-tially useful agronomic traits.

High-molecular-weight DNA was obtained from young seedlings for the AA genome species O. nivara, O. rufipogon, and O. glaberrima. In con-trast, because no inbred single-seed decent material was available for the remaining wild species, we prepared DNA from single plants that were clonally propagated at IRRI. Efforts are now underway to generate inbred seed from these wild species and that should be available from the IRRI seed bank within 2 to 3 years.


Tabl

e 15

.1. O

MA

P B

AC

libr

ary

sum

mar

ya O

ryza

spec

ies

Gen

ome

IRG

C

Acc

No.

So

urce

N

o. o

f clo

nes

Ave

rage

inse

rt

size

(kb)

G

enom

e

size

(Mb)

O

. niv

ara

AA

10

0897

In

dia

55,

296

1

61

448

O. r

ufip

ogon

A

A

1054

91

Mal

aysi

a 6

4,51

2

134

4

39

O. g

labe

rrim

a A

A

9671

7 A

fric

a 5

5,29

6

130

3

57

O. p

unct

ata

BB

10

5690

A

fric

a 3

6,86

4

142

4

25

O. o

ffici

nalis

C

C

1008

96

Thai

land

9

2,16

0

141

6

51

O. m

inut

a B

BC

C

1011

41

Phili

ppin

es

129,

024

1

25

1124

O. a

lta

CC

DD

10

5143

S.

Am

eric

a 9

2,16

0

133

10

08

O. a

ustr

alie

nsis

EE

1008

82

Aus

tralia

9

2,16

0

153

9

65

O. b

rach

yant

ha

FF

1012

32

Afr

ica

36,

864

1

31

362

O. g

ranu

lata

G

G

1021

18

Thai

land

7

3,72

8

134

8

82

O. r

idle

yi

HH

JJ

1008

21

Thai

land

12

9,02

4

127

12

83

O. c

oarc

tata

H

HK

K

1045

02

Ban

glad

esh

147,

456

1

23

ND

b

aB

AC

libr

arie

s, hi

gh d

ensi

ty fi

lters

can

be

orde

red

from

the

AG

I BA

C/E

ST R

esou

rce

Cen

ter (

ww

w.g

enom

e.ar

izon

a.ed

u);

Rep

rodu

ced

from

Am

mira

ju e

t al.

(200

6) G

enom

e R

esea

rch

16:1

40-1

47; b N

D =

not

det

erm

ined

399

Deep-coverage large-insert BAC libraries were developed for all 12 OMAP species via standard procedures developed in our laboratory over the past 10 years (Table 15.1) (Luo and Wing 2003). All libraries were quality tested for insert size and depth of coverage and were found to rep-resent at least 10 genome equivalents with average insert sizes ranging be-tween 123 kb (O. coarctata) to 161 kb (O. nivara) (Ammiraju et al. 2006). All OMAP BAC libraries were deposited in the Arizona Genomic Insti-tute’s BAC/EST Resource Center for public distribution (http://www. genome.arizona.edu).

15.3 Development of Wild Species FPC/STC Physical Maps

After BAC library construction, the libraries are then BAC end sequenced and fingerprinted. The fingerprints are assembled into contigs based on shared bands between clones using finger printed contigs(FPC) software (Soderlund et al. 2000). FPC contigs can then be aligned to the IRGSP ge-nome sequence using the associated BAC end sequences.

15.3.1 BAC End Sequencing

As shown in Table 15.2, all the BAC libraries have been end sequenced. Using O. nivara as an example, OMAP attempted to sequence 110,589 BAC ends and successfully sequenced 106,104 of these. The average high-quality sequence read length was 665 bases. All BAC end sequences and trace files can be found in the GSS section and trace archive of Gen-Bank, respectively.

15.3.2 BAC Fingerprinting

To fingerprint a BAC library, we used a modification of the SNaPshot fin-gerprinting method described by Luo et al. (2003). Briefly stated, BAC DNA is isolated using a semiautomated 96-well alkaline lysis protocol (Kim HR and Wing RA, unpublished), and then digested with five restric-tion enzymes of which four generate 5 overhangs. The corresponding 3 -OH ends are then extended using a single fluorescently labeled ddNTP and DNA polymerase. The reaction products are then separated on ABI3730XL capillary electrophoresis sequencers and the labeled frag-ments are band called using ABI fragment analysis software.

15 The Oryza Map Alignment Project (OMAP)


Tabl

e 15

.2. O

MA

P B

AC

-end

sequ

enci

ng su

mm

ary

Ory

za sp

ecie

s G

enom

e N

o. o

f rea

ds

% S

ucce

ss

afte

r tr

im

No.

of

Gen

Bank

su

bmiss

ions

Ave

rage

le

ngth

(bp)

af

ter

trim

(in

Gen

Bank

)

~Mb

se

quen

ced

(in G

enBa

nk)

%

Gen

ome

cove

rage

O. n

ivar

a A

A

11

0,58

9

96

106,

124

665

71

16

O. r

ufip

ogon

A

A

7

3,71

6

96

70,

982

704

50

11

O. g

labe

rrim

a A

A

7

3,34

4

91

66,

821

590

39

11

O. p

unct

ata

BB

73,

344

93

6

8,38

4

71

0

4

9

11

O. o

ffici

nalis

C

C

11

0,59

2

93

103,

251

717

74

11

O. m

inut

a B

BC

C

18

4,22

4

92

169,

651

559

95

8

O. a

lta

CC

DD

146,

400

88

12

8,73

2

58

6

7

5

7

O. a

ustra

liens

is EE

137,

908

93

128,

599

676

87

9

O. b

rach

yant

ha

FF

7

1,35

0

94

67,

364

672

45

13

O. g

ranu

lata

G

G

14

7,21

2

94

138,

171

674

93

11

O. r

idle

yi

HH

JJ

22

1,13

7

93

204,

729

632

129

10

O. c

oarc

tata

H

HK

K

20

8,51

0

94

195,

285

661

12

9

ND

a

Tot

al/A

vera

ge

1,

558,

326

93 1,

448,

093

654

937

11

a N

D =

not

det

erm

ined

401

As shown in Table 15.3, all 12 BAC libraries have been fingerprinted and assembled into phase I physical maps. Again, using O. nivara as an example, OMAP attempted to fingerprint 51,056 clones and achieved a 91% success rate. These fingerprints were then assembled into phase I physical maps composed of 456 contigs and 2,356 singletons.

These physical maps are now being refined as “heavily manually edited maps (HME)” using a variety of assembly parameters followed by end merging and contig alignment to the IRGSP reference sequence. Figure 15.2 shows SyMAP (Soderlund et al. 2006) alignments of HME maps for O. rufipogon (AA), O. punctata (BB), and O. brachyantha (FF). As ex-pected, there is a tremendous amount of colinearity between the wild rice species and the reference IRGSP sequence (cultivar Nipponbare of O. sativa subspecies japonica). However, several regions of structural variation can be observed, even between the two AA genome species.

All of the OMAP FPC maps produced are available on the Internet us-ing webFPC (http://www.omap.org; Pampanwar et al. 2005), and BAC end

Although Oryza separated from maize and sorghum approximately 50 million years ago (MYA) and from wheat and barley approximately 40 MYA their common evolutionary history can be traced by the colinear or-der of genetic markers across their chromosomes (Moore et al. 1995). This is particularly true for the short arm of chromosome 3, which shows large stretches of genetic marker colinearity with maize chromosomes 1 and 9, sorghum linkage group C, and barley and wheat chromosomes 4L. Such conserved synteny across the cereals suggests that rice chromosome 3 will be a good model for the study of chromosome evolution.

15.3.3 Analysis of Structural Variation Between O. sativa and the 3 AA Genome OMAP Accessions

The O. sativa ssp. japonica cv Nipponbare chromosome 3 was recently finished by the US Rice Chromosome 3 Sequencing Consortium in 2005. Cytologically, chromosome 3 is the second-largest rice chromosome, measuring 56.41 μm (or approximately 52.4 Mb) and is one of the most euchromatic (Cheng et al. 2001). Genetically, chromosome 3 is 170 cM in length (Harushima et al. 1998) and has 27 morphological mutants. In addi-tion, more than 133 agronomic genes/traits/quantitative trait loci (QTLs) and 963 cDNAs have been associated with chromosome 3 (Wu et al. 2002; http://www.shigen. nig. ac.jp/rice/oryzabase). The consortium sequenced approximately 36.1 Mb of chromosome 3 and identified 6,237 new genes (The Rice Chromosome 3 Sequencing Consortium 2005).


sequence alignments as well as the OMAP FPC maps can be found on Gramene (http://www.gramene.org; Ware et al. 2002).


Tabl

e 15

.3. O

MA

P SN

aPsh

ot/F

PC fi

nger

prin

ting

Sum

mar

y

No.

of c

ontig

s O

ryza

spec

ies

Gen

ome

Gen

ome

size

(Mb)

N

o. o

f cl

ones

FP

%

Succ

ess

Phas

e I F

PC

HM

E FP

C

No.

of

singl

eton

s

O. n

ivar

a A

A

448

51,

056

91

45

6 3

40a

2,3

56

O. r

ufip

ogon

A

A

439

33,

023

91

63

7 3

27a

1,3

05

O. g

labe

rrim

a A

A

357

33,

065

85

905

1

67a

2,0

98

O. p

unct

ata

BB

42

5 3

4,22

4

93

490

2

10a

1,4

82

O. o

ffici

nalis

C

C

651

46,

937

85

764

3

10a

2,0

52

O. m

inut

a B

BC

C

1

124

86,

861

90

3,96

2 N

Eb 9

,576

O. a

lta

CC

DD

100

8 6

3,86

0

85

2,

492

NEb

3,1

11

O. a

ustr

alie

nsis

EE

965

63,

368

86

1,40

9 N

E 2

,163

O. b

rach

yant

ha

FF

362

25,

216

78

428

2

25a

1,8

05

O. g

ranu

lata

G

G

882

64,

836

88

2,35

8 N

Eb 3

,032

O. c

oarc

tata

H

HK

K

ND

c 9

2,52

2

91

1,

250

NEb

1,8

10

O. r

idle

yi

HH

JJ

1

283

104,

393

94

2,19

0 N

Eb 5

,169

a H

ME

= he

avily

man

ually

edi

ted

map

s; bN

E =

not e

dite

d; c N

D =

not

det

erm

ined

403

Fig. 15.2. SyMAP (Soderlund et al. 2006) alignments of BAC FPC/STC contig maps of three different Oryza species (left columns) with the 12 IRGSP reference genome pseudomolecules (right columns). Horizontal lines represent BES align-ments to the IRGSP reference sequence



To obtain a detailed sample of genome expansion in O. sativa, relative to the other three AA genome species, we sequenced and annotated a sin-gle BAC from each of these species that mapped near the top of the short arm of chromosome 3. The selected O. nivara BAC had a predicted size of 220 kb based on paired BAC end sequence alignment but was found to be 178 kb following full sequencing and indicated that O. sativa was ex-panded by 42 kb in this region or O. nivara contracted by the same amount (or a combination of the two resulting in a overall difference of 42 kb). The predicted sizes of the O. rufipogon and O. glaberrima BACs were 169 kb and 230 kb, however their actual sequenced sizes were 126 kb and 148 kb, respectively thus representing overall variation of 43 kb and 82 kb respec-tively. Table 15.4 summarizes the annotation analysis and shows that not only are the insertions of transposable elements responsible for the relative expansion in O. sativa but also the presence of several new genes. The most dramatic example can be seen in the sequence comparison between O. sativa and O. glaberrima as shown in Fig. 15.4. Here, the overlapping region in O. sativa spans 230.4 kb but only 114.1 kb is conserved with O. glaberrima and contains 16 annotated genes and 2 annotated retroele-ments. The remaining 116.3 kb of unique O. sativa sequence contains 10 nonorthologous genes and 11 nonorthologous retroelements. For the O. glaberrima BAC, 34 kb of the 148.1-kb sequence is unique and con-tains three nonorthologous genes and four nonorthologous retroelements.

15.4 Summary, Conclusions, and Future Research

The domestication of rice some 10,000 years ago has severely limited the gene pool that breeders can utilize for further improvements to cultivated rice. The wild species of the genus Oryza contain a wealth of genetic di-versity that must therefore be uncovered if we are to meet the challenges of feeding the world’s expanding population in the 21st century.

Insertions and deletions in genomes play a critical role in evolution. To obtain a more in-depth understanding of the roles that insertions and deletions are playing in reshaping the genomes of Oryza, we generated minimum tiling paths of BAC clones across the entire length of chromo-some 3 from the HME maps of O. nivara (AA), O. rufipogon (AA), and O. glaberrima (AA). The predicted size of each BAC clone, based on the alignment of paired BAC end sequences on the IRGSP reference genome sequence, was then compared with the empirically determined BAC size as determined by pulsed-field gel electrophoresis. Figure 15.3 shows graphical representations of this analysis and reveals that all three rice chromosomes are undergoing chromosome-wide expansion and contraction relative to the IRGSP reference sequence.

405

Diff

eren

ce –

kb (i

nser

t siz

e\B

ES a

lignm

ent

O. nivara

O. rufipogon

O. glaberrima

Chr. 3 -Mb

Fig. 15.3. Chromosome 3 expansion/contraction analysis of structural variations in three Oryza species—O. nivara, O. rufipogon, and O. glaberrima (mapped rela-tive to O. sativa ssp. japonica IRGSP reference sequence)



Table 15.4. Summary of annotated genes, complete retrotransposons, and solo LTRs of three fully sequenced orthologous BACs in comparison to the IRGSP reference sequence

O. sativa X O. nivara Number kb Number kb Unmatched blocks 5 52 3 9 Genes in unmatched blocks 5 12 0 0 Retros/solo LTRs in unmatched blocks 7 39 1 +

unannotated 9

O. sativa X O. rufipogon Number kb Number kb

Unmatched blocks 6 60 4 16 Genes in unmatched blocks 4 12 0 0 Retros/solo LTRs in unmatched blocks 7 40 4 15

O. sativa X O. glaberrima Number kb Number kb

Unmatched blocks 5 113 5 33 Genes in unmatched blocks 10 26 3 6 Retros/solo LTRs in unmatched blocks 9 50 3 +

unannotated 16

The Oryza Map Alignment Project was designed to conduct a detailed

characterization of a single representative of each of the 10 genome types of wild rice species. The alignment of these genomes to the IRGSP refer-ence sequence will provide a comprehensive physical framework whereby numerous genome-wide applied and basic research projects can be launched to unlock the genetic potential of these wild genomes and pro-vide breeders with new candidate genes and QTLs for rice improvement.

All of the production objectives for OMAP have been completed. Our consortium is now actively mining this data set and will reevaluate the phylogenetic tree of Oryza, establish genome-wide simple sequence repeat (SSR)/single–nucleotide polymorphism (SNP) maps of all the AA genome species, investigate the transposon dynamics in Oryza and their effect on genome size variation (Piegu et al. 2006), and develop a comprehensive Oryza Rearrangement Index to determine the majority of expansion, con-traction, inversion, and translocation events with respect to the IRGSP ref-erence sequence.

Because of the massive amount of information and resources that OMAP has produced to date, and will in the future, it is obvious that our consortium alone will not be able to realize the full potential of this sys-tems biology project without collaboration and cooperation with the broader research community. We therefore propose to establish an International

407

O. glaberrima

7

123 4 8 106

5 9 11 13

172 15 18 20 25 23 21

UU H2224 2614 16 19 28

27

1 2 2614 18 2016 22

15 17 19 21 23

24 28

25 27

O. sativa ssp. japonica

Feature O. sativa Conserved O. glaberrimaSequence length (kb) 230.4 114.1 148.1# annotated genes 27 16 19# annotated retroelements 12 2 6Unique seq length (kb) 116.3 34# non-orthologous genes 11 3# non-orthologous retroelements 10 4

Orthologous retro

Non-orthologous gene Non-orthologous retro

Orthologous gene

29

Fig. 15.4. Comparative annotation of O. sativa ssp. japonica IRGSP reference se-quence versus an orthologous O. glaberrima BAC

Oryza Map Alignment Project (I-OMAP), in a similar vein as the IRGSP to help coordinate research activities utilizing this new resource. Such an I-OMAP could include the development of advance backcross (ABC) popu-lations and chromosome substitution lines (CSSLs) using the AA genome OMAP accessions. Furthermore, as sequencing technologies become more cost effective, I-OMAP could propose 6x whole-genome draft sequences of all 12 OMAP species. Having such powerful genetic and sequence re-sources available would lead to much more complete understanding of the world’s most important food crop.

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