Diversity analysis in chickpea germplasm using SNP and DArT markers
1
Manish Roorkiwal 1 , Eric J von Wettberg 2,3 , Hari Upadhyaya 1 , R Varma Penmetsa 4 , Douglas R Cook 4 , Rajeev Varshney 1,5,* To estimate genetic diversity within or between 10 Cicer species (94 accessions) covering the primary, secondary and tertiary gene pool we analyzed 5257 DArT markers and 651 KASPar SNP markers. However, allelic data for only 2763 DArT and 624 SNP markers that are polymorphic between accessions of primary and tertiary genepools were analyzed further to tackle ascertainment bias. STRUCTURE analyses showed 3 populations (kabuli, desi and pea shaped) with substantial admixture in the cultivated material, while two populations were observed among the wild species using DArT markers. Analysis of molecular variance (AMOVA) was used to partition variance among hierarchical sets of landraces and wild species at either geographical level or species level. 61% of the variation was found between species, and 39% within species. Molecular variance among the wild species was high (39%) as compared to cultivated (10%). We found widespread variation in linkage disequilibrium (LD) across the genome, with variation in patterns between the relatively homogenous domesticated and more diverse wild germplasm. Observed heterozygosity was higher in wild than cultivated for each linkage group. Our results confirm the Fertile Crescent both as the center of domestication and diversification of chickpea. Although the collection used in the present study has limitations for inferences about wild diversity, it still has higher diversity in the Fertile Crescent. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa during the Pleistocene. Abstract Diversity analysis in chickpea germplasm using SNP and DArT markers Diverse Chickpea collection 96 chickpea accessions representing 10 Cicer species 68 cultivated chickpea and 28 wild chickpea accessions 28 wild accession covered 9 different wild species ranging from primary, secondary, tertiary gene pools (GP) and one accession was perennial Based on the distribution, the germplasm was divided in three different clusters namely Geographical clusters 1 International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2 Florida International University, Florida, USA; 3 Fairchild Tropical Botanic Garden, Florida, USA; 4 University of California-Davis, Davis, CA, USA; 5 CGIAR Generation Challenge Programme, c/o CIMMYT, Mexico DF, Mexico; *Address for correspondence: [email protected] Collection sites of diversity panel Kabuli Desi Pea Ter Sec Pri Perennial Wild Cultivated STRUCTURE analysis of cultivated chickpea STRUCTURE analysis of chickpea germplasm Among Pops 61% Within Pops 39% Molecular variance among cultivated and wild Among Pops 3% Within Pops 97% Among Pops 31% Within Pops 69% Molecular variance among cultivated in seed type Molecular variance among wilds in gene pools Secondary GP Primary GP Tertiary GP 0 200 400 600 800 1000 No. of DArT PIC value range Polymorhic DArT markers 0 40 80 120 160 200 No. of SNP PIC value range Polymorphic SNP markers Polymorphism status of SNP & DArT markers 651 SNPs were used for KASPar genotyping, of which 624 were mapped LG (Hiremath et al. 2012 Plant Biotechnol J 10:716-732) 611 SNPs were polymorphic across the diverse collection 2763 were chosen for analysis our of total 5257 polymorphic DArT markers based on the presence of allele in tertiary gene pool Both markers were highly polymorphich across the germplasm with the mean PIC value of 0.2313 (SNP) and 0.2214 (DArT) Coord. 2 Coord. 1 Principal Coordinates Wild Cultivated Two major groups were identified by using Neighbor-joining tree and PCA among Cicer accessions Wild from primary gene pool were mixed with cultivated chickpea Only perennial accession was embedded among the wild from tertiary gene pool Financial support provided by CGIAR Generation Challenge Programme (GCP). Acknowledgements Genetic diversification analysis CaLG01 CaLG02 CaLG03 CaLG04 CaLG05 CaLG06 CaLG07 CaLG08 Whole genome SNP gene diversity in wild and cultivated Summary Present study suggest the possibility of gene flow among these species or incomplete lineage sorting Variation in linkage disequilibrium (LD) across the genome was observed showing different patterns between domesticated and wild germplasm Higher heterozygosity was observed in wild than cultivated for each linkage group
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Transcript of Diversity analysis in chickpea germplasm using SNP and DArT markers
Manish Roorkiwal1, Eric J von Wettberg2,3, Hari Upadhyaya1,
R Varma Penmetsa4, Douglas R Cook4, Rajeev Varshney1,5,*
To estimate genetic diversity within or between 10 Cicer species (94 accessions) covering the primary, secondary and
tertiary gene pool we analyzed 5257 DArT markers and 651 KASPar SNP markers. However, allelic data for only 2763
DArT and 624 SNP markers that are polymorphic between accessions of primary and tertiary genepools were analyzed further to
tackle ascertainment bias. STRUCTURE analyses showed 3 populations (kabuli, desi and pea shaped) with substantial admixture in
the cultivated material, while two populations were observed among the wild species using DArT markers. Analysis of molecular
variance (AMOVA) was used to partition variance among hierarchical sets of landraces and wild species at either geographical
level or species level. 61% of the variation was found between species, and 39% within species. Molecular variance among the wild
species was high (39%) as compared to cultivated (10%). We found widespread variation in linkage disequilibrium (LD) across the
genome, with variation in patterns between the relatively homogenous domesticated and more diverse wild germplasm. Observed
heterozygosity was higher in wild than cultivated for each linkage group. Our results confirm the Fertile Crescent both as the
center of domestication and diversification of chickpea. Although the collection used in the present study has limitations for
inferences about wild diversity, it still has higher diversity in the Fertile Crescent. Shared alleles between different gene pools
suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of
divergence and fusion of wild chickpea taxa during the Pleistocene.
Abstract
Diversity analysis in chickpea germplasm using
SNP and DArT markers
Diverse Chickpea collection
96 chickpea accessions
representing 10 Cicer species
68 cultivated chickpea and 28
wild chickpea accessions
28 wild accession covered 9
different wild species ranging
from primary, secondary,
tertiary gene pools (GP) and
one accession was perennial
Based on the distribution, the
germplasm was divided in
three different clusters namely
Geographical clusters
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2Florida International University, Florida, USA; 3Fairchild Tropical Botanic Garden, Florida, USA; 4University of California-Davis, Davis, CA, USA; 5CGIAR Generation Challenge Programme, c/o
CIMMYT, Mexico DF, Mexico; *Address for correspondence: [email protected]
Collection sites of diversity panel
Kabuli Desi Pea
Ter Sec Pri
Perennial
Wild Cultivated
STRUCTURE analysis of cultivated chickpea
STRUCTURE analysis of chickpea germplasm
Among Pops 61%
Within Pops 39%
Molecular variance among
cultivated and wild
Among Pops 3%
Within Pops 97%
Among Pops 31%
Within Pops 69%
Molecular variance among
cultivated in seed type Molecular variance among
wilds in gene pools
Secondary
GP Primary
GP
Tertiary
GP
0
200
400
600
800
1000
No
. o
f D
ArT
PIC value range
Polymorhic DArT markers
0
40
80
120
160
200
No
. o
f S
NP
PIC value range
Polymorphic SNP markers
Polymorphism status of SNP & DArT markers
651 SNPs were used for KASPar genotyping, of which 624 were mapped
LG (Hiremath et al. 2012 Plant Biotechnol J 10:716-732)
611 SNPs were polymorphic across the diverse collection
2763 were chosen for analysis our of total 5257 polymorphic DArT markers
based on the presence of allele in tertiary gene pool
Both markers were highly polymorphich across the germplasm with the
mean PIC value of 0.2313 (SNP) and 0.2214 (DArT)
Co
ord
. 2
Coord. 1
Principal Coordinates
Wild
Cultivated
Two major groups were identified by
using Neighbor-joining tree and PCA
among Cicer accessions
Wild from primary gene pool were
mixed with cultivated chickpea
Only perennial accession was embedded
among the wild from tertiary gene pool
Financial support provided by CGIAR Generation
Challenge Programme (GCP). Acknowledgements
Genetic diversification analysis
CaLG01 CaLG02 CaLG03 CaLG04 CaLG05 CaLG06 CaLG07 CaLG08
Whole genome SNP gene diversity in wild and cultivated
Summary Present study suggest the possibility of gene flow among these species or
incomplete lineage sorting
Variation in linkage disequilibrium (LD) across the genome was observed showing
different patterns between domesticated and wild germplasm
Higher heterozygosity was observed in wild than cultivated for each linkage group
