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Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.

Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - Sci Rep (2015)

Bottom Line: The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated.The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent.This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

ABSTRACT
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

No MeSH data available.


Genomic distribution and relative frequency of 11989 GBS-based SNPs structurally annotated on chickpea genome/genes.(A). The distribution of 11989 GBS-based genome-wide SNPs physically mapped on eight kabuli chickpea chromosomes is illustrated in the Circos circular ideogram. The outermost and innermost circles represent the different colours-coded chromosomes and distribution of SNPs, including non-synonymous SNPs (marked with red dots), respectively. (B) Frequency distribution of 15750 GBS-based SNPs mined in the intergenic regions and diverse coding and non-coding sequence components of 3371 genes annotated from kabuli genome. Number and proportion of SNPs, including synonymous and non-synonymous SNPs annotated in the coding as well as non-coding intronic and regulatory sequences of kabuli chickpea genes and intergenic regions are depicted. The URR (upstream regulatory region) and DRR (downstream regulatory region) of genes were defined as per the gene annotation information of kabuli genome (Varshney et al.6).
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f1: Genomic distribution and relative frequency of 11989 GBS-based SNPs structurally annotated on chickpea genome/genes.(A). The distribution of 11989 GBS-based genome-wide SNPs physically mapped on eight kabuli chickpea chromosomes is illustrated in the Circos circular ideogram. The outermost and innermost circles represent the different colours-coded chromosomes and distribution of SNPs, including non-synonymous SNPs (marked with red dots), respectively. (B) Frequency distribution of 15750 GBS-based SNPs mined in the intergenic regions and diverse coding and non-coding sequence components of 3371 genes annotated from kabuli genome. Number and proportion of SNPs, including synonymous and non-synonymous SNPs annotated in the coding as well as non-coding intronic and regulatory sequences of kabuli chickpea genes and intergenic regions are depicted. The URR (upstream regulatory region) and DRR (downstream regulatory region) of genes were defined as per the gene annotation information of kabuli genome (Varshney et al.6).

Mentions: The GBS-based SNPs identified from kabuli chickpea consisted of 15,750 and 28,228 reference genome- and de novo-based SNPs, respectively. The reference genome-based SNPs included 11989 SNPs that were physically mapped on eight kabuli chromosomes with an average map density of 28.9 kb (Table 1, Fig. 1A). The remaining 3761 SNPs were physically mapped on kabuli genome scaffolds. The average SNP map density was highest on kabuli chromosome 4 (20.3 kb) and lowest on chromosome 5 (39.1 kb). A higher proportion of SNPs were physically mapped on kabuli chromosome 4 (20.2%, 2,418) (Table 1). The number of SNPs physically mapped on eight kabuli and desi (Text S1, Table S3, Fig. S2A) chromosomes revealed a direct correlation with their pseudomolecule size (bp). The constructed SNP-based physical maps of desi and kabuli chromosomes could serve as references for faster selection of genome-wide SNPs for manifold high-throughput marker-aided genetic analysis, including targeted mapping of genomes and trait-regulatory genes/QTLs in wild Cicer as well as comparative genome mapping involving chickpea and other legumes. The transitions were more frequent than transversions, which made up slightly more than half (54.7%; 45099 SNPs) of the 82489 identified SNPs (Table S4). A higher frequency of A/G transitions (51.2%, 23108 SNPs) compared to C/G (30.8%, 11,510) and G/T (30.2%, 11290) transversions in both desi and kabuli genomes was apparent. In total, 15750 reference kabuli genome-based SNPs have been submitted to NCBI dbSNP (http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=NIPGR) with SNP submission (SS) accession numbers 1399931543 to 1399947292. Collectively, the integrated reference (desi and kabuli)- and de novo-based GBS strategies employed in our study for large-scale mining and high-throughput genotyping of SNPs in wild and cultivated Cicer accessions at a genome-wide scale could have multidimensional applicability in genomics-assisted breeding of chickpea.


Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea.

Bajaj D, Das S, Badoni S, Kumar V, Singh M, Bansal KC, Tyagi AK, Parida SK - Sci Rep (2015)

Genomic distribution and relative frequency of 11989 GBS-based SNPs structurally annotated on chickpea genome/genes.(A). The distribution of 11989 GBS-based genome-wide SNPs physically mapped on eight kabuli chickpea chromosomes is illustrated in the Circos circular ideogram. The outermost and innermost circles represent the different colours-coded chromosomes and distribution of SNPs, including non-synonymous SNPs (marked with red dots), respectively. (B) Frequency distribution of 15750 GBS-based SNPs mined in the intergenic regions and diverse coding and non-coding sequence components of 3371 genes annotated from kabuli genome. Number and proportion of SNPs, including synonymous and non-synonymous SNPs annotated in the coding as well as non-coding intronic and regulatory sequences of kabuli chickpea genes and intergenic regions are depicted. The URR (upstream regulatory region) and DRR (downstream regulatory region) of genes were defined as per the gene annotation information of kabuli genome (Varshney et al.6).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4513697&req=5

f1: Genomic distribution and relative frequency of 11989 GBS-based SNPs structurally annotated on chickpea genome/genes.(A). The distribution of 11989 GBS-based genome-wide SNPs physically mapped on eight kabuli chickpea chromosomes is illustrated in the Circos circular ideogram. The outermost and innermost circles represent the different colours-coded chromosomes and distribution of SNPs, including non-synonymous SNPs (marked with red dots), respectively. (B) Frequency distribution of 15750 GBS-based SNPs mined in the intergenic regions and diverse coding and non-coding sequence components of 3371 genes annotated from kabuli genome. Number and proportion of SNPs, including synonymous and non-synonymous SNPs annotated in the coding as well as non-coding intronic and regulatory sequences of kabuli chickpea genes and intergenic regions are depicted. The URR (upstream regulatory region) and DRR (downstream regulatory region) of genes were defined as per the gene annotation information of kabuli genome (Varshney et al.6).
Mentions: The GBS-based SNPs identified from kabuli chickpea consisted of 15,750 and 28,228 reference genome- and de novo-based SNPs, respectively. The reference genome-based SNPs included 11989 SNPs that were physically mapped on eight kabuli chromosomes with an average map density of 28.9 kb (Table 1, Fig. 1A). The remaining 3761 SNPs were physically mapped on kabuli genome scaffolds. The average SNP map density was highest on kabuli chromosome 4 (20.3 kb) and lowest on chromosome 5 (39.1 kb). A higher proportion of SNPs were physically mapped on kabuli chromosome 4 (20.2%, 2,418) (Table 1). The number of SNPs physically mapped on eight kabuli and desi (Text S1, Table S3, Fig. S2A) chromosomes revealed a direct correlation with their pseudomolecule size (bp). The constructed SNP-based physical maps of desi and kabuli chromosomes could serve as references for faster selection of genome-wide SNPs for manifold high-throughput marker-aided genetic analysis, including targeted mapping of genomes and trait-regulatory genes/QTLs in wild Cicer as well as comparative genome mapping involving chickpea and other legumes. The transitions were more frequent than transversions, which made up slightly more than half (54.7%; 45099 SNPs) of the 82489 identified SNPs (Table S4). A higher frequency of A/G transitions (51.2%, 23108 SNPs) compared to C/G (30.8%, 11,510) and G/T (30.2%, 11290) transversions in both desi and kabuli genomes was apparent. In total, 15750 reference kabuli genome-based SNPs have been submitted to NCBI dbSNP (http://www.ncbi.nlm.nih.gov/SNP/snp_viewTable.cgi?handle=NIPGR) with SNP submission (SS) accession numbers 1399931543 to 1399947292. Collectively, the integrated reference (desi and kabuli)- and de novo-based GBS strategies employed in our study for large-scale mining and high-throughput genotyping of SNPs in wild and cultivated Cicer accessions at a genome-wide scale could have multidimensional applicability in genomics-assisted breeding of chickpea.

Bottom Line: The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated.The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent.This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

ABSTRACT
We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66-85%) and broader natural allelic diversity (6-64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools.

No MeSH data available.