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.
Highlights
In chickpea, a plethora of array-based SNP genotyping approaches [including Illumina GoldenGate/Infinium (Bead Xpress array) and KBioscience Competitive Allele-Specific Polymerase chain reaction (KASPar) assays] are known to greatly expedite the large-scale validation and high-throughput genotyping of previously discovered SNPs in diverse accessions, for genetic diversity studies, phylogenetics and genetic linkage map construction[1,2,3,4,5]
To accelerate the process of genetic improvement through inter-specific hybridization, the understanding of molecular diversity and domestication patterns among wild and cultivated Cicer accessions representing each of the three gene pools at a genome-wide scale is essential
This process can be complemented with marker-based introgression of trait-associated novel genes, QTLs and natural allelic variants scanned from diverse wild gene pools into cultivated accessions
Summary
Genome-wide discovery and high-throughput genotyping of SNPs using a GBS assay. The sequencing of 96-plex ApeKI libraries through a GBS assay generated approximately 279.8 million raw sequence reads from 93 wild and cultivated Cicer accessions (Table S1). Approximately 83.5% (ranging from 80.2 to 89.9%) and approximately 86.8% (80.1 to 91.5%) high-quality reads were evenly distributed across 93 Cicer accessions and mapped to unique physical locations on desi and kabuli reference draft genomes, respectively (Fig. S1B) These uniquely mapped non-redundant sequence reads effectively covered approximately 20.7% (153.6 Mb) and 21.5% (159.4 Mb) [ranging from 17.4% (129.3 Mb) to 34.3% (254.1 Mb)] of desi and kabuli chickpea genomes, respectively, with an estimated size of approximately 740 Mb. Notably, 107.6 (14.5%) and 126.7 (17.1%) Mb genomic regions of desi and kabuli chickpea genomes, respectively, represented by > 90% and/or all 93 wild and cultivated Cicer accessions, were further utilized for genome-wide discovery and genotyping of SNPs among these accessions. This difference in sequenced fractions between desi and kabuli genomes encouraged
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