Abstract
Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- and intra (ICC 4958 × C. arietinum kabuli accession ICC 8261)-specific RIL mapping populations to identify the major QTL genomic regions governing flowering time in chickpea. The whole genome resequencing discovered 1635117 and 592486 SNPs exhibiting differentiation between early- and late-flowering mapping parents and bulks, constituted by pooling the homozygous individuals of extreme flowering time phenotypic trait from each of two aforesaid RIL populations. The multiple QTL-seq analysis using these mined SNPs in two RIL mapping populations narrowed-down two longer (907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea chromosome 4. This essentially identified regulatory as well as coding (non-synonymous/synonymous) novel SNP allelic variants from two efl1 (early flowering 1) and GI (GIGANTEA) genes regulating flowering time in chickpea. Interestingly, strong natural allelic diversity reduction (88–91%) of two known flowering genes especially mapped at major QTL intervals as compared to that of background genomic regions (where no flowering time QTLs were mapped; 61.8%) in cultivated vis-à-vis wild Cicer gene pools was evident inferring the significant impact of evolutionary bottlenecks on these loci during chickpea domestication. Higher association potential of coding non-synonymous and regulatory SNP alleles mined from efl1 (36–49%) and GI (33–42%) flowering genes for early and late flowering time differentiation among chickpea accessions was evident. The robustness and validity of two functional allelic variants-containing genes localized at major flowering time QTLs was apparent by their identification from multiple intra-/inter-specific mapping populations of chickpea. The functionally relevant molecular tags delineated can be of immense use for deciphering the natural allelic diversity-based domestication pattern of flowering time and expediting genomics-aided crop improvement to develop early flowering cultivars of chickpea.
Highlights
Chickpea (Cicer arietinum L.) is one of the vital food legume crops represented by two of its major cultivar types- desi and kabuli (Kumar et al, 2011) which are thought to be domesticated along with the wild ancestor C. reticulatum at Fertile Crescent around 10000 years ago (Burger et al, 2008; Toker, 2009)
Considering usefulness and broader practical applicability, multiple QTL-seq assay can be employed for rapid genomewide scanning and fine-mapping of traitlinked major genes and natural allelic-variants colocalized at robust QTLs in chickpea with minimal resource expenses
In view of afore-mentioned possibilities, a multiple QTL-seq strategy was employed in two inter- and intra-specific recombinant inbred lines (RILs) mapping populations- (C. arietinum desi accession ICC 4958 × C. reticulatum wild accession ICC 17163) and (ICC 4958 × C. arietinum kabuli accession ICC 8261)- at a genome-wide scale to delineate major genomic regions and novel natural allelic variants underlying the QTLs associated with flowering time in chickpea
Summary
Chickpea (Cicer arietinum L.) is one of the vital food legume crops represented by two of its major cultivar types- desi and kabuli (Kumar et al, 2011) which are thought to be domesticated along with the wild ancestor C. reticulatum at Fertile Crescent around 10000 years ago (Burger et al, 2008; Toker, 2009). Considering usefulness and broader practical applicability, multiple QTL-seq assay can be employed for rapid genomewide scanning and fine-mapping (positional cloning) of traitlinked major genes and natural allelic-variants colocalized at robust QTLs (well-validated in multiple mapping populations) in chickpea with minimal resource expenses This will collectively enrich our understanding on complex genetic architecture and evolutionary pattern influencing flowering time quantitative trait variation during domestication of chickpea in order to expedite its genomics-assisted crop improvement. In view of afore-mentioned possibilities, a multiple QTL-seq strategy was employed in two inter- and intra-specific RIL (recombinant inbred lines) mapping populations- (C. arietinum desi accession ICC 4958 × C. reticulatum wild accession ICC 17163) and (ICC 4958 × C. arietinum kabuli accession ICC 8261)- at a genome-wide scale to delineate major genomic (gene) regions and novel natural allelic variants underlying the QTLs associated with flowering time in chickpea
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