AUTHOR=Srivastava Rishi , Upadhyaya Hari D. , Kumar Rajendra , Daware Anurag , Basu Udita , Shimray Philanim W. , Tripathi Shailesh , Bharadwaj Chellapilla , Tyagi Akhilesh K. , Parida Swarup K. 

TITLE=A Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea

JOURNAL=Frontiers in Plant Science

VOLUME=8

YEAR=2017

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2017.01105

DOI=10.3389/fpls.2017.01105

ISSN=1664-462X

ABSTRACT=<p>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 (<italic>Cicer arietinum desi</italic> accession ICC 4958 × <italic>C reticulatum</italic> wild accession ICC 17160)- and intra (ICC 4958 × <italic>C. arietinum kabuli</italic> 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 <italic>efl1</italic> (early flowering 1) and <italic>GI</italic> (<italic>GIGANTEA</italic>) 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 <italic>Cicer</italic> 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 <italic>efl1</italic> (36–49%) and <italic>GI</italic> (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.</p>