Please use this identifier to cite or link to this item:
http://223.31.159.10:8080/jspui/handle/123456789/777
Title: | A multiple QTL-Seq strategy delineates potential genomic loci governing flowering time in chickpea |
Authors: | Srivastava, Rishi Upadhyaya, Hari D. Kumar, Rajendra Daware, Anurag Basu, Udita Shimray, Philanim W. Tripathi, Shailesh Bharadwaj, Chellapilla Tyagi, Akhilesh K. Parida, Swarup K. |
Keywords: | QTL SNP chickpea flowering time multiple QTL-seq |
Issue Date: | 2017 |
Publisher: | Frontiers Media S.A. |
Citation: | Frontiers in Plant Science, 8: 1105 |
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. |
Description: | Accepted date: 07 June 2017 |
URI: | http://59.163.192.83:8080/jspui/handle/123456789/777 |
ISSN: | 1664-462X |
Appears in Collections: | Institutional Publications |
Files in This Item:
File | Description | Size | Format | |
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Parida SK_2017_4.pdf | 1.74 MB | Adobe PDF | ![]() View/Open |
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