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A multiple QTL-Seq strategy delineates potential genomic loci governing flowering time in chickpea

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Title A multiple QTL-Seq strategy delineates potential genomic loci governing flowering time in chickpea
 
Creator Srivastava, Rishi
Upadhyaya, Hari D.
Kumar, Rajendra
Daware, Anurag
Basu, Udita
Shimray, Philanim W.
Tripathi, Shailesh
Bharadwaj, Chellapilla
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject QTL
SNP
chickpea
flowering time
multiple QTL-seq
 
Description Accepted date: 07 June 2017
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.
The financial support by the Department of Biotechnology
(DBT), Government of India to NIPGR is acknowledged.
 
Date 2017-08-14T06:26:01Z
2017-08-14T06:26:01Z
2017
 
Type Article
 
Identifier Frontiers in Plant Science, 8: 1105
1664-462X
http://59.163.192.83:8080/jspui/handle/123456789/777
http://journal.frontiersin.org/article/10.3389/fpls.2017.01105/full
https://doi.org/10.3389/fpls.2017.01105
 
Language en_US
 
Publisher Frontiers Media S.A.