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Gene associated SNP discovery in fine quality Indian Gossypium barbadense cotton through whole genome resequencing

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Title Gene associated SNP discovery in fine quality Indian Gossypium barbadense cotton through whole genome resequencing
 
Creator Katageri, Ishwarappa S
Gowda, S Anjan
N V, Mohan Kumar
Lachagari, V B Reddy
Chakravartty, Navajeet
Gupta, Saurabh
 
Subject Cotton
Gosypium barbadense
whole genome resequencing
gene associated SNPs
fiber quality
 
Description 262-272
The present study deals with the resequencing of cultivars, Suvin and BCS-23-18-7 belonging to Gossypium barbadense
which are distinctly differing in fiber qualities and seed cotton yield using Illumina Hiseq2500 sequencer. A total of
2,604,107 single nucleotide polymorphism (SNP) and 592,364 insertion and deletions (INDELs) were identified when
compared with G. barbadense reference genome. Among the 14,075 preferentially expressed genes of agronomically
important traits of cotton, we have identified 33,637 markers in the genic regions. Comparing between the variants of Suvin
and BCS-23-18-7, among the 4,929 preferentially expressed genes in fiber, only 1,128 genes have 2,453 variants and of
these 1,512 variants are non-synonymous types, leading to change at the protein level. In order to validate the presence of
these markers in the expressed genes could tag the expression and/or phenotypic variation bought by alleles of Suvin/BCS-
23-18-7, among 51 fiber elongation genes, ten genes that had high effect SNPs were utilized for real-time PCR, which
showed an extended period of expression up to 15 days post-anthesis (DPA) in Suvin. Hence, utilization of such markers for
the construction of SNP array / linkage maps would provide greater value to quantitative trait loci (QTL) mapping instead of
random genomic markers.
 
Date 2022-09-21T09:48:24Z
2022-09-21T09:48:24Z
2022-09
 
Type Article
 
Identifier 0972-5849 (print) 0975-0967 (online)
http://nopr.niscpr.res.in/handle/123456789/60522
 
Language en
 
Publisher NIScPR-CSIR,India
 
Source IJBT Vol.20(3) [July 2021]