Identification of salt stress-tolerant candidate genes in the BC2F2 population at the seedling stages of G. hirsutum and G. darwinii using NGS-based bulked segregant analysis

Salinity is a major threat to the yield and productivity of cotton seedlings. In present study, we developed BC 2 F population plants from Gossypium darwinii (5–7) hirsutum (CCRI 12–4) salt-susceptible parents identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant DNA bulks were pooled by using 30 population. Next-generation sequencing (NGS) technology for both bulks. Four significant genomic regions identified: first region located on chromosome 18 (1.86 Mb), second third 25 (1.06 Mb 1.94 Mb, respectively), fourth 8 (1.41 Mb). reads bulk1 bulk2 aligned G. genomes, respectively, leading identification 20,664,007 single-nucleotide polymorphisms (SNPs) insertions/deletions (indels). After screening, 6,573 polymorphic markers obtained after filtration regions. SNP indices in resistant susceptible Δ(SNP-index) values measured. Based higher value, six effective SNPs selected different chromosome. Six linked five genes four Further validation these carried out reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting an expression profile that showed two highly upregulated salt-tolerant species , i.e., Gohir.D05G367800 Gohir.D12G239100 ; however, opposite shown which all genes, except one, partial expression. results indicated may be We are confident this study could helpful cloning, transformation, development varieties.