Open AccessIdentification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton
Author(s) -
Caiping Cai,
Shuang Wu,
Erli Niu,
Chaoze Cheng,
Wangzhen Guo
Publication year - 2017
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/s41598-017-00617-7
Subject(s) - biology , gene , genetics , wrky protein domain , genome , gossypium , gene silencing , gene family , intron , genetic marker , gene expression , transcriptome
Intron length polymorphisms (ILPs), a type of gene-based functional marker, could themselves be related to the particular traits. Here, we developed a genome-wide cotton ILPs based on orthologs annotation from two sequenced diploid species, A-genome Gossypium arboreum and D-genome G . raimondii . We identified 10,180 putative ILP markers from 5,021 orthologous genes. Among these, 535 ILP markers from 9 gene families related to stress were selected for experimental verification. Polymorphic rates were 72.71% between G . arboreum and G . raimondii and 36.45% between G . hirsutum acc. TM-1 and G . barbadense cv. Hai7124. Furthermore, 14 polymorphic ILP markers were detected in 264 G . hirsutum accessions. Coupled with previous simple sequence repeats (SSRs) evaluations and salt tolerance assays from the same individuals, we found a total of 25 marker-trait associations involved in nine ILPs. The nine genes, temporally named as C1 to C9 , showed the various expressions in different organs and tissues, and five genes ( C3 , C4 , C5 , C7 and C9 ) were significantly upregulated after salt treatment. We verified that the five genes play important roles in salt tolerance. Particularly, silencing of C4 (encodes WRKY DNA-binding protein) and C9 (encodes Mitogen-activated protein kinase) can significantly enhance cotton susceptibility to salt stress.