Abstract
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.
Highlights
In modern crop breeding, many traits of interest such as yield, quality, and resistance to biotic or abiotic stress need to be improved simultaneously to allow crops to survive in extreme environmental conditions and to safeguard the safety of crops
We investigated the temporal and spatial expression profiles of the nine candidate genes associated with salt stress traits in different tissues and in response to salt stress treatment, and verified that the functional roles of five genes that are significantly induced by salt stress treatment by virus-induced gene silencing (VIGS) analysis
Using 9,598 genes from G. raimondii as probes, 2,528 gene sequences showed no differences between the A- and D-genome introns, and 44,966 introns from 7,070 genes showed at least one intron difference for each pair of orthologs, with the different intron-lengths ranging from 1 bp to 1,339 bp
Summary
Many traits of interest such as yield, quality, and resistance to biotic or abiotic stress need to be improved simultaneously to allow crops to survive in extreme environmental conditions and to safeguard the safety of crops. The availability of data on the whole-genome of Gossypium in different cotton species, including G. raimondii (D5)[18, 19], G. arboreum (A2)[20], G. hirsutum acc. We screened for differences in the intron-lengths of orthologous A- and D-genome genes, which have a relatively high level of similarity, by comparing genome sequences and annotation information from G. raimondii and G. arboreum, and developed a large number of gene-based ILP markers. We selected a set of ILP markers representative of genes associated with abiotic stress response pathways to experimentally validate the levels of diversity between G. arboreum and G. raimondii or between two allotetraploid cultivated species Our study provided genome-wide, gene-based ILPs marker resources in cotton, and mined effectively the genes with salt-tolerance for developing abiotic-resistance cultivars in future cotton-breeding programs
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
