Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus

Abstract

Most plants are sensitive to salt-alkali stress, and the degree of tolerance to salt-alkali stress varies from different species and varieties. In order to explore the salt-alkali stress adaptability of Brassica napus, we collected the phenotypic data of 505 B. napus accessions at seedling and mature stages under control, low and high salt-alkali soil stress conditions in Inner Mongolia of China. Six resistant and 5 sensitive materials, respectively, have been identified both in Inner Mongolia and Xinjiang Uygur Autonomous Region of China. Genome-wide association studies (GWAS) for 15 absolute values and 10 tolerance coefficients (TCs) of growth and agronomic traits were applied to investigate the genetic basis of salt-alkali tolerance of B. napus. We finally mapped 9 significant QTLs related to salt-alkali stress response and predicted 20 candidate genes related to salt-alkali stress tolerance. Some important candidate genes, including BnABA4, BnBBX14, BnVTI12, BnPYL8, and BnCRR1, were identified by combining sequence variation annotation and expression differences. The identified valuable loci and germplasms could be useful for breeding salt-alkali-tolerant B.napus varieties. This study laid a foundation for understanding molecular mechanism of salt-alkali stress adaptation and provides rich genetic resources for the large-scale production of B. napus on salt-alkali land in the future.

Genome-Wide Association Studies of Salt Tolerance at the Seed Germination Stage and Yield-Related Traits in Brassica napus L.

“…Additionally, 20 of 30 SNPs were detected simultaneously in two replicate experiments, indicating the reliability of these loci. Previous studies have explored the genetic basis of salt stress responses at the germination or seedling stage using traditional QTL mapping or GWAS analysis [13,[17][18][19][20][21][22][23]45]. Compared with the previous results, four SNPs (ChrA10: 15,189,187,15,189,200,15,189,284,15, 188, 859 bp) could be repeatedly detected at the seedling and mature stages [23], and controlled different traits, suggesting that the four SNPs are common loci that control the salt tolerance of rapeseed at different stages.…”

“…Previous studies have explored the genetic basis of salt stress responses at the germination or seedling stage using traditional QTL mapping or GWAS analysis [13,[17][18][19][20][21][22][23]45]. Compared with the previous results, four SNPs (ChrA10: 15,189,187,15,189,200,15,189,284,15, 188, 859 bp) could be repeatedly detected at the seedling and mature stages [23], and controlled different traits, suggesting that the four SNPs are common loci that control the salt tolerance of rapeseed at different stages. In addition, 33 SNPs did not overlap with salt-related SNPs identified previously, but they were less than 300kb apart.…”

“…STRS2 encodes an RNA helicase protein and is identified as an upstream negative regulator of Arabidopsis in response to multiple abiotic stresses [67]. Besides these genes, five other genes (SIED1, VAMP714, HVA22C, PGN, and CER1) related to salt tolerance are also located in the region controlling both salt tolerance and yield-related traits, of which BnHVA22C (BnaA02g14490D) has been mapped in previous studies [23,45]. Of the five genes, two genes (SIED1 and CER1) have been reported to be associated with plant growth and development.…”

“…In order to further verify the reliability of the QTLs, QTL mapping studies co-localized with the present study were collected for salt tolerance [13,[17][18][19][20][21][22][23]39] and yield-related traits including SL, SS, SMI, TSW, SYP, and DWP [10][11][12]36,48,[88][89][90][91][92][93][94][95][96][97][98][99][100][101][102][103] conducted on B. napus. QTLs from previous studies and the present study were compared to the physical genomic regions of B. napus, "Darmor-bzh".…”

“…With the development of next-generation sequencing (NGS) technology, the genome-wide association study (GWAS) has become an effective approach to map QTLs related to complex traits of crops and has been applied in various crops, such as rice, soybean, and B. napus [14][15][16]. Some QTLs and candidate genes associated with salt-tolerance-related traits at the germination and seedling stages [17][18][19][20][21][22][23] and yield-related traits [24][25][26] have gradually been identified through GWAS in B. napus. Although a number of QTLs and candidate genes have been identified for salt tolerance, the molecular mechanisms underlying the regulation of salt tolerance and yield remain unclear in B. napus.…”