Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (1): 15-27.doi: 10.3864/j.issn.0578-1752.2017.01.002

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-Wide Association Study of Root Length and Hypocotyl Length at Germination Stage Under Saline Conditions in Brassica napus

ZHANG Rui1, DENG WenYa1, YANG Liu1, WANG YaPing1, XIAO FangZhi2, HE Jian2, LU Kun1   

  1. 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715; 2 Shennong Class, Southwest University, Chongqing 400715
  • Received:2016-07-01 Online:2017-01-01 Published:2017-01-01

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Abstract: 【Objective】 Identification of the regulatory loci and candidate genes governing salt stress tolerance in Brassica napus at germination stage could lay the foundation for improvement of B. napus salt resistance. 【Method】 In this study, 317 representative B. napus inbred lines were genotyped under normal and salt-stressed conditions in a sand culture system. Significant SNPs associated with root length and hypocotyl length in B. napus under normal and saline stress conditions and their linkage disequilibrium (LD) were determined by genome-wide association studies (GWAS), based on the Brassica 60 K SNP array. Candidate genes were selected based on the combination analyses results of functional annotation of genes within the LD blocks and transcriptome analyses of seedling roots and leaves in B. napus under saline stress treatments. Accuracy of candidate gene selection was improved by real-time quantitative reverse transcriptase PCR (qRT-PCR). 【Result】 Hypocotyl length and root length of B. napus showed large variation among accessions at germination stage under normal and salt-stressed conditions, and frequency distribution revealed that all the target traits were quantitative traits and controlled by polygenic genes. Comparison of different models showed that MLM+P+K model was the optimal model. Based on this model, GWAS identified 45 loci significantly associated with target traits, including 40 and 5 SNPs associated with hypocotyl length and root length, and each of SNP explained 9.12%-14.46% and 7.67%-8.93% of phenotypic variation, respectively. Among the significantly associated SNPs, rs8970 on chromosome C04 was the most notable, since it was the only SNP, which could be repeatedly detected between root length and hypocotyl length, and associated with four traits simultaneously, explaining 7.67%-12.35% of observed phenotypic variation. Of the 11 important significantly associated SNPs, 6 SNPs were distributed in 10 to 442 kb of linkage disequilibrium (LD) blocks. By combining differentially expressed genes detected by transcriptome analysis with LD block identification, 447 genes were identified within the 11 important LD intervals, of which 15 were activated by salt stress. BnaSRO1, BnaPAGR2, BnaNPH3, BnaMYB124, BnaSAM-Mtase, BnaBIN2, BnaUMAMIT11, BnaEXPA7, BnaRPT3, BnaEF-hand and BnaF3H were most likely the candidate genes within their LD blocks. Results of qRT-PCR detection showed that 10 candidate genes were induced by salt stress treatment in root or hypocotyl at germination stage, except for BnaNPH3. In addition, tissue-specificity detection of candidate genes also showed that BnaUMAMIT11, BnaPAGR2 and BnaEXPA7mainly expressed in the root and hypocotyl at germination stage, and BnaRPT3, BnaBIN2 and BnaMYB124 possessed the highest expression in hypocotyl, confirmed that these genes might be involved in development of root and hypocotyl and salt resistance of B. napus at germination stage. 【Conclusion】 A total of 45 significantly associated SNPs controlling development and salt resistance in root and hypocotyl of B. napus at germination stage were identified by GWAS. By combined LD block identification, transcriptome analyses and functional annotation, 11 important candidate genes were screened within different LD blocks.

Key words: Brassica napus, germination, salt tolerance, genome-wide association study, transcriptome

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