油菜耐盐相关性状的全基因组关联分析及其候选基因预测

doi:10.3864/j.issn.0578-1752.2017.07.002

Abstract

Abstract: 【Objective】To find the SNP loci and candidate genes associated with salt tolerance in rapeseed, genome-wide association analysis of salt tolerance related traits in B. napus was performed. 【Method】 The seeds of 307 inbred lines of the association panel were germinated in Petri dishes under 1.2% NaCl. The control was under the sterile dH₂O. Three salt tolerances related traits, root length, fresh weight and germination rate of each line were measured seven days after planting. The relative value of root length, fresh weight and germination rate under the salt tolerance condition were calculated. The software TASSEL5.0 were employed to examine salt tolerance related traits in B. napus using a genome-wide association study with a 60K Brassica Illumina® Infinium SNP array. The software SPAGeDi v1.4 was used to calculate the relative kinship matrix comparing all pairs of the 307 accessions. STRUCTURE v2.3.4 was employed to analyze the population structure of the association panel. In this study, to avoid the false negative associations, three mixed models controlling relative kinship, K model, Q+K model and PCA +K model were chosen to determine the statistical associations between phenotypes and genotypes to evaluate the effects of population structure and relative kinship on salt tolerance related traits. The optimum model was determined according to observed P values and expected P values of all SNPs. TASSEL 5.0 was used to perform genome-wide analysis under the optimum model. Based on the physical positions of the associated SNP loci, the corresponding genomic sequences of the regions and flanking sequences (200 kb upstream and downstream of the SNPs) were extracted. The genes in the target intervals were extracted subsequently. According to the salt tolerance related genes in Arabidopsis, the homologous genes of rapeseed were screened out in the target genome interval.【Result】The association analysis identified 164 SNP loci significantly associated with the root length, 23 SNP loci with fresh weight, and 38 SNP loci with germination rate. The SNP loci which were most significantly associated with root length, fresh weight and germination rate were located on chromosomes A08, A02 and A06, and explained 23.84%, 18.59% and 31.81% of the phenotypic variance, respectively. Fifty candidate genes were found to be related to salt tolerance in the target interval of B. napus. These candidate genes include transcription factors Myb, WRKY, ABI1, bZIP, ERF1, CZF1, XERICO and some different functional genes which are regulated by the transcription factors, such as NHX1, PTR3, CAT1, HKT, CAX1, ACER, STH, STO, etc. The common salt tolerance gene BnaA03g14410D on chromosome A03 was screened out according to two different traits, root length and germination rate. In addition, the salt tolerance candidate genes contain two pairs of tandem repeats genes which are BnaA03g18900D and BnaA03g18910D located on chromosome A03 and BnaC09g19080D, BnaC09g19090D and BnaC09g19100D located on chromosome C09. Moreover, the salt tolerant candidate genes also contain two duplicated genes BnaC02g39600D and BnaC02g39630D with very close distances.【Conclusion】Totally, 225 SNP loci were detected significantly associated with salt tolerance related traits and fifty candidate genes were found.

Key words: Brassica napus, salt tolerance trait, GWAS, SNPs

HE YaJun, WU DaoMing, YOU JingCan, QIAN Wei. Genome-Wide Association Analysis of Salt Tolerance Related Traits in Brassica napus and Candidate Gene Prediction[J].Scientia Agricultura Sinica, 2017, 50(7): 1189-1201.

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