Genome-wide association study of plant height in rapeseed RIL population

doi:10.7505/j.issn.1007-9084.2016.05.001

Abstract

Abstract:

Wuhan 430062, China; 2. School of Life Sciences, Hubei University, Wuhan 430062, China; 3. Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, China)
Abstract: To increase the efficiency of molecular marker-assisted selection on plant height and ideotype, data from 3 environments were collected using recombination inbred lines (RILs) population of Brassica napus, and genotypic data from 7 877 SNPs were investigated for genome-wide association. 5 significant SNPs (Bn-scaff_15794_3-p62430, Bn-A02-p9599263, Bn-A02-p9409799, Bn-A02-p9993945 and Bn-A02-p9636219) for plant height had been identified in at least 2 environments. They were located on A02 chromosome. Compared to QTL linkage analysis, the markers (Bn-A02-p9599263 and Bn-scaff_15794_3-p62430) respectively located on the peak of QTL qPH2-2 and qPH2-4. Markers Bn-A02-p9636219 and Bn-A02-p9993945 were located in 2-LOD (log of the likehood odds ration) confidence interval for QTLs qPH2-3 and qPH2-4. Bn-A02-p9409799 was found near distance of 0.3 cM confidence interval QTL (qPH2-2). The interval range of QTL by genome-wide association studies (69.5-80.7 cM) was 24 cM shorter than that by QTL linkage analysis (60.7-95.9 cM). According to the reference genome annotation information, a candidate gene (GSBRNA2T00090973001) corresponding to the significant SNP (Bn-scaff_15794_3-p62430) was predicted, locating in 2 kb away from the SNP. These results indicated that using single RIL population for gene-wide association studies not only compensated QTL's linkage results, but also provided theoretical basis for fine mapping and gene cloning.

Key words: Brassica napus L., Recombination inbred lines (RILs), Plant height, Genome-wide association studies, SNP

HUANG Jing CHENG Ming-xing, TANG Min-qiang, ZHANG Feng-qi, ZHANG Yuan-yuan, TONG Chao-bo, LIU Yue-ying, CHENG Xiao-hui, DONG Cai-hua, HUANG Jun-yan*, LIU Sheng-yi. Genome-wide association study of plant height in rapeseed RIL population[J]. 中国油料作物学报, 2016, 38(5): 543-.

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