Scientia Agricultura Sinica ›› 2017, Vol. 50 ›› Issue (17): 3375-3385.doi: 10.3864/j.issn.0578-1752.2017.17.012

• HORTICULTURE • Previous Articles     Next Articles

Genome-Wide Association Studies for Flowering Time in Brassica rapa

GAO BaoZhen1, LIU Bo1, LI ShiKai2, LIANG JianLi1, CHENG Feng1, WANG XiaoWu1, WU Jian1   

  1. 1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081; 2Institute of horticultural crops, Yunnan Academy of Agricultural Sciences, Kunming 650205
  • Received:2017-01-20 Online:2017-09-01 Published:2017-09-01

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Abstract: 【Objective】To identify the genetic loci or candidate genes for flowering time regulation in Brassica rapa for improvement of pre-mature bolting resistance of B. rapa. 【Method】 In this study, 116 B. rapa germplasm accessions were selected to evaluate flowering time variations in greenhouse and open-field, respectively. Total genomic DNA was extracted with 1.2x re-sequenced depth. Filtering, mapping with reference by Pooled Mapping was conducted to obtain a genomic high quality SNP set. Then the population structure and linkage disequilibrium (LD) were analyzed using SNP set after condition filtering. In total 2000 SNP points were selected from all SNPs randomly to conduct phylogenetic tree analysis using PhyML software with maximum likelihood method. all high quality SNPs were used to conduct genomic linkage disequilibrium analysis with Haploview software. Genome-wide association study (GWAS) for flowering time variations was then conducted based on software TASSEL, GAPIT and R. According to the position of strong association signals and LD block, the candidate signals for flowering time were identified. Eventually, flowering time candidate genes in B. rapa were predicted by gene colinearity relationship between A. thaliana and B. rapa, and gene function annotation.【Result】The 116 B. rapa accessions showed extensive variations in flowering time. Significant variation was also observed between greenhouse and open-field environments. The distribution of flowering time under open-field was partial normal, while the flowering time distributed evenly under greenhouse. Phenotypes of flowering time were significantly correlated between different environments, indicating that genetic effect played a crucial role in regulation of flowering time. A total of 1.03 million SNPs covering genome-wide were generated by biotechnology analysis. Population structure showed that accessions from each sub-group were clustered, and had a close relationship with geographic origin in phylogenetic tree. The linkage disequilibrium decay across genome-wide was 2.3 kb, demonstrating that there were frequent recombinations and variants in 116 B. rapa accessions. A total of 54 strong signals (P＞4) were detected using mixed linear model and 87 (P＞5) using general linear model under two different environments. Thirty-three strong signals (27 loci under greenhouse, 19 loci under open-field) were saved after considering LD block (r2＞0.33), including 13 co-identified SNPs. Based on genome colinearity between A. thaliana and B. rapa, and gene function annotation, 14 candidate genes were predicted. Three candidate genes, FUL, PHYB, FPF1, were co-identified under greenhouse and open-field environments. FT1, a key gene involved in flowering time regulation was also identified under open-field condition.【Conclusion】 Correlation analysis of flowering time under different environments indicated that genetic control is a decisive effect on flowering time. A total of 33 significant associated SNPs controlling flowering time were identified by GWAS. By combining LD block, genome colinearity between A. thaliana and B. rapa, and gene annotation, 14 flowering time candidate genes were predicted.

Key words: Brassica rapa, flowering time, linkage disequilibrium, genome-wide association study, candidate gene

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