甘蓝型油菜角果长度全基因组关联分析

doi:10.3864/j.issn.0578-1752.2017.02.003

摘要/Abstract

摘要： 【目的】挖掘与油菜角果长度性状显著相关的SNP位点及候选基因，为揭示油菜角果长度性状的遗传基础和分子机制提供理论依据，为油菜产量分子标记辅助选择育种奠定基础。【方法】在江西农业大学试验地和江西省红壤研究所试验地2个环境下考察300份甘蓝型油菜自交系的角果长度性状，利用简化基因组测序技术（specific locus amplified fragment sequencing，SLAF-seq）对300份甘蓝型油菜自交系基因组DNA进行测序并分析，利用获得的均匀分布于甘蓝型油菜基因组上的201 817个群体SNP（single nucleotide polymorphism，SNP）对角果长度性状进行全基因组关联分析（genome-wide association study，GWAS），探测与油菜角果长度显著相关的SNP位点，并基于群体连锁不平衡分析结果搜寻显著SNP位点两侧100 kb范围内的基因，通过BLAST获得关联区域内基因的注释信息，根据注释信息找出与性状相关的候选基因。【结果】农大试验地角果长度表型变异幅度为46.35—107.07 mm；红壤所试验地角果长度表型变异幅度为39.41—101.35 mm，两性状在2个环境下均表现出广泛表型变异。通过一般线性模型（general linear model，GLM）关联分析，农大环境下共检测到121个角果长度显著关联的SNP位点，分布在A04、A06、A08、A09、C02、C03、C06和C09等8条染色体上，其中，A09染色体上分布最多（83个SNP），红壤所环境下检测到22个角果长度显著关联的SNP位点，其中，1个在C09染色体上，其余21个均分布于A09染色体，在两地探测到20个一致性SNP位点；通过混合线性模型（mixed linear model，MLM）分析，农大环境下共检测到5个角果长度显著关联的SNP位点，其中，3个SNP位点与红壤所环境下检测到3个SNP位点一致，所有位点均位于A09染色体上。对MLM关联分析得到的显著SNP位点两侧100 kb区域内基因进行搜寻并进行功能注释，发现多个候选基因参与调节碳水化合物的运输与合成、花器官和种子的发育、信号转导等, 它们可能通过上述功能影响油菜角果的生长，导致角果长度的差异。【结论】通过GLM和MLM两种分析方法探测到多个与油菜角果长度性状显著关联的基因位点，并在显著性位点附近搜寻到相关候选基因。

关键词: 甘蓝型油菜, 全基因组关联分析, 角果长度, SNP位点, 候选基因

Abstract: 【Objective】The objective of this study is to detect the SNP loci and determine related candidate genes affecting the silique length of B. napus significantly to reveal its genetic basis and molecular mechanism, and lay a foundation for the marker assisted selection in high yield breeding of B. napus. 【Method】In this study, the phenotype of silique length was investigated at two environments (JXAU of Nanchang and JXIRS of Jinxian) with 300 accessions of B. napus, combining with the 201,817 SNPs developed from specific locus amplified fragment sequencing (SLAF-seq) technology, the genome-wide association analysis was proceeded to detect the SNP loci affecting the silique length significantly, and the regions were scanned with 100 kb apart from the loci of SNP associated dramatically with silique length based on linkage disequilibrium analysis, and finally the candidate genes were predicted with relation to silique length by BLAST analysis.【Result】The variation ranges of silique length in the two places were 46.35-107.07 mm and 39.41-101.35 mm, respectively, which both showed extensive phenotypic variation in two environments. In addition, a total of 121 SNP loci in JXAU correlatively with silique length were excavated by general linear model (GLM), which distributed on A04, A06, A08, A09, C02, C03, C06 and C09 chromosomes, and the largest number of SNPs (83) was on A09 chromosome. Otherwise, 22 SNPs in JXIRS with 1 on C09 and 21 on A09 were detected, and there were 20 consensus SNPs under two environments. Besides, 5 SNPs in JXAU and 3 SNPs (P＜4.96E-07) in JXIRS all distributed on A09 chromosome were detected respectively using the mixed linear model (MLM), three of which were consistent in two environments. There were 40 candidate genes screened in the candidate regions with 100 kb apart from the positions of SNPs associated significantly with silique length, functional analyses showed that these genes involved in regulation of carbohydrate transportation and synthesis, flower and seed development, signal transduction and etc., which might result in the variation of silique length through affecting the growth and development of silique in B. napus. 【Conclusion】The SNP loci and candidate genes related closely with silique length of B. napus were detected in this study, thus providing a theoretical basis for the seed yield regulatory network of B. napus and molecular assisted selection of high-yield breeding of rapeseed.

Key words: Brassica napus, Genome-wide association study, silique length, SNP locus, candidate gene

周庆红，周灿，郑伟，付东辉. 甘蓝型油菜角果长度全基因组关联分析[J]. 中国农业科学, 2017, 50(2): 228-239.

ZHOU QingHong, ZHOU Can, ZHENG Wei, FU DongHui. Genome Wide Association Analysis of Silique Length in Brassica napus L.[J]. Scientia Agricultura Sinica, 2017, 50(2): 228-239.

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