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

发布时间：2018-05-03 05:39

本文选题：甘蓝型油菜 + 耐盐性状　；参考：《中国农业科学》2017年07期

【摘要】：【目的】通过对甘蓝型油菜耐盐相关性状进行全基因组关联分析,寻找可能与油菜耐盐性相关的SNP位点,发掘与油菜耐盐性有关的候选基因。【方法】以1.2%NaCl溶液作为培养液,去离子水为对照,对307个不同品系的甘蓝型油菜进行发芽试验。播种后7 d测定幼苗根长、鲜重及发芽率,计算盐胁迫下各性状相对值,并作为评价耐盐的指标。结合油菜60K SNP芯片,利用SPAGeDi v1.4软件对该群体307份甘蓝型油菜进行亲缘关系分析,并计算亲缘关系值的矩阵。利用软件STRUCTURE v2.3.4对关联群体进行了群体结构分析。为有效排除假关联的影响,将群体结构和材料间的亲缘关系考虑进关联分析中,同时进行了PCA+K模型、Q+K模型以及K模型3种混合线性模型分析和比较,根据所有SNP的 lg(P)观察值和期望值,确定每个性状GWAS分析的最优模型。采用TASSEL 5.0软件,在最优模型下对307份材料耐盐各性状的相对值分别与SNP标记进行全基因组关联分析。利用油菜基因组数据库,在显著SNP位点侧翼序列200 kb范围内提取基因。根据拟南芥中已经明确功能的耐盐相关基因,筛选出目标基因组区段内与耐盐相关的油菜同源基因。【结果】全基因组关联分析共检测到164个与根长显著关联的SNP位点,23个与鲜重显著关联的SNP位点,38个与发芽率显著关联的SNP位点。其中与根长、鲜重、发芽率最显著关联的SNP位点分别位于染色体A08、A02和A06,贡献率分别为23.84%、18.59%和31.81%。在这些显著SNP位点侧翼序列200 kb范围内发掘出可能与油菜耐盐性有关的50个候选基因。这些候选基因主要包括转录因子MYB、WRKY、ABI1、b ZIP、ERF1、CZF1、XERICO等以及一些下游受转录因子调控的不同功能基因NHX1、PTR3、CAT1、HKT、CAX1、ACER、STH、STO等。在根长和发芽率2个不同耐盐性状的分析结果中均筛选出位于A03染色体上的耐盐基因BnaA03g14410D。另外,这些耐盐候选基因中包含两组串联重复基因,分别是位于A03染色体上的BnaA03g18900D和BnaA03g18910D,位于C09染色体上的BnaC09g19080D、BnaC09g19090D和BnaC09g19100D。除此之外,耐盐候选基因中还包含2个距离非常近(中间只间隔2个基因)的重复基因BnaC02g39600D和BnaC02g39630D。【结论】共检测到225个与耐盐性状显著关联的SNP位点,筛选出50个可能与油菜耐盐性有关的候选基因。
[Abstract]:[objective] to identify the SNP sites associated with salt tolerance in Brassica napus by genome association analysis, and to identify candidate genes related to salt tolerance in Brassica napus. [methods] 1.2%NaCl solution was used as culture medium. The germination test of 307 different lines of Brassica napus was carried out in deionized water as control. The root length, fresh weight and germination rate of seedlings were measured 7 days after sowing, and the relative values of the characters under salt stress were calculated and used as an index to evaluate salt tolerance. Combined with 60K SNP microarray, SPAGeDi v1.4 software was used to analyze the phylogenetic relationship of 307 Brassica napus in this population, and the matrix of relationship value was calculated. The group structure of associated population was analyzed by software STRUCTURE v2.3.4. In order to eliminate the influence of false association, the relationship between population structure and material was taken into account in the association analysis, and the PCA K model, QK model and K model were analyzed and compared. According to the observed values and expected values of all SNP, the optimal model of GWAS analysis for each trait was determined. Under the optimal model, TASSEL 5.0 software was used to analyze the whole genome association between the relative values of each trait of salt tolerance and SNP markers. Using rapeseed genome database, the gene was extracted from the flanking sequence of significant SNP locus within 200kb. According to the salt-tolerant genes in Arabidopsis thaliana, The homologous genes related to salt tolerance in the target genome region were screened. [results] A total of 164 SNP loci were detected in the whole genome association analysis, 23 SNP loci were significantly associated with fresh weight, 38 loci were associated with hair and root length. Bud rate was significantly associated with the SNP locus. The SNP loci, which were most significantly related to root length, fresh weight and germination rate, were located on chromosome A08A02 and A06respectively, and the contribution rates were 23.848.59% and 31.81%, respectively. Fifty candidate genes which may be related to brassica napus salt tolerance were identified within the range of 200kb flanking sequence of these significant SNP loci. These candidate genes mainly include the transcription factor MYBX WRKYN ABI1nb ZIPERF1 CZF1 + XERICO, and some downstream genes, NHX1PTR3, CAT1, HKT1, CAX1, ACERCER, STHSTO, and so on. Two salt-tolerant genes, BnaA03g14410D, which were located on chromosome A03, were screened from two different salt-tolerant traits of root length and germination rate. In addition, these salt tolerance candidate genes contain two sets of tandem repeat genes, BnaA03g18900D and BnaA03g18910D located on chromosome A03, BnaC09g19080D on chromosome C09 and BnaC09g19090D and BnaC09g19100D. In addition, two repeat genes, BnaC02g39600D and BnaC02g39630D. [conclusion] 225 SNP sites were found to be significantly associated with salt tolerance traits. Fifty candidate genes that may be related to salt tolerance in rape were screened.
【作者单位】：西南大学农学与生物科技学院;
【基金】：国家重点研发计划“七大农作物育种”重点专项(2016YFD0100202) 国家自然科学基金(31671729、31301351) 中央高校基本科研业务费(XDJK2016B031)
【分类号】：S565.4

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