基于全基因组关联分析挖掘橡胶树1981'IRRDB种质胶乳总固形物候选基因

Mining of candidate genes related to total solid in latex of Hevea brasiliensis 1981'IRRDB germplasm based on genome-wide association analysis

  • 摘要: 【目的】 对橡胶树1981'IRRDB种质胶乳中总固形物进行全基因组关联分析,挖掘候选基因,为解析影响橡胶产量的分子机制从而提高橡胶树1981'IRRDB种质的产胶和排胶能力提供理论依据。【方法】 以198份橡胶树1981'IRRDB种质资源为研究对象,于2022—2024年分别对橡胶树进行割胶测产,测定最后1刀次的胶乳中的总固形物含量,并分析总固形物含量的最佳线性无偏估计值(BLUE)和最佳线性无偏预测值(BLUP)。对橡胶树1981'IRRDB种质嫩叶样本中的DNA进行重测序,对3年总固形物含量的BLUE进行全基因组关联分析,检测群体SNP位点,并筛选显著SNP位点,基于转录组数据筛选候选基因。对候选基因进行GO功能注释和KEGG信号通路富集分析以及蛋白互作预测与连锁不平衡分析,鉴定关键候选基因。【结果】 2022—2024年总固形物含量变异系数为18.62%~25.01%,总固形物含量的BLUE和BLUP变异系数分别为13.48%和2.63%,各指标均呈正态或偏正态分布。在198份橡胶树1981'IRRDB种质重测序数据中鉴定到4915181个SNP位点用于全基因组关联分析。总固形物含量全基因组关联分析共筛选到15个显著SNP位点和73个候选基因。候选基因主要富集在对刺激、化学物质、有机物质刺激的反应等GO功能条目上,以及次生代谢物、类黄酮、氰基氨基酸等物质的生物合成等KEGG信号通路上。基于不同组织转录组表达量分析、蛋白质互作预测和连锁不平衡分析,筛选出HB11G016650、HB13G002880、HB14G037800和HB16G006890这4个基因为关键候选基因,分别属于生长素响应因子(ARF)、整合因子复合体(INTS)、脱落酸受体蛋白(PYL8)和引导蛋白(DP)基因家族。连锁不平衡分析结果显示,4个关键候选基因的SNP位点不同单倍型间的总固形物含量存在明显差异。【结论】 在198份橡胶树1981'IRRDB种质中鉴定到15个与总固形物含量关联的显著SNP位点,挖掘到4个与排胶能力相关的候选基因,其中ARF可能为调控橡胶产排胶过程的关键基因。

     

    Abstract: 【Objective】 This study aimed to conduct genome-wide association analysis of total solid of latex of Hevea brasiliensis 1981'IRRDB germplasm and mine candidate genes, providing theoretical basis for elucidating the molecular mechanism of rubber production to improving latex production and flow ability of Hevea brasiliensis 1981'IRRDB germplasm. 【Method】 A total of 198 Hevea brasiliensis 1981'IRRDB germplasm resources were taken as research objects, and the Hevea brasiliensis germplasm resources were tapped and the yield was measured from 2022 to 2024. The total solid content of latex in the final tapping was measured, and the best linear unbiased estimator (BLUE) and best linear un-biased prediction (BLUP) were analyzed. The DNA from young leaf samples of Hevea brasiliensis 1981'IRRDB germplasm was resequenced. Genome-wide association analysis was performed using the BLUE of total solid content over three years to detect SNP loci in the population and screen for significant SNP loci. Candidate genes were screened based on transcriptome data. The candidate genes were subjected to GO functional annotation, KEGG signaling pathway enrichment analysis, protein interaction prediction, and linkage disequilibrium analysis to identify key candidate genes. 【Result】 From 2022 to 2024, the coefficient of variation for total solid content ranged from 18.62% to 25.01%. The coefficients of variation for BLUE and BLUP of total solid content were 13.48% and 2.63% respectively, with all traits exhibi-ting normal or skewed normal distribution. A total of 4915181 SNP loci were identified from the resequencing data of 198 Hevea brasiliensis 1981'IRRDB germplasms and were used for genome-wide association analysis. Through genome-wide association analysis for total solid content, 15 significant SNP loci and 73 candidate genes were screened. Candidate genes were mainly enriched in GO functional terms such as response to stimulus, response to chemical, and response to organic substance stimulu and KEGG signaling pathways such as biosynthesis of secondary metabolites, flavonoid, and cyanoamino acid. Based on transcriptome expression analysis of different tissues, protein interaction prediction, and linkage disequilibrium analysis, 4 genes (HB11G016650, HB13G002880, HB14G037800, and HB16G006890) were screened as key candidate genes. These genes belonged to the auxin response factor (ARF), integrator complex (INTS), abscisic acid receptor protein (PYL8), and dirigent protein (DP) gene families respectively. Linkage disequilibrium analysis revealed significant differences in total solid content among different haplotypes of the SNP loci within these 4 key candidate genes. 【Conclusion】 In 198 Hevea brasiliensis 1981'IRRDB germplasms, 15 significant SNP loci associated with total solid content are identified, and 4 candidate genes related to latex flow capacity are mined. Among these, ARF is probably a key gene regulating the processes of latex production and flow for rubber.

     

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