陆地棉早熟与产量纤维品质性状的全基因组关联分析及候选基因筛选

发布时间：2018-05-23 08:26

本文选题：陆地棉 + GWAS　；参考：《西北农林科技大学》2017年博士论文

【摘要】：棉花(Gossypium spp.)是世界上最重要的纤维作物,也是我国最主要的经济作物之一。我国是主要的产棉大国和棉纺织品出口大国,棉花在我国国民经济中占有十分重要的地位。陆地棉(Gossypium hirsutum L.)是棉花最大的四倍体栽培种,其产量占了整个棉花的95%以上。早熟、纤维品质、产量等性状是陆地棉最主要的育种目标性状,这些性状的QTL定位和基于SSR标记关联分析的研究已有大量的报道,但是基于全基因组SNP位点的全基因组关联分析(GWAS)的研究相对较少。因此从全基因组水平上解析主要育种目标性状遗传基础的研究仍不够,需要进一步开展相关研究。本研究利用355份陆地棉种质资源构成的自然群体,基于SLAF简化测序技术,检测到了能均匀分布在陆地棉26条染色体上的81,675个SNP位点;同时分2年(2014-2015)2点(河南安阳、新疆石河子)田间种植全部供试材料,调查了与早熟、纤维品质、产量相关的主要性状,开展了SNP位点与目标性状的GWAS研究及显著关联位点附近候选基因的挖掘,主要研究结果如下:通过6个早熟相关性状的GWAS研究,获得了41个与早熟相关性状显著的关联,其中29个关联所对应的SNP位点分布在Dt3染色体上。在这些显著关联的位点中,位于Dt3染色体上的SNP位点rsDt3:13562854同时与5个早熟相关性状(WGP、FT、FBP、NFFB和YPBF)显著关联,-log10(P)为6.77~10.10,能解释9.34%~14.13%的表型变异。rsDt3:13562854附近1Mb的基因组区域注释了32个基因,qRT-PCR分析发现,CotAD_01947在叶片中优势表达,2~4叶期在早熟品种叶片的表达量显著高于中晚熟品种(P0.01)。结果说明CotAD_01947是与陆地棉的早熟性相关的候选基因。通过3个产量构成性状的GWAS研究,获得12个与衣分性状显著相关的SNP位点,其中定位在At3和At4染色体上的5个SNP位点的-log10(P)6.21,能解释9.42%~12.88%的表型变异。分布在At4染色体上rsAt4:15572813和rsAt4:15573052能在4个不同的环境及BLUPs下同时与衣分显著关联;分布在At3上rsAt3:43538238、rsAt3:43631774和rsAt3:43631819能在3个不同的环境及BLUPs下同时与目标性状显著关联,说明At3和At4染色体上存在控制衣分性状的两个主效QTL。利用陆地棉(TM-1)10个不同组织的RNA-seq数据,分析发现Gh_A02G1268在5 DPA纤维中优势表达,而在种子表达量很低,是纤维5 DPA表达量的1/300,我们推测Gh_A02G1268可能在提高陆地棉衣分及纤维品质方面具有潜在的作用。通过5个纤维品质构成性状的GWAS研究,分别获得了16、10、7个与FL、FS和FU显著关联的SNP位点。在Dt7染色体上发现了两个重要基因组区段MGR1和MGR2,其中MGR1上存在有9个SNP位点均与FL显著关联;MGR2存在有2个SNP位点同时与FL、FS显著关联。在MGR1和MGR2两个区段内,存在有四个注释基因:CotAD_22823、CotAD_22824、CotAD_22825和CotAD_35088,这四个基因可能是控制FL与FS的候选基因。同时发现MGR1和MGR2,在五个生态区(YR、YZR、NW、LN和USA)品种间的优异单倍型分布频率和遗传多样性系数均存在显著的差异。YR、YZR和USA材料的优异单倍型频率显著高于NW和LN材料,新疆南疆品种的优异单倍型出现频率显著高于北疆。结果说明我国低纬度地区品种优异单倍型的出现频率要高于高纬度地区的品种。同时发现MGR1和MGR2的遗传多样性系数远低于全基因组及Dt7染色体的平均遗传多样性指数,而且优异单倍型种质的遗传多样性系数也显著低于非优异单倍型种质。这些结论支持MGR1和MGR2经历了一个人工选择过程的推论。
[Abstract]:Cotton (Gossypium spp.) is the most important fiber crop in the world and one of the most important economic crops in our country. China is the main big country of cotton producing and cotton textile export. Cotton plays a very important role in the national economy of our country. Gossypium hirsutum L. is the largest tetraploid planting seed of cotton, its production accounts for its production. More than 95% of the whole cotton, precocious, fiber quality, yield and other traits are the most important breeding target traits of upland cotton. There have been a lot of reports on the QTL location of these traits and SSR based markers association analysis, but the total genomic association analysis (GWAS) based on the whole genome SNP loci is relatively less. Therefore, the whole gene is from the whole gene. It is not enough to analyze the genetic basis of the main breeding target traits at the level of the group. The natural population of 355 terrestrial cotton germplasm resources is used in this study. Based on the simplified sequencing technology of SLAF, 81675 SNP loci that can be evenly distributed on the 26 chromophore of upland cotton are detected, and 2 years (2014-20) 15) 2 points (Anyang in Henan, Shihezi of Xinjiang) were planted in the field, and the main characters related to precocious, fiber quality and yield were investigated. The GWAS study of SNP and target traits and the mining of candidate genes near the significant associated sites were carried out. The main results were as follows: through the GWAS study of 6 precocious related traits, the results were obtained. 41 associations with the precocious correlation, of which the corresponding SNP loci of the 29 associations were distributed on the Dt3 chromosome. In these significantly associated sites, the SNP locus on the Dt3 chromosome was associated with the 5 precocious related traits (WGP, FT, FBP, NFFB and YPBF), and -log10 (P) could be interpreted. 32 genes were annotated in the genomic region of 1Mb in the vicinity of the phenotypic variation.RsDt3:13562854. QRT-PCR analysis found that CotAD_01947 was dominant in leaves, and the expression of leaves at 2~4 leaf stage was significantly higher than that of middle late maturing varieties (P0.01). The results indicated that CotAD_01947 was a candidate gene related to early maturity of land cotton. Through 3 yields, it was found that CotAD_01947 was a candidate gene for early maturity of land cotton. The GWAS study, which constitutes a trait, obtained 12 SNP loci significantly related to the properties of the linen, including -log10 (P) 6.21 of the 5 SNP loci on the At3 and At4 chromosomes, which could explain the phenotypic variation of 9.42%~12.88%. On the At4 chromosome, rsAt4:15572813 and rsAt4:15573052 can be closely related to the linen under 4 different environments and BLUPs. The distribution of rsAt3:43538238, rsAt3:43631774 and rsAt3:43631819 on At3 can be associated with the target traits at the same time in 3 different environments and BLUPs, indicating that there are RNA-seq data on the two main QTL. using 10 different tissues of Land Cotton (TM-1) on the At3 and At4 chromosomes, and that Gh_A02G1268 is found in 5 DPA fibers. The expression in the seed is very low, but the expression of the seed is very low. It is 1/300 of the 5 DPA expression of fiber. We speculate that Gh_A02G1268 may have a potential role in improving the cotton clothing and fiber quality of the land. The SNP locus which is significantly associated with FL, FS and FU, respectively, is obtained by the GWAS study of the character of 5 fiber qualities. In the Dt7 chromosome Two important genome segments MGR1 and MGR2 were found, of which 9 SNP loci on MGR1 were associated with FL; there were 2 SNP loci in MGR2 with FL and FS significantly associated. There were four annotated genes in MGR1 and MGR2 two regions: four genes may be controlled. The candidate genes of L and FS also found that the excellent haplotype distribution frequencies and genetic diversity coefficients of the five ecological regions (YR, YZR, NW, LN and USA) were significantly different in.YR, and the excellent haplotype frequency of YZR and USA materials was significantly higher than that of the materials. The frequency of the outstanding haplotypes of Xinjiang Southern Xinjiang varieties was significantly higher. The results show that the frequency of high haplotypes in low latitudes in China is higher than those of high latitudes. The genetic diversity coefficient of MGR1 and MGR2 is far lower than the average genetic diversity index of the whole and Dt7 chromosomes, and the genetic diversity coefficient of the excellent haplotype species is also significantly lower than that of non optimal ones. These results support the inference that MGR1 and MGR2 have undergone an artificial selection process.
【学位授予单位】：西北农林科技大学
【学位级别】：博士
【学位授予年份】：2017
【分类号】：S562

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