通过大豆全基因组关联分析鉴定与 21 叶绿素荧光表型相关的基因组位点。
Identification of genomic loci associated with 21chlorophyll fluorescence phenotypes by genome-wide association analysis in soybean.
机构信息
Division of Plant Science, University of Missouri, Columbia, MO, 65211, USA.
Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA.
出版信息
BMC Plant Biol. 2018 Nov 29;18(1):312. doi: 10.1186/s12870-018-1517-9.
BACKGROUND
Photosynthesis is able to convert solar energy into chemical energy in the form of biomass, but the efficiency of photosynthetic solar energy conversion is low. Chlorophyll fluorescence measurements are rapid, non-destructive, and can provide a wealth of information about the efficiencies of the photosynthetic light reaction processes. Efforts aimed at assessing genetic variation and/or mapping of genetic loci associated with chlorophyll fluorescence phenotypes have been rather limited.
RESULTS
Evaluation of SoySNP50K iSelect SNP Beadchip data from the 189 genotypes phenotyped in this analysis identified 32,453 SNPs with a minor allele frequency (MAF) ≥ 5%. A total of 288 (non-unique) SNPs were significantly associated with one or more of the 21 chlorophyll fluorescence phenotypes. Of these, 155 were unique SNPs and 100 SNPs were only associated with a single fluorescence phenotype, while 28, 11, 2, and 14 SNPs, were associated with two, three, four and five or more fluorescence phenotypes, respectively. The 288 non-unique SNPs represent 155 unique SNPs that mark 53 loci. The 155 unique SNPs included 27 that were associated with three or more phenotypes, and thus were called multi-phenotype SNPs. These 27 multi-phenotype SNPs marked 13 multi-phenotype loci (MPL) identified by individual SNPs associated with multiple chlorophyll fluorescence phenotypes or by more than one SNP located within 0.5 MB of other multi-phenotype SNPs.
CONCLUSION
A search in the genomic regions highlighted by these 13 MPL identified genes with annotations indicating involvement in photosynthetic light dependent reactions. These, as well as loci associated with only one or two chlorophyll fluorescence traits, should be useful to develop a better understanding of the genetic basis of photosynthetic light dependent reactions as a whole as well as of specific components of the electron transport chain in soybean. Accordingly, additional genetic and physiological analyses are necessary to determine the relevance and effectiveness of the identified loci for crop improvement efforts.
背景
光合作用能够将太阳能转化为生物质形式的化学能，但光合作用的太阳能转化效率较低。叶绿素荧光测量快速、无损，可以提供有关光合作用光反应过程效率的丰富信息。评估与叶绿素荧光表型相关的遗传变异和/或遗传基因座作图的努力相当有限。
结果
对本分析中表型测定的 189 个基因型的 SoySNP50K iSelect SNP Beadchip 数据进行评估，确定了 32453 个次要等位基因频率（MAF）≥5%的 SNP。共有 288 个（非独特）SNP 与 21 个叶绿素荧光表型中的一个或多个显著相关。其中，155 个是独特的 SNP，100 个 SNP 仅与单个荧光表型相关，而 28、11、2 和 14 个 SNP 分别与两个、三个、四个和五个或更多荧光表型相关。这 288 个非独特 SNP 代表标记 53 个基因座的 155 个独特 SNP。这 155 个独特 SNP 包括 27 个与三个或更多表型相关的 SNP，因此被称为多表型 SNP。这 27 个多表型 SNP 标记了 13 个由与多个叶绿素荧光表型相关的单个 SNP 或位于其他多表型 SNP 0.5MB 内的一个以上 SNP 确定的多表型基因座（MPL）。
结论
对这些 13 个 MPL 突出的基因组区域进行搜索，鉴定出具有参与光合作用光依赖反应注释的基因。这些基因座，以及与一个或两个叶绿素荧光性状相关的基因座，对于更好地了解光合作用光依赖反应的遗传基础以及大豆电子传递链的特定组件都应该是有用的。因此，需要进行额外的遗传和生理分析，以确定所鉴定的基因座对作物改良努力的相关性和有效性。
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