An Integrated Quantitative Trait Locus Map of Oil Content in Soybean, Glycine max (L.) Merr., Generated Using a Meta-Analysis Method for Mining Genes

Agricultural Sciences in China Pub Date : 2011-11-01 DOI:10.1016/S1671-2927(11)60166-1

Zhao-ming QI , Xue HAN , Ya-nan SUN , Qiong WU , Da-peng SHAN , Xiang-yu DU , Chun-yan LIU , Hong-wei JIANG , Guo-hua HU , Qing-shan CHEN

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引用次数: 20

Abstract

Soybean is a major cash crop in the world, and its oil content was one of the very important traits. Therefore, the study of gene mapping for oil content in soybean is very important for breeding application. At present, at least 130 QTL loci for soybean oil content have been published; however, the mapping results of oil content were dispersed and a coalescent public map should be established to integrate the published QTLs, and to more efficiently mine genes based on the meta-analysis method of the bioinformatics tools. This study was to construct an integrated map of QTLs for soybean oil content and accelerate the application of bioinformation resource related to oil content improvement in the practice of soybean breeding. We collected information of 130 QTLs reported over the past 20 yr for soybean oil content and used the Software BioMercator 2.1 to project QTLs from their own maps onto a reference map, which was an early-integrated map constructed by Song (2004) for oil-content quantitative trait loci (QTLs) in soybean. Gene mining was performed based on the meta-analysis by running the local ver. GENSCAN and InterProScan. The confidence interval of QTLs was efficaciously narrowed using the meta-analysis method, and 25 consensus QTLs were mapped on the reference map. Using a local version of GENSCAN, 12 805 sequences in the consensus QTL intervals were predicted. With BLAST, these predicted sequences were aligned to gene sequences from the International Protein Index database using InterProScan locally. Thirteen predicted genes were in the class of the geme ontology (GO) accession (0006631), which were involved in the fatty acid metabolic process. These genes were analyzed using BLAST at the NCBI website to examine whether they were related to oil content. Six genes were found in the oil-synthesis pathway. Twenty-five consensus QTLs and six genes were found in the oil-synthesis pathway. These results would lay the foundation for marker-assisted selection and mapping QTL precisely, and these genes will facilitate the researches on the gene mining of oil synthesis and molecular breeding in soybean.

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大豆含油量综合数量性状位点图Glycine max (L.)稳定。，使用挖掘基因的元分析方法生成

摘要大豆是世界上重要的经济作物，其含油量是其重要性状之一。因此，大豆含油量基因定位的研究对育种应用具有重要意义。目前已发表的豆油含量QTL位点至少有130个;然而，含油量的定位结果分散，需要建立一个统一的公共图谱来整合已发表的qtl，并基于生物信息学工具的荟萃分析方法更有效地挖掘基因。本研究旨在构建大豆含油量qtl综合图谱，加快提高大豆含油量相关生物信息资源在大豆育种实践中的应用。我们收集了过去20年来报道的130个大豆含油量qtl的信息，并使用软件BioMercator 2.1将他们自己的图谱中的qtl投影到参考图谱上，该参考图谱是Song(2004)构建的大豆含油量定量性状位点(qtl)的早期集成图谱。在元分析的基础上，通过运行本地程序进行基因挖掘。GENSCAN和InterProScan。采用meta分析方法有效地缩小了qtl的置信区间，并将25个一致性qtl映射到参考图谱上。利用GENSCAN的本地版本，预测了符合一致QTL区间的12 805个序列。使用BLAST，这些预测序列与InterProScan本地数据库中的基因序列进行比对。13个预测基因属于基因组本体(GO)加入(0006631)类别，参与脂肪酸代谢过程。这些基因在NCBI网站上使用BLAST进行了分析，以检查它们是否与含油量有关。在油合成途径中发现了6个基因。在油脂合成途径中发现了25个一致qtl和6个基因。这些结果将为标记辅助选择和QTL精确定位奠定基础，并为大豆油脂合成基因挖掘和分子育种研究提供依据。

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Agricultural Sciences in China AGRICULTURE, MULTIDISCIPLINARY-

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3.2 months