A soybean transcript map: Gene distribution, haplotype and single-nucleotide polymorphism analysis
A soybean transcript map: Gene distribution, haplotype and single-nucleotide polymorphism analysis
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DOI：
10.1534/genetics.107.070821
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发表时间：
2007-05-01
期刊：
影响因子：
3.3
通讯作者：
Cregan, Perry B.
中科院分区：
文献类型：
--
作者：
Choi, Ik-Young;Hyten, David L.;Cregan, Perry B.
大豆基因组的第一个遗传转录图谱是通过在三个重组近交系作图群体中的一个或多个中的1141个基因中的每一个中作图一个SNP来创建的，从而提供了基因序列在基因组的作图部分中的分布的图片。单核苷酸多态性（SNPs）是通过对表达序列标签（EST）序列进行序列标签位点（STS）重测序发现的。从最初的一组9459聚合酶链反应引物设计的一组不同的基因，4240 STS扩增和测序在每六个不同的大豆基因型。在所得到的2.44 Mbp的比对序列中，共发现了5551个SNP，包括4712个单碱基变化和839个插入缺失，平均核苷酸多样性为θ = 0.000997。相邻基因间的遗传距离与基于基因在20个大豆连锁群中随机分布的假设的理论分布的分析清楚地表明基因是聚簇的。在1141个基因中，291个基因定位在112个5-10 cM的空位中的72个，而111个基因定位在26个> 10 cM的空位中的19个。在大豆基因组图谱中增加1141个基于序列的基因标记将为大豆遗传学家提供重要的资源，用于数量性状位点的发现和基于图位的克隆，以及大豆育种家在品种改良中越来越依赖标记辅助选择。
The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Single-nucleotide polynmorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of theta = 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while I I I genes mapped in 19 of the 26 gaps > 10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.