Wen Weie, He Zhonghu, Gao Fengmei, Liu Jindong, Jin Hui, Zhai Shengnan, Qu Yanying, Xia Xianchun
College of Agronomy, Xinjiang Agricultural UniversityUrumqi, China.
National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China.
Front Plant Sci. 2017 Aug 9;8:1389. doi: 10.3389/fpls.2017.01389. eCollection 2017.
A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat ( L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.
高密度一致性图谱是小麦育种中进行基因定位、克隆及分子标记辅助选择的有力工具。本研究的目的是通过整合四个重组自交系群体的遗传图谱，构建一张基于单核苷酸多态性（SNP）的普通小麦高密度一致性图谱。利用小麦90K Infinium iSelect SNP检测法对这些群体进行基因分型。共将29,692个SNP标记定位到与21条六倍体小麦染色体相对应的21个连锁群上，覆盖2,906.86 cM，整体标记密度为10.21个标记/cM。与基于小麦90K SNP芯片的先前图谱相比，检测到22,736个（76.6%）SNP在染色体上的位置一致，而1,974个（6.7%）显示出不同的染色体位置，4,982个（16.8%）是新定位的。将本一致性图谱与小麦表达序列标签（EST）染色体 bins 图谱进行比对，可将1,221个SNP标记定位到特定的染色体 bins 上，并将819个EST整合到一致性图谱中。基于小麦基因组上的物理位置，通过斯皮尔曼等级相关系数（范围从0.69（4D）到0.97（1A, 4B, 5B和6A））对一致性图谱的标记顺序进行了验证，并且还通过与先前40K SNP一致性图谱上的遗传位置进行比较（斯皮尔曼等级相关系数范围从0.84（6D）到0.99（6A））进行了确认。先前报道的染色体重排情况在本一致性图谱中得到了证实，并鉴定出了新的假定重排。此外，通过将五个已发表的图谱与我们的图谱相结合，构建了一个包含52,607个分子标记的整合一致性图谱。这里描述的一致性图谱提供了一个高密度SNP标记图谱和可靠的SNP顺序，代表了在小麦90K阵列上SNP染色体位置映射和验证方面的一个进步。此外，它可作为数量性状位点（QTL）定位的参考，以促进小麦育种中基因和QTL的利用。
