大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果

作物基因组研究,包括基因或数量性状位点(QTL)定位、图位克隆以及物理图谱构建等,首先必须建立具有丰富标记信息的高密度遗传连锁图谱。由科丰1号和南农1138-2杂交组合衍生的重组自交系群体NJRIKY已经构建了4张大豆遗传连锁图谱,但由于遗传信息和标记数目不够充分,在基因和QTL作图时仍然存在精确度和准确度问题。为增加NJRIKY图谱密度,本研究在967对SSR引物中获得了401个多态性SSR标记。结合其他分子数据,使用作图软件Mapmaker/Exp3.0b,获得一张含有553个遗传标记,25个连锁群,总长2071.6cM,平均图距3.70cM的新遗传连锁图谱,其中SSR标记316个,RFLP标记197个,EST标记39个,形态标记1个。连锁群上大于20cM的标记间隔由原来42个减少到2个。原图谱的3个SMV抗性基因定位于D1b连锁群末端的开放区间上且仅与一个RFLP标记连锁,利用加密图谱对Rsc-3、Rsc-7、Rsc-9、Rsc-13、Rsa、Rn1和Rn3等7个SMV抗性基因重定位,全部位于D1b连锁群,与相邻分子标记距离均小于6cM,其中Rsc-9、Rn1、Rsa的距离小于1cM,Rsc-13与EST标记GMKF168a共分离。对本群体农艺性状进行QTL重定位,获得8个性状相关的42个主效QTL,其中20个QTL遗传贡献率大于10%,与原图谱比较,新定位的各QTL的标记区间明显缩短,与相邻标记的连锁更加紧密。

Density-Enhanced Genetic Linkage Map of RIL Population NJRIKY and Its Impacts on Mapping Genes and QTLs in Soybean

A high-density genetic linkage map with informative markers is essential for plant genome analysis, including gene mapping, identification of quantitative trait locus (QTL), map-based cloning, and physical map construction. Though four genetic linkage maps for the recombinant inbred line population NJRIKY derived from (Kefeng 1×Nannong 1138-2) have been established already, there are still problems of precision and accuracy in mapping genes and QTLs due to insufficiency of genetic information and number of markers. A total of 401 polymorphic SSR markers were screened out from 967 ones for density-enhancement of the previous maps. Along with other marker data, a new genetic linkage map was constructed by using Mapmaker/Exp 3.0b, with 553 markers, including 316 SSR, 197 RFLP, 39 EST and one morphologic markers, spanning 25 linkage groups, covering total length 2 071.6 cM of the soybean genome, with an average marker interval distance of 3.70 cM. In comparison with the old map, the number of gaps larger than 20 cM decreased from forty-two to two on the enhanced map. Using this map to relocate the seven SMV resistant genes, Rsc-3, Rsc-7, Rsc-9, Rsc-13, Rsa, Rn1 and Rn3 were mapped on LG D1b again with distances to the flanking markers all less than 6 cM, among them, Rsc-9, Rn1 and Rsa less than 1 cM and Rsc-13 co-segregating with EST-SSR marker GMKF168a. After re-mapping the QTLs for eight agronomic traits, 42 QTLs were detected on 12 linkage groups, with 20 of them accounted for more than 10% of the total variation, respectively, and their marker intervals obviously shortened.