An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.
An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F₂ maize population.
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DOI：
10.1186/1471-2164-15-433
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发表时间：
2014-06-04
期刊：
影响因子：
4.4
通讯作者：
Lai J
中科院分区：
文献类型：
--
作者：
Chen Z;Wang B;Dong X;Liu H;Ren L;Chen J;Hauck A;Song W;Lai J
玉米雄穗和穗构型的遗传控制。SSP.玉米）由于其与谷物产量的关系而重要。高分辨率QTL定位对于理解表型变异的分子基础至关重要。先进的群体，如重组自交系，已被广泛采用的QTL定位;然而，大的先进一代作物群体的建设是耗时和昂贵的。由于下一代测序技术的最新进展，基因分型的成本迅速下降，这为使用大的早代群体进行QTL定位产生了新的可能性。以自交系昌7 -2和787的F2代共708个为材料，采用全基因组低覆盖测序法（平均0.04×）进行基因分型。基于亲本SNP和滑动窗口法构建了包含6，533个bin标记的遗传图谱，总遗传距离为1，396 cM。该图谱的高质量和准确性通过鉴定两个已充分研究的基因r1和ba 1得到验证，r1是控制丝颜色的质量性状基因（第10号染色体），ba 1是控制雄穗分支数的基因（第3号染色体）。对该群体的雄穗和穗型3个性状进行了检测，共检测到10个QTL，其中7个与已报道的QTL重叠。编码MADS盒结构域蛋白和BTB/POZ结构域蛋白的三个基因（GRMZM 2G 316366、GRMZM 2G 492156和GRMZM 5G 805008）位于qTBN 5和qTBN 7的小间隔（长度分别为~800 Kb和1.6 Mb）中，并且可能参与雄穗结构的图案化。大多数QTL的物理间隔很小，表明该方法可以获得高分辨率的定位。构建了玉米早代群体超高密度连锁图谱。本研究为快速、高精度地检测复杂性状变异的数量基因座提供了一种有效的方法，从而有助于剖析表型变异的分子基础，以经济高效的方式加快作物育种的改进。本文的在线版本（doi：10.1186/1471-2164-15-433）包含补充材料，可供授权用户使用。
Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations. A set of 708 F2 progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method. We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion. The online version of this article (doi:10.1186/1471-2164-15-433) contains supplementary material, which is available to authorized users.