Background

The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.

Results

We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.

Conclusions

In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

中文翻译：

---

水稻三个多亲代杂交后代群体遗传连锁图谱的构建和整合

背景

基于分子标记的遗传图谱的构建是水稻遗传和基因组研究的关键步骤。来自多亲本的纯品系比双亲群体的纯品系提供更丰富的遗传变异。两个四父纯系群体（4PL1和4PL2）和一个八父纯系群体（8PL）的八个纯合开发籼稻由国际水稻研究所（IRRI）的水稻品种。据我们所知，尚无关于连锁图谱构建及其在多亲水稻群体中的整合的报道。

结果

我们构建了三个多亲群体的连锁图谱，并基于这三个图谱通过包含性复合间隔图谱（ICIM）对抽穗期（HD）和株高（PH）进行了数量性状位点（QTL）映射。从这三个单独的图构建了一个集成图，并将其用于QTL投影和荟萃分析。还基于综合图谱对这三个人群进行了QTL定位，并将图谱结果与荟萃分析的结果进行了比较。为8PL，4PL1和4PL2开发的三个连锁图分别具有5905、4354和5464箱，长度分别为1290.16、1720.01和1560.30 cM。集成地图的长度为3022.08 cM，包含10,033个容器。根据这三个连锁图，在8PL，4PL1和4PL2中检测到HD的3、7和9个QTL，而在PH中检测到6、9和10个QTL，分别。相反，通过使用整合图谱进行荟萃分析，分别确定了19个和25个QTL的HD和PH。根据集成图，分别在8PL，4PL1和4PL2中检测到HD的5、9和10个QTL，而在PH中检测到3、10和12的QTL。这49个QTL中有11个与荟萃分析的QTL相吻合。

结论

在这项研究中，我们报道了由一个八亲本重组自交系（RIL）群体构建的第一个水稻连锁图谱，以及三个多亲本群体的第一个综合图谱，它们为QTL连锁图谱，荟萃分析和水稻遗传和育种中基于图谱的克隆。