Developing new population types based on interspecific introgressions has been suggested to facilitate the discovery of novel allelic sources for traits of agronomic importance. In this study, a chromosome segment substitution line (CSSL) rice population carrying contiguous chromosomal segments of japonica Nipponbare in the genetic background of indica 9311 was developed. Meanwhile, a high-density genetic map including 655 bins covering a distance of 1480.2 Mb, with an average of 0.60 Mb between markers, was generated through a whole-genome resequencing approach. Compared with previous CSSL populations constructed from 9311 or Nipponbare, this population has a higher marker density and can effectively meet the requirements of high QTL mapping resolution. On the basis of the newly constructed high-density genetic map, a total of three major QTLs (qGP4, qGP5, and qBL4) conferring seed growth capacity after low-temperature (5 °C) treatment were detected. Among these, two QTLs shared by Nipponbare, qGP4 and qGP5, could increase germination percentage, while one QTL shared by Nipponbare, qBL4, could increase bud length after cold stress; qGP4 and qBL4 were first reported in our study. These QTLs could be highly valuable genetic factors for cold tolerance improvement in rice lines. The CSSLs carrying these QTLs not only provide an opportunity for map-based cloning of important cold tolerance QTLs but also supply useful inbred lines to improve cold tolerance in 9311. These CSSLs represent good sources of japonica tolerance QTLs (genes) for use in improving cold tolerance in indica rice directly, avoiding the genetic drag arising from incompatible epistasis effects.

已建议开发基于种间渗入的新种群类型，以促进发现具有重要农艺性状的新等位基因来源。在这项研究中，染色体片段置换系（CSSL）稻人口承载的连续染色体片段粳稻日本晴中的遗传背景籼稻开发了9311。同时，通过全基因组重测序方法生成了一个高密度遗传图谱，包括655个bin，覆盖了1480.2 Mb的距离，标记之间的平均间隔为0.60 Mb。与以前的从9311或Nipponbare构建的CSSL种群相比，该种群具有更高的标记密度，可以有效满足高QTL作图分辨率的要求。根据新构建的高密度遗传图谱，总共检测到三个主要QTL（qGP4，qGP5和qBL4），它们在低温（5°C）处理后具有种子生长能力。其中，Nipponbare共享的两个QTL qGP4和qGP5，可以增加发芽率，而日本晴共有一个QTL，qBL4，可以增加冷胁迫后的芽长。qGP4和qBL4在我们的研究中首次报道。这些QTL可能是提高水稻品系耐寒性的极有价值的遗传因素。携带这些QTL的CSSL不仅为基于地图的重要耐寒性QTL克隆提供了机会，而且还提供了有用的自交系来提高9311的耐寒性。这些CSSL代表了粳稻耐性QTL（基因）的良好来源，可用于改善耐寒性宽容籼稻直接大米，避免因不兼容互作效应引起的遗传累赘。