Genetic analysis of rice seed recovery under low-temperature conditions using a new CSSL population with a high-density genetic map in rice

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.