Mapping QTL for Seed Germinability under Low Temperature Using a New High-Density Genetic Map of Rice

Abstract

Mapping major quantitative trait loci (QTL) responsible for rice seed germinability under low temperature (GULT) can provide valuable genetic source for improving cold tolerance in rice breeding. In this study, 124 rice backcross recombinant inbred lines (BRILs) derived from a cross <i>indica</i> cv. Changhui 891 and <i>japonica</i> cv. 02428 were genotyped through re-sequencing technology. A bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. On the basis of newly constructed high-density genetic map, six QTL were detected ranging from 40 to 140 kb on Nipponbare genome. Among these, two QTL <i>qCGR8</i> and <i>qGRR11</i> alleles shared by 02428 could increase GULT and seed germination recovery rate after cold stress, respectively. However, <i>qNGR1</i> and <i>qNGR4</i> may be two major QTL affecting <i>indica</i> Changhui 891germination under normal condition. QTL <i>qGRR1</i> and <i>qGRR8</i> affected the seed germination recovery rate after cold stress and the alleles with increasing effects were shared by the Changhui 891 could improve seed germination rate after cold stress dramatically. These QTL could be a highly valuable genetic factors for cold tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying genetic basis of rice complex traits.