Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establish- ment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci （QTLs） for seed vigor by using a recombinant inbred population from a cross between rice （Oryza sativa L. ssp. indica） cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-Sb, qSV-6a, qSV- 6b, and qSV-11 influenced seedling establishment and that qSV- 5a, qSV-Sc, and qSV-8 influenced only germination. Of these, qSV-1, qSV-Sb, qSV-6a, qSV-6b, and qSV-8 were low-tempera- ture-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5cwere narrowed down to 1.13-Mbp and 4oo-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased low-temperature germination seed vigor in both normal and environments.
Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus （QTL） mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines （RILs） derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorpbic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted mark- ers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quanti- tative trait loci （QTLs） with phenotypic variation explained （PVE） values〉5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterili- ty-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construc- tion and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of in- ter-subspecies hybrid sterility and correlations with important agronomic traits in rice.
