qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.)

Abstract

Low-temperature germination (LTG) is an important agronomic trait for direct seeding of rice in temperate regions of East Asia. To dissect the genetic control of LTG, we constructed a recombinant inbred line (RIL) population derived from a cross of japonica variety USSR5 and indica variety N22. Three putative QTL involved in LTG were detected and named qLTG-7, qLTG-9 and qLTG-12. They explained 9.5, 12.12 and 7.08 % of the phenotypic variation, respectively, and the alleles from USSR5 enhanced LTG. A set of advanced backcross lines selected for the presence of qLTG-9 (with the biggest contribution of the three QTL), by both linked markers and phenotype, was used to validate qLTG-9 in different generations, years and locations. A near-isogenic line in USSR5 background with a qLTG-9 insertion from N22 had retarded germination under low-temperature conditions. Finally, qLTG-9 was fine mapped between markers L9-25D and ID-1, to a 72.3-kb region in chromosome 9, which in the Nipponbare genome contains five predicted genes. This result provides a springboard for map-based cloning of qLTG-9 and is helpful in understanding the mechanism of seed germination under low-temperature conditions.

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

“…Four new QTL; qNGR1, qNGR4, qGRR1 , and qGRR8 are newly detected QTL and never reported before, these all QTL were located on small genomic regions (40–140 kb). This result contributes to the fine mapping of these QTL and provides a foundation for understanding the mechanism of rice germination and seedling growth under low-temperature conditions (Li et al, 2013). Moreover, the BRILs harboring these QTL will serve as an excellent materials and enable us to map and study genetic basis of GULT.…”

“…Vigorous GULT is an important agricultural trait for direct seeding in rice especially at high altitudes in subtropical and tropical regions, and in areas with cold irrigated water (Fujino et al, 2004; Li et al, 2013; Mao et al, 2015; Satoh et al, 2016). Generally, GULT of japonica varieties was higher than that of indica varieties, cold resistant genes/QTL from japonica rice have been used as gene resource to improve the cold resistance in indica rice (Mao et al, 2015).…”

“…Wang Z. et al (2011) studied cold tolerance at germination stage in a japonica × indica cross, two minor QTL responsible for cold tolerance at germination were observed. Li et al (2013) found three QTL ( qLTG-7, qLTG-9 , and qLTG-12 ) associated with low-temperature germination, and qLTG-9 was fine mapped to a 72.3-kb region in chromosome 9. Among these QTL, only one QTL ( qLTG3-1 ) has been cloned (Fujino et al, 2008).…”

“…To find out the genetic basis of cold at germination stage for indica and japonica , several independent studies have been reported and some low-temperature germinability related QTL have been identified in different populations (Miura et al, 2001; Zhang et al, 2005; Jiang et al, 2006; Ji et al, 2008; Wang Z. et al, 2011; Li et al, 2013; Satoh et al, 2016). For example, Miura et al (2001) detected five low temperature germinability related QTL on chromosomes 2, 4, 5, and 11.…”

Research Advances in Rice Cold Tolerance Gene Mapping

“…Therefore, it is necessary to carry out the fine mapping of genes, and on the basis of fine positioning on the cold tolerance of rice for map cloning. Li et al [43] constructed a set of indica and japonica recombinant inbred lines USSR5 and N22 mapping groups. Under the low temperature condition, the germination ability of rice was identified, and three low-temperature germination QTLs were obtained.…”