Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice

Abstract

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.

Detection of quantitative trait loci for heading date and temperature responsiveness in a re‐sequenced, recombinant inbred line of japonica rice from Heilongjiang province, china

“…The average physical interval of bin was 128.8 kb. The maximum physical interval was 3.6 Mb and the minimum was 15 kb (Jiang et al, 2020)…”

“…A high-density bin map of the RILs was built using a sliding window approach with a slight modification (Huang, Feng, et al, 2009;Jiang et al, 2020). The bin map was constructed with 58,738 recombination breakpoints for all lines, in which each line contained 236 to 1,007 breakpoints with an average value of 405.…”

Genetic Elucidation for Response of Flowering Time to Ambient Temperatures in Asian Rice Cultivars

“…Climate change is causing large fluctuations in temperature, solar irradiation, precipitation and soil moisture, especially in the tropics [4]. At the high-latitude limits of rice cultivation; however, low temperatures at the seedling, panicle initiation and maturation stages severely decrease grain yield [5,6]. There is now an increasing demand for new cultivars that are adaptable to both effects of climate change.…”

Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

“…qSV-5c , a major QTL of radical length and germination rate under optimal and low temperature, was located between SNP3 and CAPS2, a genomic region of approximately 400 kb on chromosome 1 (Xie et al 2014 ). By progeny test, qLTG6 was delimited to a 45.8-kb physical interval between M002 and M008, and LOC_Os06g01320 was considered as a possible target gene (Jiang et al 2020 ). Currently, only two LTG-related genes, qLTG3-1 and OsSAP16 , have been cloned in rice.…”