Differentiation, evolution and utilization of natural alleles for cold adaptability at the reproductive stage in rice

Abstract

Genetic studies on cold tolerance at the reproductive stage in rice could lead to significant reductions in yield losses. However, knowledge about the genetic basis and adaptive differentiation, as well as the evolution and utilization of the underlying natural alleles, remains limited. Here, 580 rice accessions in two association panels were used to perform genome-wide association study, and 156 loci associated with cold tolerance at the reproductive stage were identified. Os01g0923600 and Os01g0923800 were identified as promising candidate genes in qCTB1t, a major associated locus. Through population genetic analyses, 22 and 29 divergent regions controlling cold adaptive differentiation inter-subspecies (Xian/Indica and Geng/Japonica) and intra-Geng, respectively, were identified. Joint analyses of four cloned cold-tolerance genes showed that they had different origins and utilizations under various climatic conditions. bZIP73 and OsAPX1 differentiating inter-subspecies evolved directly from wild rice, whereas the novel mutations CTB4a and Ctb1 arose in Geng during adaptation to colder climates. The cold-tolerant Geng accessions have undergone stronger selection under colder climate conditions than other accessions during the domestication and breeding processes. Additive effects of dominant allelic variants of four identified genes have been important in adaptation to cold in modern rice varieties. Therefore, this study provides valuable information for further gene discovery and pyramiding breeding to improve cold tolerance at the reproductive stage in rice.

Resequencing of 301 ramie accessions identifies genetic loci and breeding selection for fibre yield traits

“…Exploring and utilizing favourable alleles is an effective method for improving crop traits (Guo et al ., 2020). Substantial allelic variation was identified in ramie germplasms with respect to the fibre yield‐associated candidate genes identified in the current study, and different haplotypes showed considerable differences in fibre yield (Figure 5).…”

The time-dependent evolutionary rate of mitochondrial DNA in small mammals inferred from biogeographic calibration points with reference to the late Quaternary environmental changes in the Japanese archipelago

“…Recent work on the population dynamics of M. musculus from Myanmar showed evident population expansion in the Cytb sequence data that began about 5400 (95% CI: 2300-8000) years ago (Maung Maung Theint et al, 2020). In addition, the migration from southern China to the Japanese archipelago was deduced to have occurred 3500 years ago (Li et al, 2020b), which may be correlated with the introduction of cold-tolerant temperate japonica rice strains developed in response to the extreme environmental degradation 4200 years ago (Mao et al, 2019;Guo et al, 2020;Gutaker et al, 2020).…”

Effects of chilling at the booting and flowering stages on rice phenology and yield: A case study in Northeast China

“…At the flowering stage, ambient temperature equal to or lower than 20°C lasting for 3 days would seriously affect the seed setting rate for rice (Shinada et al., 2013). Previous studies on the impacts of chilling on rice production were based on field experiments with cold water irrigation (Han & Koh, 2000; Matsumura et al., 2012), natural chilling treatment (Guo et al., 2020) and an artificial climate chamber (Farrell et al., 2006). Such studies have two common limitations: (a) they only focussed on the low temperature or the duration of the low temperature but not the two factors together; (b) the diurnal temperature range was not taken into consideration because the treatment temperature was fixed during the daytime or night‐time.…”