Identification of Genes Related to Cold Tolerance and a Functional Allele That Confers Cold Tolerance

Abstract

Cold stress is a major factor limiting rice () production worldwide, especially at the seedling and booting stages. The identification of genes associated with cold tolerance (CT) in rice is important for sustainable food production. Here, we report the results of a genome-wide association study to identify the genetic loci associated with CT by using a 1,033-accession diversity panel. We identified five CT-related genetic loci at the booting stage. Accessions carrying multiple cold-tolerant alleles displayed a higher seed-setting rate than did accessions that had no cold-tolerant alleles or carried a single allele. At the seedling stage, eight genetic loci related to CT have been identified. Among these, was identified as the candidate gene for the genetic locus that is associated with CT in rice seedlings. A single-nucleotide polymorphism (SNP), SNP2, at position 343 in is responsible for conferring CT at the seedling stage in rice. Further analysis of the haplotype network revealed that SNP2 was present in 80.08% of the temperate accessions but only 3.8% of the ones. We used marker-assisted selection to construct a series of BCF near-isogenic lines possessing the cold-tolerant allele SNP2 When subjected to cold stress, plants carrying SNP2 survived better as seedlings and showed higher grain weight than plants carrying the SNP2 allele. The CT-related loci identified here and the functional verification of will provide genetic resources for breeding cold-tolerant varieties and for studying the molecular basis of CT in rice.

Identification of main-effect quantitative trait loci (QTLs) for low-temperature stress tolerance germination- and early seedling vigor-related traits in rice (Oryza sativa L.)

“…Compared with other cereal crops, rice is more sensitive to low-temperature stress (LTS)/cold stress (CS) as it has originated from tropical regions (Saito et al 2001;Hasanuzzaman et al 2009;Zeng et al 2017). In the temperate, tropical, and even subtropical rice-growing regions, cold stress adversely affects the rice crop throughout various growth stages, from germination to harvesting, and causes significant yield losses because of poor germination and seedling establishment, stunted growth pattern, non-vigorous plants, vast spikelet sterility, delay in flowering, and lower grain filling (Ranawake et al 2014;Martínez-Eixarch and Ellis 2015;Schläppi et al 2017;Shakiba et al 2017;Liang et al 2018;Xiao et al 2018;Najeeb et al 2019 (unpublished). Therefore, to minimize these yield losses, particularly in cold-affected regions, it is imperative to identify and develop high-yielding rice cultivars showing tolerance of LTS.…”

Genome-Wide Association of Rice Response to Blast Fungus Identifies Loci for Robust Resistance Under High Nitrogen.

“…In order to understand the possible genetic basis of the observed increased susceptibility in the high nitrogen environment, the 126 genes annotated at NIS3 were investigated (Additional le 15). We considered as good candidates genes either involved in biotic stress response (twenty-nine pathogenesisrelated genes), abiotic stress response (OsTIP3;1, [64] and RIPER6 [65]), the regulation of both stresses (OsGRXS17, [66] and OsTPR1 [67]), or nitrogen metabolism (OsPORB, [68] and a polylpolyglutamate synthetase [69]). The possible modulation of the M. oryzae pathogenicity program in response to a high nitrogen environment was also a hypothesis based on our previous results [26].…”

Marker-assisted selection in rice breeding programs in Hokkaido

“…The main advantages for genomic research focusing on improved rice varieties from Hokkaido include understanding the tolerance mechanism to abiotic stresses such as low temperature (Guo et al 2018, Jha et al 2017, Lv et al 2016, Xiao et al 2018, Zhao et al 2017. Following the optimization of the adaptability to local regions, tolerance to low temperature for stable rice production in Hokkaido can be improved (Fujino et al 2019a).…”