Genetic Analysis of Cold Tolerance at the Germination and Booting Stages in Rice by Association Mapping

Abstract

Low temperature affects the rice plants at all stages of growth. It can cause severe seedling injury and male sterility resulting in severe yield losses. Using a mini core collection of 174 Chinese rice accessions and 273 SSR markers we investigated cold tolerance at the germination and booting stages, as well as the underlying genetic bases, by association mapping. Two distinct populations, corresponding to subspecies indica and japonica showed evident differences in cold tolerance and its genetic basis. Both subspecies were sensitive to cold stress at both growth stages. However, japonica was more tolerant than indica at all stages as measured by seedling survival and seed setting. There was a low correlation in cold tolerance between the germination and booting stages. Fifty one quantitative trait loci (QTLs) for cold tolerance were dispersed across all 12 chromosomes; 22 detected at the germination stage and 33 at the booting stage. Eight QTLs were identified by at least two of four measures. About 46% of the QTLs represented new loci. The only QTL shared between indica and japonica for the same measure was qLTSSvR6-2 for SSvR. This implied a complicated mechanism of old tolerance between the two subspecies. According to the relative genotypic effect (RGE) of each genotype for each QTL, we detected 18 positive genotypes and 21 negative genotypes in indica, and 19 positive genotypes and 24 negative genotypes in japonica. In general, the negative effects were much stronger than the positive effects in both subspecies. Markers for QTL with positive effects in one subspecies were shown to be effective for selection of cold tolerance in that subspecies, but not in the other subspecies. QTL with strong negative effects on cold tolerance should be avoided during MAS breeding so as to not cancel the effect of favorable QTL at other loci.

Genome-wide Association Mapping of Cold Tolerance Genes at the Seedling Stage in Rice

“…Consistent with a previous study (Pan et al 2015), we found that both temperate and tropical japonica cultivars are more tolerant to cold stress than the IND and AUS cultivars (Fig. 1 and Additional file 1: Table S1).…”

“…Although Pan et al (2015) and Fujino et al (2015) recently reported the association mapping of cold tolerance QTLs in rice, the low resolution of SSR marker genotyping data affects the interval distance of the mapped QTLs. In this study, we mapped 67 QTLs associated with CTS in 295 rice accessions.…”

“…Cold stress is often a major limiting factor for stable rice production in temperate areas and sub-tropic areas with high altitude. Cold stress restricts the growth and development of rice at all the growth stages and results in low germination and seedling vigor, delayed seedling growth with leaf wilting and browning, prolonged duration of cultivation, pollen sterility, poor grain filling, and reduced yields (Suh et al 2010; Pan et al 2015). …”

“…Many QTLs for multiple traits were identified, such as traits associated with agronomic characteristics (Huang et al 2010; Zhao et al 2011; Yang et al 2014), and with responses to abiotic stresses (Famoso et al 2011; Pan et al 2015; Lv et al 2016), and to biotic stresses (Jia et al 2012; Wang et al 2014; Kang et al 2016; Wang et al 2015). Using GWAS, Pan et al (2015) recently mapped 51 QTLs for cold tolerance at the germination and booting stages with 174 Chinese rice accessions that were genotyped with 273 SSR markers. Fujino et al (2015) also identified 17 QTLs responsible for rice low temperature germinability in 63 Japanese varieties genotyped with 115 SSR markers and two other markers.…”

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

“…17 QTLs related to rice germinability at low temperature were detected by a GWAS analysis with the population of 63 rice varieties from Japan (Fujino et al 2015). Pan et al (2015) mapped 51 QTLs for cold tolerance at the germination and booting stages using a population of 174 Chinese rice varieties. Lv et al (2016) detected 132 QTL for nature chilling and cold-shock tolerance at the seedling stage by a GWAS analysis of 527 rice cultivars.…”