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

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.

低温会在水稻生长的全生育期对其造成影响，可引发严重的幼苗损伤与雄性不育，进而导致大幅减产。本研究以174份中国水稻种质资源构成的迷你核心种质，以及273个简单序列重复（Simple Sequence Repeat, SSR）标记为材料，通过关联作图（Association Mapping）法解析了水稻在萌发期与孕穗期的耐寒性及其潜在遗传基础。两个分别对应籼稻（indica）与粳稻（japonica）的类群，在耐寒性及其遗传基础上均存在显著差异。两个亚种在两个生育期均对低温胁迫敏感，但以幼苗存活率与结实率为评价指标时，粳稻在各生育期的耐寒性均优于籼稻。萌发期与孕穗期的耐寒性仅存在极低的相关性。共计51个控制耐寒性的数量性状位点（Quantitative Trait Locus, QTL）分布于水稻的12条染色体上，其中22个在萌发期被检测到，33个在孕穗期被检测到。有8个QTL可通过4项评价指标中的至少2项重复检测到，其中约46%的QTL为新发现的位点。两个亚种在同一评价指标下仅共享1个QTL：用于SSvR的qLTSSvR6-2，这表明两个亚种的耐寒机制存在复杂性。基于每个QTL对应的各基因型的相对基因型效应（Relative Genotypic Effect, RGE），我们在籼稻中检测到18个正向基因型与21个负向基因型，在粳稻中检测到19个正向基因型与24个负向基因型。总体而言，两个亚种中负向效应的作用强度均显著高于正向效应。在某一亚种中对耐寒性QTL具有正向效应的标记，仅可用于该亚种的耐寒性选育，而无法应用于另一亚种。在分子标记辅助选择（Marker-Assisted Selection, MAS）育种过程中，应规避对耐寒性具有强负向效应的QTL，以免抵消其他位点上有利QTL的遗传效应。