Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.

本研究共纳入200份水稻种质资源，涵盖传统地方品种、现代优良品种与古老栽培品种，其中以适应温带环境的粳稻品种为主。研究团队利用1672个单核苷酸多态性（SNP）标记开展全基因组关联研究，以挖掘与低温发芽（LTG）调控相关的染色体区域。表型鉴定通过分别测定种子在25℃与15℃条件下的生长速率完成，以此区分发芽活力与耐寒性的效应差异。正如预期，不同水稻栽培品种产生存活幼苗的能力差异显著，且受温度影响极大；此外，研究团队在种子萌发与胚芽鞘伸长过程中观察到差异化响应。相较于其他品种，被育种者传统用作耐寒亲本的品种以及部分其他具有潜在应用价值的品种（主要为意大利来源品种）的种子，在15℃条件下展现出更快的生长速率。将表型数据与粳稻品种的SNP标记组合分析后，共检测到31个存在显著关联的标记：其中7个与25℃下的生长速率相关，24个与15℃下的生长速率相关；在后者中，部分染色体区域与低温发芽相关，其余则与胚芽鞘伸长有关。各关联标记的单个效应较弱，但通过线性回归模型整合有利等位基因后，研究人员估算出27个位点可显著解释观测到的表型变异，从中筛选得到包含13个标记的核心标记组；此外，第3号和第6号染色体上的两个宽泛区域与水稻低温发芽存在稳定关联。携带更多有利等位基因的品种在两种温度下的表型值均显著提升，这证实了所标记的位点可用于粳稻低温发芽性状育种的标记辅助选择（MAS），证明了该标记工具的实用性。