Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7, 46113, Moncada, Spain.
Cooperativa de Productores de Semillas de Arroz, Sueca, Spain.
BMC Genomics. 2018 Sep 25;19(1):706. doi: 10.1186/s12864-018-5086-y.
Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle length and number of grains per panicle.
We have performed a genome wide association study using a panel of 1713 SNPs that, based on previous linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43 SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle.
We have identified loci associated with important agronomic traits among cultivars adapted to temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The detected associated markers may provide important tools for the genetic improvement of rice cultivars in temperate regions.
水稻对农业气候条件敏感，光周期是影响其适应生长地区的主要因素之一。解析适应特定环境条件的水稻群体的遗传基础是培育的基础资源。本研究分析了一组适应温带地区的粳稻品种，以开展与农艺性状（如抽穗期、株高、穗数、穗长和每穗粒数）相关的关联研究。
我们使用 1713 个 SNP 进行了全基因组关联研究，这些 SNP 基于先前的连锁不平衡估计，提供了全基因组的完整覆盖。我们总共发现了 43 个与不同性状变异相关的 SNP。鉴定的 SNP 分布在整个基因组中，除了在染色体 12 上没有发现相关 SNP。对这些标记附近区域的检查还揭示了一组与生理功能相关的基因，这些基因与农艺性状密切相关。特别值得关注的是两个与赤霉素稳态相关的基因，它们与株高和穗长有关。我们还检测到与抽穗期、穗长和每穗粒数相关的新关联位点。
我们已经鉴定出适应温带条件的品种中与重要农艺性状相关的基因座。其中一些标记与已知基因或 QTL 共定位，但关联分析也提供了新的分子标记，可以帮助阐明控制重要农艺性状的复杂遗传机制，如非依赖光周期途径的开花调控。检测到的关联标记可能为温带地区水稻品种的遗传改良提供重要工具。
