Genetic and epigenetic bases for adaptation to mega-environments in soybean

作物改良依赖于对植物遗传变异的持续利用，而缺乏变异可能会阻碍植物育种的进一步进展。遗传变异可以在育种种群中发现，也可以在基因库或世界许多地区的自然界中发现，例如作物的起源中心或多样性中心。然而，植物育种家只利用了许多作物中现有变异的一小部分，这主要是由于外来来源固有地缺乏适应目标育种环境的能力。大豆是一种作物，其中90%的北美大豆遗传变异来自35个祖先。相比之下，作为大豆原产地中心的中国存在着大量的遗传变异，可供植物育种者利用。在我们之前的NSERC发现资助中，我们已经确定了一些通用的和ME特异性的数量性状位点（QTL[U]和QTL[SP]），这些位点与产量和农艺性状有关，其中一些是独特的。高产等位基因通常由PI（外来）亲本在各自的ME中贡献，这表明来自外来种质的新的阳性等位基因有渗入的潜力。主要和次要QTL等位基因均由中国亲本贡献，其中大部分为QTL[U]，分布在加拿大、美国北部和中国。此外，与QTL[SP]相比，QTL[U]解释了更多的变异，分布在更少的连锁群体中。与特定QTL相比，通用QTL表现出更少的相互作用和更小的量级。86%的QTL[U]与其他农艺性状或种子品质性状相关，但在产量相关性状中充当QTL[U]或QTL[SP] （Palomeque et al. 2009a和2009b）。我们希望探索影响植物在不同环境中适应的差异QTL表达的潜在原因。众所周知，DNA甲基化会引起表观遗传变化，从而导致基因表达的改变。差异基因或QTL表达可能是难以确定外来来源作为适应品种杂交的潜在亲本的原因之一，因为它们的真正遗传潜力可能受到表观遗传因素的影响（或掩盖）。为了增加对中国植物种质资源的利用，进一步改善加拿大大豆，我们将研究DNA甲基化在与种子产量相关的基因组区域中的作用，作为植物适应新环境的最终指标。进一步了解DNA甲基化在不同宏观和宏观环境下QTL产量表达中的作用，将有助于制定增强外来种质资源利用的策略。这反过来又可能导致植物育种群体中种子产量选择的遗传增益增加，并加速植物育种工作的进展和经济影响。大豆等作物种子产量的持续增加将解决为全球不断增长的人口生产足够粮食供应的需求。

Crop improvement relies on continued use of genetic variation in plants and a lack of variation may impede further progress from plant breeding. Genetic variation can be found in breeding populations but also in gene banks or in nature across many regions of the world such as centres of origin or diversity for crop plants. However, only a fraction of existing variation in many crop plants has been used by plant breeders mainly due to an inherent lack of adaptation of exotic sources to target breeding environments. Soybean is a crop in which 90% of the genetic variation in North American soybeans is derived from as few as 35 ancestors. In contrast, vast amount of genetic variation exists in China as the centre of origin for soybean and may be available for use by plant breeders. In our previous NSERC Discovery grants we have identified a number of universal and ME specific Quantitative Trait Loci (QTL[U] and QTL[SP]) for yield and agronomic traits of which some were unique. Alleles for high yield have been often contributed by the PI (exotic) parent in each respective ME demonstrating the potential for introgressing new positive alleles from exotic germplasm. Both minor and major QTL alleles were contributed by the Chinese parent in the Canadian ME, the majority of them being QTL[U] across all three ME: Canada, northern U.S. and China. In addition, QTL[U] explained a greater amount of variation and were distributed across fewer linkage groups than the QTL[SP]. Universal QTL also exhibited fewer interactions and of smaller magnitude than the specific ones. Eighty-six percent of QTL[U] were associated with other agronomic or seed quality traits but acted as either QTL[U] or QTL[SP] for the yield related traits (Palomeque et al. 2009a and 2009b). We want to explore the underlying reasons for differential QTL expression that affect plant adaptation across different environments. DNA methylation is known to cause epigenetic changes that result in altered gene expression. Differential gene or QTL expression may be one of the reasons for difficulties in identifying exotic sources as potential parents for hybridization with adapted cultivars because their true genetic potential may be impacted (or masked) by epigenetic factors. In order to increase the use of plant germplasm from China to further improve soybeans in Canada, we will study the role of DNA methylation in the genomic regions that have been associated with seed yield as the ultimate measure of plants' adaptation to a new environment. An improved understanding of the role that DNA methylation plays in the expression of QTL for yield across different mega- and macro-environments will allow for the development of strategies for enhanced used of exotic germplasm. This in turn may lead to an increase in genetic gain from selection for seed yield in plant breeding populations and accelerate progress from and economic impacts of plant breeders' efforts. A continuous increase in seed yield of crops such as soybean will address the need for producing adequate food supplies for an increasing human population around the world.