Kooke Rik, Kruijer Willem, Bours Ralph, Becker Frank, Kuhn André, van de Geest Henri, Buntjer Jaap, Doeswijk Timo, Guerra José, Bouwmeester Harro, Vreugdenhil Dick, Keurentjes Joost J B
Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.)
Plant Physiol. 2016 Apr;170(4):2187-203. doi: 10.1104/pp.15.00997. Epub 2016 Feb 11.
Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
植物的数量性状由大量基因及其与环境的相互作用所控制。为了解析此类性状的遗传结构，可以通过研究基因型与表型的关系来探索物种内的自然变异。如今，将表型与数千个单核苷酸多态性标记联系起来的全基因组关联研究是进行此类分析的常见做法。然而，在许多情况下，所鉴定出的单个基因座无法完全解释遗传力估计值，这表明存在“遗传力缺失”现象。我们分析了349份拟南芥种质，发现不同形态性状存在广泛变异且遗传力较高。然而，全基因组显著关联的数量非常少。应用考虑所有单个基因座效应的基因组预测模型可能会极大地促进对植物数量性状遗传结构的阐明。在此，基因组预测模型揭示了不同形态性状的遗传结构。整合基因组预测和关联作图能够确定许多解释观察到的变异的合理候选基因。对这些基因进行了功能和序列多样性分析，并获得了许多有力证据，表明这些基因中的许多自然等位变异对表型变异有贡献。对于乙烯生物合成基因ACS11，能够鉴定出解释叶柄与叶片长度比值变异的单倍型差异。
