Peony International Institute, Beijing Advanced Innovation Center of Tree Breeding by Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
BMC Plant Biol. 2020 Jun 2;20(1):245. doi: 10.1186/s12870-020-02449-6.
Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS).
The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%).
Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.
植物数量性状的等位基因变异是由极其复杂的调控过程引起的。牡丹原产于中国，是一种特殊的观赏、药用和油料木本植物。其中的紫斑牡丹是一种珍贵的新兴木本油料作物。然而，在这个有价值的植物中，与产量性状相关的功能基因座的研究很少被鉴定。因此，为了探索 24 个产量数量性状的遗传结构，首次在 420 个无关的栽培紫斑牡丹个体中进行了关联作图，这些个体基于下一代测序（NGS）和单分子长读测序（SMLRS）。
从 959 个与产量相关的候选转录因子（TF）中开发了 58 对多态性表达序列标签简单重复序列（EST-SSR）标记，用于对 420 个紫斑牡丹品系进行基因分型。我们观察到高水平的遗传多样性（多态信息含量，PIC=0.514）和 EST-SSR 之间的低连锁不平衡（LD）。此外，通过 STRUCTURE 分析揭示了关联群体中的四个亚群。进一步的单标记关联分析鉴定出 141 个显著关联，涉及 17 个数量性状和 41 个 EST-SSR。这些位点主要来自 AP2、TCP、MYB、HSF、bHLH、GATA 和 B3 基因家族，表现出一小部分表型方差（3.79%至 37.45%）。
我们的结果总结了与紫斑牡丹产量性状相关的功能基因座的宝贵集合，并提供了一个宝贵的资源，揭示了牡丹和其他木本油料作物数量性状的等位基因变异。
