Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
Analysis of phenotypic- and Estimated Breeding Values (EBV) to dissect the genetic architecture of complex traits in a Scots pine three-generation pedigree design
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DOI：
10.1016/j.jtbi.2018.11.007
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发表时间：
2019-02-07
影响因子：
2
通讯作者：
Garcia-Gil, Maria Rosario
中科院分区：
文献类型：
--
作者：
Calleja-Rodriguez, Ainhoa;Li, Zitong;Garcia-Gil, Maria Rosario
在林木育种中，以家系为基础的数量性状基因座（QTL）研究作为剖析性状复杂性的方法和候选基因的来源是有价值的。在针叶树研究领域，我们的研究有助于评估的表型和预测育种值的QTL的鉴定，在苏格兰松（樟子松L.）的三代系谱人口的复杂性状。在3个不同地点共采集了11470株自由授粉的F2代单株，测定了其生长和适应性状。预测了它们的360个母亲的育种值，这些母亲来自两个祖父母的单杂交。采用多水平LASSO关联分析方法，利用具有相应表型的母本基因型和估计育种值（EBV）检测QTL。不同水平的基因型环境（G × E）的影响，在不同年份的网站之间，检测到的生存和高度。中度至低度狭义遗传力和EBV的准确性，发现所有性状和所有网站。我们确定了18个AFLP和12个SNP与一个或多个性状的QTL。62个QTL达到显著水平，解释的方差百分比为1.7 ~ 18.9%。在相同标记与表型或ebvQTL相关的那些情况下，ebvQTL总是解释较高比例的方差，这可能是由于估计育种值（EBV）的更准确性质。2个SNP-QTL在抗寒性、结实量、结实量和花产量等性状上表现出多效性效应。此外，我们检测到几个QTL在多个年龄的显着效果，这可以被认为是早期选择的强候选位点。跨站点检测到的一些QTL的重复性的缺乏可能是由于环境异质性所反映的基因型和QTL的环境效应。(C)2018作者由Elsevier Ltd.发布。这是CC BY-NC-ND许可下的开放获取文章。
In forest tree breeding, family-based Quantitative Trait Loci (QTL) studies are valuable as methods to dissect the complexity of a trait and as a source of candidate genes. In the field of conifer research, our study contributes to the evaluation of phenotypic and predicted breeding values for the identification of QTL linked to complex traits in a three-generation pedigree population in Scots pine (Pinus sylvestris L.). A total of 11 470 open pollinated F-2-progeny trees established at three different locations, were measured for growth and adaptive traits. Breeding values were predicted for their 360 mothers, originating from a single cross of two grand-parents. A multilevel LASSO association analysis was conducted to detect QTL using genotypes of the mothers with the corresponding phenotypes and Estimated Breeding Values (EBV). Different levels of genotype-by-environment (G x E) effects among sites at different years, were detected for survival and height. Moderate-to-low narrow sense heritabilities and EBV accuracies were found for all traits and all sites. We identified 18 AFLPs and 12 SNPs to be associated with QTL for one or more traits. 62 QTL were significant with percentages of variance explained ranging from 1.7 to 18.9%. In those cases where the same marker was associated to a phenotypic or an ebvQTL, the ebvQTL always explained higher proportion of the variance, maybe due to the more accurate nature of Estimated Breeding Values (EBV). Two SNP-QTL showed pleiotropic effects for traits related with hardiness, seed, cone and flower production. Furthermore, we detected several QTL with significant effects across multiple ages, which could be considered as strong candidate loci for early selection. The lack of reproducibility of some QTL detected across sites may be due to environmental heterogeneity reflected by the genotype- and QTL-by-environment effects. (C) 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license.