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来源: Michaela Jung et al  发布日期: 2022-05-26  访问量: 265

为了提高苹果育种的效率,需要实施基因组工具。最近,多环境苹果参考群体(apple REFPOP)被证明有助于重新发现基因座、估计基因组预测能力和研究基因型与环境的相互作用(G×E)
标签: 苹果、表型、遗传结构、基因

Genetic architecture and genomic predictive ability of apple quantitative traits across environments


Michaela Jung1,2, *, Beat Keller1,2, Morgane Roth1,3, Maria José Aranzana4,5, Annemarie Auwerkerken6, Walter Guerra7, Mehdi Al-Rifaï8, Mariusz Lewandowski9, Nadia Sanin7, Marijn Rymenants6,10, Frédérique Didelot11, Christian Dujak5, Carolina Font i Forcada4, Andrea Knauf1,2, François Laurens8, Bruno Studer2, Hélène Muranty8 ,Andrea Patocchi1

1Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
2Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
3GAFL, INRAE, 84140 Montfavet, France
4IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
5Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
6Better3fruit N.V., 3202 Rillaar, Belgium
7Research Centre Laimburg, 39040 Auer, Italy
8Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
9The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
10Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001 Leuven, Belgium
11Unité expérimentale Horticole, INRAE, F-49000 Angers, France


Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18–0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of traitenvironment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency

为了提高苹果育种的效率,需要实施基因组工具。最近,多环境苹果参考群体(apple REFPOP)被证明有助于重新发现基因座、估计基因组预测能力和研究基因型与环境的相互作用(G×E)。到目前为止,使用苹果REFPOP只调查了两个物候性状,尽管在剖析遗传结构和报告苹果育种中其他关键性状的预测能力时,群体可能很有价值。在这里,我们使用apple REFPOP展示了欧洲6个地区30个数量性状的对比遗传结构和基因组预测能力。使用GWAS共发现59个稳定的和277个位置特异性关联,其中69.2%是新的,而41个已审查的出版物。使用主效应单变量、主效应多变量、多环境单变量和多环境多变量模型估计平均基因组预测能力为0.18–0.88。G×E占表型变异的24%。这项最全面的苹果基因组研究提供了性状生物学知识和预测模型,可以很容易地应用于标记辅助或基因组选择,从而提高育种效率



Thirty phenotypic traits related to phenology, productivity, fruit size, outer fruit, inner fruit, and vigor were evaluated at up to six locations of the apple REFPOP during up to three seasons (2018–2020). Trunk diameter was measured in 2017 in some locations, enabling for a trunk increment calculation for 2018. The traits were recorded as described in the Supplementary Methods, the measurements being performed either visually or using automatic devices (sorting machine Greefa iQS4 v.1.0, the instrument Pimprenelle (Setop, France)). Two phenology traits measured in 2018, i.e. f loral emergence and harvest date, were previously analyzed by Jung et al. [36].

在三个季节(2018-2020)内,在苹果REFPOP的六个地点,对与表型、生产力、果实大小、外部果实、内部果实和活力相关的30个表型性状进行了评估。2017年,在一些地方测量了树干直径,从而可以计算2018年的树干增量。按照补充方法中的描述记录性状,通过目视或使用自动装置(分选机Greefa iQS4 v.1.0,器Pimprenelle(法国Setop))进行测量。Jung等人之前分析了2018年测得的两个物候特征,即花期出苗和收获日期。