Kondo Fumiya, Kumanomido Yui, D'Andrea Mariasilvia, Palombo Valentino, Ahmed Nahed, Futatsuyama Shino, Nemoto Kazuhiro, Matsushima Kenichi
Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake Cho, Sakyo-Ku, Kyoto, 606-8502, Japan.
Department of Science and Technology, Graduate School of Medicine, Science and Technology, Shinshu University, Minamiminowa, Nagano, 399-4598, Japan.
Mol Genet Genomics. 2025 Jan 21;300(1):15. doi: 10.1007/s00438-024-02224-4.
Chili pepper (Capsicum spp.) fruits are used as vegetables, spices, and ornamental plants, necessitating various fruit characteristics. However, their genetic improvement is challenging through conventional crossbreeding due to the quantitative traits, which makes it difficult to predict phenotypes in the progeny. As a breakthrough, we focused on phenotypic simulation via genomic prediction (GP) and aimed to clarify its utility for fruit-related traits in chili peppers. The present study used 291 C. annuum accessions, including two populations: inbred lines and F accessions derived from 20 inbred parents. We collected data of fruit length, width, shape index (length/width), weight, and pericarp thickness, and obtained single nucleotide polymorphism data via multiplexed inter-simple sequence repeat genotyping by sequencing. We simulated the fruit-related traits in the F accessions by inputting their estimated genotypes (based on their parents) into the GP model using the GBLUP-GAUSS model, which was shown to be the most accurate regardless of population or trait differences in the present study. As a result, we observed strong positive correlations (r = 0.833-0.908) between the simulated and observed phenotypic values across all traits, suggesting that accurate ranking of F progenies based on fruit-related traits can be achieved using parental information. This is the first report demonstrating the utility of phenotypic simulation via GP in chili pepper breeding, offering valuable insights for its application in this field.
辣椒（辣椒属）果实被用作蔬菜、香料和观赏植物，因此需要具备各种果实特性。然而，由于其数量性状，通过传统杂交育种对其进行遗传改良具有挑战性，这使得预测后代的表型变得困难。作为一项突破，我们专注于通过基因组预测（GP）进行表型模拟，旨在阐明其在辣椒果实相关性状方面的实用性。本研究使用了291份辣椒材料，包括两个群体：自交系和来自20个自交亲本的F代材料。我们收集了果实长度、宽度、形状指数（长度/宽度）、重量和果皮厚度的数据，并通过多重简单序列重复测序基因分型获得了单核苷酸多态性数据。我们使用GBLUP-GAUSS模型，将F代材料的估计基因型（基于其亲本）输入到GP模型中，模拟了F代材料的果实相关性状，在本研究中，无论群体或性状差异如何，该模型都被证明是最准确的。结果，我们观察到所有性状的模拟表型值与观察到的表型值之间都存在很强的正相关（r = 0.833 - 0.908），这表明利用亲本信息可以实现基于果实相关性状对F代后代进行准确排名。这是第一份证明通过GP进行表型模拟在辣椒育种中的实用性的报告，为其在该领域的应用提供了有价值的见解。
