Detecting a novel locus associated with pellicle peelability in Japanese chestnut populations preselected for a major peelability gene
Detecting a novel locus associated with pellicle peelability in Japanese chestnut populations preselected for a major peelability gene
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DOI：
10.1016/j.scienta.2022.111446
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发表时间：
2022-08-18
影响因子：
4.3
通讯作者：
Saito, Toshihiro
中科院分区：
文献类型：
--
作者：
Nishio, Sogo;Hayashi, Takeshi;Saito, Toshihiro
剥壳性是板栗最重要的性状之一。)育种。以往的研究表明，板栗的脱皮性受一个主要的隐性脱皮基因（MRPG）控制。该基因座已被有效地用于栗子育种中的标记辅助选择，但也可能存在次要的基因座，将进一步提高育种的剥性效率。我们基于BayesB的变分近似版本进行了全基因组关联研究（GWAS），使用27个品种和mrpg预选群体，包括来自22个科的520个F1幼苗。利用双酶切酶切位点相关DNA测序（ddRAD-Seq），我们获得了9164个标签单核苷酸多态性。由于可剥性的表型值分布非常不对称，并且由于MRPG的预选而在高端出现峰值，因此我们将原始数据集转换为反正态转换值和分类得分，并使用GWAS对两组转换数据进行分析。在CCR1.0F_56177061位点鉴定出一个可剥性数量性状位点（QTL），后验概率分别为0.68和1.00。CCR1.0F_56177061基因型的平均值为CC、CT、TT分别为60.4%、63.7%和86.5%。结果表明，CCR1.0F_56177061基因型与板栗剥壳性存在显著的相关性，该QTL将为板栗剥壳性的改良提供参考。
Peelability is one of the most important traits in Japanese chestnut (Castanea crenata Sieb. et Zucc.) breeding. Previous studies revealed that the peelability of Japanese chestnut is controlled by a major recessive peeling gene (MRPG). This locus has been used effectively for marker-assisted selection in chestnut breeding programs, but there are also likely to be minor loci that would further improve the efficiency of breeding for peelability. We conducted a genome-wide association study (GWAS) based on a variational approximation version of BayesB using 27 cultivars and MRPG-preselected populations consisting of 520 F1 seedlings from 22 families. Using double-digest restriction site-associated DNA sequencing (ddRAD-Seq), we obtained 9164 tag single-nucleotide polymorphisms. Because the phenotypic values of peelability were distributed very asymmetrically, with a peak at the high end due to the preselection for MRPG, we converted the original data set to both inverse normal transformed values and categorical scores, and we analyzed both sets of converted data by GWAS. In both an-alyses, a quantitative trait locus (QTL) for peelability at CCR1.0F_56177061 was identified with posterior probability values of 0.68 and 1.00, respectively. The average values of genotypes at CCR1.0F_56177061 for cultivars and seedlings in this study were 60.4% (peelability rate) for CC, 63.7% for CT, and 86.5% for TT. This analysis reveals a significant association between CCR1.0F_56177061 genotype and peelability, indicating that this newly identified QTL will be useful for improving peelability in chestnut breeding programs.