Apple fruit cover color is an important appearance trait determining fruit quality, high degree of fruit cover color or completely red fruit skin is also the ultimate breeding goal. MdMYB1 has repeatedly been reported as a major gene controlling apple fruit cover color. There are also multiple minor‐effect genes affecting degree of fruit cover color (DFC). This study was to identify genome‐wide quantitative trait loci (QTLs) and to develop genomics‐assisted prediction for apple DFC. The DFC phenotype data of 9,422 hybrids from five full‐sib families of Malus asiatica ‘Zisai Pearl’, M. domestica ‘Red Fuji’, ‘Golden Delicious’, and ‘Jonathan’ were collected in 2014–2017. The phenotype varied considerably among hybrids with the same MdMYB1 genotype. Ten QTLs for DFC were identified using MapQTL and bulked segregant analysis via sequencing. From these QTLs, ten candidate genes were predicted, including MdMYB1 from a year‐stable QTL on chromosome 9 of ‘Zisai Pearl’ and ‘Red Fuji’. Then, kompetitive allele‐specific polymerase chain reaction (KASP) markers were designed on these candidate genes and 821 randomly selected hybrids were genotyped. The genotype effects of the markers were estimated. MdMYB1‐1 (represented by marker H162) exhibited a partial dominant allelic effect on MdMYB1‐2 and showed non‐allelic epistasis on markers H1245 and G6. Finally, a non‐additive QTL‐based genomics assisted prediction model was established for DFC. The Pearson's correlation coefficient between the genomic predicted value and the observed phenotype value was 0.5690. These results can be beneficial for apple genomics‐assisted breeding and may provide insights for understanding the mechanism of fruit coloration.

中文翻译：

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基于数量性状基因座的基因组学辅助预测苹果果实色泽的程度

苹果果实的覆盖颜色是决定果实品质的重要外观特征，高度的果实覆盖颜色或完全红色的果皮也是最终的育种目标。MdMYB1已被反复报道为控制苹果果实色泽的主要基因。还有多个影响果皮颜色（DFC）程度的次要基因。这项研究旨在鉴定全基因组定量性状基因座（QTL），并开发苹果DFC的基因组学辅助预测。在2014–2017年，收集了来自五个全同胞亚洲苹果，“紫菜珍珠”，“家蝇M ”，“红富士”，“金冠”和“乔纳森”的9,422个杂种的DFC表型数据。在具有相同MdMYB1的杂种中，表型差异很大基因型。使用MapQTL鉴定了10个DFC的QTL，并通过测序进行了大批量分离物分析。从这些个QTL，十个候选基因进行了预测，其中包括MdMYB1从“Zisai珍珠”和“红富士”染色体9年稳定的QTL。然后，在这些候选基因上设计竞争性等位基因特异性聚合酶链反应（KASP）标记，并对821个随机选择的杂种进行基因分型。估计了标记的基因型效应。MdMYB1-1（由标记H162表示）对MdMYB1-2具有部分显性等位基因作用并在标记H1245和G6上显示非等位基因上位。最后，为DFC建立了基于QTL的非加性基因组辅助预测模型。基因组预测值和观察到的表型值之间的皮尔逊相关系数为0.5690。这些结果对于苹果基因组学辅助育种可能是有益的，并且可能为理解水果着色的机理提供见解。