Retention of flesh texture attributes during cold storage is critical for the long-term maintenance of fruit quality. The genetic variations determining flesh firmness and crispness retainability are not well understood. The objectives of this study are to identify gene markers based on quantitative trait loci (QTLs) and to develop genomics-assisted prediction (GAP) models for apple flesh firmness and crispness retainability. Phenotype data of 2664 hybrids derived from three Malus domestica cultivars and a M. asiatica cultivar were collected in 2016 and 2017. The phenotype segregated considerably with high broad-sense heritability of 83.85% and 83.64% for flesh firmness and crispness retainability, respectively. Fifty-six candidate genes were predicted from the 62 QTLs identified using bulked segregant analysis and RNA-seq. The genotype effects of the markers designed on each candidate gene were estimated. The genomics-predicted values were obtained using pyramiding marker genotype effects and overall mean phenotype values. Fivefold cross-validation revealed that the prediction accuracy was 0.5541 and 0.6018 for retainability of flesh firmness and crispness, respectively. An 8-bp deletion in the MdERF3 promoter disrupted MdDOF5.3 binding, reduced MdERF3 expression, relieved the inhibition on MdPGLR3, MdPME2, and MdACO4 expression, and ultimately decreased flesh firmness and crispness retainability. A 3-bp deletion in the MdERF118 promoter decreased its expression by disrupting the binding of MdRAVL1, which increased MdPGLR3 and MdACO4 expression and reduced flesh firmness and crispness retainability. These results provide insights regarding the genetic variation network regulating flesh firmness and crispness retainability, and the GAP models can assist in apple breeding.

中文翻译：

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MdERF3和MdERF118自然变异在苹果果肉硬度/脆性保持性中的作用以及基于QTL的基因组学辅助预测的发展

在冷藏期间保留果肉质地属性对于长期保持水果品质至关重要。决定果肉紧实度和脆性保持性的遗传变异尚不十分清楚。这项研究的目的是基于定量性状基因座（QTL）鉴定基因标记，并开发苹果果肉硬度和脆性保留性的基因组学辅助预测（GAP）模型。来自3个家蝇和一个亚洲分枝杆菌的2664个杂种的表型数据该品种于2016年和2017年收集。该表型明显分离，具有较高的广义遗传力，其肉的紧实度和脆性保持力分别为83.85％和83.64％。使用大量分离子分析和RNA序列分析，从62个QTL中预测了56个候选基因。估计了在每个候选基因上设计的标记的基因型效应。使用金字塔标记基因型效应和总体平均表型值获得基因组预测值。五重交叉验证显示，对肉的坚挺性和松脆性的保留率的预测准确度分别为0.5541和0.6018。MdERF3启动子中的8 bp缺失破坏了MdDOF5.3的结合，降低了MdERF3的表达，减轻了对MdDOF5.3的抑制作用。MdPGLR3，MdPME2和MdACO4的表达，最终降低了肉的硬度和松脆性。MdERF118启动子中的3 bp缺失通过破坏MdRAVL1的结合而降低了其表达，MdRAVL1的结合增加了MdPGLR3和MdACO4的表达，并降低了肉的硬度和松脆性。这些结果提供了有关调节果肉硬度和脆性保持性的遗传变异网络的见识，并且GAP模型可以帮助苹果育种。