The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified in crops. However, the underlying mechanisms of the RGA remain poorly understood, especially in apple rootstocks. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Bulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., large RGA) and ‘M9’ (M. pumila Mill., small RGA). With RNA sequencing (RNA-seq) and parental resequencing, six major functional genes were identified and constituted two genetic variation networks for the RGA. Two single nucleotide polymorphisms (SNPs) of the MdLAZY1 promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP of MdDREB2A and MdIAA1 affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within the MdNPR5 promoter damaged the interaction between MdNPR5 and MdLBD41, while one SNP of MdLBD41 interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on the MdNPR5 promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°. Six diagnostic markers, SNP592, G122, b13, Z312, S1272, and S1288, were used to identify two intricate genetic variation networks that control the RGA and may provide new insights into the accuracy of the molecular markers. The QTLs and SNP markers can potentially be used to select deep-rooted apple rootstocks.

中文翻译：

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复杂的遗传变异网络控制苹果不定根生长角度

根部生长角度（RGA）通常决定植物的生根深度，这对于植物的固着和非生物胁迫耐受性都非常重要。已经在农作物中鉴定了一些RGA的定量性状基因座（QTL）。但是，RGA的基本机制仍然知之甚少，尤其是在苹果砧木中。这项研究的目的是鉴定QTL，验证遗传变异网络并开发苹果砧木中RGA的分子标记。使用1955年苹果砧木品种'Baleng Crab'（Malusrobista Rehd。，大型RGA）和'M9'（M. pumila Mill。，小型RGA）的杂种，通过测序（BSA-seq）进行的大量分离物测序确定了25个RGA QTL。 。通过RNA测序（RNA-seq）和亲本重测序，鉴定了六个主要功能基因，并构成了RGA的两个遗传变异网络。MdLAZY1启动子的两个单核苷酸多态性（SNPs）破坏了MdDREB2A和MdHSFB3的结合位点，而MdDREB2A和MdIAA1的一个SNP分别影响了MdDREB2A / MdHSFB3和MdIAA1 / MdLAZY1的相互作用。MdNPR5启动子中的一个SNP破坏了MdNPR5与MdLBD41之间的相互作用，而MdLBD41的一个SNP中断了MdLBD41 / MdbHLH48相互作用，从而影响了MdLBD41在MdNPR5启动子上的结合能力。在每个QTL间隔中，在候选基因上设计了26个SNP标记，标记效应在0.22°-26.11°之间变化。六个诊断标记SNP592，G122，b13，Z312，S1272和S1288被用于识别控制RGA的两个复杂的遗传变异网络，并可能为分子标记的准确性提供新的见解。