Intricate genetic variation networks control the adventitious root growth angle in apple

BackgroundThe 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.ResultsBulked segregant analysis by sequencing (BSA-seq) identified 25 QTLs for RGA using 1955 hybrids of the apple rootstock cultivars ‘Baleng Crab’ (Malus robustaRehd., large RGA) and ‘M9’ (M. pumilaMill., 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 theMdLAZY1promoter damaged the binding sites of MdDREB2A and MdHSFB3, while one SNP ofMdDREB2AandMdIAA1affected the interactions of MdDREB2A/MdHSFB3 and MdIAA1/MdLAZY1, respectively. A SNP within theMdNPR5promoter damaged the interaction betweenMdNPR5and MdLBD41, while one SNP ofMdLBD41interrupted the MdLBD41/MdbHLH48 interaction that affected the binding ability of MdLBD41 on theMdNPR5promoter. Twenty six SNP markers were designed on candidate genes in each QTL interval, and the marker effects varied from 0.22°-26.11°.ConclusionsSix 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.