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

Abstract

Background 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. Results 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°. Conclusions 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.

Analysis of the Small Auxin-Up RNA (SAUR) Genes Regulating Root Growth Angle (RGA) in Apple

“…MdSAUR60 , MdSAUR62 , MdSAUR69 and MdSAUR71 were mapped in QTL M10.1, and MdSAUR84 was located in QTL B13.2 ( Figure 4 ). The previous kompetitive allele-specific PCR (KASP) assay showed [ 25 ], the RGA of hybrids with the A:G genotype of marker Z3658 in QTL M10.1 were large, but had no significant difference from those with the A:A genotype ( Figure S1 ). However, significantly larger RGA values were detected in hybrids with T:G than in hybrids with T:T genotype of the marker b13 in QTL B13.2 ( Figure S1 ).…”

“…Network analysis of AppleMDO webtools could predict some proteins that positively or negatively regulate the target protein, which contributes to finding the primary target proteins with more regulatory proteins [ 25 , 42 ]. In our study, 25 MdSAURs , screened from expression and allelic variations, were further analyzed based on the network analysis of AppleMDO webtools.…”

“…MdSAUR family numbers were achieved using the resequence database of ‘BC’ and ‘M9’ [ 25 , 46 ]. The locations and sequences of all MdSAURs were found via searching against the gene database of AppleMDO ( (accessed on 22 October 2020) using the identity document (ID) of the gene [ 23 ].…”

“…In RNA-seq of hybrids from ‘BC’ and ‘M9’, the expression patterns of MdSAURs were analyzed at 7 d (stems) and 14 d (roots) after cutting [ 25 ]. To further characterize the expression of selected MdSAUR genes, tissue samples were also collected from ‘BC’ and ‘M9’ at 7 d (stems) and 14 d (roots) after cutting.…”

“…Therefore, it is necessary to further identify the MdSAUR gene family in this new apple genome. In our previous study, the BSA-seq and RNA-seq of hybrids from ‘M9’ and ‘BC’ were analyzed, which contributes to further screening of MdSAUR genes regulating RGA from expression and allelic variation [ 25 ].…”