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

Caixia Zheng,Ting Wu,Xuefeng Xu,Zhenhai Han,Xinzhong Zhang,Fei Shen,Yi Wang

doi:10.1186/s12864-020-07257-8

Abstract

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 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°.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.

Highlights

The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance
A point mutation of MdDREB2A-Baleng Crab (BC) (592 C to T), MdDR EB2A-BC (p), could not interact with MdHSFB3 at all (Fig. 3e and Fig. S7B). These results indicated that the SNP592 T/C of MdDREB2A altered its ability to interact with MdHSFB3
A total of 25 significant Quantitative trait locus (QTL) were identified, 11 of which were mapped on the maternal parent ‘BC’, eight were mapped on the pollen parent ‘M9’, and six were located on both parents

Summary

Introduction

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. The objective of this study was to identify QTLs, validate genetic variation networks, and develop molecular markers for the RGA in apple rootstock. Dwarfing rootstock is widely used as an ideal method for achieving high-density planting of apple [1]. Apple trees that are grafted on dwarfing rootstocks usually have a relatively shallow root system, which leads to poor anchorage and increased sensitivity to ambient stress from, for example, wind or water logging [2]. Plants with shallow roots are often vulnerable to environmental stresses such as drought, cold, and salinity [3, 4], Gravity, light, and water potential are major environmental factors that affect the RGA [11].

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