Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

BMC Genomics
Jing LiuZhenhai Han

Abstract

Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock. A total of 3258 hybrids derived from the apple rootstock cultivars 'Baleng Crab' (Malus robusta Rehd., tolerant) × 'M9' (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt-alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt-alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkal...Continue Reading

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Methods Mentioned

BETA
salt
RNA-seq
PCR
MDA
ubiquitination
transgenic

Software Mentioned

SNP VIEWER
Burrows
BSATOS
Wheeler Alignment
GAP
AppleMDO webtools

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