Single Nucleotide Polymorphism Detection for Peach Gummosis Disease Resistance by Genome-Wide Association Study.

Xiongwei Li,Huijuan Jia,Weichao Fang,Jing Jin,Zhongshan Gao,Lirong Wang,Ke Cao,Xianan Zhang,Jingyi Zhou,Mingshen Su,Minghao Zhang,Jihong Du,Jiabo Wang,Kexin Gan,Huijuan Zhou,Zhengwen Ye

doi:10.3389/fpls.2021.763618

Abstract

Peach gummosis is one of the most widespread and destructive diseases. It causes growth stunting, yield loss, branch, trunk, and tree death, and is becoming a restrictive factor in healthy and sustainable development of peach production. Although a locus has been identified based on bi-parental quantitative trait locus (QTL) mapping, selection of gummosis-resistant cultivars remains challenging due to the lack of resistant parents and of the complexity of an inducing factor. In this study, an integrated approach of genome-wide association study (GWAS) and comparative transcriptome was used to elucidate the genetic architecture associated with the disease using 195 accessions and 145,456 genome-wide single nucleotide polymorphisms (SNPs). The broad-sense and narrow-sense heritabilities were estimated using 2-year phenotypic data and genotypic data, which gave high values of 70 and 73%, respectively. Evaluation of population structure by neighbor-joining and principal components analysis (PCA) clustered all accessions into three major groups and six subgroups, mainly according to fruit shape, hairy vs. glabrous fruit skin, pedigree, geographic origin, and domestication history. Five SNPs were found to be significantly associated with gummosis disease resistance, of which SNPrs285957, located on chromosome6 across 28 Mb, was detected by both the BLINK and the FarmCPU model. Six candidate genes flanked by or harboring the significant SNPs, previously implicated in biotic stress tolerance, were significantly associated with this resistance. Two highly resistant accessions were identified with low disease severity, which could be potential sources of resistance genes for breeding. Our results provide a fresh insight into the genetic control of peach gummosis disease.

Highlights

Peach [Prunus persica (L.) Batsch] is one of the most economically important deciduous fruit from the Rosaceae family (Li et al, 2013)
The results demonstrated the existence of a group of accessions highly resistant to gummosis disease
The present study is the first to identify multiple genetic factors involved in peach gummosis using genome-wide association study (GWAS) by using a substantial number of peach germplasm accessions

Summary

Introduction

Peach [Prunus persica (L.) Batsch] is one of the most economically important deciduous fruit from the Rosaceae family (Li et al, 2013). Gummosis is a nonspecific disease response to pathogen infection, mechanical injury, drought and cold stress, or insect attack It is characterized by a gum exudation from tree trunks, branches, and fruits in several fruit species, such as peach (Britton and Hendrix, 1982), almond (Popovicet al., 2021), apricot (Liu et al, 2015), sweet cherry (Zhang L. et al, 2019), and in citrus (Fan et al, 2011). The gum exudation on trunks, scaffold limbs, and branches significantly supresses tree growth and fruit yield of susceptible peach varieties It is one of the most destructive peach diseases in the south of China (Fan et al, 2011) and the southeastern United States (Weaver, 1974; Britton and Hendrix, 1982). Botryosphaeria dothidea is the most common cause of the disease in a large number of hosts worldwide (Britton and Hendrix, 1982; Mancero-Castillo et al, 2018), while Lasiodiplodia theobromae has proven to be the most virulent, causing the largest lesions and most copious gummosis in China (Fan et al, 2011)

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Conclusion