77种葡萄砧木基因型的全基因组重测序、多样性分析及抗逆性分析

Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes.

作者信息

Wang Peipei, Zhao Fanggui, Zheng Ting, Liu Zhongjie, Ji Xinglong, Zhang Zhichang, Pervaiz Tariq, Shangguan Lingfei, Fang Jinggui

机构信息

College of Horticulture, Qingdao Agricultural University, Qingdao, China.

College of Horticulture, Nanjing Agricultural University, Nanjing, China.

出版信息

Front Plant Sci. 2023 Feb 9;14:1102695. doi: 10.3389/fpls.2023.1102695. eCollection 2023.

DOI:10.3389/fpls.2023.1102695

PMID:36844076

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9947647/

Abstract

INTRODUCTION

Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes.

METHODS

To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study.

RESULTS

About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of and , originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits.

DISCUSSION

This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated and could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

摘要

引言

葡萄砧木因其对各种环境具有更高的适应性，在全球葡萄产业发展中发挥着关键作用，评估葡萄基因型之间的遗传多样性对于基因型的保存和利用至关重要。

方法

为分析葡萄砧木的遗传多样性以更好地了解多重抗性性状，本研究对77份常见葡萄砧木种质进行了全基因组重测序。

结果

从77份葡萄砧木中产生了约6450亿个基因组测序数据，平均深度约为15.5倍，据此生成了系统发育聚类并探索了葡萄砧木的驯化过程。结果表明，这77份砧木起源于五个祖先成分。通过系统发育、主成分和同源性分析，这77份葡萄砧木被分为十组。值得注意的是，原产于中国且通常被认为对生物和非生物胁迫具有更强抗性的野生资源和从其他群体中细分出来。进一步分析表明，77份砧木基因型之间存在高水平的连锁不平衡，共挖掘出2805889个单核苷酸多态性（SNP），葡萄砧木的全基因组关联研究（GWAS）分析定位到631、13、9、2、810和44个SNP位点，这些位点与对根瘤蚜、根结线虫、盐、干旱、寒冷和涝渍性状的抗性有关。