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Journal of Integrative Agriculture  2022, Vol. 21 Issue (8): 2291-2304    DOI: 10.1016/S2095-3119(21)63881-9
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Mining of candidate genes for grape berry cracking using a genome-wide association study

ZHANG Chuan1, 2*, WU Jiu-yun2*, CUI Li-wen3, FANG Jing-gui1

1 College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China

2 Turpan Research Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Turpan 838000, P.R.China

3 College of Agro-grassland Sciences, Nanjing Agricultural University, Nanjing 210095, P.R.China

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摘要  

为了更好地了解葡萄浆果开裂的遗传基础,我们对不同葡萄品种进行了全基因组关联研究(GWAS)。基于混合线性模型(MLM),我们在两年内分别检测到五个和两个与浆果开裂指数和浆果开裂类型相关的单核苷酸多态性(SNP)位点;这些位点主要分布在四条染色体上,即1、2、3和18号染色体。这些相关的SNP位点与10个独特的候选浆果开裂基因相关。基因表达模式表明,易裂果品种的候选基因表达比抗裂果品种丰富。葡萄浆果是一个由多个基因控制的复杂性状,主要涉及包括多聚半乳糖醛酸酶、铜转运蛋白和受体样蛋白相关基因,这些候选浆果开裂基因的高表达可能促进浆果开裂的发生。本研究有助于阐明浆果开裂的遗传机制




Abstract  

Fruit cracking is a common phenomenon during the growth and development of horticultural crops that seriously affects fruit yield and quality.  However, there are few studies on the mining of candidate genes related to berry cracking.  To better understand the genetic basis of grape berry cracking, we conducted a genome-wide association study (GWAS) of grape varieties.  Based on the mixed linear model (MLM), we detected five single nucleotide polymorphism (SNP) loci associated with berry-cracking index and two SNP loci associated with berry-cracking type in two years.  These loci were mainly distributed on four chromosomes, namely 1, 2, 3, and 18, and were associated with ten unique candidate berry-cracking genes.  The gene expression patterns indicated that the candidate genes in the susceptible berry-cracking variety were more abundant than in the resistant berry-cracking variety.  Grape berry-cracking is a complex trait controlled by multiple genes, mainly including genes involved in polygalacturonase, copper transporter, and receptor-like proteins.  The high expression of the candidate berry-cracking genes may promote the occurrence of berry cracking, so the present study helps to further elucidate the genetic mechanism of berry cracking.

Keywords:  berry-cracking index       berry-cracking type       GWAS       MLM       SNP  
Received: 12 May 2021   Accepted: 01 April 2022
Fund: The authors are grateful for the National Key Research and Development Program of China (2019YFD1000101), the China Agriculture Research System of MOF and MARA (CARS-29-yc-1); and Crop Resources Protection Program of Ministry of Agriculture and Rural Affairs of China (2130135–34).
About author:  ZHANG Chuan, E-mail: 2016204005@njau.edu.cn; WU Jiu-yun, E-mail: kobewjy@163.com; Correspondence FANG Jing-gui, Tel/Fax: +86-25-84395217, E-mail: fanggg@njau.edu.cn * These authors contributed equally to this study.

Cite this article: 

ZHANG Chuan, WU Jiu-yun, CUI Li-wen, FANG Jing-gui. 2022. Mining of candidate genes for grape berry cracking using a genome-wide association study. Journal of Integrative Agriculture, 21(8): 2291-2304.

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