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Journal of Integrative Agriculture
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Construction of the first high-density genetic linkage map and the identification of QTLs and key candidate genes associated with fruit size for Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]

Jing Zhang1,3*, Tao Chen2*, Yan Wang1, 3, Hao Wang1, Zhenshan Liu1, Qing Chen1, 3, Wen He1, 3, Shaofeng Yang1, Haoru Tang1, Xiaorong Wang1, 3#

1 College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China

2 College of Life science, Sichuan Agricultural University, Yaan, 625014, China

3 Key Laboratory of Agricultural Bioinformatics (Ministry of Education), Sichuan Agricultural University, Chengdu, 611130, China

Highlights:

1. The first SNP-based genetic linkage map was constructed, including eight linkage groups with a total length of 1,185.24 cM and a resolution of 0.41 cM.

2. A total of 49 non-redundant QTLs were identified for five fruit size-related traits and ten multi-trait QTL clusters were further detected from these loci.

3. Seven key fruit size-related candidates were identified by transcriptomic analysis, association analysis and RT-qPCR validation.

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摘要  

果实大小是中国樱桃[Cerasus pseudocerasus (Lindl.) G.Don]重要果实品质性状。本研究中,我们从两份中国樱桃地方种质构建的F1分离群体中筛选出200个子代开展特异性位点扩增片段测序(specific locus amplified fragment sequencing,SLAF-seq),构建了首个基于单核苷酸多态性(single nucleotide polymorphism,SNP)标记的中国樱桃高密度遗传连锁图谱,基于两年表型数据开展果实大小相关数量性状位点(quantitative trait lociQTL),及多性状共定位QTLmulti-trait QTL clustersmuQTL)的鉴定,并通过果实关键发育阶段转录组分析,SNP挖掘与实时荧光定量PCRquantitative real-time PCRRT-qPCR)验证在QTL簇中筛选关键候选基因。整合遗传连锁图谱由2919SNP标记构成,包含8个连锁群,总图距1185.24 cM,分辨率为0.41 cM5个果实大小相关性状中,共检测到107QTLs,合并去冗余后获得49个非冗余QTLs。其中12个非冗余位点在两年中稳定检测到,包含9对数优势比logarithm of oddsLOD)介于3.01~4.72,表型变异解释率(phenotypic variation explainedPVE)介于6.69%~10.30%的高置信度位点。此外,检测到10个由3~4个性状共定位QTL簇。在这些QTL簇区间内,转录组分析鉴定出23个与果实大小相关的候选基因,功能主要富集于植物激素合成、代谢与信号转导(如IAAs)、细胞扩展与增殖(如RLF)及细胞壁代谢(如NAC)通路,经关联分析和RT-qPCR验证,7个候选基因可能在调控果实大小方面发挥关键作用本研究成果为利用分子育种技术遗传改良中国樱桃果实大小提供了重要理论依据。



Abstract  

Fruit size is a crucial fruit quality trait for Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]. Herein, we constructed the first single nucleotide polymorphism (SNP)-based high-density genetic linkage map for Chinese cherry by applying specific locus amplified fragment sequencing to 200 progenies selected from an F1 segregating population derived from two Chinese cherry landraces. Fruit size-related quantitative trait loci (QTLs) and QTLs co-located by multiple traits (multi-trait QTL clusters, muQTLs) were identified based on phenotypic data for two years. We discovered key candidate genes within muQTLs through transcriptomic analyses of fruits from crucial developmental stages, SNP detection and RT-qPCR validation. Integrated linkage map was constructed using 2,919 SNPs, comprising eight linkage groups with a total length of 1,185.24 cM and a resolution of 0.41 cM. A total of 107 QTLs were identified for five fruit size-related traits and subsequently merged into 49 non-redundant QTLs. Twelve non-redundant loci were consistently detected across two years, including nine high-confidence loci with logarithm of odds (LOD) scores of 3.014.72 and phenotypic variation explained (PVE) of 6.69%10.30%. Furthermore, ten muQTLs were co-located by three or four traits. Within muQTLs, 23 fruit size-related candidate genes identified by transcriptomic analysis were predominantly enriched in phytohormone-related biosynthesis, metabolism and signal transduction (e.g., IAA), cell expansion and proliferation (e.g., RLF), and cell wall metabolism (e.g., NAC), among which seven candidates were further validated to exert putative crucial functions in governing fruit size via RT-qPCR. This study provides helpful support for genetic improvement by molecular breeding in Chinese cherry.

Keywords:  Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]       high-density genetic linkage map              fruit size-related traits              QTLs (quantitative trait loci)              key candidate genes  
Online: 14 September 2026  
Fund: 

This study was financially supported by National Natural Science Foundation of Chinese (No. 31801826), Sichuan Science and Technology Program (No. 20YYJC2929, No. 2019JDTD0010), Cherry Resources Sharing and Service Platform of Sichuan Province and Tianfu Talent Project of Sichuan Tianfu New Area (No. 2021- CF02-0162396-RC-4096). 

About author:  * These authors contributed equally to this study. #Correspondence Xiaorong Wang, E-mail: wangxr@sicau.edu.cn

Cite this article: 

Jing Zhang, Tao Chen, Yan Wang, Hao Wang, Zhenshan Liu, Qing Chen, Wen He, Shaofeng Yang, Haoru Tang, Xiaorong Wang. 2026. Construction of the first high-density genetic linkage map and the identification of QTLs and key candidate genes associated with fruit size for Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don]. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2026.09.026

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