果树学报2025，Vol.42Issue(5)：979-992,14.DOI:10.13925/j.cnki.gsxb.20240644
新疆甜瓜种质资源遗传多样性及果肉硬度性状GWAS分析
Genetic diversity and GWAS analysis of flesh hardness trait in Xinjiang melon germplasm resources
摘要
Abstract
[Objective]Melon,as an important global fruit and vegetable crop,is highly influenced by fruit flesh hardness and other quality traits,which directly affect its market competitiveness.Melon is widely cultivated worldwide and holds significant economic value,especially in Xinjiang,China,which serves as a major production hub.Xinjiang is the home to a diverse array of melon varieties,with key cultivation areas including Hami,Turpan,Korla and Changji.In recent years,the melon planting area has continued to expand,with Xinjiang accounting for one-third of the national production.However,the Xinjiang melon industry faces challenges such as severe homogenization,a reliance on a limited number of parental lines for breeding,and low breeding efficiency.Conducting genetic diversity analy-ses of melon germplasm and identifying key trait-associated genes and loci can provide critical informa-tion for developing genetic improvement strategies.This,in turn,can promote varietal diversity and en-hance the industry's market competitiveness.Flesh hardness is a key quality characteristic,however,and little research has been reported on the genetic basis of fruit flesh hardness in melon.This study aims to analyze the genetic diversity and population structure of melon germplasm and to locate genes associated to flesh hardness.[Methods]High-throughput sequencing technology was used to analyze the genomes of 292 melon accessions from around the world,constructing a large-scale genetic varia-tion map.The Neighbor-Joining Method was applied to calculate the genetic distance matrix,and a phy-logenetic tree was built.Genome-wide association analysis(GWAS)and haplotype analysis were per-formed in conjunction with the flesh hardness trait.[Results]The melon germplasm population was di-vided into two distinct branches:Branch Ⅰ(Pop1)and Branch Ⅱ(Pop2).Pop1 predominantly clus-tered local varieties from Xinjiang of China,Japan and the former Soviet Union,with Xinjiang varieties making up the majority(90.84％).Pop2 was mainly composed of cultivated varieties,widely distributed across various regions,including multiple provinces of China(Xinjiang,Shaanxi,Taiwan,Gansu,Inner Mongolia and Liaoning),Japan,the former Soviet Union,the United States,Canada,Iran,Turkey,Hun-gary,South Africa and India,with Xinjiang varieties constituting 67.5％.Genome-wide linkage disequi-librium(LD)analysis confirmed significant differences in genetic diversity and population structure be-tween the two groups.LD analysis revealed that the LD decay distance for the entire melon germplasm population was 49.2 kb when r2 decreased to half(r2=0.33).However,when analyzed separately,the LD decay distances for landraces and cultivated varieties were 57 kb and 45.9 kb,respectively,indicat-ing that cultivated varieties exhibited a faster LD decay rate than landraces.This suggests that cultivat-ed varieties have undergone stronger selective pressures and genetic drift.Furthermore,nucleotide di-versity analysis showed that the nucleotide diversity of cultivated varieties(2.537× 10-3)was significant-ly(p＜0.01)higher than that of landraces(1.989× 10-3),further supporting the idea of rapid evolution in genetic diversity among cultivated varieties.Through GWAS,we explored the variation of flesh traits,especially the important agronomic trait of flesh hardness.Based on phenotypic and genotypic data,we identified a significant association signal on chromosome 8 of the melon genome(Chr08:2815957_2831112;P=2.36e-07).This region contained 11 significant associated SNPs,which explained 9.04％of the phenotypic variation.Functional annotation revealed that this region harbored candidate genes re-lated to cell wall biosynthesis and remodeling,like inositol monophosphatase(MELO3C007440.2)and nucleotide-sugar transporter(MELO3C007449.2).These genes may influence flesh hardness by regulat-ing the synthesis and remodeling of pectin and cell wall polysaccharides.Five SNPs were found in the coding region of MELO3C007451.2,which were in strong linkage disequilibrium,allowing the popula-tion to be divided into four haplotypes.The 98.05％of local varieties carried the hap001 haplotype.Hap004 haplotype materials exhibited soft and brittle characteristics,while hard materials carried hap001,hap002 and hap003 haplotypes.[Conclusion]The high geographical and cultivation environ-ment differentiation of melon germplasm reflects significant genetic differences between local and culti-vated varieties,especially the diversified geographical origins of Xinjiang melons.The study identified candidate genes associated with melon flesh hardness,including MELO3C007434,MELO3C007435,MELO3C007436,MELO3C007437,MELO3C007438,MELO3C007439,MELO3C007440 and ME-LO3C007441,which were confirmed as selection genes related to the differentiation between wild and cultivated species.We speculate that these genes may play a key role in the domestication process of flesh hardness from wild to cultivated species.In addition,candidate genes like inositol monophospha-tase(MELO3C007440.2)and nucleotide-sugar transporter(MELO3C007449.2),involved in pectin and cell wall polysaccharide synthesis,may be important regulatory factors influencing flesh hardness.Fur-thermore,we discovered several haplotypes associated with flesh hardness in the population,and the differences in these haplotypes were closely related to phenotypic variation in flesh texture.Notably,haplotype differentiation showed a clear association between hard and soft flesh samples,highlighting the connection between genotype and phenotype.This study provides new molecular markers for the ge-netic improvement of melon flesh hardness and other quality traits,laying the foundation for marker-as-sisted selection in melon breeding.关键词
甜瓜/全基因组关联分析/果肉硬度Key words
Cucumis melo L./Genome-wide association analysis(GWAS)/Flesh hardness分类
园艺学与植物营养学引用本文复制引用
朱婉婷,李江峰,詹倩如,耍振阳,朱迎春,郭艳霞,骆翔..新疆甜瓜种质资源遗传多样性及果肉硬度性状GWAS分析[J].果树学报,2025,42(5):979-992,14.基金项目
河南省农业援疆项目(202107) （202107）
新疆人才发展基金重点人才计划项目(XJARS-06-22) （XJARS-06-22）
新疆维吾尔自治区重点研发计划项目(2023B02017-2) （2023B02017-2）
