Genotype_data.hmp.csv

Understanding the genetic control of fruit composition traits in interspecific grapevines (<i>Vitis</i><i> </i>spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections of the North Dakota Grape Germplasm Enhancement Program. This study spanned three seasons (2020-to-2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable QTL associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K+ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTL on chromosomes 1-5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (BLUPs and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.

解析种间葡萄（*Vitis* spp.，葡萄属）果实组成性状的遗传调控机制，对于培育具备理想果实化学特性的新品种至关重要。为解决这一科学问题，本研究依托北达科他州葡萄种质改良计划的3份优良选系，构建了包含587份基因型材料的关联分析群体，并开展全基因组关联分析（genome-wide association study, GWAS）。本试验周期涵盖2020至2022年共3个生长季，每个生长季内设置3个不同采样时间点，累计开展9次表型鉴定，共测定9项果实性状。针对多数糖、酸相关性状，在多个表型鉴定事件中，于第6、16和17号染色体上检测到多个效应显著且稳定的数量性状基因座（quantitative trait locus, QTL）关联信号。尤为值得关注的是，位于16号染色体上的假定糖转运蛋白基因Vitvi16g00860与Vitvi16g00861，可介导糖分与钾离子跨膜运输，经鉴定其与本研究涉及的全部糖、酸性状均存在显著关联。此外，在1至5号、7号、14号及18号染色体上还检测到多个数量性状基因座，可调控不同表型鉴定事件中的多项果实品质性状。本研究通过对显著单核苷酸多态性（single nucleotide polymorphism, SNP）位点附近基因进行基因本体（gene ontology, GO）注释分析，解析了性状间的功能关联并筛选候选基因。同时，本研究还探讨了不同表型数据形式（最佳线性无偏预测值Best Linear Unbiased Prediction, BLUPs与原始未校正表型值）对部分数量性状基因座关联信号检测的抑制效应。本项全基因组关联分析以葡萄果实品质为研究核心，系统解析了相关性状的遗传结构，为分子育种学家进一步改良葡萄果实品质提供了必要的理论依据与研究基础。