da Silva Linge Cassia, Cai Lichun, Fu Wanfang, Clark John, Worthington Margaret, Rawandoozi Zena, Byrne David H, Gasic Ksenija
Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States.
Department of Horticulture, Michigan State University, East Lansing, MI, United States.
Front Plant Sci. 2021 Feb 25;12:644799. doi: 10.3389/fpls.2021.644799. eCollection 2021.
Peach is one of the most important fruit crops in the world, with the global annual production about 24.6 million tons. The United States is the fourth-largest producer after China, Spain, and Italy. Peach consumption has decreased over the last decade, most likely due to inconsistent quality of the fruit on the market. Thus, marker-assisted selection for fruit quality traits is highly desired in fresh market peach breeding programs and one of the major goals of the RosBREED project. The ability to use DNA information to select for desirable traits would enable peach breeders to efficiently plan crosses and select seedlings with desired quality traits early in the selection process before fruiting. Therefore, we assembled a multi-locus genome wide association study (GWAS) of 620 individuals from three public fresh market peach breeding programs (Arkansas, Texas, and South Carolina). The material was genotyped using 9K SNP array and the traits were phenotyped for three phenological (bloom date, ripening date, and days after bloom) and 11 fruit quality-related traits (blush, fruit diameter, fruit weight, adherence, fruit firmness, redness around pit, fruit texture, pit weight, soluble solid concentration, titratable acidity, and pH) over three seasons (2010, 2011, and 2012). Multi-locus association analyses, carried out using mrMLM 4.0 and FarmCPU R packages, revealed a total of 967 and 180 quantitative trait nucleotides (QTNs), respectively. Among the 88 consistently reliable QTNs detected using multiple multi-locus GWAS methods and/or at least two seasons, 44 were detected for the first time. Fruit quality hotspots were identified on chromosomes 1, 3, 4, 5, 6, and 8. Out of 566 candidate genes detected in the genomic regions harboring the QTN clusters, 435 were functionally annotated. Gene enrichment analyses revealed 68 different gene ontology (GO) terms associated with fruit quality traits. Data reported here advance our understanding of genetic mechanisms underlying important fruit quality traits and further support the development of DNA tools for breeding.
桃是世界上最重要的水果作物之一，全球年产量约为2460万吨。美国是继中国、西班牙和意大利之后的第四大生产国。在过去十年中，桃的消费量有所下降，这很可能是由于市场上水果质量不稳定所致。因此，在鲜食桃育种计划中，利用标记辅助选择果实品质性状的需求非常迫切，这也是RosBREED项目的主要目标之一。利用DNA信息选择理想性状的能力将使桃育种者能够在结果前的选择过程早期有效地规划杂交并选择具有所需品质性状的幼苗。因此，我们对来自三个公共鲜食桃育种计划（阿肯色州、得克萨斯州和南卡罗来纳州）的620个个体进行了多位点全基因组关联研究（GWAS）。使用9K SNP阵列对材料进行基因分型，并在三个季节（2010年、2011年和2012年）对三个物候性状（开花日期、成熟日期和开花后天数）和11个果实品质相关性状（红晕、果实直径、果实重量、附着性、果实硬度、果核周围红色、果实质地、果核重量、可溶性固形物浓度、可滴定酸度和pH值）进行表型分析。使用mrMLM 4.0和FarmCPU R软件包进行的多位点关联分析分别揭示了总共967个和180个数量性状核苷酸（QTN）。在使用多种多位点GWAS方法和/或至少两个季节检测到的88个始终可靠的QTN中，有44个是首次检测到的。在第1、3、4、5、6和8号染色体上鉴定出了果实品质热点区域。在包含QTN簇的基因组区域中检测到的566个候选基因中，有435个进行了功能注释。基因富集分析揭示了68个与果实品质性状相关的不同基因本体（GO）术语。本文报道的数据推进了我们对重要果实品质性状潜在遗传机制的理解，并进一步支持了用于育种的DNA工具的开发。
