Abstract
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.
Highlights
Peach [Prunus persica (L.) Batsch] is a diploid species, with a short juvenile period (2–4 years), relatively simple genome (∼230 Mbp), and one of the best genetically characterized deciduous trees (Verde et al, 2013)
Six hundred twenty individuals from the three fresh market public peach breeding programs were evaluated for 14 different fruit quality traits over 3 years (2010–2012) (Table 1)
The Ripening date (RD), fruit weight (FW), Fruit firmness (FF), Pit weight (PW), soluble solid concentration (SSC), and pH, as well as the categorical traits Blush, ADH, Redness around Pit (RP), and fruit texture (FT) were evaluated in three seasons (2010–2012)
Summary
Peach [Prunus persica (L.) Batsch] is a diploid species, with a short juvenile period (2–4 years), relatively simple genome (∼230 Mbp), and one of the best genetically characterized deciduous trees (Verde et al, 2013). Peach is the third most cultivated temperate tree fruit in the world, after apple and pear, with a world production of approximately 24.6 million tons (Food and Agricultural Organization of the United Nations (FAOSTAT), 2018). Peach consumption has declined over the past decades. In the United States, peach per capita consumption decreased to 1.3 kg per year compared to ∼3 kg per year in the 1980s (Minas et al, 2018). Inconsistent and low fruit quality is recognized as the major limiting factor for consumer acceptance and, the low rates of peach consumption (Cirilli et al, 2016). Peach breeders have always selected for fruit quality with respect to size, color and firmness, as well as tried to expand harvest season (Laurens et al, 2018). More emphasis is on other traits such as internal quality and postharvest traits (Elsadr et al, 2019)
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