Identification and characterization of QTLs for blush, soluble solids concentration (SSC), and titratable acidity (TA) in peach through a multi-family approach

Abstract

25Background: Fruit quality traits have a significant effect on consumer acceptance and 26 subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic 27 bases of key fruit quality traits is essential for industry to improve fruit quality and increase 28 consumption. A Bayesian approach embedded in the FlexQTL software increases the 29 accuracy of QTL mapping and the probability of identifying new and validating known QTLs 30 across a wide range of genetic backgrounds. 31Results: Phenotypic data of seven F1 low to medium chill full-sib families were collected over 32 two years at two locations and genotyped using the 9K SNP Illumina array. One major QTL 33 for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% 34 of the total phenotypic variance and showed three QTL alleles of different effects. For SSC, 35 one QTL was mapped on LG5 at 60-72cM and explained from 17 to 39% of the phenotypic 36 variance. A major QTL for TA that co-localized with the major locus for low-acid fruit (D-locus) 37 was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. 38The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. 39This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is 40 homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and 41 predictive SNP marker(s) associated with desired QTL alleles. 42 Conclusions:A multi-family-based QTL discovery approach enhanced the ability to discover 43 a new TA QTL and validated other QTLs which were reported in previous studies. Identified 44 predictive SNPs and their original sources will facilitate the selection of parents and/or 45 seedlings that have desired haplotype alleles. Our findings will help peach breeders develop 46 new predictive, DNA-based molecular marker tests for routine use in marker-assisted 3 Background 51Peach [Prunus persica (L.) Batsch] is the third most important temperate fruit crop globally in terms of 52 production [1]. Peach fruit quality traits such as flesh texture, color, sweetness, acidity, and other 53 organoleptic attributes affect consumer preference and consumption [2]. Most of these traits are 54 quantitatively inherited and their genetic control is still unclear [3]. 55In the last decade, the rate of fresh consumption has decreased from 2.3 to 1.3 kg per capita per 56year in the U.S. [4]. The lack of consistent quality (poor firmness, lack of flavor, low level of 57 sweetness, and non-ripening fruit) is a main reason consumers do not purchase peaches [5]. The 58 primary reason for poor quality is harvesting at immature stages, a lack of good postharvest handling 59 practices, the need for high yields but not necessarily high quality to make production profitable and 60 the relative ease for selecting for external versus internal fruit traits. Consumers are willing to pay more 61 for fruits of better quality [6] which is the reason for developing branded fru...