Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach

Abstract

Background: Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time. Results: Phenotypic data of seven F 1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles. Conclusions: A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.

Mapping and Characterization QTLs for Phenological Traits in Seven Pedigree-connected Peach Families

“…Finally, Prupe.4G185800 [73] and Prupe.4G187100 [74] genes that were reported to be associated with the regulation of the anthocyanin biosynthetic pathway in peach. Hence, these results confirming the pleiotropic effect of the RD on several quality traits including blush that was previously reported [15,16,34,35,39].…”

“…Likewise, the examination of the relative effects of haplotypes and estimated QTL genotypes revealed a series of QTL alleles of different effect at this locus that we coined Q1, Q2, q1, and q2. The use of multi-parent populations for finding multiple functional alleles of different effect was also reported for two acidity QTLs/genes in apple by Verma, et al [51] and for the blush QTL in peach using the current germplasm by Rawandoozi, et al [16]. In our germplasm the RD QTL on LG4 co-localized with a QTL for soluble solids concentration (SSC) and blush reported by Rawandoozi, et al [16].…”

“…The use of multi-parent populations for finding multiple functional alleles of different effect was also reported for two acidity QTLs/genes in apple by Verma, et al [51] and for the blush QTL in peach using the current germplasm by Rawandoozi, et al [16]. In our germplasm the RD QTL on LG4 co-localized with a QTL for soluble solids concentration (SSC) and blush reported by Rawandoozi, et al [16]. These co-localizations had also been reported by other studies [15,34,52].…”

“…Moreover, the Pedigree-Based Analysis (PBA) approach [12,13] that uses multiple pedigree-linked families allows the discovery of more QTL or QTL-alleles per locus across a range of genetic backgrounds. This approach has facilitated the identification of QTLs for blush [14][15][16], ripening date [15,17,18], soluble solids content [15][16][17][18], fruit weight, and titratable acidity [15,17,19].…”

Non-structural Carbohydrate Metabolism in the Flesh of Stone Fruits of the Genus Prunus (Rosaceae) – A Review

“…The genes for the invertases, SuSy, SPS and SDH present in the peach genome are shown in Table 2. Amongst these, a SuSy (Prupe.5G241700.1) is a candidate gene for controlling the SSC because it is within the interval (located between 12 and 18 Mbp of chromosome 5) of a Quantitative Trait Loci linked to SSC (Nuñez-Lillo et al, 2019;Rawandoozi et al, 2020).…”