QTL mapping of pomological traits in peach and related species breeding germplasm

Abstract

Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those Electronic supplementary material The online version of this article (previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in markerassisted breeding.

Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps

“…These positions are also consistent with markers developed for sub-acidic traits in peach ) and with the colocalization of QTLs for TA and pH on LG5 (Fresnedo-Ramírez et al 2015). On the contrary, any equivalent QTL on LG5 was found in apricot for malic acid (which is synonymous with TA) and pH (Salazar et al 2013), even in peach ).…”

“…More recently, attempts have been made to map QTLs in peach using the newly developed SNP genotyping array v1 . Several QTLs that control traits such as chilling and heat requirements , blush (Frett et al 2014), maturity date Fresnedo-Ramírez et al 2015;Nuñez-Lillo et al 2015) or other pomological traits such as fruit weight, soluble solids content or pH (Fresnedo-Ramírez et al 2015) have been mapped. Moreover, the current analytical techniques are more powerful for large-scale phenotyping than older methods, and new traits related to fruit quality are being incorporated in QTL analysis.…”

Two QTL characterized for soft scald and soggy breakdown in apple (Malus × domestica) through pedigree-based analysis of a large population of interconnected families

“…PBA has been made a more attractive approach in apple through guidelines on the composition of the study germplasm (Peace et al 2014), high throughput genomewide genotyping capabilities through SNP arrays (Chagné et al 2012;Bianco et al 2014Bianco et al , 2016, the availability of sets of pedigreed full-sib families (Peace et al 2014), and standardized phenotyping procedures for some major traits (Evans et al 2011a). This approach has been increasingly utilized in a variety of Rosaceous fruit species, including strawberry (Whitaker 2011;Roach et al 2016;Mangandi et al 2017), peach (Fresnedo-Ramírez et al 2015Mora et al 2017), cherry (Rosyara et al 2013;Stegmeir et al 2014;Sandefur et al 2016), and apple (Schmitz et al 2013;Bink et al 2014;Guan et al 2015, Allard et al 2016Durand et al 2017).…”

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

“…A major SSC QTL was consistently detected in the middle region of LG4 close to the maturity date (MD) locus in intraspecific full-sib families [3]. Minor QTLs have also been reported on LG1, 2, 3, 5, 6, 7, and 8 [14,21].…”

“…Fruit acidity, like SSC, impacts consumer acceptance and is considered a major selection criterion in breeding [2,22]. Low fruit acidity is associated with the major locus D-locus located on the proximal end of LG5 [15,21,22]. Several additional QTLs with minor effects have been mapped on five other LGs: LG1 and LG6 [15] and LG2, 3, and 7 [21].…”