ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)

Abstract

Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL),-diameter (FD),-weight (FW) and-soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F 1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24-35%, 21-42%, 24-54% and 23-50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1 723 G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F 1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

“…Likewise, our AX-184477629 marker linked to TSS on 3B is in the same chromosome region as the SSC1 QTL controlling soluble solids content 30 we found in GWAS/QTL published data only a few additional fruit quality QTL located on the same chromosomes as those detected here. Among them are the FW QTL on 5B and the TSS QTL on 5A previously reported 38 on the same chromosomes but in different regions. Thus, thanks to the originality of European accessions included in our study, the genetic diversity of the panel allowed us to reveal new QTL and associated SNP markers, even for well-studied fruit quality traits such as FW and TSS.…”

Strawberry breeding for improved flavor

“…Genome-wide association study and QTL mapping QTL mapping has been applied frequently for many fruit quality traits including SSC, thanks to handheld refractometers that provide rapid measurements. Biparental (Castro & Lewers, 2016;Lerceteau-Köhler et al, 2012;Natarajan et al, 2020;Rey-Serra et al, 2021;Vallarino et al, 2019;Zorrilla-Fontanesi et al, 2011) and pedigree connected populations (Verma et al, 2017) have been investigated for SSC QTLs using different marker technologies identifying many SSC QTL, yet with few consensus QTL across multiple populations/environments. Moreover, a GWAS analysis with a small sample collection found no significant markers correlating with SSC (Cockerton et al, 2021).…”

“…The genetic control of SSC appears to be complex. Though quantitative trait locus (QTL) have been detected in different studies (Castro & Lewers, 2016; Lerceteau‑Köhler et al., 2012; Natarajan et al., 2020; Vallarino et al., 2019; Verma et al., 2017), few have been stable across environments and breeding programs. Nevertheless, multiple studies have shown moderate heritability and the ability to make gains from selection (Gezan et al., 2017).…”

QTL associated with Gummy Stem Blight (GSB) resistance in watermelon

“…CAPS/HRM markers have been reported for 'PMR 5' resistance to powdery mildew race 5 in melon [21]. GBS and ddRAD-seq techniques have been used for mapping genes and development of markers in several plant species such as rapeseed, soybean, maize, strawberry and melon [22][23][24][25]. Among these assays, HRM and Kompetitive allele specific PCR (KASP) assays have relatively simple, fast, and cost-effective approaches.…”