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 F1 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 A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 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.
Highlights
The cultivated strawberry (Fragaria × ananassa), an economically important berry crop, is favored across the globe due to its characteristic aesthetic property, flavor, nutritional value and health benefitting anti-oxidative content (AlvarezSuarez et al 2014; Henning et al 2010)
The genomic DNA of strawberry genotypes were double digested with PstI and MspI restriction enzymes to generate ddRAD-seq representation libraries which were subsequently sequenced using Illumina HiSeq 2000 platform
Based on strict single nucleotide polymorphisms (SNPs) filtration criteria, a total of 12,698 high quality SNPs were retained from the mapped reads
Summary
The cultivated strawberry (Fragaria × ananassa), an economically important berry crop, is favored across the globe due to its characteristic aesthetic property, flavor, nutritional value and health benefitting anti-oxidative content (AlvarezSuarez et al 2014; Henning et al 2010). Compared to other economically important fruits, genetic control of key traits of cultivated strawberry is yet to be completely understood. Fragaria × ananassa has undergone complex evolutionary changes during its evolutionary journey starting from wild diploid progenitors to the current cultivated octoploid (2n = 8 × = 56) species (Potter et al 2000). Evidences from recent studies indicate three diploid progenitors namely, F. vesca, F. nubicola and F. orientalis; or F. orientalis, F. iinumae and F. vesca or F. mandshurica (Edger et al 2019; Rousseau-Gueutin and Gaston 2009), which lead to the extant octoploid species with four relatively similar sub-genomic components (Rousseau-Gueutin and Gaston 2009; Sargent et al 2016; Tennessen et al 2014). The complexity of the genetics of this species can be attributed to the various combinations of gene interactions between the multiple alleles, complex meiotic behaviors and highly heterozygous nature of the species (Lerceteau-Köhler et al 2003; Rousseau-Gueutin et al 2008; Spigler et al 2010; Weebadde et al 2008)
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