Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

Abstract

Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line ‘Wongyo 3115’, using long- and short-read sequencing technologies. The assembly of ‘Wongyo 3115’ produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the ‘Wongyo 3115’ reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the ‘BS F2’ populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the ‘Wongyo 3115’ genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of ‘BS F2’ obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.

Genome-Wide Analysis of MYB10 Transcription Factor in Fragaria and Identification of QTLs Associated with Fruit Color in Octoploid Strawberry

“…Fruit skin color exhibited normal distribution in F 2 progenies, while achene color and flesh color biased to red and white, respectively (Figure 5B). QTLs controlling fruit color were analyzed using bin map of 'BS F 2 (II)' [12] and the color-related traits evaluated for 2019 and 2020. QTLs detected on the common physical position in 'Wongyo 3115' genome were combined to one.…”

“…The fruit color related traits of the 'BS F 2 (II)' population were evaluated as two to three scales (Table S2). QTL analysis was performed using the phenotypes of 2019 and 2020 and genetic map constructed by Lee and Manivannan et al [12]. Composite interval mapping of Windows QTL Cartographer 2.5 [36] with default option was used for QTL analysis.…”

“…The recent advancements in next generation sequencing enabled the availability of the whole genome sequence of diploid and octoploid strawberry. The reference genomes of heterozygous 'Camarosa' [11] and homozygous 'Wongyo 3115' [12] cultivated strawberries can facilitate the understating of gene regulation and development of markers associated with fruit colors in octoploid strawberry.…”

QTL Analysis for Chlorophyll Content in Strawberry (Fragaria × ananassa Duch.) Leaves

“…The octoploid strawberry (Fragaria × ananassa) is a vital horticultural crop worldwide. The consumption and the economic value of strawberries have been increasing due to its flavor, pleasant aroma, antioxidant characteristics, and other important health advantages [19,20]. The completion of the whole genome sequencing of strawberry implies that research on the strawberries genome has entered into a new era [19,21].…”

“…The consumption and the economic value of strawberries have been increasing due to its flavor, pleasant aroma, antioxidant characteristics, and other important health advantages [19,20]. The completion of the whole genome sequencing of strawberry implies that research on the strawberries genome has entered into a new era [19,21]. In the past few years, with the rapid development of next generation sequencing (NGS)-based molecular marker technologies, it has become achievable to construct a high density genetic map of strawberries.…”