Diallelic SNP marker development and genetic linkage map construction in octoploid strawberry (Fragaria × ananassa) through next-generation resequencing and high-resolution melting analysis

Lee, Ye Rin; Kim, Jinhee; Lee, Sun Yi; Lee, Jundae

doi:10.1007/s13580-019-00223-8

Cited by 8 publications

(11 citation statements)

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“…The homozygosity of 'Wongyo 3115' has been validated, using the SNP markers in our previous report (Lee et al, 2020). Our assembly strategy incorporated the hybrid approaches with short-and long-read sequencing technologies to acquire the promising genome sequence assembly.…”

Section: Discussionmentioning

confidence: 98%

“…Furthermore, we compared the 'Wongyo 3115' physical map with previously reported octoploid strawberry genetic maps (Supplementary Dataset 4). Linkage groups of 'Redgauntlet' × 'Hapil' F 1 (Alarfaj et al, 2021) matched with individual chromosomes, while some of the linkage groups displayed breakage on 'Sulhyang' × 'Senga-sengana' F 1 (Lee et al, 2020) and '232' × '1,392' F 1 (Sánchez-Sevilla et al, 2015). All the linkage groups matched with chromosomes 1-2, 1-4, 3-2, and 6-2 showed collinearity between genetic position and physical position in 'Wongyo 3115', except the linkage group LG6.4 of 'Redgauntlet' × 'Hapil' F 1 and LG1-1 of 'Sulhyang' × 'Senga-sengana' F 1 aligned with Chr6-2 and 1-4, respectively (Supplementary Figure 6).…”

Section: Construction Of a High-density Genetic Linkage Mapmentioning

confidence: 97%

“…'Wongyo 3115' produces pink-colored fruits with high firmness and a high sugar/acid ratio in comparison with other inbred lines. The homozygosity of 'Wongyo 3115' was investigated, using the genome-wide high-resolution meltingbased SNP markers, and the results suggested that 96.6% of the genome in 'Wongyo 3115' is homozygous (Lee et al, 2020). The homozygous cultivar 'Wongyo 3115' can reduce complexity of the genome assembly process, and its ancestor 'Benihoppe' is a major cultivar of Japanese origin with various desirable characters (Mochizuki et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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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)

et al. 2021

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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.

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Section: Discussionmentioning

confidence: 98%

Section: Construction Of a High-density Genetic Linkage Mapmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

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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)

et al. 2021

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“…Genomic DNA was extracted from young leaves of each F 2 individual according to the method described by Lee et al [39]. The DNA was dissolved in 100 µL of distilled water and treated with 0.1 µL of 10 mg•mL −1 RNase solution (Bio Basic Canada Inc., Ontario, Canada).…”

Section: Dna Extractionmentioning

confidence: 99%

Construction of an Onion (Allium cepa L.) Genetic Linkage Map Using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

Choi

Kim

Lee

2020

Plants

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Anthocyanins, the pigmented flavonoids responsible for red and blue colors in horticultural products, promote human health by preventing cancers and lowering the risk of cardiovascular disease. Red onions contain several cyanidin- and peonidin-based anthocyanins. In this study, we constructed a single-nucleotide polymorphism (SNP)-based genetic linkage map in an F2 segregating population derived from a cross between the inbred line ‘SP3B’ (yellow bulb) and the doubled haploid line ‘H6′ (red bulb) to identify quantitative trait loci (QTLs) for total anthocyanin content of onion bulbs using a genotyping-by-sequencing (GBS) analysis based on a reference gene set. A total of 101.9 Gbp of raw sequences were generated using an Illumina HiSeq 2500 system and a total of 1625 SNP loci were identified with the criteria of three minimum depths, lower than 30% missing rate, and more than 5% minor allele frequency. As a result, an onion genetic linkage map consisting of 319 GBS-based SNP loci and 34 high-resolution melting (HRM) markers was constructed with eight linkage groups and a total genetic distance of 881.4 cM. In addition, the linkage groups were assigned to corresponding chromosomes by comparison with the reference genetic map OH1×5225 through marker development based on common transcripts. The analysis revealed one major QTL, qAS7.1, for anthocyanin synthesis and two significant QTLs, qAC4.1 and qAC4.2, for anthocyanin content. The QTL qAS7.1, located on chromosome 7 with a phenotypic variation of 87.61%, may be a dihydroflavonol 4-reductase (DFR) gene that determines whether the bulb color is red or yellow. The QTLs qAC4.1 and qAC4.2 are separately positioned on chromosome 4 with R2 values of 19.43% and 26.28%, respectively. This map and QTL information will contribute to marker development and breeding for high anthocyanin content in bulb onion.

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“…At present, there are several methods for SNP detection, such as pyrosequencing, 7 restriction fragment length polymorphism (PCR-RFLP), uorescent quantitative PCR (TaqMan PCR), 8 mass array method (Mass assay), 9 and high-resolution melting (HRM). 10 They are difficult to be widely used due to expensive professional equipment, difficulty in automation, low sensitivity, difficulty in optimization, and so forth.…”

Section: Introductionmentioning

confidence: 99%

Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip

2021

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Diallelic SNP marker development and genetic linkage map construction in octoploid strawberry (Fragaria × ananassa) through next-generation resequencing and high-resolution melting analysis

Cited by 8 publications

References 58 publications

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)

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)

Construction of an Onion (Allium cepa L.) Genetic Linkage Map Using Genotyping-by-Sequencing Analysis with a Reference Gene Set and Identification of QTLs Controlling Anthocyanin Synthesis and Content

Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip

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