SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

Lee, Ji Hee; Natarajan, Sathishkumar; Biswas, Manosh Kumar; Shirasawa, Kenta; Isobe, Sachiko; Kim, Hoy‐Taek; Park, Jong-In; Seong, Chi Nam; Nou, Ill Sup

doi:10.1371/journal.pone.0201229

Cited by 25 publications

(16 citation statements)

References 48 publications

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“…Anthocyanins, type of From genotyping-by-sequencing (GBS), 175 SNPs and 57 from Fluidigm SNP assays were used for the construction of an onion genetic map, which consisted of eight linkage groups and covered a total length of 1339.5 cM [34]. A total of 1904 SNPs were discovered in 192 Korean short-day onion inbred lines using double digest restriction site-associated DNA sequencing (ddRAD-seq) [35].…”

Section: Introductionmentioning

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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Section: Introductionmentioning

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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“…Restriction site associated DNA sequencing (RAD-seq) a newly developed high-throughput approach conferring comprehensive understanding of genetic evolution based on SNPs [32,33]. In addition, RAD-seq technology is a widely used for the construction high-density genetic map [34,35]. Lee et al performed paired-end double digested restriction site-associated DNA sequencing (RAD-seq) and identified 1904 SNPs in 192 onion inbred lines [35].…”

Section: Discussionmentioning

confidence: 99%

“…In addition, RAD-seq technology is a widely used for the construction high-density genetic map [34,35]. Lee et al performed paired-end double digested restriction site-associated DNA sequencing (RAD-seq) and identified 1904 SNPs in 192 onion inbred lines [35]. The number of 1904 SNPs in 192 onion inbred lines by Lee et al was significantly lower than the number of 162,321 high quality SNPs and total 680,825 SNPs in 122 onion accessions in our study.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing

Fang

Liu

et al. 2020

PLoS ONE

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Lou onion (Allium fistulosum L. var. viviparum) is an abundant source of flavonols which provides additional health benefits to diseases. Genome-wide specific length amplified fragment (SLAF) sequencing method is a rapidly developed deep sequencing technologies used for selection and identification of genetic loci or markers. This study aimed to elucidate the genetic diversity of 122 onion accessions in China using the SLAF-seq method. A set of 122 onion accessions including 107 A.fistulosum L. var. viviparum Makino, 3 A.fistulosum L. var. gigantum Makino, 3 A.mongolicum Regel and 9 A.cepa L. accessions (3 whites, 3 reds and 3 yellows) from different regions in China were enrolled. Genomic DNA was isolated from young leaves and prepared for the SLAF-seq, which generated a total of 1,387.55 M reads and 162,321 high quality SNPs (integrity >0.5 and MAF >0.05). These SNPs were used for the construction of neighbor-joining phylogenetic tree, in which 10 A.fistulosum L. var. viviparum Makino accessions from Yinchuan (Ningxia province) and Datong (Qinghai province) had close genetic relationship. The 3 A.cepa L. clusters (red, white and yellow) had close genetic relationship especially with the 97 A.fistulosum L. var. viviparum Makino accessions. Population structure analysis suggested entire population could be clustered into 3 groups, while principal component analysis (PCA) showed there were 4 genetic groups. We confirmed the SLAF-seq approach was effective in genetic diversity analysis in red onion accessions. The key findings would provide a reference to the Lou onion germplasm in China.

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“…Recently, the double digest restriction site-associated DNA sequencing (ddRAD-seq) approach was used for SNP discovery in inbred lines of Korean short-day onion. A total of 1904 SNPs were discovered and used in population structure analyses and genetic relationship studies ( Lee et al, 2018 ) . Such SNPs or SSRs developed using NGS technologies can be helpful in developing precise linkage maps and managing genetic resources in onion as well as other related Allium species.…”

Section: Survey Methodologymentioning

confidence: 99%

Omics approaches inAlliumresearch: Progress and way ahead

Khandagale

Krishna

Roylawar

et al. 2020

PeerJ

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Background The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. Method In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. Results Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. Conclusion All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

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SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

Cited by 25 publications

References 48 publications

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

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

Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing

Omics approaches inAlliumresearch: Progress and way ahead

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