Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm
Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and popula...
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| Veröffentlicht in: | Genes 2019-10, Vol.10 (10), p.822 |
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| creator | Lee, Kyung Jun Lee, Jung-Ro Sebastin, Raveendar Shin, Myoung-Jae Kim, Seong-Hoon Cho, Gyu-Taek Hyun, Do Yoon |
| description | Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs. |
| doi_str_mv | 10.3390/genes10100822 |
| format | Article |
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The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes10100822</identifier><identifier>PMID: 31635343</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>agrobiodiversity ; breeding programs ; Citrullus - genetics ; Citrullus lanatus ; discriminant analysis ; Enzymes ; fruits ; Genetic diversity ; Genetic resources ; genetic variation ; Genomes ; Genotype ; Genotyping ; genotyping by sequencing ; Genotyping Techniques - methods ; Germplasm ; Polymorphism ; Polymorphism, Single Nucleotide ; Population ; Population genetics ; Population structure ; Rural development ; Seed Bank ; seed industry ; Sequence Analysis, DNA - methods ; Single-nucleotide polymorphism ; Software ; South Korea ; vegetables ; watermelons</subject><ispartof>Genes, 2019-10, Vol.10 (10), p.822</ispartof><rights>2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2019 by the authors. 2019</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c448t-9e1b3e7a8fb6dbf608becae5fda8167cf119a2531f58c712402c1c14d8117da03</citedby><cites>FETCH-LOGICAL-c448t-9e1b3e7a8fb6dbf608becae5fda8167cf119a2531f58c712402c1c14d8117da03</cites><orcidid>0000-0002-8972-0391 ; 0000-0003-3244-4266</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826620/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826620/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53770,53772</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31635343$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee, Kyung Jun</creatorcontrib><creatorcontrib>Lee, Jung-Ro</creatorcontrib><creatorcontrib>Sebastin, Raveendar</creatorcontrib><creatorcontrib>Shin, Myoung-Jae</creatorcontrib><creatorcontrib>Kim, Seong-Hoon</creatorcontrib><creatorcontrib>Cho, Gyu-Taek</creatorcontrib><creatorcontrib>Hyun, Do Yoon</creatorcontrib><title>Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.</description><subject>agrobiodiversity</subject><subject>breeding programs</subject><subject>Citrullus - genetics</subject><subject>Citrullus lanatus</subject><subject>discriminant analysis</subject><subject>Enzymes</subject><subject>fruits</subject><subject>Genetic diversity</subject><subject>Genetic resources</subject><subject>genetic variation</subject><subject>Genomes</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>genotyping by sequencing</subject><subject>Genotyping Techniques - methods</subject><subject>Germplasm</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Rural development</subject><subject>Seed Bank</subject><subject>seed industry</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Software</subject><subject>South Korea</subject><subject>vegetables</subject><subject>watermelons</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkU1LxDAQhoMorqx79CoFL3qo5qttehH8XIUFD6t4DGk6XSNtWpN2Yf-9WVbF9WISmAzz8DLzDkJHBJ8zluOLBVjwBBOMBaU76IDijMWc02T313-EJt6_43A4phgn-2jESMoSxtkBep4Gid7o6NYswXnTr6Ir7yG8MipWUai2_aozdrHO5vAxgNXr7HR6PT-LjI1eVQ-ugbq1AXZNVyvfHKK9StUeJl9xjF7u755vHuLZ0_Tx5moWa85FH-dACgaZElWRlkWVYlGAVpBUpRIkzXRFSK5owkiVCJ0RGtrXRBNeCkKyUmE2Rpcb3W4oGig12N6pWnbONMqtZKuM3K5Y8yYX7VKmgqYpXQucfgm4Nozme9kYr6GulYV28JJyjtM8z4X4H2U4y1jwOAvoyR_0vR2cDU5ImnARLg3ej1G8obRrvXdQ_fRNsFxvV25tN_DHv4f9ob93yT4BAsqgMQ</recordid><startdate>20191018</startdate><enddate>20191018</enddate><creator>Lee, Kyung Jun</creator><creator>Lee, Jung-Ro</creator><creator>Sebastin, Raveendar</creator><creator>Shin, Myoung-Jae</creator><creator>Kim, Seong-Hoon</creator><creator>Cho, Gyu-Taek</creator><creator>Hyun, Do Yoon</creator><general>MDPI AG</general><general>MDPI</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-8972-0391</orcidid><orcidid>https://orcid.org/0000-0003-3244-4266</orcidid></search><sort><creationdate>20191018</creationdate><title>Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm</title><author>Lee, Kyung Jun ; 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The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>31635343</pmid><doi>10.3390/genes10100822</doi><orcidid>https://orcid.org/0000-0002-8972-0391</orcidid><orcidid>https://orcid.org/0000-0003-3244-4266</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | agrobiodiversity breeding programs Citrullus - genetics Citrullus lanatus discriminant analysis Enzymes fruits Genetic diversity Genetic resources genetic variation Genomes Genotype Genotyping genotyping by sequencing Genotyping Techniques - methods Germplasm Polymorphism Polymorphism, Single Nucleotide Population Population genetics Population structure Rural development Seed Bank seed industry Sequence Analysis, DNA - methods Single-nucleotide polymorphism Software South Korea vegetables watermelons |
| title | Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm |
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