Genetic Heterogeneity in Cowpea Genotypes ( Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms
Cowpeas ( L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide p...
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| Veröffentlicht in: | Genes 2024-06, Vol.15 (6), p.764 |
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| creator | Dikane, Goitsemang Mahlomola Hendry Sedibe, Moosa Mahmood |
| description | Cowpeas (
L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide polymorphisms (SNPs) in wide-genomic analyses of genetic diversity. The aim of this study was to assess the heterogeneity in cowpea genotypes using DArTseq-derived SNPs. A total of 92 cowpea genotypes were selected, and their fourteen-day-old leaves were freeze-dried for five days. DNA was extracted using the CTAB protocol, genotyped using DArTseq, and analysed using DArTsoft14. A total of 33,920 DArTseq-derived SNPs were recalled for filtering analysis, with a final total of 16,960 SNPs. The analyses were computed using vcfR, poppr, and ape in R Studio v1.2.5001-3 software. The heatmap revealed that the TVU 9596 (SB26), Orelu (SB72), 90K-284-2 (SB55), RV 403 (SB17), and RV 498 (SB16) genotypes were heterogenous. The mean values for polymorphic information content, observed heterozygosity, expected heterozygosity, major allele frequency, and the inbreeding coefficient were 0.345, 0.386, 0.345, 0.729, and 0.113, respectively. Moreover, they validated the diversity of the evaluated cowpea genotypes, which could be used for potential breeding programmes and management of cowpea germplasm. |
| doi_str_mv | 10.3390/genes15060764 |
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L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide polymorphisms (SNPs) in wide-genomic analyses of genetic diversity. The aim of this study was to assess the heterogeneity in cowpea genotypes using DArTseq-derived SNPs. A total of 92 cowpea genotypes were selected, and their fourteen-day-old leaves were freeze-dried for five days. DNA was extracted using the CTAB protocol, genotyped using DArTseq, and analysed using DArTsoft14. A total of 33,920 DArTseq-derived SNPs were recalled for filtering analysis, with a final total of 16,960 SNPs. The analyses were computed using vcfR, poppr, and ape in R Studio v1.2.5001-3 software. The heatmap revealed that the TVU 9596 (SB26), Orelu (SB72), 90K-284-2 (SB55), RV 403 (SB17), and RV 498 (SB16) genotypes were heterogenous. The mean values for polymorphic information content, observed heterozygosity, expected heterozygosity, major allele frequency, and the inbreeding coefficient were 0.345, 0.386, 0.345, 0.729, and 0.113, respectively. Moreover, they validated the diversity of the evaluated cowpea genotypes, which could be used for potential breeding programmes and management of cowpea germplasm.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes15060764</identifier><identifier>PMID: 38927700</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Agricultural production ; Bar codes ; Flavonoids ; Gene frequency ; Genetic analysis ; Genetic diversity ; Genetic Heterogeneity ; Genomes ; Genomic analysis ; Genotype ; Genotype & phenotype ; Genotyping Techniques - methods ; Germplasm ; Heterozygosity ; Inbreeding ; Polymorphism ; Polymorphism, Single Nucleotide ; Proprietary ; Proteins ; Seeds ; Single-nucleotide polymorphism ; Vigna - genetics ; Vigna unguiculata</subject><ispartof>Genes, 2024-06, Vol.15 (6), p.764</ispartof><rights>2024 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 (https://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>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c302t-a61a0599b51bafb1641167f0e6f12b763d732674573a78984ffafa8826c0fa023</cites><orcidid>0000-0001-6247-4891</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/PMC11202451/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11202451/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38927700$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dikane, Goitsemang Mahlomola Hendry</creatorcontrib><creatorcontrib>Sedibe, Moosa Mahmood</creatorcontrib><title>Genetic Heterogeneity in Cowpea Genotypes ( Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms</title><title>Genes</title><addtitle>Genes (Basel)</addtitle><description>Cowpeas (
L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide polymorphisms (SNPs) in wide-genomic analyses of genetic diversity. The aim of this study was to assess the heterogeneity in cowpea genotypes using DArTseq-derived SNPs. A total of 92 cowpea genotypes were selected, and their fourteen-day-old leaves were freeze-dried for five days. DNA was extracted using the CTAB protocol, genotyped using DArTseq, and analysed using DArTsoft14. A total of 33,920 DArTseq-derived SNPs were recalled for filtering analysis, with a final total of 16,960 SNPs. The analyses were computed using vcfR, poppr, and ape in R Studio v1.2.5001-3 software. The heatmap revealed that the TVU 9596 (SB26), Orelu (SB72), 90K-284-2 (SB55), RV 403 (SB17), and RV 498 (SB16) genotypes were heterogenous. The mean values for polymorphic information content, observed heterozygosity, expected heterozygosity, major allele frequency, and the inbreeding coefficient were 0.345, 0.386, 0.345, 0.729, and 0.113, respectively. Moreover, they validated the diversity of the evaluated cowpea genotypes, which could be used for potential breeding programmes and management of cowpea germplasm.</description><subject>Agricultural production</subject><subject>Bar codes</subject><subject>Flavonoids</subject><subject>Gene frequency</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>Genetic Heterogeneity</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Genotype</subject><subject>Genotype & phenotype</subject><subject>Genotyping Techniques - methods</subject><subject>Germplasm</subject><subject>Heterozygosity</subject><subject>Inbreeding</subject><subject>Polymorphism</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Proprietary</subject><subject>Proteins</subject><subject>Seeds</subject><subject>Single-nucleotide polymorphism</subject><subject>Vigna - genetics</subject><subject>Vigna unguiculata</subject><issn>2073-4425</issn><issn>2073-4425</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</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>eNpdkc1v1DAQxS0EolXpkSuyxGV7SBl_xE5OqN3CFmkFSG3hGDnZSeoqiVPbKdorfzleWqqWucxI76enN3qEvGVwLEQJHzocMbAcFGglX5B9DlpkUvL85ZN7jxyGcANpJHCA_DXZE0XJtQbYJ79XySLahp5jRO92hjZuqR3p0v2a0NCku7idMNAF_WG70dB57GbbzL2Jhq6P6U_TT0f0Ktixo2cn_jLgLV2sTi-OsjP09g439CJJPdKvc9Oji3aD9Lvrt4Pz07UNQ3hDXrWmD3j4sA_I1edPl8vzbP1t9WV5ss4aATxmRjEDeVnWOatNWzMlGVO6BVQt47VWYqMFV1rmWhhdlIVsW9OaouCqgdYAFwfk473vNNcDbhocozd9NXk7GL-tnLHVc2W011Xn7irGOHCZs-SweHDw7nbGEKvBhgb73ozo5lAJ0LyAlEwl9P1_6I2b_Zj--0sJrmWxi5TdU413IXhsH9MwqHYNV88aTvy7py880v_6FH8AfH2hpg</recordid><startdate>20240611</startdate><enddate>20240611</enddate><creator>Dikane, Goitsemang Mahlomola Hendry</creator><creator>Sedibe, Moosa Mahmood</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>5PM</scope><orcidid>https://orcid.org/0000-0001-6247-4891</orcidid></search><sort><creationdate>20240611</creationdate><title>Genetic Heterogeneity in Cowpea Genotypes ( Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms</title><author>Dikane, Goitsemang Mahlomola Hendry ; Sedibe, Moosa Mahmood</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c302t-a61a0599b51bafb1641167f0e6f12b763d732674573a78984ffafa8826c0fa023</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Agricultural production</topic><topic>Bar codes</topic><topic>Flavonoids</topic><topic>Gene frequency</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>Genetic Heterogeneity</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Genotype</topic><topic>Genotype & phenotype</topic><topic>Genotyping Techniques - methods</topic><topic>Germplasm</topic><topic>Heterozygosity</topic><topic>Inbreeding</topic><topic>Polymorphism</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Proprietary</topic><topic>Proteins</topic><topic>Seeds</topic><topic>Single-nucleotide polymorphism</topic><topic>Vigna - genetics</topic><topic>Vigna unguiculata</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dikane, Goitsemang Mahlomola Hendry</creatorcontrib><creatorcontrib>Sedibe, Moosa Mahmood</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dikane, Goitsemang Mahlomola Hendry</au><au>Sedibe, Moosa Mahmood</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic Heterogeneity in Cowpea Genotypes ( Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms</atitle><jtitle>Genes</jtitle><addtitle>Genes (Basel)</addtitle><date>2024-06-11</date><risdate>2024</risdate><volume>15</volume><issue>6</issue><spage>764</spage><pages>764-</pages><issn>2073-4425</issn><eissn>2073-4425</eissn><abstract>Cowpeas (
L. Walp) have been credible constituents of nutritious food and forage in human and animal diets since the Neolithic era. The modern technique of Diversity Array Technology (DArTseq) is both cost-effective and rapid in producing thousands of high-throughputs, genotyped, single nucleotide polymorphisms (SNPs) in wide-genomic analyses of genetic diversity. The aim of this study was to assess the heterogeneity in cowpea genotypes using DArTseq-derived SNPs. A total of 92 cowpea genotypes were selected, and their fourteen-day-old leaves were freeze-dried for five days. DNA was extracted using the CTAB protocol, genotyped using DArTseq, and analysed using DArTsoft14. A total of 33,920 DArTseq-derived SNPs were recalled for filtering analysis, with a final total of 16,960 SNPs. The analyses were computed using vcfR, poppr, and ape in R Studio v1.2.5001-3 software. The heatmap revealed that the TVU 9596 (SB26), Orelu (SB72), 90K-284-2 (SB55), RV 403 (SB17), and RV 498 (SB16) genotypes were heterogenous. The mean values for polymorphic information content, observed heterozygosity, expected heterozygosity, major allele frequency, and the inbreeding coefficient were 0.345, 0.386, 0.345, 0.729, and 0.113, respectively. Moreover, they validated the diversity of the evaluated cowpea genotypes, which could be used for potential breeding programmes and management of cowpea germplasm.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38927700</pmid><doi>10.3390/genes15060764</doi><orcidid>https://orcid.org/0000-0001-6247-4891</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Agricultural production Bar codes Flavonoids Gene frequency Genetic analysis Genetic diversity Genetic Heterogeneity Genomes Genomic analysis Genotype Genotype & phenotype Genotyping Techniques - methods Germplasm Heterozygosity Inbreeding Polymorphism Polymorphism, Single Nucleotide Proprietary Proteins Seeds Single-nucleotide polymorphism Vigna - genetics Vigna unguiculata |
| title | Genetic Heterogeneity in Cowpea Genotypes ( Vigna unguiculata L. Walp) Using DArTseq (GBS)-Derived Single Nucleotide Polymorphisms |
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