Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers
The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic...
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| Veröffentlicht in: | Acta agriculturae Scandinavica. Section B, Soil and plant science Soil and plant science, 2020-08, Vol.70 (6), p.495-506 |
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| container_title | Acta agriculturae Scandinavica. Section B, Soil and plant science |
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| creator | Tigist, Shiferaw G. Melis, Rob Sibiya, Julia Amelework, Beyene A. Keneni, Gemechu Tegene, Asheber |
| description | The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p |
| doi_str_mv | 10.1080/09064710.2020.1779339 |
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The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identification and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.</description><identifier>ISSN: 0906-4710</identifier><identifier>EISSN: 1651-1913</identifier><identifier>DOI: 10.1080/09064710.2020.1779339</identifier><language>eng</language><publisher>Abingdon: Taylor & Francis</publisher><subject>Beans ; Clusters ; Common bean ; Discriminant analysis ; Gene polymorphism ; Genetic analysis ; Genetic distance ; Genetic diversity ; Genotypes ; Genotyping ; Germplasm ; Insects ; Markers ; Nucleotides ; Phaseolus vulgaris ; Phenotypic variations ; Phenotyping ; Polymorphism ; population structure ; Single-nucleotide polymorphism ; SNP genotyping ; Variance analysis ; Zabrotes subfasciatus</subject><ispartof>Acta agriculturae Scandinavica. Section B, Soil and plant science, 2020-08, Vol.70 (6), p.495-506</ispartof><rights>2020 Informa UK Limited, trading as Taylor & Francis Group 2020</rights><rights>2020 Informa UK Limited, trading as Taylor & Francis Group</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c404t-b4acc6e8f5b5345dabc7674b2606930e0b08c01930907cc8369e67b7558d24fe3</citedby><cites>FETCH-LOGICAL-c404t-b4acc6e8f5b5345dabc7674b2606930e0b08c01930907cc8369e67b7558d24fe3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids></links><search><creatorcontrib>Tigist, Shiferaw G.</creatorcontrib><creatorcontrib>Melis, Rob</creatorcontrib><creatorcontrib>Sibiya, Julia</creatorcontrib><creatorcontrib>Amelework, Beyene A.</creatorcontrib><creatorcontrib>Keneni, Gemechu</creatorcontrib><creatorcontrib>Tegene, Asheber</creatorcontrib><title>Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers</title><title>Acta agriculturae Scandinavica. Section B, Soil and plant science</title><description>The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identification and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.</description><subject>Beans</subject><subject>Clusters</subject><subject>Common bean</subject><subject>Discriminant analysis</subject><subject>Gene polymorphism</subject><subject>Genetic analysis</subject><subject>Genetic distance</subject><subject>Genetic diversity</subject><subject>Genotypes</subject><subject>Genotyping</subject><subject>Germplasm</subject><subject>Insects</subject><subject>Markers</subject><subject>Nucleotides</subject><subject>Phaseolus vulgaris</subject><subject>Phenotypic variations</subject><subject>Phenotyping</subject><subject>Polymorphism</subject><subject>population structure</subject><subject>Single-nucleotide polymorphism</subject><subject>SNP genotyping</subject><subject>Variance analysis</subject><subject>Zabrotes subfasciatus</subject><issn>0906-4710</issn><issn>1651-1913</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNp9Uc2O0zAQjhBIlIVHQLLEZVeiix3HcXIDrZZlpSI4wIWLNXYmrYsTB9vpkhfkuXBp4YgP9nj0_YzmK4qXjF4z2tA3tKV1JfOvpGVuSdly3j4qVqwWbM1axh8XqyNmfQQ9LZ7FuKf58Iavil93OGKyhnT2gCHatBAYwS3RRuJ7Yvww-JFohJFcft5BRO_mSA6z20LIkM31Fdni6NMyYSS9DyRgpiYYDZLkyUf8aQ2cBR4QD9aRy2-gg08ZH2fdQzQW0hyvXpM52nFLjpdDMs7GoU-2QzJ5tww-TDsbhzxdR6bdyTKPPUD4nud-XjzpwUV8cX4viq_vb7_cfFhvPt3d37zbrE1Fq7TWFRhTY9MLLXglOtBG1rLSZU3rllOkmjaGsly2VBrT8LrFWmopRNOVVY_8org_6XYe9moKNvsvyoNVfxo-bBWEvE6HiknGWl2CbBAqLVhba4G0Ek0JtCubLmu9OmlNwf-YMSa193PIy4-qrLikDS-pyChxQpngYwzY_3NlVB3jV3_jV8f41Tn-zHt74tkxxzLAgw-uUwkW50Mfcj42Kv5_id89j7p0</recordid><startdate>20200817</startdate><enddate>20200817</enddate><creator>Tigist, Shiferaw G.</creator><creator>Melis, Rob</creator><creator>Sibiya, Julia</creator><creator>Amelework, Beyene A.</creator><creator>Keneni, Gemechu</creator><creator>Tegene, Asheber</creator><general>Taylor & Francis</general><general>Taylor & Francis LLC</general><general>Taylor & Francis Group</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7ST</scope><scope>7T7</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>SOI</scope><scope>DOA</scope></search><sort><creationdate>20200817</creationdate><title>Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers</title><author>Tigist, Shiferaw G. ; Melis, Rob ; Sibiya, Julia ; Amelework, Beyene A. ; Keneni, Gemechu ; Tegene, Asheber</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c404t-b4acc6e8f5b5345dabc7674b2606930e0b08c01930907cc8369e67b7558d24fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Beans</topic><topic>Clusters</topic><topic>Common bean</topic><topic>Discriminant analysis</topic><topic>Gene polymorphism</topic><topic>Genetic analysis</topic><topic>Genetic distance</topic><topic>Genetic diversity</topic><topic>Genotypes</topic><topic>Genotyping</topic><topic>Germplasm</topic><topic>Insects</topic><topic>Markers</topic><topic>Nucleotides</topic><topic>Phaseolus vulgaris</topic><topic>Phenotypic variations</topic><topic>Phenotyping</topic><topic>Polymorphism</topic><topic>population structure</topic><topic>Single-nucleotide polymorphism</topic><topic>SNP genotyping</topic><topic>Variance analysis</topic><topic>Zabrotes subfasciatus</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tigist, Shiferaw G.</creatorcontrib><creatorcontrib>Melis, Rob</creatorcontrib><creatorcontrib>Sibiya, Julia</creatorcontrib><creatorcontrib>Amelework, Beyene A.</creatorcontrib><creatorcontrib>Keneni, Gemechu</creatorcontrib><creatorcontrib>Tegene, Asheber</creatorcontrib><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environment Abstracts</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Acta agriculturae Scandinavica. Section B, Soil and plant science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tigist, Shiferaw G.</au><au>Melis, Rob</au><au>Sibiya, Julia</au><au>Amelework, Beyene A.</au><au>Keneni, Gemechu</au><au>Tegene, Asheber</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers</atitle><jtitle>Acta agriculturae Scandinavica. Section B, Soil and plant science</jtitle><date>2020-08-17</date><risdate>2020</risdate><volume>70</volume><issue>6</issue><spage>495</spage><epage>506</epage><pages>495-506</pages><issn>0906-4710</issn><eissn>1651-1913</eissn><abstract>The objective of this study was to examine the genetic diversity present among 297 common bean genotypes using 2554 SNPs and 12 insects and seed-related traits. The phenotyping was done under laboratory condition while the genotyping was conducted by using the Illumina SNP BeadChip. High phenotypic diversity among traits were recorded, ranging from 0.87 to 0.96, with a mean of 0.92. Principal component and discriminant analyses identified four PCs and three discriminant functions, which explained 82% and 100% of the total phenotypic variations among genotypes, respectively. Polymorphic Information Content ranged from 0.21 to 0.38, with a mean of 0.34. The mean gene diversity among genotypes ranged from 0.24 to 0.50, with a mean of 0.44. Genetic distance ranged from 0.19 to 0.82, with a mean of 0.62, while the phenotypic distance ranged from 0.00 to 1.00, with a mean of 0.64 were observed aamong genotypes. The analysis of molecular variance revealed highly significant differences (p<0.001) among and within individuals and among populations. Both the SNP and the phenotypic markers grouped the 297 genotypes into two major distinct clusters and three sub-clusters. This information is useful for identification and development of common bean germplasm with economically valuable traits and the conservation and utilization of genotypes.</abstract><cop>Abingdon</cop><pub>Taylor & Francis</pub><doi>10.1080/09064710.2020.1779339</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Beans Clusters Common bean Discriminant analysis Gene polymorphism Genetic analysis Genetic distance Genetic diversity Genotypes Genotyping Germplasm Insects Markers Nucleotides Phaseolus vulgaris Phenotypic variations Phenotyping Polymorphism population structure Single-nucleotide polymorphism SNP genotyping Variance analysis Zabrotes subfasciatus |
| title | Genetic diversity analysis of common bean (Phaseolus vulgaris L.) genotypes for resistance to Mexican bean weevil (Zabrotes subfasciatus), using single nucleotide polymorphism and phenotypic markers |
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