Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers
Abstract Background Assessment of genetic diversity of Vigna unguiculata (L.) Walp (cowpea) accessions using informative molecular markers is imperative for their genetic improvement and conservation. Use of efficacious molecular markers to obtain the required knowledge of the genetic diversity with...
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BMC
2017-11-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-017-0567-6 |
| _version_ | 1818139351935090688 |
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| author | David Okeh Igwe Celestine Azubike Afiukwa Benjamin Ewa Ubi Kenneth Idika Ogbu Omena Bernard Ojuederie George Nkem Ude |
| author_facet | David Okeh Igwe Celestine Azubike Afiukwa Benjamin Ewa Ubi Kenneth Idika Ogbu Omena Bernard Ojuederie George Nkem Ude |
| author_sort | David Okeh Igwe |
| collection | DOAJ |
| description | Abstract Background Assessment of genetic diversity of Vigna unguiculata (L.) Walp (cowpea) accessions using informative molecular markers is imperative for their genetic improvement and conservation. Use of efficacious molecular markers to obtain the required knowledge of the genetic diversity within the local and regional germplasm collections can enhance the overall effectiveness of cowpea improvement programs, hence, the comparative assessment of Inter-simple sequence repeat (ISSR) and Start codon targeted (SCoT) markers in genetic diversity of V. unguiculata accessions from different regions in Nigeria. Comparative analysis of the genetic diversity of eighteen accessions from different locations in Nigeria was investigated using ISSR and SCoT markers. DNA extraction was done using Zymogen Kit according to its manufacturer’s instructions followed by amplifications with ISSR and SCoT and agarose gel electrophoresis. The reproducible bands were scored for analyses of dendrograms, principal component analysis, genetic diversity, allele frequency, polymorphic information content, and population structure. Results Both ISSR and SCoT markers resolved the accessions into five major clusters based on dendrogram and principal component analyses. Alleles of 32 and 52 were obtained with ISSR and SCoT, respectively. Numbers of alleles, gene diversity and polymorphic information content detected with ISSR were 9.4000, 0.7358 and 0.7192, while SCoT yielded 11.1667, 0.8158 and 0.8009, respectively. Polymorphic loci were 70 and 80 in ISSR and SCoT, respectively. Both markers produced high polymorphism (94.44–100%). The ranges of effective number of alleles (Ne) were 1.2887 ± 0.1797–1.7831 ± 0.2944 and 1.7416 ± 0.0776–1.9181 ± 0.2426 in ISSR and SCoT, respectively. The Nei’s genetic diversity (H) ranged from 0.2112 ± 0.0600–0.4335 ± 0.1371 and 0.4111 ± 0.0226–0.4778 ± 0.1168 in ISSR and SCoT, respectively. Shannon’s information index (I) from ISSR and SCoT were 0.3583 ± 0.0639–0.6237 ± 0.1759 and 0.5911 ± 0.0233–0.6706 ± 0.1604. Total gene diversity (Ht), gene diversity within population (Hs), coefficient of gene differentiation (Gst) and level of gene flow (Nm) revealed by ISSR were 0.4498, 0.3203, 0.2878 and 1.2371 respectively, while SCoT had 0.4808, 0.4522, 0.0594 and 7.9245. Conclusions Both markers showed highest genetic diversity in accessions from Ebonyi. Our study demonstrated that SCoT markers were more efficient than ISSR for genetic diversity studies in V. unguiculata and can be integrated in the exploration of their genetic diversity for improvement and germplasm utilization. |
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| spelling | doaj.art-f24deaebe18b4a5ab552cf64a7ea08b82022-12-22T01:11:08ZengBMCBMC Genetics1471-21562017-11-0118111310.1186/s12863-017-0567-6Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markersDavid Okeh Igwe0Celestine Azubike Afiukwa1Benjamin Ewa Ubi2Kenneth Idika Ogbu3Omena Bernard Ojuederie4George Nkem Ude5Department of Biotechnology, Ebonyi State UniversityDepartment of Biotechnology, Ebonyi State UniversityDepartment of Biotechnology, Ebonyi State UniversityDepartment of Biotechnology, Ebonyi State UniversityDepartment of Biological Sciences, College of Natural and Applied Sciences, Bells University of TechnologyDepartment of Natural Sciences, Bowie State UniversityAbstract Background Assessment of genetic diversity of Vigna unguiculata (L.) Walp (cowpea) accessions using informative molecular markers is imperative for their genetic improvement and conservation. Use of efficacious molecular markers to obtain the required knowledge of the genetic diversity within the local and regional germplasm collections can enhance the overall effectiveness of cowpea improvement programs, hence, the comparative assessment of Inter-simple sequence repeat (ISSR) and Start codon targeted (SCoT) markers in genetic diversity of V. unguiculata accessions from different regions in Nigeria. Comparative analysis of the genetic diversity of eighteen accessions from different locations in Nigeria was investigated using ISSR and SCoT markers. DNA extraction was done using Zymogen Kit according to its manufacturer’s instructions followed by amplifications with ISSR and SCoT and agarose gel electrophoresis. The reproducible bands were scored for analyses of dendrograms, principal component analysis, genetic diversity, allele frequency, polymorphic information content, and population structure. Results Both ISSR and SCoT markers resolved the accessions into five major clusters based on dendrogram and principal component analyses. Alleles of 32 and 52 were obtained with ISSR and SCoT, respectively. Numbers of alleles, gene diversity and polymorphic information content detected with ISSR were 9.4000, 0.7358 and 0.7192, while SCoT yielded 11.1667, 0.8158 and 0.8009, respectively. Polymorphic loci were 70 and 80 in ISSR and SCoT, respectively. Both markers produced high polymorphism (94.44–100%). The ranges of effective number of alleles (Ne) were 1.2887 ± 0.1797–1.7831 ± 0.2944 and 1.7416 ± 0.0776–1.9181 ± 0.2426 in ISSR and SCoT, respectively. The Nei’s genetic diversity (H) ranged from 0.2112 ± 0.0600–0.4335 ± 0.1371 and 0.4111 ± 0.0226–0.4778 ± 0.1168 in ISSR and SCoT, respectively. Shannon’s information index (I) from ISSR and SCoT were 0.3583 ± 0.0639–0.6237 ± 0.1759 and 0.5911 ± 0.0233–0.6706 ± 0.1604. Total gene diversity (Ht), gene diversity within population (Hs), coefficient of gene differentiation (Gst) and level of gene flow (Nm) revealed by ISSR were 0.4498, 0.3203, 0.2878 and 1.2371 respectively, while SCoT had 0.4808, 0.4522, 0.0594 and 7.9245. Conclusions Both markers showed highest genetic diversity in accessions from Ebonyi. Our study demonstrated that SCoT markers were more efficient than ISSR for genetic diversity studies in V. unguiculata and can be integrated in the exploration of their genetic diversity for improvement and germplasm utilization.http://link.springer.com/article/10.1186/s12863-017-0567-6Vigna unguiculataISSR markersSCoT markersGenetic diversityShannon’s information indexPolymorphism |
| spellingShingle | David Okeh Igwe Celestine Azubike Afiukwa Benjamin Ewa Ubi Kenneth Idika Ogbu Omena Bernard Ojuederie George Nkem Ude Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers BMC Genetics Vigna unguiculata ISSR markers SCoT markers Genetic diversity Shannon’s information index Polymorphism |
| title | Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers |
| title_full | Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers |
| title_fullStr | Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers |
| title_full_unstemmed | Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers |
| title_short | Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers |
| title_sort | assessment of genetic diversity in vigna unguiculata l walp accessions using inter simple sequence repeat issr and start codon targeted scot polymorphic markers |
| topic | Vigna unguiculata ISSR markers SCoT markers Genetic diversity Shannon’s information index Polymorphism |
| url | http://link.springer.com/article/10.1186/s12863-017-0567-6 |
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