Genetic diversity and population structure analysis of Grass pea (Lathyrus sativus L.) accessions collected from North-Western Ethiopia using SSR markers
Grass pea ( Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to t...
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Published in | Genetic resources and crop evolution Vol. 69; no. 3; pp. 1247 - 1260 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
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01.03.2022
Springer Nature B.V |
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Abstract | Grass pea (
Lathyrus sativus
L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to the presence of a neurotoxin that causes lathyrism in the crop, it has been neglected and underutilized. As a necessary first step towards, therefore, this investigation was undertaken to assess the genetic diversity and population structure that existed within grass pea accessions collected from North-West Ethiopia using simple sequence repeat markers. Twenty-five grass pea accessions collected from the Ethiopian Biodiversity Institute were planted at the College of Agricultural Science, Ebonyi State University, Nigeria. The genomic DNA was extracted using Quick-DNA™ ZR Plant/Seed Miniprep Kit and amplified in an ABI Veriti PCR machine with 10 pairs of SSR markers in IITA, Ibadan, Nigeria. Out of 10 SSR primers, only eight primers were polymorphic. A total of 41 alleles were detected with an average of 5.13. The Polymorphism Information Content and Gene Diversity values ranged from 0.074 to 0.944 with a mean of 0.474 and 0.536 respectively. The largest pairwise genetic distance (0.365) was detected between North Gondar and East Gojjam populations. The ФPT (analog of FST test) estimated through AMOVA were 0.24, 0.20, and 0.05 for within accessions, among regions, and population within regions respectively. The highest genetic differentiation value (76%) resides within accessions followed by 20% among regions. Both the population structure and cluster analyses grouped the 25 grass pea accessions into two distinct subgroups. This grouping pattern indicates the presence of gene flow among geographic regions. In general, the findings of this study indicate that despite few numbers of SSR markers it was possible to detect genetic diversity among grass pea accessions indicating the power of the SSR marker in picking up the existing genetic diversity within the studied accessions. |
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AbstractList | Grass pea (
Lathyrus sativus
L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to the presence of a neurotoxin that causes lathyrism in the crop, it has been neglected and underutilized. As a necessary first step towards, therefore, this investigation was undertaken to assess the genetic diversity and population structure that existed within grass pea accessions collected from North-West Ethiopia using simple sequence repeat markers. Twenty-five grass pea accessions collected from the Ethiopian Biodiversity Institute were planted at the College of Agricultural Science, Ebonyi State University, Nigeria. The genomic DNA was extracted using Quick-DNA™ ZR Plant/Seed Miniprep Kit and amplified in an ABI Veriti PCR machine with 10 pairs of SSR markers in IITA, Ibadan, Nigeria. Out of 10 SSR primers, only eight primers were polymorphic. A total of 41 alleles were detected with an average of 5.13. The Polymorphism Information Content and Gene Diversity values ranged from 0.074 to 0.944 with a mean of 0.474 and 0.536 respectively. The largest pairwise genetic distance (0.365) was detected between North Gondar and East Gojjam populations. The ФPT (analog of FST test) estimated through AMOVA were 0.24, 0.20, and 0.05 for within accessions, among regions, and population within regions respectively. The highest genetic differentiation value (76%) resides within accessions followed by 20% among regions. Both the population structure and cluster analyses grouped the 25 grass pea accessions into two distinct subgroups. This grouping pattern indicates the presence of gene flow among geographic regions. In general, the findings of this study indicate that despite few numbers of SSR markers it was possible to detect genetic diversity among grass pea accessions indicating the power of the SSR marker in picking up the existing genetic diversity within the studied accessions. Grass pea (Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used as an alternative source of protein to reduce malnutrition for resource-poor people and farmers leaving in marginal areas. However, due to the presence of a neurotoxin that causes lathyrism in the crop, it has been neglected and underutilized. As a necessary first step towards, therefore, this investigation was undertaken to assess the genetic diversity and population structure that existed within grass pea accessions collected from North-West Ethiopia using simple sequence repeat markers. Twenty-five grass pea accessions collected from the Ethiopian Biodiversity Institute were planted at the College of Agricultural Science, Ebonyi State University, Nigeria. The genomic DNA was extracted using Quick-DNA™ ZR Plant/Seed Miniprep Kit and amplified in an ABI Veriti PCR machine with 10 pairs of SSR markers in IITA, Ibadan, Nigeria. Out of 10 SSR primers, only eight primers were polymorphic. A total of 41 alleles were detected with an average of 5.13. The Polymorphism Information Content and Gene Diversity values ranged from 0.074 to 0.944 with a mean of 0.474 and 0.536 respectively. The largest pairwise genetic distance (0.365) was detected between North Gondar and East Gojjam populations. The ФPT (analog of FST test) estimated through AMOVA were 0.24, 0.20, and 0.05 for within accessions, among regions, and population within regions respectively. The highest genetic differentiation value (76%) resides within accessions followed by 20% among regions. Both the population structure and cluster analyses grouped the 25 grass pea accessions into two distinct subgroups. This grouping pattern indicates the presence of gene flow among geographic regions. In general, the findings of this study indicate that despite few numbers of SSR markers it was possible to detect genetic diversity among grass pea accessions indicating the power of the SSR marker in picking up the existing genetic diversity within the studied accessions. |
Author | Ilesanmi, Oluyinka Oselebe, Happiness Mekonen, Desalegn Abebe Abraham, Adane Afiukwa, Celestine Abebe, Tiegist Dejene |
Author_xml | – sequence: 1 givenname: Desalegn Abebe orcidid: 0000-0001-7929-5638 surname: Mekonen fullname: Mekonen, Desalegn Abebe email: desalegn.abebe16@arari.gov.et organization: Amhara Agricultural Research Institute (ARARI), Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University (AASTU) – sequence: 2 givenname: Adane surname: Abraham fullname: Abraham, Adane organization: Department of Biotechnology, College of Biological and Chemical Engineering, Addis Ababa Science and Technology University (AASTU), Department of Biological Science and Biotechnology, Botswana International University of Science and Technology – sequence: 3 givenname: Happiness surname: Oselebe fullname: Oselebe, Happiness organization: Department of Crop Production and Landscape Management, Faculty of Agriculture and Natural Resources Management, Ebonyi State University – sequence: 4 givenname: Celestine surname: Afiukwa fullname: Afiukwa, Celestine organization: Department of Biotechnology, Faculty of Science, Ebonyi State University – sequence: 5 givenname: Oluyinka surname: Ilesanmi fullname: Ilesanmi, Oluyinka organization: International Institute of Tropical Agriculture (IITA) – sequence: 6 givenname: Tiegist Dejene surname: Abebe fullname: Abebe, Tiegist Dejene organization: College of Agriculture and Environmental Sciences, Bahir Dar University |
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Cites_doi | 10.5897/AJAR.9000582 10.1007/s10681-012-0702-4 10.1071/CP19557 10.1186/1471-2229-14-65 10.1016/j.cj.2016.06.008 10.1007/BF02910401 10.1023/A:1003520721375 10.1093/genetics/164.4.1567 10.1111/j.1365-294X.2005.02553.x 10.1111/pbr.12268 10.1515/znc-2007-11-1215 10.1016/j.cj.2018.03.004 10.1093/bioinformatics/bti282 10.2298/GENSR1802395U 10.1007/s00425-018-03084-0 10.2298/GENSR2002777A 10.1590/1678-4324-2020190150 10.1017/S0014479720000356 10.22271/09746315.2020.v16.i1.1287 10.1508/cytologia.80.457 10.1023/A:1023923813312 10.1111/j.1471-8286.2005.01155.x 10.1023/A:1023087903679 10.1111/1755-0998.12387 10.1111/j.1439-0523.2011.01935.x 10.3390/ijms22020685 10.5958/0976-0571.2015.00027.2 10.3390/agronomy10081182 10.25130/tjas.v21i1.477 10.1007/s11032-011-9662-y 10.1007/s10722-005-5680-0 10.1371/journal.pone.0118542 10.1007/s12686-011-9548-7 10.1093/genetics/155.2.945 10.1007/s10722-010-9589-x 10.1111/j.1439-0523.2007.01407.x |
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Snippet | Grass pea (
Lathyrus sativus
L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used... Grass pea (Lathyrus sativus L.) is a legume crop known to be an excellent source of protein, tolerant to drought, waterlogging, and salinity. The crop is used... |
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SubjectTerms | Agricultural sciences Agriculture Biodiversity Biomarkers Biomedical and Life Sciences Crops Deoxyribonucleic acid DNA Drought Gene flow Gene polymorphism Genetic analysis Genetic distance Genetic diversity Grass peas Grasses Lathyrus sativus Legumes Life Sciences Lupinosis Malnutrition Peas Plant extracts Plant Genetics and Genomics Plant Physiology Plant Sciences Plant Systematics/Taxonomy/Biogeography Polymorphism Population Population genetics Population structure Protein sources Proteins Research Article Structural analysis Subgroups Toxins Waterlogging |
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Title | Genetic diversity and population structure analysis of Grass pea (Lathyrus sativus L.) accessions collected from North-Western Ethiopia using SSR markers |
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