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Ongom PO, Fatokun C, Togola A, Garcia-Oliveira AL, Ng EH, Kilian A, Lonardi S, Close TJ, Boukar O. A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea ( Vigna unguiculata (L.) Walp). Int J Genomics 2024; 2024:9912987. [PMID: 38235497 PMCID: PMC10791481 DOI: 10.1155/2024/9912987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/04/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024] Open
Abstract
Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array. The panel's usefulness was assessed using 376 genotypes from different populations of known genetic backgrounds. The panel was informative, with over 78% of SNPs exceeding a minor allele frequency of 0.20. The panel decoded three stratifications in the constituted population, as was expected. Linkage disequilibrium (LD) decay was correctly depicted as slower in a biparental subset than in other populations. A known flower and seed coat color gene region was located on chromosome Vu07, suggesting that the mid-density panel may be used to hypothesize genomic regions underlying target traits in cowpea. Unexpected heterozygosity was detected in some lines and highly among F1 progenies, divulging the panel's potential application in germplasm purity and hybridity verification. The study unveils the potential of an excellent genomic resource that can be tapped to enhance the development of improved cowpea cultivars.
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Affiliation(s)
| | - Christian Fatokun
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Abou Togola
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
| | - Ana Luisa Garcia-Oliveira
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, UN Avenue, PO Box, Nairobi 1041-00621, Kenya
- Department of Molecular Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar, India
| | - Eng Hwa Ng
- Excellence in Breeding Platform, International Maize and Wheat Improvement Center (CIMMYT), Los Baños, Laguna 4031, Philippines
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd., University of Canberra, Montana St., Bruce, ACT 2617, Australia
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
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Raina A, Khan S. Field assessment of yield and its contributing traits in cowpea treated with lower, intermediate, and higher doses of gamma rays and sodium azide. FRONTIERS IN PLANT SCIENCE 2023; 14:1188077. [PMID: 37521916 PMCID: PMC10382141 DOI: 10.3389/fpls.2023.1188077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Across the globe, plant breeders of different organizations are working in collaboration to bring preferred traits to crops of economic importance. Among the traits, "high yielding potential" is the most important as it is directly associated with food security and nutrition, one of the sustainable development goals. The Food and Agriculture Organization acknowledges plant breeders' role and efforts in achieving local and global food security and nutrition. Recognizing the importance of pulses and increasing pressure on food security, the United Nations General Assembly declared 2016 the "International year of Pulses" owing to their preferred traits such as climate change resilience, wide adaptability, low agriculture input, and protein- and nutrient-rich crops. Keeping all these developments in consideration, we initiated an induced mutagenesis program by treating cowpea (Vigna unguiculata L. Walp.) with different doses of gamma rays and sodium azide aiming to enhance the yielding potential of an otherwise outstanding variety viz., Gomati VU-89 and Pusa-578. We noticed a substantial increase in mean values of agronomic traits in putative mutants raised from seeds treated with lower and intermediate doses of mutagens. Statistical analysis such as correlation, path, hierarchical clustering analysis (HCA), and principal component analysis (PCA) were used to assess the difference between mutagenized and control populations. A significant and positive correlation of yield with yield-attributing traits was recorded. However, among all the yield attributing traits, seeds per pod (SPP) depicted the maximum direct impact upon yield, and therefore, working on this trait may yield better results. A widely used PCA revealed 40.46% and 33.47% of the total variation for var. Gomati VU-89 and var. Pusa-578, respectively. Cluster analysis clustered treated and control populations into separate clusters with variable cluster sizes. Cluster V in the variety Gomati VU-89 and cluster V and VI in the variety Pusa 578 comprised of putative mutants were higher yielding and hence could be recommended for selection in future breeding programs. We expect to release such mutant lines for farmer cultivation in Northern parts of India depending on the performance of such high-yielding mutant lines at multilocations.
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Affiliation(s)
- Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, India
- Botany Section, Women’s College, Aligarh Muslim University, Aligarh, India
| | - Samiullah Khan
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, India
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Kumar B, Singh AK, Bahuguna RN, Pareek A, Singla‐Pareek SL. Orphan crops: A genetic treasure trove for hunting stress tolerance genes. Food Energy Secur 2022. [DOI: 10.1002/fes3.436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Brijesh Kumar
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
| | - Anil Kumar Singh
- ICAR‐National Institute for Plant Biotechnology LBS Centre New Delhi India
| | - Rajeev Nayan Bahuguna
- Center for Advanced Studies on Climate Change Dr. Rajendra Prasad Central Agricultural University Bihar Pusa, Samastipur India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences Jawaharlal Nehru University New Delhi India
| | - Sneh L. Singla‐Pareek
- Plant Stress Biology Group International Centre for Genetic Engineering and Biotechnology New Delhi India
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Gumede MT, Gerrano AS, Amelework AB, Modi AT. Analysis of Genetic Diversity and Population Structure of Cowpea ( Vigna unguiculata (L.) Walp) Genotypes Using Single Nucleotide Polymorphism Markers. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243480. [PMID: 36559592 PMCID: PMC9780845 DOI: 10.3390/plants11243480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/01/2022] [Accepted: 12/09/2022] [Indexed: 05/14/2023]
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources.
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Affiliation(s)
- Mbali Thembi Gumede
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plant Institute, Private Bag X293, Pretoria 0001, South Africa
- Correspondence:
| | - Abe Shegro Gerrano
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plant Institute, Private Bag X293, Pretoria 0001, South Africa
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Assefa Beyene Amelework
- Agricultural Research Council—Vegetables, Industrial and Medicinal Plant Institute, Private Bag X293, Pretoria 0001, South Africa
| | - Albert Thembinkosi Modi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg 3209, South Africa
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Dorvlo IK, Amenorpe G, Amoatey HM, Amiteye S, Kutufam JT, Afutu E, Asare-Bediako E, Darkwa AA. Improvement in cowpea variety Videza for traits of extra earliness and higher seed yield. Heliyon 2022; 8:e12059. [PMID: 36561698 PMCID: PMC9763773 DOI: 10.1016/j.heliyon.2022.e12059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 06/20/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022] Open
Abstract
The cowpea variety Videza, which was used as the control, matures early (70 days after planting), although it produces low yields. Gamma irradiation mutagenesis was used to induce Videza into extra-early maturing and higher yielding mutant genotypes. A single seed descend population was developed for radio-sensitivity test, and a Lethal Dose 50 (LD50) of 240.5 Gy was determined, and applied from a cobalt-60 (60Co) source, to acutely mass irradiate 1800 Videza seeds, at the Ghana Atomic Energy Commission. The irradiated seeds (M1) were planted to produce M2 seeds bearing plants and subsequently advanced to M3 plants for selection of nine induced plants based on extra earliness and significantly higher seed yields than the parental control. It took 48 days after planting (DAP) for the genotype coded P1N02#1 to reach 50 % maturity followed by 52 DAP for genotypes with codes P4N03#3; P3N01#5; P5N05#6, P4N14#7, P5N07#8, P5N05#10 and 54 DAP for genotype P4N14#11. P1N06#9 had the highest yield (97.38 g/plant), followed by P5N05#10 (95.97 g/plant), P1N08#13 (81.24 g/plant), P2N09#12 (73.94 g/plant), P6N10#19 (70.83 g/plant), P1N06#20 (65.36 kg/plant), P5N07#14 (61.23 g/plant), P4N14# (58.05 g/plant) and P1N08#17 (56.23 g/plant). M3 seeds were advanced to M4 plants for a Preliminary Yield Trial which revealed that induced plants P5N05#10 (1235 kg/ha), P2N09#12 (1206 kg/ha), P5N07#14 (1185 kg/ha), P1N06#20 (1171 kg/ha), P1N06#9 (1051 kg/ha), P1N08#13 (1041 kg/ha), and P6N10#19 (999 kg/ha) outperformed the control (517 kg/ha) and two other commercial varieties. Overall, the two highest performing candidates for further evaluation for varietal release were P5N05#10 and P2N09#12.
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Affiliation(s)
- Innocent Kwaku Dorvlo
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Godwin Amenorpe
- Biotechnology and Nuclear Agricultural Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), Accra, Ghana,Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana,Corresponding author.
| | - Harry Mensah Amoatey
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing. School of Nuclear and Allied Sciences, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Jacob Teye Kutufam
- Biotechnology and Nuclear Agricultural Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), Accra, Ghana
| | - Emmanuel Afutu
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Elvis Asare-Bediako
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Alfred Anthony Darkwa
- Department of Crop Science, School of Agriculture, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast, Ghana
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Zaki HEM, Radwan KSA. Estimates of genotypic and phenotypic variance, heritability, and genetic advance of horticultural traits in developed crosses of cowpea ( Vigna unguiculata [L.] Walp). FRONTIERS IN PLANT SCIENCE 2022; 13:987985. [PMID: 36237497 PMCID: PMC9551400 DOI: 10.3389/fpls.2022.987985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Cowpea, in addition to being a food and feed crop, plays a key role in sustainable farming. The present study's goal is to develop new high-yielding cowpea varieties. A Field experiment was carried out across 3 summer seasons and the breeding program included 28 distinct cowpea varieties, out of which five potential parents were selected for this investigation. Local cultivars, i.e., Cream 7 'Cr7', Dokki 331 'D331', Commercial 1 'Com1', and introduced cultivars, i.e., Colossus 'Col' and Asian Introduction 'AI' were utilized to produce six crosses in two generations apart; F1 and F2: Col x AI, Col x Com1, Cr7 x AI, Cr7 x Com1, D331 x AI, and D331 x Com1. 'AI' and 'Com1' were superior in pod length, pod diameter, number of seeds/pod and seeds weight/pod, whereas 'Col', 'Cr7' and 'D331' were superior in seeds yield/plant, number of pods/plant and the least number of aborted ovules/pod. The genotypes/crosses showed greater genotypic variance (GV) than phenotypic variance (PV) for number of pods/plant, pod length, number of seeds/pod, number of aborted ovules/pod, fresh pod weight, seeds weight/pod, and seeds yield/plant. All studied variables showed high heritability (H%) in genotypes/crosses, despite the exception of seeds weight/pod, which ranged from 29.14 in 'D331' to 83.7 in F2 of Col x Com1. F2 plants and their parents' genotypes showed greater H%. Cr7 x AI developed the most H%, 99.04% for number of pods/plant. D331 x Com1 and Cr7 x AI exhibited moderate H% for fresh pod weight in F1, but all other crosses had high H%. F1 and F2 crosses yielded moderate to high GCV and PCV for number of seeds/pod. Variations in parental genotypes and crossings reflect genetic diversity and the possibility of selection. Crossing with 'AI,' and 'Com1' genotypes enhanced the performance of the other varieties, 'Col', 'D331' and 'Cr7'. Cr7 x Com1 and D331 x AI were selected as the most promising crosses for cowpea breeding programs.
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Affiliation(s)
- Haitham E. M. Zaki
- Horticulture Department, Faculty of Agriculture, Minia University, El-Minia, Egypt
- Applied Biotechnology Department, University of Technology and Applied Sciences-Sur, Sur, Oman
| | - Khlode S. A. Radwan
- Plant Pathology Department, Faculty of Agriculture, Minia University, El-Minia, Egypt
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7
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Sodedji FAK, Agbahoungba S, Agoyi EE, Kafoutchoni MK, Choi J, Nguetta SPA, Assogbadjo AE, Kim HY. Diversity, population structure, and linkage disequilibrium among cowpea accessions. THE PLANT GENOME 2021; 14:e20113. [PMID: 34275189 DOI: 10.1002/tpg2.20113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 05/27/2023]
Abstract
Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor-joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005-0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48-0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80-100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome-wide association studies on quality attributes and critical agronomic traits in cowpea.
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Affiliation(s)
- Frejus Ariel Kpedetin Sodedji
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, Abidjan, Lagunes, 22 BP 461, Côte d'Ivoire
| | - Symphorien Agbahoungba
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Eric Echikintho Agoyi
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
| | - Médard Konoutan Kafoutchoni
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Simon-Pierre Assanvo Nguetta
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, Abidjan, Lagunes, 22 BP 461, Côte d'Ivoire
| | - Achille Ephrem Assogbadjo
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Ho-Youn Kim
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
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Gbedevi KM, Boukar O, Ishikawa H, Abe A, Ongom PO, Unachukwu N, Rabbi I, Fatokun C. Genetic Diversity and Population Structure of Cowpea [ Vigna unguiculata (L.) Walp.] Germplasm Collected from Togo Based on DArT Markers. Genes (Basel) 2021; 12:1451. [PMID: 34573433 PMCID: PMC8465771 DOI: 10.3390/genes12091451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Crop genetic diversity is a sine qua non for continuous progress in the development of improved varieties, hence the need for germplasm collection, conservation and characterization. Over the years, cowpea has contributed immensely to the nutrition and economic life of the people in Togo. However, the bulk of varieties grown by farmers are landraces due to the absence of any serious genetic improvement activity on cowpea in the country. In this study, the genetic diversity and population structure of 255 cowpea accessions collected from five administrative regions and the agricultural research institute of Togo were assessed using 4600 informative diversity array technology (DArT) markers. Among the regions, the polymorphic information content (PIC) ranged from 0.19 to 0.27 with a mean value of 0.25. The expected heterozygosity (He) varied from 0.22 to 0.34 with a mean value of 0.31, while the observed heterozygosity (Ho) varied from 0.03 to 0.07 with an average of 0.05. The average inbreeding coefficient (FIS) varied from 0.78 to 0.89 with a mean value of 0.83, suggesting that most of the accessions are inbred. Cluster analysis and population structure identified four groups with each comprising accessions from the six different sources. Weak to moderate differentiation was observed among the populations with a genetic differentiation index varying from 0.014 to 0.117. Variation was highest (78%) among accessions within populations and lowest between populations (7%). These results revealed a moderate level of diversity among the Togo cowpea germplasm. The findings of this study constitute a foundation for genetic improvement of cowpea in Togo.
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Affiliation(s)
- Kodjo M. Gbedevi
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
- Life and Earth Sciences Institute (Including Health and Agriculture), Pan African University, University of Ibadan, Ibadan 200284, Oyo State, Nigeria
| | - Ousmane Boukar
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
| | - Haruki Ishikawa
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
| | - Ayodeji Abe
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan 200284, Oyo State, Nigeria;
| | - Patrick O. Ongom
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
| | - Nnanna Unachukwu
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
| | - Ismail Rabbi
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
| | - Christian Fatokun
- Cowpea Breeding Unit, International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Road, Ibadan 200001, Oyo State, Nigeria; (O.B.); (H.I.); (P.O.O.); (N.U.); (I.R.); (C.F.)
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9
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Che P, Chang S, Simon MK, Zhang Z, Shaharyar A, Ourada J, O'Neill D, Torres-Mendoza M, Guo Y, Marasigan KM, Vielle-Calzada JP, Ozias-Akins P, Albertsen MC, Jones TJ. Developing a rapid and highly efficient cowpea regeneration, transformation and genome editing system using embryonic axis explants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:817-830. [PMID: 33595147 DOI: 10.1101/738971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/11/2021] [Indexed: 05/21/2023]
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) is one of the most important legume crops planted worldwide, but despite decades of effort, cowpea transformation is still challenging due to inefficient Agrobacterium-mediated transfer DNA delivery, transgenic selection and in vitro shoot regeneration. Here, we report a highly efficient transformation system using embryonic axis explants isolated from imbibed mature seeds. We found that removal of the shoot apical meristem from the explants stimulated direct multiple shoot organogenesis from the cotyledonary node tissue. The application of a previously reported ternary transformation vector system provided efficient Agrobacterium-mediated gene delivery, while the utilization of spcN as selectable marker enabled more robust transgenic selection, plant recovery and transgenic plant generation without escapes and chimera formation. Transgenic cowpea plantlets developed exclusively from the cotyledonary nodes at frequencies of 4% to 37% across a wide range of cowpea genotypes. CRISPR/Cas-mediated gene editing was successfully demonstrated. The transformation principles established here could also be applied to other legumes to increase transformation efficiencies.
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Affiliation(s)
- Ping Che
- Corteva Agriscience, Johnston, Iowa, 50131, USA
| | | | | | - Zhifen Zhang
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia Tifton Campus, Tifton, GA, 31973, USA
| | | | | | | | - Mijael Torres-Mendoza
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, 36821, México
| | - Yinping Guo
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia Tifton Campus, Tifton, GA, 31973, USA
| | - Kathleen M Marasigan
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia Tifton Campus, Tifton, GA, 31973, USA
| | - Jean-Philippe Vielle-Calzada
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, Guanajuato, 36821, México
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia Tifton Campus, Tifton, GA, 31973, USA
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Che P, Chang S, Simon MK, Zhang Z, Shaharyar A, Ourada J, O’Neill D, Torres‐Mendoza M, Guo Y, Marasigan KM, Vielle‐Calzada J, Ozias‐Akins P, Albertsen MC, Jones TJ. Developing a rapid and highly efficient cowpea regeneration, transformation and genome editing system using embryonic axis explants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:817-830. [PMID: 33595147 PMCID: PMC8252785 DOI: 10.1111/tpj.15202] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/11/2021] [Indexed: 05/21/2023]
Abstract
Cowpea (Vigna unguiculata (L.) Walp.) is one of the most important legume crops planted worldwide, but despite decades of effort, cowpea transformation is still challenging due to inefficient Agrobacterium-mediated transfer DNA delivery, transgenic selection and in vitro shoot regeneration. Here, we report a highly efficient transformation system using embryonic axis explants isolated from imbibed mature seeds. We found that removal of the shoot apical meristem from the explants stimulated direct multiple shoot organogenesis from the cotyledonary node tissue. The application of a previously reported ternary transformation vector system provided efficient Agrobacterium-mediated gene delivery, while the utilization of spcN as selectable marker enabled more robust transgenic selection, plant recovery and transgenic plant generation without escapes and chimera formation. Transgenic cowpea plantlets developed exclusively from the cotyledonary nodes at frequencies of 4% to 37% across a wide range of cowpea genotypes. CRISPR/Cas-mediated gene editing was successfully demonstrated. The transformation principles established here could also be applied to other legumes to increase transformation efficiencies.
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Affiliation(s)
- Ping Che
- Corteva AgriscienceJohnstonIowa50131USA
| | - Shujun Chang
- Corteva AgriscienceJohnstonIowa50131USA
- Present address:
Benson Hill Biosystems1100 Corporate Square Dr. Suite 150St. LouisMO63132USA
| | | | - Zhifen Zhang
- Department of Horticulture and Institute of Plant Breeding, Genetics & GenomicsUniversity of Georgia Tifton CampusTiftonGA31973USA
| | - Ahmed Shaharyar
- Corteva AgriscienceJohnstonIowa50131USA
- Present address:
Benson Hill Biosystems1100 Corporate Square Dr. Suite 150St. LouisMO63132USA
| | - Jesse Ourada
- Corteva AgriscienceJohnstonIowa50131USA
- Present address:
Benson Hill Biosystems1100 Corporate Square Dr. Suite 150St. LouisMO63132USA
| | | | - Mijael Torres‐Mendoza
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la BiodiversidadCINVESTAV IrapuatoGuanajuato36821México
| | - Yinping Guo
- Department of Horticulture and Institute of Plant Breeding, Genetics & GenomicsUniversity of Georgia Tifton CampusTiftonGA31973USA
| | - Kathleen M. Marasigan
- Department of Horticulture and Institute of Plant Breeding, Genetics & GenomicsUniversity of Georgia Tifton CampusTiftonGA31973USA
| | - Jean‐Philippe Vielle‐Calzada
- Group of Reproductive Development and Apomixis, UGA Laboratorio Nacional de Genómica para la BiodiversidadCINVESTAV IrapuatoGuanajuato36821México
| | - Peggy Ozias‐Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & GenomicsUniversity of Georgia Tifton CampusTiftonGA31973USA
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Alghamdi SS, Khan MA, Migdadi HM, El-Harty EH, Afzal M, Farooq M. Biochemical and molecular characterization of cowpea landraces using seed storage proteins and SRAP marker patterns. Saudi J Biol Sci 2019; 26:74-82. [PMID: 30622409 PMCID: PMC6319192 DOI: 10.1016/j.sjbs.2018.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/04/2018] [Accepted: 09/16/2018] [Indexed: 11/15/2022] Open
Abstract
Seven landraces of cowpea [Vigna unguiculata (L.) Walp.] were assessed for genetic variability in total proteins, protein fractions viz. albumins, globulins, prolamins, and glutelins by SDS-polyacrylamide gel electrophoresis and DNA polymorphism using sequence-related amplified polymorphisms (SRAP) markers. The solubility-based protein fractionation data indicated that the salt soluble fraction (globulin) and water-soluble fraction (albumin) proteins were the predominant fractions in cowpea seeds comprising 45-50.3% and 31.2-35.5% of total soluble proteins, respectively. The electrophoretic pattern revealed the molecular heterogeneity among total proteins as well as different protein fractions. The molecular weights of protein bands obtained by SDS-PAGE varied between 10 to 250, 15 to 110, 15 to 150, and 15 to 130 kDa for total proteins, albumins, globulins, and glutelins, respectively. A large number of bands were found common to the various landraces, indicative of their close relationship with one another. However, a few bands distinctive to some specific landraces were also detected, indicating varietal differences. A 34 SRAP primer pair combination generated a total of 1003 amplicons (loci) showed 100% polymorphism with an average of 0.93 polymorphism information content (PIC) value. Landraces displayed an average 0.50 similarity coefficient which clustered the landraces corresponding to their growth habit in main clusters and to their geographical origin in subcultures. Molecular and biochemical analysis were correlated with a medium level (Mantel test, r = 0.56, P < 0.02). These findings revealed that seed proteins and DNA polymorphism provide valuable information regarding the variability among landraces and this information could be utilized for breeding purposes in the enhancement of protein quality and quantity in grain legumes.
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Affiliation(s)
- Salem S. Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Muhammad A. Khan
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Hussein M. Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- National Center for Agriculture and Extension. P.O Box: 639, Baq'a 19381, Jordan
| | - Ehab H. El-Harty
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Muhammad Afzal
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Muhammad Farooq
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 123, Oman
- Department of Agronomy, University of Agriculture, Faisalabad 38040, Pakistan
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 PMCID: PMC5343864 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Affiliation(s)
- Nacira Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Centro de Investigaciones Agropecuarias-INTA, Instituto de Fisiología y Recursos Genéticos Vegetales, Córdoba X5000, Argentina.
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Ailin Liu
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Leo Kan
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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