1
|
Fiscus CJ, Herniter IA, Tchamba M, Paliwal R, Muñoz-Amatriaín M, Roberts PA, Abberton M, Alaba O, Close TJ, Oyatomi O, Koenig D. The pattern of genetic variability in a core collection of 2,021 cowpea accessions. G3 (BETHESDA, MD.) 2024; 14:jkae071. [PMID: 38708794 DOI: 10.1093/g3journal/jkae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 05/07/2024]
Abstract
Cowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world's largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations originating in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA Cowpea Core Collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.
Collapse
Affiliation(s)
- Christopher J Fiscus
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Ira A Herniter
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Marimagne Tchamba
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Rajneesh Paliwal
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | | | - Philip A Roberts
- Department of Nematology, University of California, Riverside, Riverside, CA 92521, USA
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Oluwafemi Alaba
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Olaniyi Oyatomi
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Sodedji FAK, Ryu D, Choi J, Agbahoungba S, Assogbadjo AE, N’Guetta SPA, Jung JH, Nho CW, Kim HY. Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea ( Vigna unguiculata L. Walp). Int J Mol Sci 2022; 23:ijms23073696. [PMID: 35409065 PMCID: PMC8998333 DOI: 10.3390/ijms23073696] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/01/2023] Open
Abstract
The development and promotion of biofortified foods plants are a sustainable strategy for supplying essential micronutrients for human health and nutrition. We set out to identify quantitative trait loci (QTL) associated with carotenoid content in cowpea sprouts. The contents of carotenoids, including lutein, zeaxanthin, and β-carotene in sprouts of 125 accessions were quantified via high-performance liquid chromatography. Significant variation existed in the profiles of the different carotenoids. Lutein was the most abundant (58 ± 12.8 mg/100 g), followed by zeaxanthin (14.7 ± 3.1 mg/100 g) and β-carotene (13.2 ± 2.9 mg/100 g). A strong positive correlation was observed among the carotenoid compounds (r ≥ 0.87), indicating they can be improved concurrently. The accessions were distributed into three groups, following their carotenoid profiles, with accession C044 having the highest sprout carotenoid content in a single cluster. A total of 3120 genome-wide SNPs were tested for association analysis, which revealed that carotenoid biosynthesis in cowpea sprouts is a polygenic trait controlled by genes with additive and dominance effects. Seven loci were significantly associated with the variation in carotenoid content. The evidence of variation in carotenoid content and genomic regions controlling the trait creates an avenue for breeding cowpea varieties with enhanced sprouts carotenoid content.
Collapse
Affiliation(s)
- Frejus Ariel Kpedetin Sodedji
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- Non-Timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), Cotonou 05 BP 1752, Benin; (S.A.); (A.E.A.)
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, 22 BP 582 Abidjan 22, Abidjan 582, Côte d’Ivoire;
| | - Dahye Ryu
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
| | - Symphorien Agbahoungba
- Non-Timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), Cotonou 05 BP 1752, Benin; (S.A.); (A.E.A.)
| | - Achille Ephrem Assogbadjo
- Non-Timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), Cotonou 05 BP 1752, Benin; (S.A.); (A.E.A.)
| | - Simon-Pierre Assanvo N’Guetta
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, 22 BP 582 Abidjan 22, Abidjan 582, Côte d’Ivoire;
| | - Je Hyeong Jung
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
| | - Chu Won Nho
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Ho-Youn Kim
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung 25451, Korea; (F.A.K.S.); (D.R.); (J.C.); (J.H.J.); (C.W.N.)
- Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence: ; Tel.: +82-33-650-3580
| |
Collapse
|