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Girma G, Tirfessa A, Bejiga T, Seyoum A, Mekonen M, Nega A, Gebreyohannes A, Ayana G, Nida H, Mengiste T, Ejeta G, Tesso T. Assessing genetic, racial, and geographic diversity among Ethiopian sorghum landraces and implications for heterotic potential for hybrid sorghum breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:46. [PMID: 38911335 PMCID: PMC11190104 DOI: 10.1007/s11032-024-01483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 05/30/2024] [Indexed: 06/25/2024]
Abstract
The wealth of sorghum genetic resources in Africa has not been fully exploited for cultivar development in the continent. Hybrid cultivars developed from locally evolved germplasm are more likely to possess a well-integrated assembly of genes for local adaptation, productivity, quality, as well as for defensive traits and broader stability. A subset of 560 sorghum accessions of known fertility reaction representing the major botanical races and agro-ecologies of Ethiopia were characterized for genetic, agronomic and utilization parameters to lay a foundation for cultivar improvement and parental selection for hybrid breeding. Accessions were genotyped using a genotyping by sequencing (GBS) generating 73,643 SNPs for genetic analysis. Significant genetic variability was observed among accessions with Admixture and Discriminant Analysis of Principal Components where 67% of the accessions fell into K=10 clusters with membership coefficient set to > 0.6. The pattern of aggregation of the accessions partially overlapped with racial category and agro-ecological adaptation. Majority of the non-restorer (B-line) accessions primarily of the bicolor race from the wet highland ecology clustered together away from two clusters of fertility restorer (R-line) accessions. Small members of the B accessions were grouped with the R clusters and in vice-versa while significant numbers of both B and R accessions were spread between the major clusters. Such pattern of diversity along with the complementary agronomic data based information indicate the potential for heterosis providing the foundation for initiating hybrid breeding program based on locally adapted germplasm. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01483-8.
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Affiliation(s)
- Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Alemu Tirfessa
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Tamirat Bejiga
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Amare Seyoum
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Moges Mekonen
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Amare Nega
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Adane Gebreyohannes
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Getachew Ayana
- Ethiopian Institute of Agricultural Research, Melkassa Research Center, P.O.Box 432, Adama, Ethiopia
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
| | - Tesfaye Tesso
- Department of Agronomy, Purdue University, West Lafayette, IN 47907 USA
- Department of Agronomy, Kansas State University, Manhattan, KS 66506 USA
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Gimode DM, Ochieng G, Deshpande S, Manyasa EO, Kondombo CP, Mikwa EO, Avosa MO, Kunguni JS, Ngugi K, Sheunda P, Jumbo MB, Odeny DA. Validation of sorghum quality control (QC) markers across African breeding lines. THE PLANT GENOME 2024; 17:e20438. [PMID: 38409578 DOI: 10.1002/tpg2.20438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi-arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi-Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro-ecologies. Varietal purity and correct confirmation of new crosses are essential for the integrity and efficiency of a breeding program. We used 49 quality control (QC) kompetitive allele-specific PCR single nucleotide polymorphism (SNP) markers to genotype 716 breeding lines. Note that 46 SNPs were polymorphic with the top 10 most informative revealing polymorphism information content (PIC), minor allele frequency (MAF), and observed heterozygosity (Ho) of 0.37, 0.43, and 0.02, respectively, and explaining 45% of genetic variance within the first two principal components (PC). Thirty-nine markers were highly informative across 16 Burkina Faso breeding lines, out of which the top 10 revealed average PIC, MAF, and Ho of 0.36, 0.39, and 0.05, respectively. Discriminant analysis of principal components done using top 30 markers separated the breeding lines into five major clusters, three of which were distinct. Six of the top 10 most informative markers successfully confirmed hybridization of crosses between genotypes IESV240, KARIMTAMA1, F6YQ212, and FRAMIDA. A set of 10, 20, and 30 most informative markers are recommended for routine QC applications. Future effort should focus on the deployment of these markers in breeding programs for enhanced genetic gain.
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Affiliation(s)
- Davis M Gimode
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Grace Ochieng
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-arid Tropics-Patancheru, Patancheru, Telangana, India
| | - Eric O Manyasa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Clarisse P Kondombo
- Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Erick O Mikwa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Millicent O Avosa
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | | | - Kahiu Ngugi
- Department of Plant Science & Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Patrick Sheunda
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
- The Kenya Seed Company Limited, Kitale Branch, Kitale, Kenya
| | - McDonald Bright Jumbo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
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Mudaki P, Wamalwa LN, Muui CW, Nzuve F, Muasya RM, Nguluu S, Kimani W. Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers. J Mol Evol 2023:10.1007/s00239-023-10108-1. [PMID: 37147402 DOI: 10.1007/s00239-023-10108-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/02/2023] [Indexed: 05/07/2023]
Abstract
Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.
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Affiliation(s)
- Phoebe Mudaki
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Lydia N Wamalwa
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Catherine W Muui
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi, Kenya
| | - Felister Nzuve
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | | | - Simon Nguluu
- South Eastern Kenya University (SEKU), Kitui, Kenya
| | - Wilson Kimani
- International Livestock Research Institute (ILRI), Nairobi, Kenya.
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Wondimu Z, Dong H, Paterson AH, Worku W, Bantte K. Genome-wide association study reveals genomic loci influencing agronomic traits in Ethiopian sorghum ( Sorghum bicolor (L.) Moench) landraces. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:32. [PMID: 37312746 PMCID: PMC10248676 DOI: 10.1007/s11032-023-01381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/11/2023] [Indexed: 06/15/2023]
Abstract
Uncovering the genetic basis of agronomic traits in sorghum landraces that have adapted to various agro-climatic conditions would contribute to sorghum improvement efforts around the world. To identify quantitative trait nucleotides (QTNs) associated with nine agronomic traits in a panel of 304 sorghum accessions collected from diverse environments across Ethiopia (considered to be the center of origin and diversity), multi-locus genome-wide association studies (ML-GWAS) were performed using 79,754 high quality single nucleotide polymorphism (SNP) markers. Association analyses using six ML-GWAS models identified a set of 338 significantly (LOD ≥ 3)-associated QTNs for nine agronomic traits of sorghum accessions evaluated in two environments (E1 and E2) and their combined dataset (Em). Of these, 121 reliable QTNs, including 13 for flowering time (DF), 13 for plant height (PH), 9 for tiller number (TN), 15 for panicle weight (PWT), 30 for grain yield per panicle (GYP), 12 for structural panicle mass (SPM), 13 for hundred seed weight (HSW), 6 for grain number per panicle (GNP), and 10 for panicle exertion (PE) were consistently detected by at least three ML-GWAS methods and/or in two different environments. Notably, Ethylene responsive transcription factor gene AP2/ERF, known for regulation of plant growth, and the sorghum Terminal flower1/TF1 gene, which functions in the control of floral architecture, were identified as strong candidate genes associated with PH and HSW, respectively. This study provides an entry point for further validation studies to elucidate complex mechanisms controlling important agronomic traits in sorghum. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01381-5.
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Affiliation(s)
- Zeleke Wondimu
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Hongxu Dong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602 USA
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602 USA
| | - Walelign Worku
- College of Agriculture, Hawassa University, P.O. Box 05, Hawassa, Ethiopia
| | - Kassahun Bantte
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
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Amombo E, Ashilenje D, Hirich A, Kouisni L, Oukarroum A, Ghoulam C, El Gharous M, Nilahyane A. Exploring the correlation between salt tolerance and yield: research advances and perspectives for salt-tolerant forage sorghum selection and genetic improvement. PLANTA 2022; 255:71. [PMID: 35190912 PMCID: PMC8860782 DOI: 10.1007/s00425-022-03847-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/25/2022] [Indexed: 05/18/2023]
Abstract
MAIN CONCLUSION Some salt stress response mechanisms can translate into sorghum forage yield and thus act as targets for genetic improvement. Sorghum is a drought-tolerant cereal that is widely grown in the vast Africa's arid and semi-arid areas. Apart from drought, salinity is a major abiotic factor that, in addition to natural causes, has been exacerbated by increased poor anthropological activities. The importance of sorghum as a forage crop in saline areas has yet to be fully realized. Despite intraspecific variation in salt tolerance, sorghum is generally moderately salt-tolerant, and its productivity in saline soils can be remarkably limited. This is due to the difficulty of replicating optimal field saline conditions due to the great heterogeneity of salt distribution in the soil. As a promising fodder crop for saline areas, classic phenotype-based selection methods can be integrated with modern -omics in breeding programs to simultaneously address salt tolerance and production. To enable future manipulation, selection, and genetic improvement of sorghum with high yield and salt tolerance, here, we explore the potential positive correlations between the reliable indices of sorghum performance under salt stress at the phenotypic and genotypic level. We then explore the potential role of modern selection and genetic improvement programs in incorporating these linked salt tolerance and yield traits and propose a mechanism for future studies.
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Affiliation(s)
- Erick Amombo
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Dennis Ashilenje
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Abdelaziz Hirich
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Lamfeddal Kouisni
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
| | - Abdallah Oukarroum
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Cherki Ghoulam
- AgroBioSciences Department (AgBS), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Center of Agrobiotechnology and Bioengineering, Labelled Research Unit CNRST, Cadi Ayyad University (UCA), Marrakech, Morocco
| | - Mohamed El Gharous
- Agricultural Innovation and Technology Transfer Center (AITTC), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Abdelaziz Nilahyane
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco.
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Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Geleta M. Genetic Diversity and Population Structure of Sorghum [ Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers. FRONTIERS IN PLANT SCIENCE 2022; 12:799482. [PMID: 35069657 PMCID: PMC8766336 DOI: 10.3389/fpls.2021.799482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/03/2021] [Indexed: 05/17/2023]
Abstract
Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy-Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.
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Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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