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Dossa EN, Shimelis H, Shayanowako AIT. Genetic diversity analysis of tropical and sub-tropical maize germplasm for Striga resistance and agronomic traits with SNP markers. PLoS One 2024; 19:e0306263. [PMID: 39106250 DOI: 10.1371/journal.pone.0306263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/13/2024] [Indexed: 08/09/2024] Open
Abstract
Striga hermonthica (Sh) and S. asiatica (Sa) are major parasitic weeds limiting cereal crop production and productivity in sub-Saharan Africa (SSA). Under severe infestation, Striga causes yield losses of up to 100%. Breeding for Striga-resistant maize varieties is the most effective and economical approach to controlling the parasite. Well-characterized and genetically differentiated maize germplasm is vital to developing inbred lines, hybrids, and synthetic varieties with Striga resistance and desirable product profiles. The objective of this study was to determine the genetic diversity of 130 tropical and sub-tropical maize inbred lines, hybrids, and open-pollinated varieties germplasm using phenotypic traits and single nucleotide polymorphism (SNP) markers to select Striga-resistant and complementary genotypes for breeding. The test genotypes were phenotyped with Sh and Sa infestations using a 13x10 alpha lattice design with two replications. Agro-morphological traits and Striga-resistance damage parameters were recorded under a controlled environment. Further, high-density Diversity Array Technology Sequencing-derived SNP markers were used to profile the test genotypes. Significant phenotypic differences (P<0.001) were detected among the assessed genotypes for the assessed traits. The SNP markers revealed mean gene diversity and polymorphic information content of 0.34 and 0.44, respectively, supporting the phenotypic variation of the test genotypes. Higher significant variation was recorded within populations (85%) than between populations using the analysis of molecular variance. The Structure analysis allocated the test genotypes into eight major clusters (K = 8) in concordance with the principal coordinate analysis (PCoA). The following genetically distant inbred lines were selected, displaying good agronomic performance and Sa and Sh resistance: CML540, TZISTR25, TZISTR1248, CLHP0303, TZISTR1174, TZSTRI113, TZDEEI50, TZSTRI115, CML539, TZISTR1015, CZL99017, CML451, CML566, CLHP0343 and CML440. Genetically diverse and complementary lines were selected among the tropical and sub-tropical maize populations that will facilitate the breeding of maize varieties with Striga resistance and market-preferred traits.
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Affiliation(s)
- Emeline N Dossa
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Admire I T Shayanowako
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
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Mbe JO, Dzidzienyo DK, Abah SP, Njoku DN, Onyeka J, Tongoona P, Egesi C. Novel SNP markers and other stress-related genomic regions associated with nitrogen use efficiency in cassava. FRONTIERS IN PLANT SCIENCE 2024; 15:1376520. [PMID: 38638347 PMCID: PMC11024350 DOI: 10.3389/fpls.2024.1376520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Cassava productivity is constrained by low soil nitrogen, which is predominant in most cassava-growing regions in the tropics and subtropical agroecology. Improving the low nitrogen tolerance of cassava has become an important breeding objective. The current study aimed to develop cassava varieties with improved nitrogen use efficiency by identifying genomic regions and candidate genes linked to nitrogen use efficiency in cassava. A genome-wide association study (GWAS) was performed using the Genome Association and Prediction Integrated Tool (GAPIT). A panel of 265 diverse cassava genotypes was phenotyped for 10 physiological and agronomic traits under optimum and low-nitrogen regimes. Whole-genome genotyping of these cassava cloneswas performed using the Diversity Arrays Technology (DArTseq) sequencing platform. A total of 68,814 single nucleotide polymorphisms (SNPs) were identified, which were spread across the entire 18 chromosomes of the cassava genome, of which 52 SNPs at various densities were found to be associated with nitrogen use efficiency in cassava and other yield-related traits. The putative genes identified through GWAS, especially those with significant associated SNP markers for NUE and related traits have the potential, if deployed appropriately, to develop cassava varieties with improved nitrogen use efficiency, which would translate to a reduction in the economic and environmental cost of cassava production.
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Affiliation(s)
- Joseph Okpani Mbe
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Daniel Kwadjo Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Biotechnology Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Simon Peter Abah
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Damian Ndubuisi Njoku
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Joseph Onyeka
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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Jhu MY, Ellison EE, Sinha NR. CRISPR gene editing to improve crop resistance to parasitic plants. Front Genome Ed 2023; 5:1289416. [PMID: 37965302 PMCID: PMC10642197 DOI: 10.3389/fgeed.2023.1289416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Parasitic plants pose a significant threat to global agriculture, causing substantial crop losses and hampering food security. In recent years, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene-editing technology has emerged as a promising tool for developing resistance against various plant pathogens. Its application in combating parasitic plants, however, remains largely unexplored. This review aims to summarise current knowledge and research gaps in utilising CRISPR to develop resistance against parasitic plants. First, we outline recent improvements in CRISPR gene editing tools, and what has been used to combat various plant pathogens. To realise the immense potential of CRISPR, a greater understanding of the genetic basis underlying parasitic plant-host interactions is critical to identify suitable target genes for modification. Therefore, we discuss the intricate interactions between parasitic plants and their hosts, highlighting essential genes and molecular mechanisms involved in defence response and multilayer resistance. These include host resistance responses directly repressing parasitic plant germination or growth and indirectly influencing parasitic plant development via manipulating environmental factors. Finally, we evaluate CRISPR-mediated effectiveness and long-term implications for host resistance and crop improvement, including inducible resistance response and tissue-specific activity. In conclusion, this review highlights the challenges and opportunities CRISPR technology provides to combat parasitic plants and provides insights for future research directions to safeguard global agricultural productivity.
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Affiliation(s)
- Min-Yao Jhu
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Evan E. Ellison
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Neelima R. Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, United States
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Rouamba A, Shimelis H, Drabo I, Mrema E, Ojiewo CO, Mwadzingeni L, Rathore A. Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet. Sci Rep 2023; 13:17152. [PMID: 37821558 PMCID: PMC10567810 DOI: 10.1038/s41598-023-44046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023] Open
Abstract
Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha-1) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers' and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits.
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Affiliation(s)
- Armel Rouamba
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
- Institute of Environment and Agricultural Research, 01 BP 476, Ouagadougou, Burkina Faso.
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Inoussa Drabo
- Institute of Environment and Agricultural Research, 01 BP 476, Ouagadougou, Burkina Faso
| | - Emmanuel Mrema
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
- Tanzania Agriculture Research Institute, Tumbi Center, P.O. Box 306, Tabora, Tanzania
| | - Christopher Ochieng Ojiewo
- International Maize and Wheat Improvement Center, CIMMYT - ICRAF, House, United Nations Avenue, Gigiri, Nairobi, Kenya
| | - Learnmore Mwadzingeni
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
- Seed Co Limited, 1 Shamwari Road, Stapleford, P.O. Box WGT 64 Westage, Harare, Zimbabwe
| | - Abhishek Rathore
- Excellence in Breeding Platform (EiB), International Maize and Wheat Improvement Center, CIMMYT, Hyderabad, Telangana, India
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Chaudhary N, Salgotra RK, Chauhan BS. Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security. Genes (Basel) 2023; 14:1770. [PMID: 37761910 PMCID: PMC10530810 DOI: 10.3390/genes14091770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes.
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Affiliation(s)
- Neeraj Chaudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Bhagirath Singh Chauhan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD 4343, Australia
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Dossa EN, Shimelis H, Mrema E, Shayanowako ATI, Laing M. Genetic resources and breeding of maize for Striga resistance: a review. FRONTIERS IN PLANT SCIENCE 2023; 14:1163785. [PMID: 37235028 PMCID: PMC10206272 DOI: 10.3389/fpls.2023.1163785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/07/2023] [Indexed: 05/28/2023]
Abstract
The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.
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Affiliation(s)
- Emeline Nanou Dossa
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Emmanuel Mrema
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Tanzania Agricultural Research Institute, Tumbi Center, Tabora, Tanzania
| | | | - Mark Laing
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Harnessing plant resistance against Striga spp. parasitism in major cereal crops for enhanced crop production and food security in Sub-Saharan Africa: a review. Food Secur 2023. [DOI: 10.1007/s12571-023-01345-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
AbstractGiven their long-lasting seed viability, 15–20-year lifespan and their high seed production levels, a significant impact of parasitic plant Striga spp. on African food production is inevitable. Over the last decades, climate change has increasingly favoured the adaptability, spread and virulence of major Striga species, S. hermonthica and S. asiatica, across arable land in Sub-Saharan Africa (SSA). These parasitic weeds are causing important yield losses on several staple food crops and endangering food and nutritional security in many SSA countries. Losses caused by Striga spp. are amplified by low soil fertility and recurrent droughts. The impact of Striga parasitism has been characterized through different phenotypic and genotypic traits assessment of their host plants. Among all control strategies, host-plant resistance remains the most pro-poor, easy-to-adopt, sustainable and eco-friendly control strategy against Striga parasitism. This review highlights the impact of Striga parasitism on food security in SSA and reports recent results related to the genetic basis of different agronomic, pheno-physiological and biochemical traits associated with the resistance to Striga in major African cereal food crops.
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Okunlola G, Badu-Apraku B, Ariyo O, Agre P, Offernedo Q, Ayo-Vaughan M. Genome-wide association studies of Striga resistance in extra-early maturing quality protein maize inbred lines. G3 (BETHESDA, MD.) 2023; 13:jkac237. [PMID: 36073937 PMCID: PMC9911053 DOI: 10.1093/g3journal/jkac237] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/03/2022] [Indexed: 11/14/2022]
Abstract
Identification of genes associated with Striga resistance is invaluable for accelerating genetic gains in breeding for Striga resistance in maize. We conducted a genome-wide association study to identify genomic regions associated with grain yield and other agronomic traits under artificial Striga field infestation. One hundred and forty-one extra-early quality protein maize inbred lines were phenotyped for key agronomic traits. The inbred lines were also genotyped using 49,185 DArTseq markers from which 8,143 were retained for population structure analysis and genome wide-association study. Cluster analysis and population structure revealed the presence of 3 well-defined genetic groups. Using the mixed linear model, 22 SNP markers were identified to be significantly associated with grain yield, Striga damage at 10 weeks after planting, number of emerged Striga plants at 8 and 10 weeks after planting and ear aspect. The identified SNP markers would be useful for breeders for marker-assisted selection to accelerate the genetic enhancement of maize for Striga resistance in sub-Saharan Africa after validation.
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Affiliation(s)
- Gbemisola Okunlola
- Maize Improvement Programme, International Institute of Tropical Agriculture, IITA, Oyo Road, Ibadan 200001, Oyo ,5320, Nigeria
- Department of Plant Breeding and Seed Technology, Federal University of Agriculture, Abeokuta 110124, Ogun, 2240, Nigeria
| | - Baffour Badu-Apraku
- Maize Improvement Programme, International Institute of Tropical Agriculture, IITA, Oyo Road, Ibadan 200001, Oyo ,5320, Nigeria
| | - Omolayo Ariyo
- Department of Plant Breeding and Seed Technology, Federal University of Agriculture, Abeokuta 110124, Ogun, 2240, Nigeria
| | - Paterne Agre
- Maize Improvement Programme, International Institute of Tropical Agriculture, IITA, Oyo Road, Ibadan 200001, Oyo ,5320, Nigeria
| | - Queen Offernedo
- Maize Improvement Programme, International Institute of Tropical Agriculture, IITA, Oyo Road, Ibadan 200001, Oyo ,5320, Nigeria
| | - Moninuola Ayo-Vaughan
- Department of Plant Breeding and Seed Technology, Federal University of Agriculture, Abeokuta 110124, Ogun, 2240, Nigeria
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Badu-Apraku B, Adewale S, Paterne A, Offornedo Q, Gedil M. Mapping quantitative trait loci and predicting candidate genes for Striga resistance in maize using resistance donor line derived from Zea diploperennis. Front Genet 2023; 14:1012460. [PMID: 36713079 PMCID: PMC9877281 DOI: 10.3389/fgene.2023.1012460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
The parasitic weed, Striga is a major biological constraint to cereal production in sub-Saharan Africa (SSA) and threatens food and nutrition security. Two hundred and twenty-three (223) F2:3 mapping population involving individuals derived from TZdEI 352 x TZEI 916 were phenotyped for four Striga-adaptive traits and genotyped using the Diversity Arrays Technology (DArT) to determine the genomic regions responsible for Striga resistance in maize. After removing distorted SNP markers, a genetic linkage map was constructed using 1,918 DArTseq markers which covered 2092.1 cM. Using the inclusive composite interval mapping method in IciMapping, twenty-three QTLs influencing Striga resistance traits were identified across four Striga-infested environments with five stable QTLs (qGY4, qSC2.1, qSC2.2, qSC5, and qSC6) detected in more than one environment. The variations explained by the QTLs ranged from 4.1% (qSD2.3) to 14.4% (qSC7.1). Six QTLs each with significant additive × environment interactions were also identified for grain yield and Striga damage. Gene annotation revealed candidate genes underlying the QTLs, including the gene models GRMZM2G077002 and GRMZM2G404973 which encode the GATA transcription factors, GRMZM2G178998 and GRMZM2G134073 encoding the NAC transcription factors, GRMZM2G053868 and GRMZM2G157068 which encode the nitrate transporter protein and GRMZM2G371033 encoding the SBP-transcription factor. These candidate genes play crucial roles in plant growth and developmental processes and defense functions. This study provides further insights into the genetic mechanisms of resistance to Striga parasitism in maize. The QTL detected in more than one environment would be useful for further fine-mapping and marker-assisted selection for the development of Striga resistant and high-yielding maize cultivars.
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Calderón-González Á, Pérez-Vich B, Pouilly N, Boniface MC, Louarn J, Velasco L, Muños S. Association mapping for broomrape resistance in sunflower. FRONTIERS IN PLANT SCIENCE 2023; 13:1056231. [PMID: 36714707 PMCID: PMC9875907 DOI: 10.3389/fpls.2022.1056231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance. METHODS The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments. RESULTS AND DISCUSSION The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.
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Affiliation(s)
- Álvaro Calderón-González
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Johann Louarn
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
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12
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Genome-Wide Association Study Revealed SNP Alleles Associated with Seed Size Traits in African Yam Bean ( Sphenostylis stenocarpa (Hochst ex. A. Rich.) Harms). Genes (Basel) 2022; 13:genes13122350. [PMID: 36553617 PMCID: PMC9777823 DOI: 10.3390/genes13122350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/26/2022] [Accepted: 12/09/2022] [Indexed: 12/16/2022] Open
Abstract
Seed size is an important yield and quality-determining trait in higher plants and is also crucial to their evolutionary fitness. In African yam bean (AYB), seed size varies widely among different accessions. However, the genetic basis of such variation has not been adequately documented. A genome-wide marker-trait association study was conducted to identify genomic regions associated with four seed size traits (seed length, seed width, seed thickness, and 100-seed weight) in a panel of 195 AYB accessions. A total of 5416 SNP markers were generated from the diversity array technology sequence (DArTseq) genotype-by-sequencing (GBS)- approach, in which 2491 SNPs were retained after SNP quality control and used for marker-trait association analysis. Significant phenotypic variation was observed for the traits. Broad-sense heritability ranged from 50.0% (seed width) to 66.4% (seed length). The relationships among the traits were positive and significant. Genome-wide association study (GWAS) using the general linear model (GLM) and the mixed linear model (MLM) approaches identified 12 SNP markers significantly associated with seed size traits across the six test environments. The 12 makers explained 6.5-10.8% of the phenotypic variation. Two markers (29420334|F|0-52:C>G-52:C>G and 29420736|F|0-57:G>T-57:G>T) with pleiotropic effects associated with seed width and seed thickness were found. A candidate gene search identified five significant markers (100026424|F|0-37:C>T-37:C>T, 100041049|F|0-42:G>C-42:G>C, 100034480|F|0-31:C>A-31:C>A, 29420365|F|0-55:C>G-55:C>G, and 29420736|F|0-57:G>T-57:G>T) located close to 43 putative genes whose encoding protein products are known to regulate seed size traits. This study revealed significant makers not previously reported for seed size in AYB and could provide useful information for genomic-assisted breeding in AYB.
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Zhang L, Ding Y, Xu J, Gao X, Cao N, Li K, Feng Z, Cheng B, Zhou L, Ren M, Lu X, Bao Z, Tao Y, Xin Z, Zou G. Selection Signatures in Chinese Sorghum Reveals Its Unique Liquor-Making Properties. FRONTIERS IN PLANT SCIENCE 2022; 13:923734. [PMID: 35755652 PMCID: PMC9218943 DOI: 10.3389/fpls.2022.923734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.
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Affiliation(s)
- Liyi Zhang
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jianxia Xu
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xu Gao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ning Cao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Kuiying Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhou Feng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, China
| | - Bing Cheng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Lengbo Zhou
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, China
| | - Xiaochun Lu
- Institute of Sorghum Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Zhigui Bao
- Shanghai OE Biotech Co., Ltd., Shanghai, China
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, United States
| | - Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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14
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Bhadmus OA, Badu-Apraku B, Adeyemo OA, Agre PA, Queen ON, Ogunkanmi AL. Genome-Wide Association Analysis Reveals Genetic Architecture and Candidate Genes Associated with Grain Yield and Other Traits under Low Soil Nitrogen in Early-Maturing White Quality Protein Maize Inbred Lines. Genes (Basel) 2022; 13:genes13050826. [PMID: 35627211 PMCID: PMC9141126 DOI: 10.3390/genes13050826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 02/01/2023] Open
Abstract
Maize production in the savannas of sub-Saharan Africa (SSA) is constrained by the low nitrogen in the soils. The identification of quantitative trait loci (QTL) conferring tolerance to low soil nitrogen (low-N) is crucial for the successful breeding of high-yielding QPM maize genotypes under low-N conditions. The objective of this study was to identify QTLs significantly associated with grain yield and other low-N tolerance-related traits under low-N. The phenotypic data of 140 early-maturing white quality protein maize (QPM) inbred lines were evaluated under low-N. The inbred lines were genotyped using 49,185 DArTseq markers, from which 7599 markers were filtered for population structure analysis and genome-wide association study (GWAS). The inbred lines were grouped into two major clusters based on the population structure analysis. The GWAS identified 24, 3, 10, and 3 significant SNPs respectively associated with grain yield, stay-green characteristic, and plant and ear aspects, under low-N. Sixteen SNP markers were physically located in proximity to 32 putative genes associated with grain yield, stay-green characteristic, and plant and ear aspects. The putative genes GRMZM2G127139, GRMZM5G848945, GRMZM2G031331, GRMZM2G003493, GRMZM2G067964, GRMZM2G180254, on chromosomes 1, 2, 8, and 10 were involved in cellular nitrogen assimilation and biosynthesis, normal plant growth and development, nitrogen assimilation, and disease resistance. Following the validation of the markers, the putative candidate genes and SNPs could be used as genomic markers for marker-assisted selection, to facilitate genetic gains for low-N tolerance in maize production.
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Affiliation(s)
- Olatunde A. Bhadmus
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
- Correspondence:
| | - Oyenike A. Adeyemo
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
| | - Paterne A. Agre
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Offornedo N. Queen
- International Institute of Tropical Agriculture, IITA, PMB 5320 Oyo Road, Ibadan 200285, Nigeria; (P.A.A.); (O.N.Q.)
| | - Adebayo L. Ogunkanmi
- Department of Cell Biology and Genetics, University of Lagos, Lagos 101017, Nigeria; (O.A.B.); (O.A.A.); (A.L.O.)
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15
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Woods P, Lehner KR, Hein K, Mullen JL, McKay JK. Root Pulling Force Across Drought in Maize Reveals Genotype by Environment Interactions and Candidate Genes. FRONTIERS IN PLANT SCIENCE 2022; 13:883209. [PMID: 35498695 PMCID: PMC9051544 DOI: 10.3389/fpls.2022.883209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.
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Affiliation(s)
- Patrick Woods
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Kevin R. Lehner
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Kirsten Hein
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Jack L. Mullen
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - John K. McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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16
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Hyten DL. Genotyping Platforms for Genome-Wide Association Studies: Options and Practical Considerations. Methods Mol Biol 2022; 2481:29-42. [PMID: 35641757 DOI: 10.1007/978-1-0716-2237-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) in crops requires genotyping platforms that are capable of producing accurate high density genotyping data on hundreds of plants in a cost-effective manner. Currently there are multiple commercial platforms available that are being effectively used across crops. These platforms include genotyping arrays such as the Illumina Infinium arrays and the Applied Biosystems Axiom Arrays along with a variety of resequencing methods. These methods are being used to genotype tens of thousands of markers up to millions of markers on GWAS panels. They are being used on crops with simple genomes to crops with very complex, large, polyploid genomes. Depending on the crop and the goal of the GWAS, there are several options and practical considerations to take into account when selecting a genotyping technology to ensure that the right coverage, accuracy, and cost for the study is achieved.
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Affiliation(s)
- David L Hyten
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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17
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Stanley AE, Menkir A, Ifie B, Paterne AA, Unachukwu NN, Meseka S, Mengesha WA, Bossey B, Kwadwo O, Tongoona PB, Oladejo O, Sneller C, Gedil M. Association analysis for resistance to Striga hermonthica in diverse tropical maize inbred lines. Sci Rep 2021; 11:24193. [PMID: 34921181 PMCID: PMC8683441 DOI: 10.1038/s41598-021-03566-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers’ lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.
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Affiliation(s)
- A E Stanley
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana.,International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - A Menkir
- International Institute of Tropical Agriculture, Ibadan, Nigeria.
| | - B Ifie
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - A A Paterne
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - N N Unachukwu
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - S Meseka
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - W A Mengesha
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - B Bossey
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - O Kwadwo
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - P B Tongoona
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | - O Oladejo
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - C Sneller
- Ohio Agriculture Research and Development Center, Ohio State University, Wooster, OH, USA
| | - M Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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18
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Uchendu K, Njoku DN, Paterne A, Rabbi IY, Dzidzienyo D, Tongoona P, Offei S, Egesi C. Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava. FRONTIERS IN PLANT SCIENCE 2021; 12:770434. [PMID: 34975953 PMCID: PMC8719520 DOI: 10.3389/fpls.2021.770434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 06/14/2023]
Abstract
Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.
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Affiliation(s)
- Kelechi Uchendu
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | | | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Samuel Offei
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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19
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Kavuluko J, Kibe M, Sugut I, Kibet W, Masanga J, Mutinda S, Wamalwa M, Magomere T, Odeny D, Runo S. GWAS provides biological insights into mechanisms of the parasitic plant (Striga) resistance in sorghum. BMC PLANT BIOLOGY 2021; 21:392. [PMID: 34418971 PMCID: PMC8379865 DOI: 10.1186/s12870-021-03155-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/02/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite. RESULTS We used laboratory assays - rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attachments were identified. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors. CONCLUSIONS Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.
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Affiliation(s)
- Jacinta Kavuluko
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Magdaline Kibe
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Irine Sugut
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Willy Kibet
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Joel Masanga
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Sylvia Mutinda
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
- Pan African University of Science Technology and Innovation, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Titus Magomere
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Steven Runo
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi, Kenya.
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20
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Genome-Wide Association Studies for Striga asiatica Resistance in Tropical Maize. Int J Genomics 2021; 2021:9979146. [PMID: 34239920 PMCID: PMC8238628 DOI: 10.1155/2021/9979146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 11/17/2022] Open
Abstract
Striga asiatica L. is a parasitic weed in cereal crops including maize leading to tremendous yield losses up to 100% under severe infestation. The available S. asiatica control methods include cultural control options such as uprooting and burning the Striga plants before they flower, field sanitation, crop rotation, intercropping, organic matter usage, improved fallows, and application of herbicides. Resource limitation among smallholder farmers renders almost all of the control methods impossible. Development and use of Striga resistant genotypes are seen as the most feasible management option. Marker identification formulates tools that are faster, cheaper, and easier to utilise in breeding for S. asiatica resistance which has low heritability. The objective of this study was to identify single nucleotide polymorphism (SNP) markers for Striga resistance using the genome-wide association study (GWAS). Genotyping by sequencing was done on tropical maize inbred lines followed by their evaluation for Striga resistance. Analysis of variance showed significant (p < 0.05) variation among evaluated genotypes for Striga resistance traits such as germination distance, germination percentage, haustoria root attachments, total Striga plants emerged, total biomass, and growth rate. There were also significant differences (p < 0.05) for cobs, leaves, stems, and roots weight. The broad sense heritability was fairly high (up to 61%) for most traits. The means for derived traits on stress tolerance indices were subjected to a t-test, and significant differences (p < 0.05) were found for leaves, stem, roots, shoots, and total biomass. The Manhattan plots from GWAS showed the presence of three SNP markers on chromosome numbers 5, 6, and 7 for total Striga plants emerged. The identified markers for resistance to S. asiatica should be validated and utilised to breed for Striga resistance in tropical maize.
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21
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Jamil M, Kountche BA, Al-Babili S. Current progress in Striga management. PLANT PHYSIOLOGY 2021; 185:1339-1352. [PMID: 33793943 PMCID: PMC8133620 DOI: 10.1093/plphys/kiab040] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/18/2021] [Indexed: 05/20/2023]
Abstract
The Striga, particularly S. he rmonthica, problem has become a major threat to food security, exacerbating hunger and poverty in many African countries. A number of Striga control strategies have been proposed and tested during the past decade, however, further research efforts are still needed to provide sustainable and effective solutions to the Striga problem. In this paper, we provide an update on the recent progress and the approaches used in Striga management, and highlight emerging opportunities for developing new technologies to control this enigmatic parasite.
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Affiliation(s)
- Muhammad Jamil
- Division of Biological and Environmental Sciences and Engineering, the BioActives Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Boubacar A Kountche
- Division of Biological and Environmental Sciences and Engineering, the BioActives Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Salim Al-Babili
- Division of Biological and Environmental Sciences and Engineering, the BioActives Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Author for communication:
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22
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Yacoubou A, Zoumarou Wallis N, Menkir A, Zinsou VA, Onzo A, Garcia‐Oliveira AL, Meseka S, Wende M, Gedil M, Agre P. Breeding maize ( Zea mays) for Striga resistance: Past, current and prospects in sub-saharan africa. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2021; 140:195-210. [PMID: 34239217 PMCID: PMC8248382 DOI: 10.1111/pbr.12896] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 12/21/2020] [Indexed: 05/21/2023]
Abstract
Striga hermonthica, causes up to 100% yield loss in maize production in Sub-Saharan Africa. Developing Striga-resistant maize cultivars could be a major component of integrated Striga management strategies. This paper presents a comprehensive overview of maize breeding activities related to Striga resistance and its management. Scientific surveys have revealed that conventional breeding strategies have been used more than molecular breeding strategies in maize improvement for Striga resistance. Striga resistance genes are still under study in the International Institute for Tropical Agriculture (IITA) maize breeding programme. There is also a need to discover QTL and molecular markers associated with such genes to improve Striga resistance in maize. Marker Assistance Breeding is expected to increase maize breeding efficiency with complex traits such as resistance towards Striga because of the complex nature of the host-parasite relationship and its intersection with other environmental factors. Conventional alongside molecular tools and technical controls are promising methods to effectively assess Striga in Sub-Saharan Africa.
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Affiliation(s)
- Abdoul‐Madjidou Yacoubou
- Laboratoire de Phytotechnie, d’Amélioration et de Protection des Plantes (LaPAPP)Département des Sciences et Techniques de Production Végétale (STPV)Faculté d’AgronomieUniversité de ParakouParakouBénin
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
- Institut National des Recherches Agricoles du Bénin01 BP 884CotonouBénin
| | - Nouhoun Zoumarou Wallis
- Laboratoire de Phytotechnie, d’Amélioration et de Protection des Plantes (LaPAPP)Département des Sciences et Techniques de Production Végétale (STPV)Faculté d’AgronomieUniversité de ParakouParakouBénin
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
| | - Valerien A. Zinsou
- Laboratoire de Phytotechnie, d’Amélioration et de Protection des Plantes (LaPAPP)Département des Sciences et Techniques de Production Végétale (STPV)Faculté d’AgronomieUniversité de ParakouParakouBénin
| | - Alexis Onzo
- Laboratoire de Phytotechnie, d’Amélioration et de Protection des Plantes (LaPAPP)Département des Sciences et Techniques de Production Végétale (STPV)Faculté d’AgronomieUniversité de ParakouParakouBénin
| | | | - Silvestro Meseka
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
| | - Mengesha Wende
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
| | - Paterne Agre
- International Institute of Tropical Agriculture (IITA)Oyo RoadPMB 5320IbadanNigeria
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23
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Gowda M, Makumbi D, Das B, Nyaga C, Kosgei T, Crossa J, Beyene Y, Montesinos-López OA, Olsen MS, Prasanna BM. Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:941-958. [PMID: 33388884 PMCID: PMC7925482 DOI: 10.1007/s00122-020-03744-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/02/2020] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.
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Affiliation(s)
- Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya.
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Christine Nyaga
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Titus Kosgei
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
- Moi University, P. O. Box 3900-30100, Eldoret, Kenya
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, D.F, Mexico
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | | | - Michael S Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
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24
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Badu-Apraku B, Adewale S, Paterne AA, Gedil M, Toyinbo J, Asiedu R. Identification of QTLs for grain yield and other traits in tropical maize under Striga infestation. PLoS One 2020; 15:e0239205. [PMID: 32925954 PMCID: PMC7489516 DOI: 10.1371/journal.pone.0239205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/02/2020] [Indexed: 12/02/2022] Open
Abstract
Striga is an important biotic factor limiting maize production in sub-Saharan Africa and can cause yield losses as high as 100%. Marker-assisted selection (MAS) approaches hold a great potential for improving Striga resistance but requires identification and use of markers associated with Striga resistance for adequate genetic gains from selection. However, there is no report on the discovery of quantitative trait loci (QTL) for resistance to Striga in maize under artificial field infestation. In the present study, 198 BC1S1 families obtained from a cross involving TZEEI 29 (Striga resistant inbred line) and TZEEI 23 (Striga susceptible inbred line) plus the two parental lines were screened under artificial Striga-infested conditions at two Striga-endemic locations in Nigeria in 2018, to identify QTL associated with Striga resistance indicator traits, including grain yield, ears per plant, Striga damage and number of emerged Striga plants. Genetic map was constructed using 1,386 DArTseq markers distributed across the 10 maize chromosomes, covering 2076 cM of the total genome with a mean spacing of 0.11 cM between the markers. Using composite interval mapping (CIM), fourteen QTL were identified for key Striga resistance/tolerance indicator traits: 3 QTL for grain yield, 4 for ears per plant and 7 for Striga damage at 10 weeks after planting (WAP), across environments. Putative candidate genes which encode major transcription factor families WRKY, bHLH, AP2-EREBPs, MYB, and bZIP involved in plant defense signaling were detected for Striga resistance/tolerance indicator traits. The QTL detected in the present study would be useful for rapid transfer of Striga resistance/tolerance genes into Striga susceptible but high yielding maize genotypes using MAS approaches after validation. Further studies on validation of the QTL in different genetic backgrounds and in different environments would help verify their reproducibility and effective use in breeding for Striga resistance/tolerance.
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Affiliation(s)
- Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- * E-mail:
| | - Samuel Adewale
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Johnson Toyinbo
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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25
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Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement. Genes (Basel) 2020; 11:genes11091054. [PMID: 32906687 PMCID: PMC7565678 DOI: 10.3390/genes11091054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 01/30/2023] Open
Abstract
Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.
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