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Habte N, Girma G, Xu X, Liao CJ, Adeyanju A, Hailemariam S, Lee S, Okoye P, Ejeta G, Mengiste T. Haplotypes at the sorghum ARG4 and ARG5 NLR loci confer resistance to anthracnose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:106-123. [PMID: 38111157 DOI: 10.1111/tpj.16594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
Sorghum anthracnose caused by the fungus Colletotrichum sublineola (Cs) is a damaging disease of the crop. Here, we describe the identification of ANTHRACNOSE RESISTANCE GENES (ARG4 and ARG5) encoding canonical nucleotide-binding leucine-rich repeat (NLR) receptors. ARG4 and ARG5 are dominant resistance genes identified in the sorghum lines SAP135 and P9830, respectively, that show broad-spectrum resistance to Cs. Independent genetic studies using populations generated by crossing SAP135 and P9830 with TAM428, fine mapping using molecular markers, comparative genomics and gene expression studies determined that ARG4 and ARG5 are resistance genes against Cs strains. Interestingly, ARG4 and ARG5 are both located within clusters of duplicate NLR genes at linked loci separated by ~1 Mb genomic region. SAP135 and P9830 each carry only one of the ARG genes while having the recessive allele at the second locus. Only two copies of the ARG5 candidate genes were present in the resistant P9830 line while five non-functional copies were identified in the susceptible line. The resistant parents and their recombinant inbred lines carrying either ARG4 or ARG5 are resistant to strains Csgl1 and Csgrg suggesting that these genes have overlapping specificities. The role of ARG4 and ARG5 in resistance was validated through sorghum lines carrying independent recessive alleles that show increased susceptibility. ARG4 and ARG5 are located within complex loci displaying interesting haplotype structures and copy number variation that may have resulted from duplication. Overall, the identification of anthracnose resistance genes with unique haplotype stucture provides a foundation for genetic studies and resistance breeding.
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Affiliation(s)
- Nida Habte
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Xiaochen Xu
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Sara Hailemariam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Pascal Okoye
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, 47907, USA
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Cuevas HE, Knoll JE, Prom LK, Stutts LR, Vermerris W. Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1249555. [PMID: 37929175 PMCID: PMC10623324 DOI: 10.3389/fpls.2023.1249555] [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: 06/28/2023] [Accepted: 10/04/2023] [Indexed: 11/07/2023]
Abstract
Sweet sorghum is an attractive feedstock for the production of renewable chemicals and fuels due to the readily available fermentable sugars that can be extracted from the juice, and the additional stream of fermentable sugars that can be obtained from the cell wall polysaccharides in the bagasse. An important selection criterion for new sweet sorghum germplasm is resistance to anthracnose, a disease caused by the fungal pathogen Colletotrichum sublineolum. The identification of novel anthracnose-resistance sources present in sweet sorghum germplasm offers a fast track towards the development of new resistant sweet sorghum germplasm. We established a sweet sorghum diversity panel (SWDP) of 272 accessions from the USDA-ARS National Plant Germplasm (NPGS) collection that includes landraces from 22 countries and advanced breeding material, and that represents ~15% of the NPGS sweet sorghum collection. Genomic characterization of the SWDP identified 171,954 single nucleotide polymorphisms (SNPs) with an average of one SNP per 4,071 kb. Population structure analysis revealed that the SWDP could be stratified into four populations and one admixed group, and that this population structure could be aligned to sorghum's racial classification. Results from a two-year replicated trial of the SWDP for anthracnose resistance response in Texas, Georgia, Florida, and Puerto Rico showed 27 accessions to be resistant across locations, while 145 accessions showed variable resistance response against local pathotypes. A genome-wide association study identified 16 novel genomic regions associated with anthracnose resistance. Four resistance loci on chromosomes 3, 6, 8 and 9 were identified against pathotypes from Puerto Rico, and two resistance loci on chromosomes 3 and 8 against pathotypes from Texas. In Georgia and Florida, three resistance loci were detected on chromosomes 4, 5, 6 and four on chromosomes 4, 5 (two loci) and 7, respectively. One resistance locus on chromosome 2 was effective against pathotypes from Texas and Puerto Rico and a genomic region of 41.6 kb at the tip of chromosome 8 was associated with resistance response observed in Georgia, Texas, and Puerto Rico. This publicly available SWDP and the extensive evaluation of anthracnose resistance represent a valuable genomic resource for the improvement of sorghum.
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Affiliation(s)
- Hugo E. Cuevas
- USDA-ARS, Tropical Agriculture Research Station, Mayagüez, Puerto Rico
| | - Joseph E. Knoll
- USDA-ARS, Crop Genetics and Breeding Research, Tifton, GA, United States
| | - Louis K. Prom
- USDA-ARS, Southern Plains Agriculture Research Center, College Station, TX, United States
| | - Lauren R. Stutts
- Graduate Program in Plant Molecular & Cellular Biology, University of Florida, Gainesville, FL, United States
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL, United States
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Cruet-Burgos C, Morris GP, Rhodes DH. Characterization of grain carotenoids in global sorghum germplasm to guide genomics-assisted breeding strategies. BMC PLANT BIOLOGY 2023; 23:165. [PMID: 36977987 PMCID: PMC10045421 DOI: 10.1186/s12870-023-04176-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Crop biofortification is a successful strategy to ameliorate Vitamin A deficiency. Sorghum is a good candidate for vitamin A biofortification, as it is a staple food in regions with high prevalence of vitamin A deficiency. β-carotene-the main provitamin A carotenoid-is below the target concentration in sorghum grain, therefore biofortification breeding is required. Previous studies found evidence that sorghum carotenoid variation is oligogenic, suggesting that marker-assisted selection can be an appropriate biofortification method. However, we hypothesize that sorghum carotenoids have both oligogenic and polygenic components of variation. Genomics-assisted breeding could accelerate breeding efforts, but there exists knowledge gaps in the genetics underlying carotenoid variation, as well as appropriate germplasm to serve as donors. RESULTS In this study, we characterized carotenoids in 446 accessions from the sorghum association panel and carotenoid panel using high-performance liquid chromatography, finding high carotenoid accessions not previously identified. Genome-wide association studies conducted with 345 accessions, confirmed that zeaxanthin epoxidase is a major gene underlying variation for not only zeaxanthin, but also lutein and β-carotene. High carotenoid lines were found to have limited genetic diversity, and originated predominantly from only one country. Potential novel genetic diversity for carotenoid content was identified through genomic predictions in 2,495 accessions of unexplored germplasm. Oligogenic variation of carotenoids was confirmed, as well as evidence for polygenic variation, suggesting both marker-assisted selection and genomic selection can facilitate breeding efforts. CONCLUSIONS Sorghum vitamin A biofortification could be beneficial for millions of people who rely on it as a dietary staple. Carotenoid content in sorghum is low, but high heritability suggests that increasing concentrations through breeding is possible. Low genetic diversity among high carotenoid lines might be the main limitation for breeding efforts, therefore further germplasm characterization is needed to assess the feasibility of biofortification breeding. Based on germplasm here evaluated, most countries' germplasm lacks high carotenoid alleles, thus pre-breeding will be needed. A SNP marker within the zeaxanthin epoxidase gene was identified as a good candidate for use in marker-assisted selection. Due to the oligogenic and polygenic variation of sorghum grain carotenoids, both marker-assisted selection and genomic selection can be employed to accelerate breeding efforts.
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Affiliation(s)
- Clara Cruet-Burgos
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
| | - Geoffrey P Morris
- Department of Soil & Crop Science, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Davina H Rhodes
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, 80523, USA
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Xiong W, Liao L, Ni Y, Gao H, Yang J, Guo Y. The Effects of Epicuticular Wax on Anthracnose Resistance of Sorghum bicolor. Int J Mol Sci 2023; 24:ijms24043070. [PMID: 36834482 PMCID: PMC9964091 DOI: 10.3390/ijms24043070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/17/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Cuticular waxes are mixtures of hydrophobic compounds covering land plant surfaces and play key roles in plant resistance to abiotic and biotic stresses. However, it is still not clear whether the epicuticular wax could protect the plants from infection by anthracnose, one of the most important plant diseases worldwide, which seriously infects sorghum and causes great yield loss. In this study, Sorghum bicolor L., an important C4 crop with high wax coverage, was selected to analyze the relationship between epicuticular wax (EW) and anthracnose resistance. In vitro analysis indicated that the sorghum leaf wax significantly inhibited the anthracnose mycelium growth of anthracnose on potato dextrose agar (PDA) medium, with the plaque diameter smaller than that grown on medium without wax. Then, the EWs were removed from the intact leaf with gum acacia, followed by the inoculation of Colletotrichum sublineola. The results indicated that the disease lesion was remarkably aggravated on leaves without EW, which showed decreased net photosynthetic rate and increased intercellular CO2 concentrations and malonaldehyde content three days after inoculation. Transcriptome analysis further indicated that 1546 and 2843 differentially expressed genes (DEGs) were regulated by C. sublineola infection in plants with and without EW, respectively. Among the DEG encoded proteins and enriched pathways regulated by anthracnose infection, the cascade of the mitogen-activated protein kinases (MAPK) signaling pathway, ABC transporters, sulfur metabolism, benzoxazinoid biosynthesis, and photosynthesis were mainly regulated in plants without EW. Overall, the EW increases plant resistance to C. sublineola by affecting physiological and transcriptome responses through sorghum epicuticular wax, improving our understanding of its roles in defending plants from fungi and ultimately benefiting sorghum resistance breeding.
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Affiliation(s)
- Wangdan Xiong
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Longxin Liao
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yu Ni
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Hanchi Gao
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Jianfeng Yang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanjun Guo
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao Agricultural University, Qingdao 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence:
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Boatwright JL, Sapkota S, Jin H, Schnable JC, Brenton Z, Boyles R, Kresovich S. Sorghum Association Panel whole-genome sequencing establishes cornerstone resource for dissecting genomic diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:888-904. [PMID: 35653240 PMCID: PMC9544330 DOI: 10.1111/tpj.15853] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 05/26/2023]
Abstract
Association mapping panels represent foundational resources for understanding the genetic basis of phenotypic diversity and serve to advance plant breeding by exploring genetic variation across diverse accessions. We report the whole-genome sequencing (WGS) of 400 sorghum (Sorghum bicolor (L.) Moench) accessions from the Sorghum Association Panel (SAP) at an average coverage of 38× (25-72×), enabling the development of a high-density genomic marker set of 43 983 694 variants including single-nucleotide polymorphisms (approximately 38 million), insertions/deletions (indels) (approximately 5 million), and copy number variants (CNVs) (approximately 170 000). We observe slightly more deletions among indels and a much higher prevalence of deletions among CNVs compared to insertions. This new marker set enabled the identification of several novel putative genomic associations for plant height and tannin content, which were not identified when using previous lower-density marker sets. WGS identified and scored variants in 5-kb bins where available genotyping-by-sequencing (GBS) data captured no variants, with half of all bins in the genome falling into this category. The predictive ability of genomic best unbiased linear predictor (GBLUP) models was increased by an average of 30% by using WGS markers rather than GBS markers. We identified 18 selection peaks across subpopulations that formed due to evolutionary divergence during domestication, and we found six Fst peaks resulting from comparisons between converted lines and breeding lines within the SAP that were distinct from the peaks associated with historic selection. This population has served and continues to serve as a significant public resource for sorghum research and demonstrates the value of improving upon existing genomic resources.
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Affiliation(s)
- J. Lucas Boatwright
- Department of Plant and Environmental SciencesClemson UniversityClemsonSouth Carolina29634USA
- Advanced Plant TechnologyClemson UniversityClemsonSouth Carolina29634USA
| | - Sirjan Sapkota
- Advanced Plant TechnologyClemson UniversityClemsonSouth Carolina29634USA
| | - Hongyu Jin
- Center for Plant Science Innovation and Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraska68588USA
| | - James C. Schnable
- Center for Plant Science Innovation and Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNebraska68588USA
| | | | - Richard Boyles
- Department of Plant and Environmental SciencesClemson UniversityClemsonSouth Carolina29634USA
- Pee Dee Research and Education CenterClemson UniversityFlorenceSouth Carolina29506USA
| | - Stephen Kresovich
- Department of Plant and Environmental SciencesClemson UniversityClemsonSouth Carolina29634USA
- Advanced Plant TechnologyClemson UniversityClemsonSouth Carolina29634USA
- Feed the Future Innovation Lab for Crop ImprovementCornell UniversityIthacaNew York14850USA
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Mohammed A, Bekeko Z, Yusufe M, Sulyok M, Krska R. Fungal Species and Multi-Mycotoxin Associated with Post-Harvest Sorghum (Sorghum bicolor (L.) Moench) Grain in Eastern Ethiopia. Toxins (Basel) 2022; 14:toxins14070473. [PMID: 35878211 PMCID: PMC9315719 DOI: 10.3390/toxins14070473] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/03/2022] [Accepted: 07/07/2022] [Indexed: 02/05/2023] Open
Abstract
Sorghum is the main staple food crop in developing countries, including Ethiopia. However, sorghum grain quantity and quality are affected by contaminating fungi both under field and post-harvest stage. The aim of the current study was to assessed fungal species and multi-mycotoxins associated with sorghum grain in post-harvest samples collected from eastern Ethiopia. Fungal genera of Aspergillus, Alternaria, Bipolaris, Fusarium, Mucor, Penicillium, and Rhizoctonia were recovered in the infected grain. A liquid chromatography-tandem mass spectrometric (LC-MS/MS) was used for quantification of multiple mycotoxins/fungal metabolites. Overall, 94 metabolites were detected and grouped into eight categories. All metabolites were detected either in one or more samples. Among major mycotoxins and derivatives, deoxynivalenol (137 μg/kg), zearalenone (121 μg/kg), ochratoxin A (115 μg/kg), and fumonisin B1 (112 μg/kg) were detected with maximum concentrations, while aflatoxin B1 had relatively lower concentrations (23.6 μg/kg). Different emerging mycotoxins were also detected, with tenuazonic acid (1515 μg/kg) occurring at the maximum concentration among Alternaria metabolites. Fusaric acid (2786 μg/kg) from Fusarium metabolites and kojic acid (4584 μg/kg) were detected with the maximum concentration among Fusarium and Aspergillus metabolites, respectively. Unspecific metabolites were recognized with neoechinulin A (1996 μg/kg) at the maximum concentration, followed by cyclo (L-Pro-L-Tyr) (574 μg/kg) and cyclo (L-Pro-L-Val) (410 μg/kg). Moreover, metabolites form other fungal genera and bacterial metabolites were also detected at varying levels. Apparently, the study revealed that sorghum grains collected across those districts were significantly contaminated with co-occurrences of several mycotoxins. Farmers should be the main target groups to be trained on the improved management of sorghum production.
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Affiliation(s)
- Abdi Mohammed
- School of Plant Sciences, College of Agriculture and Environmental Sciences, Haramaya University, Dire Dawa P.O. Box 138, Ethiopia;
- Correspondence: ; Tel.: +251-953953442
| | - Zelalem Bekeko
- School of Plant Sciences, College of Agriculture and Environmental Sciences, Haramaya University, Dire Dawa P.O. Box 138, Ethiopia;
| | - Mawardi Yusufe
- Institute of Technology, Food Sciences and Post-harvest Technology, Haramaya University, Dire Dawa P.O. Box 138, Ethiopia;
| | - Michael Sulyok
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna Konrad Lorenzstr. 20, A-3430 Tulln, Austria; (M.S.); (R.K.)
| | - Rudolf Krska
- Institute of Bioanalytics and Agro-Metabolomics, Department of Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna Konrad Lorenzstr. 20, A-3430 Tulln, Austria; (M.S.); (R.K.)
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, University Road, Belfast BT7 1NN, UK
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8
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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
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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Pandian BA, Sexton-Bowser S, Prasad PV, Jugulam M. Current status and prospects of herbicide-resistant grain sorghum (Sorghum bicolor). PEST MANAGEMENT SCIENCE 2022; 78:409-415. [PMID: 34532972 DOI: 10.1002/ps.6644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Grain sorghum is a versatile crop, which can thrive under limited water and other inputs. However, crop loss from weed infestation continues to be a major constraint in grain sorghum production. Particularly, post-emergence grass weed control is a great challenge in grain sorghum due to the lack of herbicide options. Unlike in other major crops, such as maize or soybean, herbicide-resistant sorghum technology that can facilitate weed control throughout crop growing season is not available to growers yet. The development of herbicide-resistant sorghum can have potential to improve weed management, including post-emergence grass weed control. One of the major concerns in the development of such technology in sorghum is escape of resistance traits into weedy relatives of sorghum (e.g. shattercane and johnsongrass). This review focuses on sources of herbicide resistance in sorghum, the status of the development of herbicide-resistant sorghum technologies, overview of breeding methods, and limitations in the development of such sorghum technology as well as economic benefits for sorghum growers. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Balaji A Pandian
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | | | - Pv Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, USA
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
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10
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Silva TN, Thomas JB, Dahlberg J, Rhee SY, Mortimer JC. Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:646-664. [PMID: 34644381 PMCID: PMC8793871 DOI: 10.1093/jxb/erab450] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/10/2021] [Indexed: 05/09/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.
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Affiliation(s)
- Tallyta N Silva
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jason B Thomas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Jeff Dahlberg
- Joint BioEnergy Institute, Emeryville, CA, USA
- UC-ANR-KARE, 9240 S. Riverbend Ave, Parlier, CA, USA
| | - Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
- Correspondence: or
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, SA, Australia
- Correspondence: or
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11
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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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12
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Mengistu G, Shimelis H, Assefa E, Lule D. Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]. PLoS One 2021; 16:e0261461. [PMID: 34929013 PMCID: PMC8687563 DOI: 10.1371/journal.pone.0261461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.
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Affiliation(s)
- Girma Mengistu
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
- * E-mail:
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Ermias Assefa
- Ethiopian Biotechnology Institute, Bioinformatics and Genomics Research Directorate (BGRD), Addis Ababa, Ethiopia
| | - Dagnachew Lule
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
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13
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Xin Z, Wang M, Cuevas HE, Chen J, Harrison M, Pugh NA, Morris G. Sorghum genetic, genomic, and breeding resources. PLANTA 2021; 254:114. [PMID: 34739592 PMCID: PMC8571242 DOI: 10.1007/s00425-021-03742-w] [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: 04/16/2021] [Accepted: 09/28/2021] [Indexed: 05/24/2023]
Abstract
Sorghum research has entered an exciting and fruitful era due to the genetic, genomic, and breeding resources that are now available to researchers and plant breeders. As the world faces the challenges of a rising population and a changing global climate, new agricultural solutions will need to be developed to address the food and fiber needs of the future. To that end, sorghum will be an invaluable crop species as it is a stress-resistant C4 plant that is well adapted for semi-arid and arid regions. Sorghum has already remained as a staple food crop in many parts of Africa and Asia and is critically important for animal feed and niche culinary applications in other regions, such as the United States. In addition, sorghum has begun to be developed into a promising feedstock for forage and bioenergy production. Due to this increasing demand for sorghum and its potential to address these needs, the continuous development of powerful community resources is required. These resources include vast collections of sorghum germplasm, high-quality reference genome sequences, sorghum association panels for genome-wide association studies of traits involved in food and bioenergy production, mutant populations for rapid discovery of causative genes for phenotypes relevant to sorghum improvement, gene expression atlas, and online databases that integrate all resources and provide the sorghum community with tools that can be used in breeding and genomic studies. Used in tandem, these valuable resources will ensure that the rate, quality, and collaborative potential of ongoing sorghum improvement efforts is able to rival that of other major crops.
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA.
| | - Mingli Wang
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - Hugo E Cuevas
- Tropical Agriculture Research Station, USDA-ARS, Mayagüez, 00680, Puerto Rico
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Melanie Harrison
- Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA, 30223, USA
| | - N Ace Pugh
- Plant Stress and Germplasm Development Unit, Crop Systems Research Laboratory, USDA-ARS, 3810, 4th Street, Lubbock, TX, 79424, USA
| | - Geoffrey Morris
- Crop Quantitative Genomics, Soil and Crop Sciences, Colorado State University, Plant Sciences Building, Fort Collins, CO, 80523, USA
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14
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Cuevas HE, Cruet-Burgos CM, Prom LK, Knoll JE, Stutts LR, Vermerris W. The inheritance of anthracnose (Colletotrichum sublineola) resistance in sorghum differential lines QL3 and IS18760. Sci Rep 2021; 11:20525. [PMID: 34654899 PMCID: PMC8519964 DOI: 10.1038/s41598-021-99994-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 10/05/2021] [Indexed: 01/10/2023] Open
Abstract
Anthracnose caused by the fungal pathogen C. sublineola is an economically important constraint on worldwide sorghum production. The most effective strategy to safeguard yield is through the introgression of resistance alleles. This requires elucidation of the genetic basis of the different resistance sources that have been identified. In this study, 223 recombinant inbred lines (RILs) derived from crossing anthracnose-differentials QL3 (96 RILs) and IS18760 (127 RILs) with the common susceptible parent PI609251 were evaluated at four field locations in the United States (Florida, Georgia, Texas, and Puerto Rico) for their anthracnose resistance response. Both RIL populations were highly susceptible to anthracnose in Florida and Georgia, while in Puerto Rico and Texas they were segregating for anthracnose resistance response. A genome scan using a composite linkage map of 982 single nucleotide polymorphisms (SNPs) detected two genomic regions of 4.31 and 0.85 Mb on chromosomes 4 and 8, respectively, that explained 10–27% of the phenotypic variation in Texas and Puerto Rico. In parallel, a subset of 43 RILs that contained 67% of the recombination events were evaluated against anthracnose pathotypes from Arkansas (2), Puerto Rico (2) and Texas (4) in the greenhouse. A genome scan showed that the 7.57 Mb region at the distal end of the short arm of chromosome 5 is associated with the resistance response against the pathotype AMP-048 from Arkansas. Comparative analysis identified the genomic region on chromosome 4 overlaps with an anthracnose resistance locus identified in another anthracnose-differential line, SC414-12E, indicating this genomic region is of interest for introgression in susceptible sorghum germplasm. Candidate gene analysis for the resistance locus on chromosome 5 identified an R-gene cluster that has high similarity to another R-gene cluster associated with anthracnose resistance on chromosome 9.
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Affiliation(s)
- Hugo E Cuevas
- USDA-Agricultural Research Service-Tropical Agriculture Research Station, Mayagüez, Puerto Rico.
| | - Clara M Cruet-Burgos
- USDA-Agricultural Research Service-Tropical Agriculture Research Station, Mayagüez, Puerto Rico.,Department of Biology, University of Puerto Rico-Mayaguez Campus, Mayagüez, Puerto Rico
| | - Louis K Prom
- USDA-Agricultural Research Service-Southern Plains Agriculture Research Center, College Station, TX, USA
| | - Joseph E Knoll
- USDA-Agricultural Research Service, Crop Genetics and Breeding Research, Tifton, GA, USA
| | - Lauren R Stutts
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, USA
| | - Wilfred Vermerris
- Department of Microbiology and Cell Science, UF Genetics Institute, and Florida Center for Renewable Fuels and Chemicals, University of Florida, Gainesville, FL, USA
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15
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Ahn E, Prom LK, Hu Z, Odvody G, Magill C. Genome-wide association analysis for response of Senegalese sorghum accessions to Texas isolates of anthracnose. THE PLANT GENOME 2021; 14:e20097. [PMID: 33900689 DOI: 10.1002/tpg2.20097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
Anthracnose disease of sorghum is caused by Colletotrichum sublineola, a filamentous fungus. The genetic basis of resistance to anthracnose in sorghum is largely unclear, especially in Senegalese sorghum germplasm. In this study, 163 Senegalese sorghum accessions were evaluated for response to C. sublineola, and a genome-wide association study (GWAS) was performed to identify genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Germplasm diversity analysis showed low genetic diversity and slow linkage disequilibrium (LD) decay among the Senegalese accessions. Phenotypic analysis resulted in relatively low differences to C. sublineola among the tested population. Genome-wide association study did not identify any significant association based on a strict threshold for the number of SNPs available. However, individual analysis of the top eight SNPs associated with relative susceptibility and resistance identified candidate genes that have been shown to play important roles in plant stress tolerance in previous studies. This study identifies sorghum genes whose annotated properties have known roles in host defense and thus identify them as candidates for use in breeding for resistance to anthracnose.
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Affiliation(s)
- Ezekiel Ahn
- Dep. of Plant Pathology & Microbiology, Texas A&M Univ., College Station, TX, 77843, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
| | - Zhenbin Hu
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, TX, 78406, USA
| | - Clint Magill
- Dep. of Plant Pathology & Microbiology, Texas A&M Univ., College Station, TX, 77843, USA
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16
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Ackerman A, Wenndt A, Boyles R. The Sorghum Grain Mold Disease Complex: Pathogens, Host Responses, and the Bioactive Metabolites at Play. FRONTIERS IN PLANT SCIENCE 2021; 12:660171. [PMID: 34122480 PMCID: PMC8192977 DOI: 10.3389/fpls.2021.660171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Grain mold is a major concern in sorghum [Sorghum bicolor (L.) Moench] production systems, threatening grain quality, safety, and nutritional value as both human food and livestock feed. The crop's nutritional value, environmental resilience, and economic promise poise sorghum for increased acreage, especially in light of the growing pressures of climate change on global food systems. In order to fully take advantage of this potential, sorghum improvement efforts and production systems must be proactive in managing the sorghum grain mold disease complex, which not only jeopardizes agricultural productivity and profitability, but is also the culprit of harmful mycotoxins that warrant substantial public health concern. The robust scholarly literature from the 1980s to the early 2000s yielded valuable insights and key comprehensive reviews of the grain mold disease complex. Nevertheless, there remains a substantial gap in understanding the complex multi-organismal dynamics that underpin the plant-pathogen interactions involved - a gap that must be filled in order to deliver improved germplasm that is not only capable of withstanding the pressures of climate change, but also wields robust resistance to disease and mycotoxin accumulation. The present review seeks to provide an updated perspective of the sorghum grain mold disease complex, bolstered by recent advances in the understanding of the genetic and the biochemical interactions among the fungal pathogens, their corresponding mycotoxins, and the sorghum host. Critical components of the sorghum grain mold disease complex are summarized in narrative format to consolidate a collection of important concepts: (1) the current state of sorghum grain mold in research and production systems; (2) overview of the individual pathogens that contribute to the grain mold complex; (3) the mycotoxin-producing potential of these pathogens on sorghum and other substrates; and (4) a systems biology approach to the understanding of host responses.
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Affiliation(s)
- Arlyn Ackerman
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
| | - Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, The School of Integrated Plant Sciences, Cornell University, Ithaca, NY, United States
| | - Richard Boyles
- Cereal Grains Breeding and Genetics, Pee Dee Research and Education Center, Department of Plant & Environmental Sciences, Clemson University, Florence, SC, United States
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18
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Wondimu Z, Dong H, Paterson AH, Worku W, Bantte K. Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm. G3-GENES GENOMES GENETICS 2021; 11:6237486. [PMID: 33871028 PMCID: PMC8495740 DOI: 10.1093/g3journal/jkab087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/07/2021] [Indexed: 11/17/2022]
Abstract
Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.
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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, Georgia 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
| | - Walelign Worku
- College of Agriculture, Hawassa University, PO Box 05, Hawassa, Ethiopia
| | - Kassahun Bantte
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
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19
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Ruperao P, Thirunavukkarasu N, Gandham P, Selvanayagam S, Govindaraj M, Nebie B, Manyasa E, Gupta R, Das RR, Odeny DA, Gandhi H, Edwards D, Deshpande SP, Rathore A. Sorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain. FRONTIERS IN PLANT SCIENCE 2021; 12:666342. [PMID: 34140962 PMCID: PMC8204017 DOI: 10.3389/fpls.2021.666342] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.
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Affiliation(s)
- Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | - Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | | | | | - Baloua Nebie
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, Mali
| | - Eric Manyasa
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Roma Rani Das
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - Damaris A. Odeny
- Sorghum Breeding Program, International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Harish Gandhi
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Santosh P. Deshpande
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- Santosh P. Deshpande
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- *Correspondence: Abhishek Rathore
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Abreha KB, Ortiz R, Carlsson AS, Geleta M. Understanding the Sorghum- Colletotrichum sublineola Interactions for Enhanced Host Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:641969. [PMID: 33959139 PMCID: PMC8093437 DOI: 10.3389/fpls.2021.641969] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/22/2021] [Indexed: 05/09/2023]
Abstract
Improving sorghum resistance is a sustainable method to reduce yield losses due to anthracnose, a devastating disease caused by Colletotrichum sublineola. Elucidating the molecular mechanisms of sorghum-C. sublineola interactions would help identify biomarkers for rapid and efficient identification of novel sources for host-plant resistance improvement, understanding the pathogen virulence, and facilitating resistance breeding. Despite concerted efforts to identify resistance sources, the knowledge about sorghum-anthracnose interactions remains scanty. Hence, in this review, we presented an overview of the current knowledge on the mechanisms of sorghum-C. sublineola molecular interactions, sources of resistance for sorghum breeding, quantitative trait loci (QTL), and major (R-) resistance gene sequences as well as defense-related genes associated with anthracnose resistance. We summarized current knowledge about C. sublineola populations and its virulence. Illustration of the sorghum-C. sublineola interaction model based on the current understanding is also provided. We highlighted the importance of genomic resources of both organisms for integrated omics research to unravel the key molecular components underpinning compatible and incompatible sorghum-anthracnose interactions. Furthermore, sorghum-breeding strategy employing rapid sorghum germplasm screening, systems biology, and molecular tools is presented.
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