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Birhanu C, Girma G, Mekbib F, Nida H, Tirfessa A, Lule D, Bekeko Z, Ayana G, Bejiga T, Bedada G, Tola M, Legesse T, Alemu H, Admasu S, Bekele A, Mengiste T. Exploring the genetic basis of anthracnose resistance in Ethiopian sorghum through a genome-wide association study. BMC Genomics 2024; 25:677. [PMID: 38977981 PMCID: PMC11229211 DOI: 10.1186/s12864-024-10545-2] [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: 03/21/2024] [Accepted: 06/20/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Sorghum anthracnose is a major disease that hampers the productivity of the crop globally. The disease is caused by the hemibiotrophic fungal pathogen Colletotrichum sublineola. The identification of anthracnose-resistant sorghum genotypes, defining resistance loci and the underlying genes, and their introgression into adapted cultivars are crucial for enhancing productivity. In this study, we conducted field experiments on 358 diverse accessions of Ethiopian sorghum. Quantitative resistance to anthracnose was evaluated at locations characterized by a heavy natural infestation that is suitable for disease resistance screening. RESULTS The field-based screening identified 53 accessions that were resistant across locations, while 213 accessions exhibited variable resistance against local pathotypes. Genome-wide association analysis (GWAS) was performed using disease response scores on 329 accessions and 83,861 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS). We identified 38 loci significantly associated with anthracnose resistance. Interestingly, a subset of these loci harbor genes encoding receptor-like kinases (RLK), nucleotide-binding leucine-rich repeats (NLRs), stress-induced antifungal tyrosine kinase that have been previously implicated in disease resistance. A SNP on chromosome 4 (S04_66140995) and two SNPs on chromosome 2 (S02_75784037, S02_2031925), localized with-in the coding region of genes that encode a putative stress-induced antifungal kinase, an F-Box protein, and Xa21-binding RLK that were strongly associated with anthracnose resistance. We also identified highly significant associations between anthracnose resistance and three SNPs linked to genes (Sobic.002G058400, Sobic.008G156600, Sobic.005G033400) encoding an orthologue of the widely known NLR protein (RPM1), Leucine Rich Repeat family protein, and Heavy Metal Associated domain-containing protein, respectively. Other SNPs linked to predicted immune response genes were also significantly associated with anthracnose resistance. CONCLUSIONS The sorghum germplasm collections used in the present study are genetically diverse. They harbor potentially useful, yet undiscovered, alleles for anthracnose resistance. This is supported by the identification of novel loci that are enriched for disease resistance regulators such as NLRs, LRKs, Xa21-binding LRK, and antifungal proteins. The genotypic data available for these accessions offer a valuable resource for sorghum breeders to effectively improve the crop. The genomic regions and candidate genes identified can be used to design markers for molecular breeding of sorghum diseases resistance.
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Affiliation(s)
- Chemeda Birhanu
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Firew Mekbib
- Haramaya University, P.O. Box 138, Dire Dawa, Ethiopia
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Alemu Tirfessa
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Dagnachew Lule
- Agricultural Transformation Institute, P.O. Box 708, Addis Ababa, Ethiopia
| | | | - Getachew Ayana
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Tamirat Bejiga
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Gudeta Bedada
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Meseret Tola
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Tokuma Legesse
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Habtamu Alemu
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Solomon Admasu
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | | | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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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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Sun X, Li A, Ma G, Zhao S, Liu L. Transcriptome analysis provides insights into the bases of salicylic acid-induced resistance to anthracnose in sorghum. PLANT MOLECULAR BIOLOGY 2022; 110:69-80. [PMID: 35793006 DOI: 10.1007/s11103-022-01286-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Key Message Transcriptome analysis of SA sensitive and tolerant lines indicates that SA enhances anthracnose resistance in sorghum by upregulating the expression of some immune-related genes and pathways.Abstract Anthracnose caused by the hemibiotrophic pathogen Colletotrichum sublineolum is one of the most destructive diseases of sorghum, the fifth most important cereal crop in the world. Salicylic acid (SA) is a phytohormone essential for plant immunity; however, the role of SA in sorghum resistance to anthracnose has not been well explored. In this study, we found that Colletotrichum sublineolum infection induced the expression of SA-responsive genes and that exogenous SA enhanced resistance to anthracnose in the sorghum line BTx623. To rule out the possibility that SA triggers anthracnose resistance in sorghum by its direct toxic function on pathogen, an SA-tolerant line, WHEATLAND, was identified, and we found that SA treatment could not induce anthracnose resistance in WHEATLAND. Then, SA-induced transcriptome changes during Colletotrichum sublineolum infection in BTx623 and WHEATLAND were analyzed to explore the molecular mechanism of SA-triggered resistance. SA pretreatment regulated the expression of 2125 genes in BTx623 but only 524 genes in WHEATLAND during Colletotrichum sublineolum infection. The cutin, suberine and wax biosynthesis pathway involved in the plant immune response and the flavonoid biosynthesis pathway involved in anthracnose resistance were enriched in BTx623-specifically upregulated genes. Additionally, some immune-related genes, including multiple resistance genes, were differentially expressed in BTx623 and WHEATLAND. Taken together, our results revealed the mechanisms of SA-induced anthracnose resistance in sorghum at the transcriptional level and shed light on the possibility of enhancing sorghum resistance to anthracnose by activating the SA signaling pathway by molecular breeding.
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Affiliation(s)
- Xue Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Aixia Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Guojing Ma
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Shuangyi Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Lijing Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China.
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