1
|
Vela S, Wolf ESA, Rollins JA, Cuevas HE, Vermerris W. Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola. FRONTIERS IN FUNGAL BIOLOGY 2024; 5:1437344. [PMID: 39220294 PMCID: PMC11362643 DOI: 10.3389/ffunb.2024.1437344] [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: 05/23/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024]
Abstract
In warm and humid regions, the productivity of sorghum is significantly limited by the fungal hemibiotrophic pathogen Colletotrichum sublineola, the causal agent of anthracnose, a problematic disease of sorghum (Sorghum bicolor (L.) Moench) that can result in grain and biomass yield losses of up to 50%. Despite available genomic resources of both the host and fungal pathogen, the molecular basis of sorghum-C. sublineola interactions are poorly understood. By employing a dual-RNA sequencing approach, the molecular crosstalk between sorghum and C. sublineola can be elucidated. In this study, we examined the transcriptomes of four resistant sorghum accessions from the sorghum association panel (SAP) at varying time points post-infection with C. sublineola. Approximately 0.3% and 93% of the reads mapped to the genomes of C. sublineola and Sorghum bicolor, respectively. Expression profiling of in vitro versus in planta C. sublineola at 1-, 3-, and 5-days post-infection (dpi) indicated that genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), and membrane transporters increased in expression during the transition from the biotrophic to the necrotrophic phase (3 dpi). The hallmark of the pathogen-associated molecular pattern (PAMP)-triggered immunity in sorghum includes the production of reactive oxygen species (ROS) and phytoalexins. The majority of effector candidates secreted by C. sublineola were predicted to be localized in the host apoplast, where they could interfere with the PAMP-triggered immunity response, specifically in the host ROS signaling pathway. The genes encoding critical molecular factors influencing pathogenicity identified in this study are a useful resource for subsequent genetic experiments aimed at validating their contributions to pathogen virulence. This comprehensive study not only provides a better understanding of the biology of C. sublineola but also supports the long-term goal of developing resistant sorghum cultivars.
Collapse
Affiliation(s)
- Saddie Vela
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Emily S. A. Wolf
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
| | - Jeffrey A. Rollins
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Hugo E. Cuevas
- United States Department of Agriculture, Agricultural Research Service, Tropical Agriculture Research Station, Mayagüez, PR, United States
| | - Wilfred Vermerris
- Plant Molecular & Cellular Biology Graduate Program, University of Florida, Gainesville, FL, United States
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, Gainesville, FL, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Wolf ESA, Vela S, Cuevas HE, Vermerris W. A Sorghum F-Box Protein Induces an Oxidative Burst in the Defense Against Colletotrichum sublineola. PHYTOPATHOLOGY 2024; 114:405-417. [PMID: 37717251 DOI: 10.1094/phyto-06-23-0184-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The hemibiotrophic fungal pathogen Colletotrichum sublineola is the causal agent of anthracnose in sorghum (Sorghum bicolor), resulting in leaf blight, stalk rot, and head blight in susceptible genotypes, with yield losses of up to 50%. The development of anthracnose-resistant cultivars can reduce reliance on fungicides and provide a more sustainable and economical means for disease management. A previous genome-wide association study of the sorghum association panel identified the candidate resistance gene Sobic.005G172300 encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum accession SC110, which harbored the resistance allele, and three accessions that harbored a susceptible allele. Only in SC110 did the expression of Sobic.005G172300 increase during the biotrophic phase of infection. Subsequent transcriptome analysis, gene co-expression networks, and gene regulatory networks of inoculated and mock-inoculated seedlings of resistant and susceptible accessions suggest that the increase in expression of Sobic.005G172300 induces an oxidative burst by lowering the concentration of ascorbic acid during the biotrophic phase of infection. Based on gene regulatory network analysis, the protein encoded by Sobic.005G172300 is proposed to target proteins involved in the biosynthesis of ascorbic acid for polyubiquitination through the SCF E3 ubiquitin ligase, causing their degradation via the proteasome.
Collapse
Affiliation(s)
- Emily S A Wolf
- Plant Molecular & Cellular Biology graduate program, University of Florida, Gainesville, FL 32611
| | - Saddie Vela
- Plant Molecular & Cellular Biology graduate program, University of Florida, Gainesville, FL 32611
| | - Hugo E Cuevas
- U.S. Department of Agriculture-Agricultural Research Service, Tropical Agriculture Research Station, Mayagüez, PR 00680
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, University of Florida, Gainesville, FL 32611
- University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611
| |
Collapse
|
4
|
Zou X, Zhang J, Cheng T, Guo Y, Zhang L, Han X, Liu C, Wan Y, Ye X, Cao X, Song C, Zhao G, Xiang D. New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health. FRONTIERS IN PLANT SCIENCE 2023; 14:1301445. [PMID: 38107010 PMCID: PMC10722300 DOI: 10.3389/fpls.2023.1301445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/19/2023]
Abstract
As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.
Collapse
Affiliation(s)
- Xin Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Jieyu Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Ting Cheng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yangyang Guo
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Li Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiao Han
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xiaoning Cao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Chao Song
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gang Zhao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| |
Collapse
|
5
|
La Borde N, Rajewski J, Dweikat I. Novel QTL for chilling tolerance at germination and early seedling stages in sorghum. Front Genet 2023; 14:1129460. [PMID: 37007950 PMCID: PMC10052408 DOI: 10.3389/fgene.2023.1129460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Sorghum (Sorghum bicolor L.) a drought tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importanceorghum’s originated from tropical regions rendering the crop to be cold sensitive. Low temperature stresses such as chilling and frost greatly affect the agronomic performance of sorghum and limit its geographical distribution, posing a major problem in temperate environments when sorghum is planted early. Understanding the genetic basis of wide adaptability and of sorghum would facilitate molecular breeding programs and studies of other C4 crops. The objective of this study is to conduct quantitative trait loci analysis using genotying by sequencing for early seed germination and seedling cold tolerance in two sorghum recombinant inbred lines populations. To accomplish that, we used two populations of recombinant inbred lines (RIL) developed from crosses between cold-tolerant (CT19, ICSV700) and cold-sensitive (TX430, M81E) parents. The derived RIL populations were evaluated for single nucleotide polymorphism (SNP) using genotype-by-sequencing (GBS) in the field and under controlled environments for their response to chilling stress. Linkage maps were constructed with 464 and 875 SNPs for the CT19 X TX430 (C1) and ICSV700 X M81 E (C2) populations respectively. Using quantitative trait loci (QTL) mapping, we identified QTL conferring tolerance to chilling tolerance at the seedling stage. A total of 16 and 39 total QTL were identified in the C1 and C2 populations, respectively. Two major QTL were identified in the C1 population, and three major QTL were mapped in the C2 population. Comparisons between the two populations and with previously identified QTL show a high degree of similarity in QTL locations. Given the amount of co-localization of QTL across traits and the direction of allelic effect supports that these regions have a pleiotropic effect. These QTL regions were also identified to be highly enriched for genes encoding chilling stress and hormonal response genes. This identified QTL can be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.
Collapse
|
6
|
Mewa DB, Lee S, Liao C, Adeyanju A, Helm M, Lisch D, Mengiste T. ANTHRACNOSE RESISTANCE GENE2 confers fungal resistance in sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:308-326. [PMID: 36441009 PMCID: PMC10108161 DOI: 10.1111/tpj.16048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
Sorghum is an important food and feed crop globally; its production is hampered by anthracnose disease caused by the fungal pathogen Colletotrichum sublineola (Cs). Here, we report identification and characterization of ANTHRACNOSE RESISTANCE GENE 2 (ARG2) encoding a nucleotide-binding leucine-rich repeat (NLR) protein that confers race-specific resistance to Cs strains. ARG2 is one of a cluster of several NLR genes initially identified in the sorghum differential line SC328C that is resistant to some Cs strains. This cluster shows structural and copy number variations in different sorghum genotypes. Different sorghum lines carrying independent ARG2 alleles provided the genetic validation for the identity of the ARG2 gene. ARG2 expression is induced by Cs, and chitin induces ARG2 expression in resistant but not in susceptible lines. ARG2-mediated resistance is accompanied by higher expression of defense and secondary metabolite genes at early stages of infection, and anthocyanin and zeatin metabolisms are upregulated in resistant plants. Interestingly, ARG2 localizes to the plasma membrane when transiently expressed in Nicotiana benthamiana. Importantly, ARG2 plants produced higher shoot dry matter than near-isogenic lines carrying the susceptible allele suggesting an absence of an ARG2 associated growth trade-off. Furthermore, ARG2-mediated resistance is stable at a wide range of temperatures. Our observations open avenues for resistance breeding and for dissecting mechanisms of resistance.
Collapse
Affiliation(s)
- Demeke B. Mewa
- Department of Botany and Plant Pathology, Purdue University915 W. State St.West LafayetteIN47907USA
| | - Sanghun Lee
- Department of Botany and Plant Pathology, Purdue University915 W. State St.West LafayetteIN47907USA
| | - Chao‐Jan Liao
- Department of Botany and Plant Pathology, Purdue University915 W. State St.West LafayetteIN47907USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University915 W. State St.West LafayetteIN47907USA
| | - Matthew Helm
- United States Department of Agriculture, Agricultural Research Service, Crop Production and Pest Control Research UnitWest LafayetteIN47907USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University915 W. State St.West LafayetteIN47907USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University915 W. State St.West LafayetteIN47907USA
| |
Collapse
|
7
|
Lee S, Fu F, Liao CJ, Mewa DB, Adeyanju A, Ejeta G, Lisch D, Mengiste T. Broad-spectrum fungal resistance in sorghum is conferred through the complex regulation of an immune receptor gene embedded in a natural antisense transcript. THE PLANT CELL 2022; 34:1641-1665. [PMID: 35018449 PMCID: PMC9048912 DOI: 10.1093/plcell/koab305] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 06/12/2023]
Abstract
Sorghum (Sorghum bicolor), the fifth most widely grown cereal crop globally, provides food security for millions of people. Anthracnose caused by the fungus Colletotrichum sublineola is a major disease of sorghum worldwide. We discovered a major fungal resistance locus in sorghum composed of the nucleotide-binding leucine-rich repeat receptor gene ANTHRACNOSE RESISTANCE GENE1 (ARG1) that is completely nested in an intron of a cis-natural antisense transcript (NAT) gene designated CARRIER OF ARG1 (CARG). Susceptible genotypes express CARG and two alternatively spliced ARG1 transcripts encoding truncated proteins lacking the leucine-rich repeat domains. In resistant genotypes, elevated expression of an intact allele of ARG1, attributed to the loss of CARG transcription and the presence of miniature inverted-repeat transposable element sequences, resulted in broad-spectrum resistance to fungal pathogens with distinct virulence strategies. Increased ARG1 expression in resistant genotypes is also associated with higher histone H3K4 and H3K36 methylation. In susceptible genotypes, lower ARG1 expression is associated with reduced H3K4 and H3K36 methylation and increased expression of NATs of CARG. The repressive chromatin state associated with H3K9me2 is low in CARG-expressing genotypes within the CARG exon and higher in genotypes with low CARG expression. Thus, ARG1 is regulated by multiple mechanisms and confers broad-spectrum, strong resistance to fungal pathogens.
Collapse
Affiliation(s)
| | | | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Demeke B Mewa
- 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
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | | |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
|
10
|
Genomic Dissection of Anthracnose ( Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14. G3-GENES GENOMES GENETICS 2020; 10:1403-1412. [PMID: 32102832 PMCID: PMC7144069 DOI: 10.1534/g3.120.401121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.
Collapse
|
11
|
Cuevas HE, Prom LK. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection. BMC Genomics 2020; 21:88. [PMID: 31992189 PMCID: PMC6988227 DOI: 10.1186/s12864-020-6489-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
Background The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. Results We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. Conclusions The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.
Collapse
Affiliation(s)
- Hugo E Cuevas
- USDA-ARS, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Avenue, Mayaguez, 00680, Puerto Rico
| | - Louis K Prom
- USDA-ARS, Southern Plains Agriculture Research Center, College Station, TX, 77845, USA.
| |
Collapse
|
12
|
Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm. G3-GENES GENOMES GENETICS 2019; 9:2879-2885. [PMID: 31289022 PMCID: PMC6723129 DOI: 10.1534/g3.119.400350] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The National Plant Germplasm System (NPGS) Ethiopian sorghum [Sorghum bicolor (L.) Moench] collection of the United States is an important genetic resource for sorghum improvement. Anthracnose (Colletotrichum sublineolum) is one of the most harmful fungal diseases in humid sorghum production regions. Although multiple resistance sources have been identified in temperate-adapted germplasm in the Sorghum Association Panel (SAP), these resistance loci explain a limited portion of the total variation, and sources of resistance from tropical germplasm are not available for breeding programs at temperate regions. Using a core set of 335 previously genotyped NPGS Ethiopian accessions, we identified 169 accessions resistant to anthracnose. To identify resistance loci, we merged the genotypic and anthracnose response data for both NPGS Ethiopian germplasm and the SAP and performed genome-wide association scans using 219,037 single nucleotide polymorphisms and 617 accessions. The integrated data set enabled the detection of a locus on chromosome 9 present in the SAP at a low frequency. The locus explains a limited portion of the observed phenotypic variation (r2 = 0.31), suggesting the presence of other resistance loci. The locus in chromosome 9 was constituted by three R genes clustered within a 47-kb region. The presence of multiple sources of resistance in NPGS Ethiopian germplasm and SAP requires the inclusion of other resistance response evaluation that could revealed others low frequency resistance alleles in the panel.
Collapse
|
13
|
Hu Z, Olatoye MO, Marla S, Morris GP. An Integrated Genotyping-by-Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes. THE PLANT GENOME 2019; 12:180044. [PMID: 30951089 DOI: 10.3835/plantgenome2018.06.0044] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mining crop genomic variation can facilitate the genetic research of complex traits and molecular breeding. In sorghum [ L. (Moench)], several large-scale single nucleotide polymorphism (SNP) datasets have been generated using genotyping-by-sequencing of KI reduced representation libraries. However, data reuse has been impeded by differences in reference genome coordinates among datasets. To facilitate reuse of these data, we constructed and characterized an integrated 459,304-SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome. The SNP distribution showed high enrichment in subtelomeric chromosome arms and in genic regions (48% of SNPs) and was highly correlated ( = 0.82) to the distribution of KI restriction sites. The genetic structure reflected population differences by botanical race, as well as familial structure among recombinant inbred lines (RILs). Faster linkage disequilibrium decay was observed in the diversity panel than in the RILs, as expected, given the greater opportunity for recombination in diverse populations. To validate the quality and utility of the integrated SNP dataset, we used genome-wide association studies (GWAS) of genebank phenotype data, precisely mapping several known genes (e.g and ) and identifying novel associations for other traits. We further validated the dataset with GWAS of new and published plant height and flowering time data in a nested association mapping population, precisely mapping known genes and identifying epistatic interactions underlying both traits. These findings validate this integrated SNP dataset as a useful genomics resource for sorghum genetics and breeding.
Collapse
|
14
|
Jang YJ, Seo M, Hersh CP, Rhee SJ, Kim Y, Lee GP. An evolutionarily conserved non-synonymous SNP in a leucine-rich repeat domain determines anthracnose resistance in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:473-488. [PMID: 30446794 DOI: 10.1007/s00122-018-3235-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
A non-synonymous SNP of CC-NBS-LRR was firstly mapped to confer resistance to anthracnose in watermelon. Newly proposed LRR domain harboring the SNP is evolutionary conserved in the Cucurbitaceae and Fabaceae. Anthracnose disease caused by Colletotrichum devastates many plants. Despite the importance of the disease, the mechanisms of resistance against it are poorly understood. Here, we identified a non-synonymous single-nucleotide polymorphism (SNP) located in a leucine-rich repeat domain as a marker for resistance to anthracnose race 1 in watermelon, using a combination of genetic analyses. We validated this SNP in segregating populations and 59 watermelon accessions using high-resolution melting assays and Sanger sequencing. We demonstrated that the resulting arginine-to-lysine substitution is particularly conserved among the Cucurbitaceae and Fabaceae. We identified a conserved motif, IxxLPxSxxxLYNLQTLxL, found in 1007 orthologues/paralogues from 89 plant species, and discovered that residue 18 of this motif could determine resistance to disease caused by external invaders. This study provides a step forward in understanding anthracnose resistance in watermelon, as well as functional and evolutionary insight into leucine-rich repeat proteins.
Collapse
Affiliation(s)
- Yoon Jeong Jang
- Department of Integrative Plant Science, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Minseok Seo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sun-Ju Rhee
- Department of Plant Sciences, The University of Cambridge, Cambridge, CB2 3EA, UK
| | - Yongjae Kim
- Partner Seeds Co., Ltd., Anseong, 17601, Republic of Korea
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Anseong, 17546, Republic of Korea.
| |
Collapse
|
15
|
Cuevas HE, Prom LK, Cooper EA, Knoll JE, Ni X. Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum) Resistance in the U.S. Sorghum Association Panel. THE PLANT GENOME 2018; 11:170099. [PMID: 30025025 DOI: 10.3835/plantgenome2017.11.0099] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The productivity and profitability of sorghum [ (L.) Moench] is reduced by susceptibility to fungal diseases, such as anthracnose ( P. Henn.). A limited number of resistant accessions are present in the temperate-adapted germplasm; other exotic sources of resistance are not currently available for breeding programs. Among 335 accessions available to breeders from a previously genotyped sorghum association panel (SAP), we found that 75 were resistant to anthracnose. A phylogenetic analysis of these accessions showed high genetic diversity and multiple resistance sources. Genome-wide association scans (GWAS) were conducted using 268,289 single-nucleotide polymorphisms to identify loci associated with anthracnose resistance. Using logistic regressions for binary measures of resistance responses, we identified three loci within a region on chromosome 5 that have been previously associated with three sources of anthracnose resistance. A GWAS limited to Caudatum germplasm identified an association with a region on chromosome 1 and with the same previous region on chromosome 5. Candidate genes within these loci were related to R-gene families, signaling cascades, and transcriptional reprogramming, suggesting that the resistance response is controlled by multiple defense mechanisms. The strategic integration of exotic resistant germplasm into the SAP is needed to identify additional rare resistance alleles via GWAS.
Collapse
|
16
|
Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
| |
Collapse
|
17
|
Lopez JR, Erickson JE, Munoz P, Saballos A, Felderhoff TJ, Vermerris W. QTLs Associated with Crown Root Angle, Stomatal Conductance, and Maturity in Sorghum. THE PLANT GENOME 2017; 10. [PMID: 28724080 DOI: 10.3835/plantgenome2016.04.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three factors that directly affect the water inputs in cropping systems are root architecture, length of the growing season, and stomatal conductance to water vapor (). Deeper-rooted cultivars will perform better under water-limited conditions because they can access water stored deeper in the soil profile. Reduced limits transpiration rate () and thus throughout the vegetative phase conserves water that may be used during grain filling in water-limited environments. Additionally, growing early-maturing varieties in regions that rely on soil-stored water is a key water management strategy. To further our understanding of the genetic basis underlying root depth, growing season length, and we conducted a quantitative trait locus (QTL) study. A QTL for crown root angle (a proxy for root depth) new to sorghum was identified in chromosome 3. For , a QTL in chromosome seven was identified. In a follow-up field study it was determined that the QTL for was associated with reduced but not with net carbon assimilation rate () or shoot biomass. No differences in guard-cell length or stomatal density were observed among the lines, leading to the conclusion that the observed differences in must be explained by partial stomatal closure. The well-studied maturity gene was identified in the QTL for maturity. The transgressive segregation of the population was explained by the possible interaction of with other loci. Finally, the most probable position of the genes underlying the QTLs and candidate genes were proposed.
Collapse
|
18
|
Bhadauria V, Ramsay L, Bett KE, Banniza S. QTL mapping reveals genetic determinants of fungal disease resistance in the wild lentil species Lens ervoides. Sci Rep 2017; 7:3231. [PMID: 28607439 PMCID: PMC5468239 DOI: 10.1038/s41598-017-03463-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 11/08/2022] Open
Abstract
Lens ervoides, a wild relative of lentil is an important source of allelic diversity for enhancing the genetic resistance of the cultivated species against economically important fungal diseases, such as anthracnose and Stemphylium blight caused by Colletotrichum lentis and Stemphylium botryosum, respectively. To unravel the genetic control underlying resistance to these fungal diseases, a recombinant inbred line (RIL) population (n = 94, F9) originating from a cross between two L. ervoides accessions, L01-827A and IG 72815, was genotyped on the Illumina HiSeq 2500 platform. A total of 289.07 million 100 bp paired-end reads were generated, giving an average 7.53-fold genomic coverage to the RILs and identifying 2,180 high-quality SNPs that assembled in 543 unique haplotypes. Seven linkage groups were resolved among haplotypes, equal to the haploid chromosome number in L. ervoides. The genetic map spanned a cumulative distance of 740.94 cM. Composite interval mapping revealed five QTLs with a significant association with resistance to C. lentis race 0, six QTLs for C. lentis race 1 resistance, and three QTLs for S. botryosum resistance. Taken together, the data obtained in the study reveal that the expression of resistance to fungal diseases in L. ervoides is a result of rearrangement of resistant alleles contributed by both parental accessions.
Collapse
Affiliation(s)
- Vijai Bhadauria
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
- Swift Current Research and Development Center, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - Larissa Ramsay
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Kirstin E Bett
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Sabine Banniza
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada.
| |
Collapse
|