1
|
Ahn E, Prom LK, Park S, Hu Z, Magill CW. Genome-Wide Association Analysis Uncovers Genes Associated with Resistance to Head Smut Pathotype 5 in Senegalese Sorghum Accessions. PLANTS (BASEL, SWITZERLAND) 2024; 13:977. [PMID: 38611506 PMCID: PMC11013943 DOI: 10.3390/plants13070977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
A newly documented pathotype 5 of the soil-borne fungus Sporisorium reilianum, causing head smut in sorghum, was tested against 153 unexplored Senegalese sorghum accessions. Among the 153 sorghum accessions tested, 63 (41%) exhibited complete resistance, showing no signs of infection by the fungus. The remaining 90 accessions (59%) displayed varying degrees of susceptibility. Sorghum responses against S. reilianum were explored to analyze the potential link with previously known seed morphology-related traits and new phenotype data from 59 lines for seed weight. A genome-wide association study (GWAS) screened 297,876 SNPs and identified highly significant associations (p < 1 × 10-5) with head smut resistance in sorghum. By mapping these significant SNPs to the reference genome, this study revealed 35 novel candidate defense genes potentially involved in disease resistance.
Collapse
Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA;
| | - Sunchung Park
- USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Zhenbin Hu
- USDA-ARS Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Clint W. Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77843, USA
| |
Collapse
|
2
|
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.
Collapse
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:
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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
|
7
|
Stutts LR, Vermerris W. Elucidating Anthracnose Resistance Mechanisms in Sorghum-A Review. PHYTOPATHOLOGY 2020; 110:1863-1876. [PMID: 33100146 DOI: 10.1094/phyto-04-20-0132-rvw] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sorghum (Sorghum bicolor) is the fifth most cultivated cereal crop in the world, traditionally providing food, feed, and fodder, but more recently also fermentable sugars for the production of renewable fuels and chemicals. The hemibiotrophic fungal pathogen Colletotrichum sublineola, the causal agent of anthracnose disease in sorghum, is prevalent in the warm and humid climates where much of the sorghum is cultivated and poses a serious threat to sorghum production. The use of anthracnose-resistant sorghum germplasm is the most environmentally and economically sustainable way to protect sorghum against this pathogen. Even though multiple anthracnose resistance loci have been mapped in diverse sorghum germplasm in recent years, the diversity in C. sublineola pathotypes at the local and regional levels means that these resistance genes are not equally effective in different areas of cultivation. This review summarizes the genetic and cytological data underlying sorghum's defense response and describes recent developments that will enable a better understanding of the interactions between sorghum and C. sublineola at the molecular level. This includes releases of the sorghum genome and the draft genome of C. sublineola, the use of next-generation sequencing technologies to identify gene expression networks activated in response to infection, and improvements in methodologies to validate resistance genes, notably virus-induced and transgenic gene silencing approaches.
Collapse
Affiliation(s)
- Lauren R Stutts
- Graduate Program in Plant Molecular & Cellular Biology, University of Florida, Gainesville, FL 32610
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science, UF Genetics Institute, and Florida Center for Renewable Fuels and Chemicals, University of Florida, Gainesville, FL 32610
| |
Collapse
|
8
|
Fu F, Girma G, Mengiste T. Global mRNA and microRNA expression dynamics in response to anthracnose infection in sorghum. BMC Genomics 2020; 21:760. [PMID: 33143636 PMCID: PMC7641857 DOI: 10.1186/s12864-020-07138-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Anthracnose is a damaging disease of sorghum caused by the fungal pathogen Colletotrichum sublineolum. Genome-wide mRNA and microRNA (miRNA) profiles of resistant and susceptible sorghum genotypes were studied to understand components of immune responses, and fungal induced miRNA and target gene networks. RESULTS A total of 18 mRNA and 12 miRNA libraries from resistant and susceptible sorghum lines were sequenced prior to and after inoculation with C. sublineolum. Significant differences in transcriptomes of the susceptible and resistant genotypes were observed with dispersion distance and hierarchical cluster tree analyses. Of the total 33,032 genes predicted in the sorghum genome, 19,593 were induced by C. sublineolum, and 15,512 were differentially expressed (DEGs) between the two genotypes. The resistant line was marked by significant reprogramming of the transcriptome at 24 h post inoculation (hpi), and a decrease at 48 hpi, whereas the susceptible line displayed continued changes in gene expression concordant with elevated fungal growth in the susceptible genotype. DEGs encode proteins implicated in diverse functions including photosynthesis, synthesis of tetrapyrrole, carbohydrate and secondary metabolism, immune signaling, and chitin binding. Genes encoding immune receptors, MAPKs, pentatricopeptide repeat proteins, and WRKY transcription factors were induced in the resistant genotype. In a parallel miRNA profiling, the susceptible line displayed greater number of differentially expressed miRNAs than the resistant line indicative of a widespread suppression of gene expression. Interestingly, we found 75 miRNAs, including 36 novel miRNAs, which were differentially expressed in response to fungal inoculation. The expression of 50 miRNAs was significantly different between resistant and susceptible lines. Subsequently, for 35 differentially expressed miRNAs, the corresponding 149 target genes were identified. Expression of 56 target genes were significantly altered after inoculation, showing inverse expression with the corresponding miRNAs. CONCLUSIONS We provide insights into genome wide dynamics of mRNA and miRNA profiles, biological and cellular processes underlying host responses to fungal infection in sorghum. Resistance is correlated with early transcriptional reprogramming of genes in various pathways. Fungal induced genes, miRNAs and their targets with a potential function in host responses to anthracnose were identified, opening avenues for genetic dissection of resistance mechanisms.
Collapse
Affiliation(s)
- Fuyou Fu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
- Present address: Agriculture and Agri-Food Canada, Plant Gene Resources of Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| |
Collapse
|
9
|
Elango D, Xue W, Chopra S. Genome wide association mapping of epi-cuticular wax genes in Sorghum bicolor. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1727-1737. [PMID: 32801499 PMCID: PMC7415066 DOI: 10.1007/s12298-020-00848-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 06/11/2020] [Accepted: 07/07/2020] [Indexed: 05/25/2023]
Abstract
Sorghum accumulates epi-cuticular wax (EW) in leaves, sheaths, and culms. EW reduces the transpirational and nontranspirational (nonstomatal) water loss and protects the plant from severe drought stress in addition to imparting resistance against insect pests. Results presented here are from the analysis of EW content of 387 diverse sorghum accessions and its genome-wide association study (GWAS). EW content in sorghum leaves ranged from 0.1 to 29.7 mg cm-2 with a mean value of 5.1 mg cm-2. GWAS using 265,487 single nucleotide polymorphisms identified thirty-seven putative genes associated (P < 9.89E-06) with EW biosynthesis and transport in sorghum. Major EW biosynthetic genes identified included 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, an Ankyrin repeat protein, a bHLH-MYC, and an R2R3-MYB transcription factor. Genes involved in EW regulation or transport included an ABC transporter, a Lipid exporter ABCA1, a Multidrug resistance protein, Inositol 1, 3, 4-trisphosphate 5/6-kinase, and a Cytochrome P450. This GWA study thus demonstrates the potential for genetic manipulation of EW content in sorghum for better adaptation to biotic and abiotic stress.
Collapse
Affiliation(s)
- Dinakaran Elango
- Department of Plant Science, Penn State University, University Park, PA USA
| | - Weiya Xue
- Department of Plant Science, Penn State University, University Park, PA USA
| | - Surinder Chopra
- Department of Plant Science, Penn State University, University Park, PA USA
| |
Collapse
|
10
|
Ahn E, Hu Z, Perumal R, Prom LK, Odvody G, Upadhyaya HD, Magill C. Genome wide association analysis of sorghum mini core lines regarding anthracnose, downy mildew, and head smut. PLoS One 2019; 14:e0216671. [PMID: 31086384 PMCID: PMC6516728 DOI: 10.1371/journal.pone.0216671] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/26/2019] [Indexed: 02/04/2023] Open
Abstract
In previous studies, a sorghum mini core collection was scored over several years for response to Colletotrichum sublineola, Peronosclerospora sorghi, and Sporisorium reilianum, the causal agents of the disease anthracnose, downy mildew, and head smut, respectively. The screening results were combined with over 290,000 Single nucleotide polymorphic (SNP) loci from an updated version of a publicly available genotype by sequencing (GBS) dataset available for the mini core collection. GAPIT (Genome Association and Prediction Integrated Tool) R package was used to identify chromosomal locations that differ in disease response. When the top scoring SNPs were mapped to the most recent version of the published sorghum genome, in each case, a nearby and most often the closest annotated gene has precedence for a role in host defense.
Collapse
Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Ramasamy Perumal
- Kansas State University, Agricultural Research Center, Hays, Kansas, United States of America
| | - Louis K. Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, Texas, United States of America
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, Texas, United States of America
| | - Hari D. Upadhyaya
- ICRISAT, Patancheru, Telangana, India
- King Abdulaziz University, Jeddah, Saudi Arabia
| | - Clint Magill
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, United States of America
| |
Collapse
|
11
|
Prom LK, Ahn E, Isakeit T, Magill C. GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1389-1396. [PMID: 30688991 DOI: 10.1007/s00122-019-03285-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
SNPs identify prospective genes related to response to Colletotrichum sublineola (anthracnose) in the sorghum association panel lines. Sorghum association panel (SAP) lines were scored over several years for response to Colletotrichum sublineola, the causal agent of the disease anthracnose. Known resistant and susceptible lines were included each year to verify successful inoculation. Over 79,000 single-nucleotide polymorphic (SNP) loci from a publicly available genotype by sequencing dataset available for the SAP lines were used with TASSEL association mapping software to identify chromosomal locations associated with differences in disease response. When the top-scoring SNPs were mapped to the published sorghum genome, in each case, the nearest annotated gene has precedence for a role in host defense.
Collapse
Affiliation(s)
- Louis K Prom
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA.
| | - Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| |
Collapse
|
12
|
Assis R. Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. Genome Biol Evol 2019; 11:207-219. [PMID: 30398650 PMCID: PMC6331041 DOI: 10.1093/gbe/evy245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 02/02/2023] Open
Abstract
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.
Collapse
Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park
| |
Collapse
|
13
|
Singh AK, Singh R, Subramani R, Kumar R, Wankhede DP. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals. Curr Genomics 2016; 17:177-92. [PMID: 27252585 PMCID: PMC4869005 DOI: 10.2174/1389202917666160202215308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023] Open
Abstract
Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.
Collapse
Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajkumar Subramani
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | | |
Collapse
|
14
|
Kulwal PL. Association Mapping and Genomic Selection—Where Does Sorghum Stand? COMPENDIUM OF PLANT GENOMES 2016. [DOI: 10.1007/978-3-319-47789-3_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
15
|
Zhu Y, Yin Y, Yang K, Li J, Sang Y, Huang L, Fan S. Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.). BMC Genomics 2015; 16:614. [PMID: 26283231 PMCID: PMC4539690 DOI: 10.1186/s12864-015-1822-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 08/07/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. RESULTS SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. CONCLUSIONS High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.
Collapse
Affiliation(s)
- Yufeng Zhu
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Yanfei Yin
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Keqiang Yang
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Jihong Li
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Yalin Sang
- College of Forestry, Shandong Agricultural University, No.61 Daizong Load, Taian, Shandong Provence, 271018, P. R. China.
| | - Long Huang
- Biomarker Technologies Corporation, Beijing, P. R. China.
| | - Shu Fan
- Biomarker Technologies Corporation, Beijing, P. R. China.
| |
Collapse
|
16
|
Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of stress tolerance. Food Energy Secur 2015. [DOI: 10.1002/fes3.54] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- 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
| |
Collapse
|
17
|
Mace E, Tai S, Innes D, Godwin I, Hu W, Campbell B, Gilding E, Cruickshank A, Prentis P, Wang J, Jordan D. The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes. BMC PLANT BIOLOGY 2014; 14:253. [PMID: 25928459 PMCID: PMC4189741 DOI: 10.1186/s12870-014-0253-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/20/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. RESULTS In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. CONCLUSIONS NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the "arms race" with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.
Collapse
Affiliation(s)
- Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | | | - David Innes
- DAFFQ, Cooper's Plains, Brisbane, QLD, Australia.
| | - Ian Godwin
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, Australia.
| | | | | | - Edward Gilding
- The Institute of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Peter Prentis
- Queensland University of Technology, Brisbane, QLD, Australia.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
| |
Collapse
|