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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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Ali S, Freire LGD, Rezende VT, Noman M, Ullah S, Abdullah, Badshah G, Afridi MS, Tonin FG, de Oliveira CAF. Occurrence of Mycotoxins in Foods: Unraveling the Knowledge Gaps on Their Persistence in Food Production Systems. Foods 2023; 12:4314. [PMID: 38231751 DOI: 10.3390/foods12234314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024] Open
Abstract
In this review, the intricate issue about the occurrence levels of mycotoxins in foods is discussed aiming to underline the main knowledge gaps on the persistence of these toxicants in the food production system. Mycotoxins have been a key challenge to the food industry, economic growth, and consumers' health. Despite a breadth of studies over the past decades, the persistence of mycotoxins in foods remain an overlooked concern that urges exploration. Therefore, we aimed to concisely underline the matter and provide possible biochemical and metabolic details that can be relevant to the food sector and overall public health. We also stress the application of computational modeling, high-throughput omics, and high-resolution imaging approaches, which can provide insights into the structural and physicochemical characteristics and the metabolic activities which occur in a stored cereal grain's embryo and endosperm and their relationship with storage fungi and mycotoxins on a cellular level. In addition, there is a need for extensive collaborative network and funding, which will play a key role in finding effective solutions against the persistence of mycotoxins at the genetic and molecular to metabolic levels in the food system.
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Affiliation(s)
- Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Lucas Gabriel Dionisio Freire
- Department of Food Engineering, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Vanessa Theodoro Rezende
- Faculty of Veterinary and Animal Science (FMVZ), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Muhammad Noman
- Plant Molecular Physiology, Department of Biology, Federal University of Lavras (UFLA), Lavras 37200-000, MG, Brazil
| | - Sana Ullah
- Department of Food Engineering, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Abdullah
- Department of Health and Biological Sciences, Abasyn University Peshawar (AUP), Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Gul Badshah
- Department of Chemistry, Federal University of Paraná (UFPR), Curitiba 81530-000, PR, Brazil
| | - Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras (UFLA), Lavras 37200-900, MG, Brazil
| | - Fernando Gustavo Tonin
- Department of Biosystems Engineering, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
| | - Carlos Augusto Fernandes de Oliveira
- Department of Food Engineering, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga 13635-900, SP, Brazil
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Yu T, Zhang J, Cao J, Li S, Cai Q, Li X, Li S, Li Y, He C, Ma X. Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize ( Zea maize L.) through a Genome-Wide Association Study. Curr Issues Mol Biol 2023; 45:9634-9655. [PMID: 38132448 PMCID: PMC10742315 DOI: 10.3390/cimb45120602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.
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Affiliation(s)
- Tao Yu
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jianguo Zhang
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jingsheng Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Shujun Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Quan Cai
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Xin Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Sinan Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Yunlong Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
| | - Changan He
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer 161000, China
| | - Xuena Ma
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.C.); (Q.C.); (X.L.); (X.M.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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Ayesiga SB, Rubaihayo P, Oloka BM, Dramadri IO, Sserumaga JP. Genome-wide association study and pathway analysis to decipher loci associated with Fusarium ear rot resistance in tropical maize germplasm. GENETIC RESOURCES AND CROP EVOLUTION 2023; 71:2435-2448. [PMID: 39026943 PMCID: PMC11252232 DOI: 10.1007/s10722-023-01793-4] [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: 08/04/2023] [Accepted: 10/25/2023] [Indexed: 07/20/2024]
Abstract
Breeding for host resistance is the most efficient and environmentally safe method to curb the spread of fusarium ear rot (FER). However, conventional breeding for resistance to FER is hampered by the complex polygenic nature of this trait, which is highly influenced by environmental conditions. This study aimed to identify genomic regions, single nucleotide polymorphisms (SNPs), and putative candidate genes associated with FER resistance as well as candidate metabolic pathways and pathway genes involved in it. A panel of 151 tropical inbred maize lines were used to assess the genetic architecture of FER resistance over two seasons. During the study period, seven SNPs associated with FER resistance were identified on chromosomes 1, 2, 4, 5, and 9, accounting for 4-11% of the phenotypic variance. These significant markers were annotated into four genes. Seven significant metabolic pathways involved in FER resistance were identified using the Pathway Association Study Tool, the most significant being the superpathway of the glyoxylate cycle. Overall, this study confirmed that resistance to FER is indeed a complex mechanism controlled by several small to medium-effect loci. Our findings may contribute to fast-tracking the efforts to develop disease-resistant maize lines through marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s10722-023-01793-4.
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Affiliation(s)
- Stella Bigirwa Ayesiga
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
- National Livestock Resources Research Institute, National Agricultural Research Organization, PO Box 5704, Kampala, Uganda
| | - Patrick Rubaihayo
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Bonny Michael Oloka
- Department of Horticultural Sciences, North Carolina State University, Raleigh, NC USA
| | - Isaac Ozinga Dramadri
- Department of Agricultural Production, College of Agriculture and Environmental Sciences, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Julius Pyton Sserumaga
- National Livestock Resources Research Institute, National Agricultural Research Organization, PO Box 5704, Kampala, Uganda
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Santiago R, Ramos AJ, Cao A, Malvar RA, Butrón A. Inbred Selection for Increased Resistance to Kernel Contamination with Fumonisins. Toxins (Basel) 2023; 15:444. [PMID: 37505713 PMCID: PMC10467120 DOI: 10.3390/toxins15070444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/27/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
In temperate world-wide regions, maize kernels are often infected with the fumonisin-producing fungus Fusarium verticillioides which poses food and feed threats to animals and humans. As maize breeding has been revealed as one of the main tools with which to reduce kernel contamination with fumonisins, a pedigree selection program for increased resistance to Fusarium ear rot (FER), a trait highly correlated with kernel fumonisin content, was initiated in 2014 with the aim of obtaining inbred lines (named EPFUM) with resistance to kernel contamination with fumonisins and adapted to our environmental conditions. The new released EPFUM inbreds, their parental inbreds, hybrids involving crosses of one or two EPFUM inbreds, as well as commercial hybrids were evaluated in the current study. The objectives were (i) to assess if inbreds released by that breeding program were significantly more resistant than their parental inbreds and (ii) to examine if hybrids derived from EPFUM inbreds could be competitive based on grain yield and resistance to FER and fumonisin contamination. Second-cycle inbreds obtained through this pedigree selection program did not significantly improve the levels of resistance to fumonisin contamination of their parental inbreds; however, most EPFUM hybrids showed significantly better resistance to FER and fumonisin contamination than commercial hybrids did. Although European flint materials seem to be the most promising reservoirs of alleles with favorable additive and/or dominance effects for resistance to kernel contamination with fumonisins, marketable new Reid × Lancaster hybrids have been detected as they combine high resistance and yields comparable to those exhibited by commercial hybrids. Moreover, the white kernel hybrid EPFUM-4 × EP116 exploits the genetic variability within the European flint germplasm and can be an alternative to dent hybrid cultivation because white flint grain can lead to higher market prices.
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Affiliation(s)
- Rogelio Santiago
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra, Spain; (R.S.); (A.C.); (R.A.M.)
| | - Antonio J. Ramos
- Applied Mycology Unit, Department of Food Technology, Engineering and Science, University of Lleida, Agrotecnio-CERCA Center, Av. Rovira Roure 191, 25198 Lleida, Spain;
| | - Ana Cao
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra, Spain; (R.S.); (A.C.); (R.A.M.)
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra, Spain; (R.S.); (A.C.); (R.A.M.)
| | - Ana Butrón
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra, Spain; (R.S.); (A.C.); (R.A.M.)
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Ma L, Yu Y, Li C, Wang P, Liu K, Ma W, Wang W, Fan Y, Xiong Z, Jiang T, Zhang J, Wang Z, Wang J, Zhang H, Bao Y. Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene Pb3 Encoding NLR Protein. Int J Mol Sci 2022; 23:ijms232214032. [PMID: 36430507 PMCID: PMC9698523 DOI: 10.3390/ijms232214032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Rice blast is a worldwide fungal disease that seriously affects the yield and quality of rice. Identification of resistance genes against rice blast disease is one of the effective ways to control this disease. However, panicle blast resistance genes, which are useful in the fields, have rarely been studied due to the difficulty in phenotypic identification and the environmental influences. Here, panicle blast resistance-3 (Pb3) was identified by a genome-wide association study (GWAS) based on the panicle blast resistance phenotypes of 230 Rice Diversity Panel I (RDP-I) accessions with 700,000 single-nucleotide polymorphism (SNP) markers. A total of 16 panicle blast resistance loci (PBRLs) within three years including one repeated locus PBRL3 located in chromosome 11 were identified. In addition, 7 genes in PBRL3 were identified as candidate genes by haplotype analysis, which showed significant differences between resistant and susceptible varieties. Among them, one nucleotide-binding domain and Leucine-rich Repeat (NLR) gene Pb3 was highly conserved in multiple resistant rice cultivars, and its expression was significantly induced after rice blast inoculation. Evolutionary analysis showed that Pb3 was a typical disease resistance gene containing coiled-coil, NB-ARC, and LRR domains. T-DNA insertion mutants and CRISPR lines of Pb3 showed significantly reduced panicle blast resistance. These results indicate that Pb3 is a panicle blast resistance gene and GWAS is a rapid method for identifying panicle blast resistance in rice.
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Affiliation(s)
- Lu Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yao Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Changqing Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Panting Wang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kunquan Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjing Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunxin Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziwei Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tingting Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingran Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhixue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongsheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongmei Bao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Akohoue F, Miedaner T. Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1050891. [PMID: 36388551 PMCID: PMC9662303 DOI: 10.3389/fpls.2022.1050891] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Fusarium (FER) and Gibberella ear rots (GER) are the two most devastating diseases of maize (Zea mays L.) which reduce yield and affect grain quality worldwide, especially by contamination with mycotoxins. Genetic improvement of host resistance to effectively tackle FER and GER diseases requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. We applied improved meta-analysis algorithms to re-analyze 224 QTL identified in 15 studies based on dense genome-wide single nucleotide polymorphisms (SNP) in order to identify meta-QTL (MQTL) and colocalized genomic loci for fumonisin (FUM) and deoxynivalenol (DON) accumulation, silk (SR) and kernel (KR) resistances of both FER and GER, kernel dry-down rate (KDD) and husk coverage (HC). A high-resolution genetic consensus map with 36,243 loci was constructed and enabled the projection of 164 of the 224 collected QTL. Candidate genes (CG) mining was performed within the most refined MQTL, and identified CG were cross-validated using publicly available transcriptomic data of maize under Fusarium graminearum infection. The meta-analysis revealed 40 MQTL, of which 29 were associated each with 2-5 FER- and/or GER-related traits. Twenty-eight of the 40 MQTL were common to both FER and GER resistances and 19 MQTL were common to silk and kernel resistances. Fourteen most refined MQTL on chromosomes 1, 2, 3, 4, 7 and 9 harbored a total of 2,272 CG. Cross-validation identified 59 of these CG as responsive to FER and/or GER diseases. MQTL ZmMQTL2.2, ZmMQTL9.2 and ZmMQTL9.4 harbored promising resistance genes, of which GRMZM2G011151 and GRMZM2G093092 were specific to the resistant line for both diseases and encoded "terpene synthase21 (tps21)" and "flavonoid O-methyltransferase2 (fomt2)", respectively. Our findings revealed stable refined MQTL harboring promising candidate genes for use in breeding programs for improving FER and GER resistances with reduced mycotoxin accumulation. These candidate genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted backcross breeding strategies.
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Cao A, de la Fuente M, Gesteiro N, Santiago R, Malvar RA, Butrón A. Genomics and Pathways Involved in Maize Resistance to Fusarium Ear Rot and Kernel Contamination With Fumonisins. FRONTIERS IN PLANT SCIENCE 2022; 13:866478. [PMID: 35586219 PMCID: PMC9108495 DOI: 10.3389/fpls.2022.866478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Fusarium verticillioides is a causal agent of maize ear rot and produces fumonisins, which are mycotoxins that are toxic to animals and humans. In this study, quantitative trait loci (QTLs) and bulk-segregant RNA-seq approaches were used to uncover genomic regions and pathways involved in resistance to Fusarium ear rot (FER) and to fumonisin accumulation in maize kernels. Genomic regions at bins 4.07-4.1, 6-6.01, 6.04-6.05, and 8.05-8.08 were related to FER resistance and/or reduced fumonisin levels in kernels. A comparison of transcriptomes between resistant and susceptible inbred bulks 10 days after inoculation with F. verticillioides revealed 364 differentially expressed genes (DEGs). In the resistant inbred bulks, genes involved in sink metabolic processes such as fatty acid and starch biosynthesis were downregulated, as well as those involved in phytosulfokine signaling and many other genes involved in cell division; while genes involved in secondary metabolism and compounds/processes related to resistance were upregulated, especially those related to cell wall biosynthesis/rearrangement and flavonoid biosynthesis. These trends are indicative of a growth-defense trade-off. Among the DEGs, Zm00001d053603, Zm00001d035562, Zm00001d037810, Zm00001d037921, and Zm00001d010840 were polymorphic between resistant and susceptible bulks, were located in the confidence intervals of detected QTLs, and showed large differences in transcript levels between the resistant and susceptible bulks. Thus, they were identified as candidate genes involved in resistance to FER and/or reduced fumonisin accumulation.
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Affiliation(s)
- Ana Cao
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
| | | | | | - Rogelio Santiago
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Pontevedra, Spain
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia (CSIC), Pontevedra, Spain
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Gangurde SS, Xavier A, Naik YD, Jha UC, Rangari SK, Kumar R, Reddy MSS, Channale S, Elango D, Mir RR, Zwart R, Laxuman C, Sudini HK, Pandey MK, Punnuri S, Mendu V, Reddy UK, Guo B, Gangarao NVPR, Sharma VK, Wang X, Zhao C, Thudi M. Two decades of association mapping: Insights on disease resistance in major crops. FRONTIERS IN PLANT SCIENCE 2022; 13:1064059. [PMID: 37082513 PMCID: PMC10112529 DOI: 10.3389/fpls.2022.1064059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties.
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Affiliation(s)
- Sunil S. Gangurde
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Alencar Xavier
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | | - Uday Chand Jha
- Indian Council of Agricultural Research (ICAR), Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | | | - Raj Kumar
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - M. S. Sai Reddy
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Sonal Channale
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Reyazul Rouf Mir
- Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Sopore, India
| | - Rebecca Zwart
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
| | - C. Laxuman
- Zonal Agricultural Research Station (ZARS), Kalaburagi, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish K. Pandey
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Somashekhar Punnuri
- College of Agriculture, Family Sciences and Technology, Dr. Fort Valley State University, Fort Valley, GA, United States
| | - Venugopal Mendu
- Department of Plant Science and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Umesh K. Reddy
- Department of Biology, West Virginia State University, West Virginia, WV, United States
| | - Baozhu Guo
- Crop Genetics and Breeding Research, United States Department of Agriculture (USDA) - Agriculture Research Service (ARS), Tifton, GA, United States
| | | | - Vinay K. Sharma
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
| | - Mahendar Thudi
- Dr. Rajendra Prasad Central Agricultural University (RPCAU), Bihar, India
- Crop Health Center, University of Southern Queensland (USQ), Toowoomba, QLD, Australia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China
- *Correspondence: Mahendar Thudi, ; Chuanzhi Zhao,
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Gesteiro N, Cao A, Santiago R, Malvar RA, Butrón A. Genomics of maize resistance to kernel contamination with fumonisins using a multiparental advanced generation InterCross maize population (MAGIC). BMC PLANT BIOLOGY 2021; 21:596. [PMID: 34915847 PMCID: PMC8675497 DOI: 10.1186/s12870-021-03380-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/17/2021] [Indexed: 06/01/2023]
Abstract
Maize kernel is exposed to several fungal species, most notably Fusarium verticillioides, which can contaminate maize kernels with fumonisins. In an effort to increase genetic gains and avoid the laborious tasks of conventional breeding, the use of marker-assisted selection or genomic selection programs was proposed. To this end, in the present study a Genome Wide Association Study (GWAS) was performed on 339 RILs of a Multiparental Advanced Generation InterCross (MAGIC) population that had previously been used to locate Quantitative Trait Locus (QTL) for resistance to Fusarium Ear Rot (FER). Six QTLs for fumonisin content were detected in the bins 3.08, 4.07, 4.10, 7.03-7.04, 9.04-9.05 and 10.04-10.5. Five of the six QTLs collocate in regions where QTLs for FER were also found. However, the genetic variation for fumonisin content in kernel is conditioned by many other QTLs of small effect that could show QTL x environment interaction effects. Although a genomic selection approach to directly reduce fumonisin content in the kernel could be suitable, improving resistance to fumonisin content by genomic selection for FER would be more advisable.
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Affiliation(s)
- Noemi Gesteiro
- Misión Biológica de Galicia (CSIC), Box 28, 36080, Pontevedra, Spain
| | - Ana Cao
- Misión Biológica de Galicia (CSIC), Box 28, 36080, Pontevedra, Spain
| | - Rogelio Santiago
- Departamento Biología Vegetal y Ciencias del Suelo, Facultad de Biología, Universidad de Vigo, Unidad Asociada Agrobiología Ambiental, Calidad de Suelos y Plantas, As Lagoas Marcosende, 36310 Vigo, Spain
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC), Box 28, 36080, Pontevedra, Spain
| | - Ana Butrón
- Misión Biológica de Galicia (CSIC), Box 28, 36080, Pontevedra, Spain
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11
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Muhammad A, Li J, Hu W, Yu J, Khan SU, Khan MHU, Xie G, Wang J, Wang L. Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models. Sci Rep 2021; 11:6767. [PMID: 33762669 PMCID: PMC7990932 DOI: 10.1038/s41598-021-86127-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Wheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.
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Affiliation(s)
- Ali Muhammad
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
- Department of Agriculture, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jianguo Li
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Hu
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Yu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, 311300, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guosheng Xie
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jibin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, 100 Daxue Rd., Nanning, Guangxi, China.
- College of Plant Science and Technology & Biomass and Bioenergy Research Center, Huazhong Agricultural University, Wuhan, 430070, China.
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12
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Santiago R, Cao A, Malvar RA, Butrón A. Genomics of Maize Resistance to Fusarium Ear Rot and Fumonisin Contamination. Toxins (Basel) 2020; 12:E431. [PMID: 32629954 PMCID: PMC7404995 DOI: 10.3390/toxins12070431] [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: 06/10/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/13/2022] Open
Abstract
Food contamination with mycotoxins is a worldwide concern, because these toxins produced by several fungal species have detrimental effects on animal and/or human health. In maize, fumonisins are among the toxins with the highest threatening potential because they are mainly produced by Fusarium verticillioides, which is distributed worldwide. Plant breeding has emerged as an effective and environmentally safe method to reduce fumonisin levels in maize kernels, but although phenotypic selection has proved effective for improving resistance to fumonisin contamination, further resources should be mobilized to meet farmers' needs. Selection based on molecular markers linked to quantitative trait loci (QTL) for resistance to fumonisin contamination or/and genotype values obtained using prediction models with markers distributed across the whole genome could speed up breeding progress. Therefore, in the current paper, previously identified genomic regions, genes, and/or pathways implicated in resistance to fumonisin accumulation will be reviewed. Studies done until now have provide many markers to be used by breeders, but to get further insight on plant mechanisms to defend against fungal infection and to limit fumonisin contamination, the genes behind those QTLs should be identified.
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Affiliation(s)
- Rogelio Santiago
- Departamento de Biología Vegetal y Ciencias del Suelo, Facultad de Biología, Universidad de Vigo, As Lagoas Marcosende, Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), 36310 Vigo, Spain;
| | - Ana Cao
- Misión Biológica de Galicia (CSIC), Apdo. 28, 36080 Pontevedra, Spain; (A.C.); (R.A.M.)
| | - Rosa Ana Malvar
- Misión Biológica de Galicia (CSIC), Apdo. 28, 36080 Pontevedra, Spain; (A.C.); (R.A.M.)
| | - Ana Butrón
- Misión Biológica de Galicia (CSIC), Apdo. 28, 36080 Pontevedra, Spain; (A.C.); (R.A.M.)
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13
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A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel. G3-GENES GENOMES GENETICS 2020; 10:1685-1696. [PMID: 32156690 PMCID: PMC7202023 DOI: 10.1534/g3.119.400987] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.
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López-Malvar A, Butrón A, Samayoa LF, Figueroa-Garrido DJ, Malvar RA, Santiago R. Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates. BMC PLANT BIOLOGY 2019; 19:519. [PMID: 31775632 PMCID: PMC6882159 DOI: 10.1186/s12870-019-2135-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/13/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND The structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidation of maize genetic variations that contribute to variation for stem hydroxycinnamate content could simplify breeding for cell wall strengthening by using markers linked to the most favorable genetic variants in marker-assisted selection or genomic selection approaches. RESULTS A genome-wide association study was conducted using a subset of 282 inbred lines from a maize diversity panel to identify single nucleotide polymorphisms (SNPs) associated with stem cell wall hydroxycinnamate content. A total of 5, 8, and 2 SNPs were identified as significantly associated to p-coumarate, ferulate, and total diferulate concentrations, respectively in the maize pith. Attending to particular diferulate isomers, 3, 6, 1 and 2 SNPs were related to 8-O-4 diferulate, 5-5 diferulate, 8-5 diferulate and 8-5 linear diferulate contents, respectively. This study has the advantage of being done with direct biochemical determinations instead of using estimates based on Near-infrared spectroscopy (NIRS) predictions. In addition, novel genomic regions involved in hydroxycinnamate content were found, such as those in bins 1.06 (for FA), 4.01 (for PCA and FA), 5.04 (for FA), 8.05 (for PCA), and 10.03 and 3.06 (for DFAT and some dimers). CONCLUSIONS The effect of individual SNPs significantly associated with stem hydroxycinnamate content was low, explaining a low percentage of total phenotypic variability (7 to 10%). Nevertheless, we spotlighted new genomic regions associated with the accumulation of cell-wall-bound hydroxycinnamic acids in the maize stem, and genes involved in cell wall modulation in response to biotic and abiotic stresses have been proposed as candidate genes for those quantitative trait loci (QTL). In addition, we cannot rule out that uncharacterized genes linked to significant SNPs could be implicated in dimer formation and arobinoxylan feruloylation because genes involved in those processes have been poorly characterized. Overall, genomic selection considering markers distributed throughout the whole genome seems to be a more appropriate breeding strategy than marker-assisted selection focused in markers linked to QTL.
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Affiliation(s)
- A López-Malvar
- Facultad de Biología, Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, As Lagoas Marcosende, 36310, Vigo, Spain.
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Vigo, Spain.
| | - A Butrón
- Misión Biológica de Galicia (CSIC), Pazo de Salcedo, Carballeira 8, 36143, Pontevedra, Spain
| | - L F Samayoa
- Department of Crop and Soil Sciences, North Carolina State University Raleigh, Raleigh, NC, 27695-7620, USA
| | - D J Figueroa-Garrido
- Facultad de Biología, Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, As Lagoas Marcosende, 36310, Vigo, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Vigo, Spain
| | - R A Malvar
- Misión Biológica de Galicia (CSIC), Pazo de Salcedo, Carballeira 8, 36143, Pontevedra, Spain
| | - R Santiago
- Facultad de Biología, Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, As Lagoas Marcosende, 36310, Vigo, Spain
- Agrobiología Ambiental, Calidad de Suelos y Plantas (UVIGO), Unidad Asociada a la MBG (CSIC), Vigo, Spain
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