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Balconi C, Galaretto A, Malvar RA, Nicolas SD, Redaelli R, Andjelkovic V, Revilla P, Bauland C, Gouesnard B, Butron A, Torri A, Barata AM, Kravic N, Combes V, Mendes-Moreira P, Murariu D, Šarčević H, Schierscher-Viret B, Vincent M, Zanetto A, Kessel B, Madur D, Mary-Huard T, Pereira A, Placinta DD, Strigens A, Charcosset A, Goritschnig S. Genetic and Phenotypic Evaluation of European Maize Landraces as a Tool for Conservation and Valorization of Agrobiodiversity. BIOLOGY 2024; 13:454. [PMID: 38927334 PMCID: PMC11201045 DOI: 10.3390/biology13060454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
The ECPGR European Evaluation Network (EVA) for Maize involves genebanks, research institutions, and private breeding companies from nine countries focusing on the valorization of maize genetic resources across Europe. This study describes a diverse collection of 626 local landraces and traditional varieties of maize (Zea mays L.) from nine European genebanks, including criteria for selection of the collection and its genetic and phenotypic diversity. High-throughput pool genotyping grouped the landraces into nine genetic groups with a threshold of 0.6 admixture, while 277 accessions were designated admixed and likely to have resulted from previous breeding activities. The grouping correlated well with the geographic origins of the collection, also reflecting the various pathways of introduction of maize to Europe. Phenotypic evaluations of 588 accessions for flowering time and plant architecture in multilocation trials over three years confirmed the great diversity within the collection, although phenotypic clusters only partially correlated with the genetic grouping. The EVA approach promotes conservation of genetic resources and opens an opportunity to increase genetic variability for developing improved varieties and populations for farmers, with better adaptation to specific environments and greater tolerance to various stresses. As such, the EVA maize collection provides valuable sources of diversity for facing climate change due to the varieties' local adaptation.
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Affiliation(s)
- Carlotta Balconi
- CREA—Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy; (R.R.); (A.T.)
| | - Agustin Galaretto
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Rosa Ana Malvar
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas, Pazo de Salcedo Carballeira, 8 Salcedo, 36143 Pontevedra, Spain; (R.A.M.)
| | - Stéphane D. Nicolas
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Rita Redaelli
- CREA—Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy; (R.R.); (A.T.)
| | - Violeta Andjelkovic
- Maize Research Institute Zemun Polje, 11000 Belgrade, Serbia; (V.A.); (N.K.)
| | - Pedro Revilla
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas, Pazo de Salcedo Carballeira, 8 Salcedo, 36143 Pontevedra, Spain; (R.A.M.)
| | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Brigitte Gouesnard
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University Montpellier, F-34398 Montpellier, France (M.V.); (A.Z.)
| | - Ana Butron
- Misión Biológica de Galicia Consejo Superior de Investigaciones Científicas, Pazo de Salcedo Carballeira, 8 Salcedo, 36143 Pontevedra, Spain; (R.A.M.)
| | - Alessio Torri
- CREA—Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy; (R.R.); (A.T.)
| | - Ana Maria Barata
- Banco Português de Germoplasma Vegetal, Quinta de S. José, S.Pedro de Merelim, 4700-859 Braga, Portugal;
| | - Natalija Kravic
- Maize Research Institute Zemun Polje, 11000 Belgrade, Serbia; (V.A.); (N.K.)
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Pedro Mendes-Moreira
- Coimbra School of Agriculture, Polytechnic University of Coimbra (ESAC-IPC), 3045-093 Coimbra, Portugal; (P.M.-M.); (A.P.)
- CERNAS—Research Centre for Natural Resources, Environment and Society, Bencanta, 3045-601 Coimbra, Portugal
| | - Danela Murariu
- Suceava Genebank, B-Dul. 1 Mai 17, 720224 Suceava, Romania; (D.M.); (D.D.P.)
| | - Hrvoje Šarčević
- Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia;
| | | | - Morgane Vincent
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University Montpellier, F-34398 Montpellier, France (M.V.); (A.Z.)
| | - Anne Zanetto
- UMR AGAP Institut, CIRAD, INRAE, Institut Agro, University Montpellier, F-34398 Montpellier, France (M.V.); (A.Z.)
| | - Bettina Kessel
- KWS SAAT SE & Co. KGaA, Grimsehlstr. 31, 37574 Einbeck, Germany;
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
- INRAE, UMR MIA Paris-Saclay, Université Paris-Saclay, AgroParisTech, 91120 Paris, France
| | - André Pereira
- Coimbra School of Agriculture, Polytechnic University of Coimbra (ESAC-IPC), 3045-093 Coimbra, Portugal; (P.M.-M.); (A.P.)
- CERNAS—Research Centre for Natural Resources, Environment and Society, Bencanta, 3045-601 Coimbra, Portugal
| | | | - Alexandre Strigens
- DSP—Delley Semences et Plantes SA, Route de Portalban 40, 1567 Delley, Switzerland;
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Université Paris-Saclay, 12 route 128, 91190 Gif-sur-Yvette, France; (A.G.); (S.D.N.); (C.B.); (V.C.); (D.M.); (T.M.-H.); (A.C.)
| | - Sandra Goritschnig
- ECPGR, Alliance of Bioversity International and CIAT, Via di San Domenico 1, 00153 Rome, Italy
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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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Mastrangelo AM, Hartings H, Lanzanova C, Balconi C, Locatelli S, Cassol H, Valoti P, Petruzzino G, Pecchioni N. Genetic Diversity within a Collection of Italian Maize Inbred Lines: A Resource for Maize Genomics and Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:336. [PMID: 38337869 PMCID: PMC10857507 DOI: 10.3390/plants13030336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
Genetic diversity is fundamental for studying the complex architecture of the traits of agronomic importance, controlled by major and minor loci. Moreover, well-characterized germplasm collections are essential tools for dissecting and analyzing genetic and phenotypic diversity in crops. A panel of 360 entries, a subset of a larger collection maintained within the GenBank at CREA Bergamo, which includes the inbreds derived from traditional Italian maize open-pollinated (OP) varieties and advanced breeding ones (Elite Inbreds), was analyzed to identify SNP markers using the tGBS® genotyping-by-sequencing technology. A total of 797,368 SNPs were found during the initial analysis. Imputation and filtering processes were carried out based on the percentage of missing data, redundant markers, and rarest allele frequencies, resulting in a final dataset of 15,872 SNP markers for which a physical map position was identified. Using this dataset, the inbred panel was characterized for linkage disequilibrium (LD), genetic diversity, population structure, and genetic relationships. LD decay at a genome-wide level indicates that the collection is a suitable resource for association mapping. Population structure analyses, which were carried out with different clustering methods, showed stable grouping statistics for four groups, broadly corresponding to 'Insubria', 'Microsperma', and 'Scagliolino' genotypes, with a fourth group composed prevalently of elite accessions derived from Italian and US breeding programs. Based on these results, the CREA Italian maize collection, genetically characterized in this study, can be considered an important tool for the mapping and characterization of useful traits and associated loci/alleles, to be used in maize breeding programs.
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Affiliation(s)
- Anna Maria Mastrangelo
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Hans Hartings
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Chiara Lanzanova
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Carlotta Balconi
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Sabrina Locatelli
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Helga Cassol
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Paolo Valoti
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
| | - Giuseppe Petruzzino
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
| | - Nicola Pecchioni
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, SS 673 Metri 25200, 71122 Foggia, Italy; (G.P.); (N.P.)
- CREA-Centro di Ricerca Cerealicoltura e Colture Industriali/Research Centre for Cereal and Industrial Crops, Via Stezzano 24, 24126 Bergamo, Italy; (H.H.); (C.L.); (C.B.); (S.L.); (H.C.); (P.V.)
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Omondi DO, Dida MM, Berger DK, Beyene Y, Nsibo DL, Juma C, Mahabaleswara SL, Gowda M. Combination of linkage and association mapping with genomic prediction to infer QTL regions associated with gray leaf spot and northern corn leaf blight resistance in tropical maize. Front Genet 2023; 14:1282673. [PMID: 38028598 PMCID: PMC10661943 DOI: 10.3389/fgene.2023.1282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Among the diseases threatening maize production in Africa are gray leaf spot (GLS) caused by Cercospora zeina and northern corn leaf blight (NCLB) caused by Exserohilum turcicum. The two pathogens, which have high genetic diversity, reduce the photosynthesizing ability of susceptible genotypes and, hence, reduce the grain yield. To identify population-based quantitative trait loci (QTLs) for GLS and NCLB resistance, a biparental population of 230 lines derived from the tropical maize parents CML511 and CML546 and an association mapping panel of 239 tropical and sub-tropical inbred lines were phenotyped across multi-environments in western Kenya. Based on 1,264 high-quality polymorphic single-nucleotide polymorphisms (SNPs) in the biparental population, we identified 10 and 18 QTLs, which explained 64.2% and 64.9% of the total phenotypic variance for GLS and NCLB resistance, respectively. A major QTL for GLS, qGLS1_186 accounted for 15.2% of the phenotypic variance, while qNCLB3_50 explained the most phenotypic variance at 8.8% for NCLB resistance. Association mapping with 230,743 markers revealed 11 and 16 SNPs significantly associated with GLS and NCLB resistance, respectively. Several of the SNPs detected in the association panel were co-localized with QTLs identified in the biparental population, suggesting some consistent genomic regions across genetic backgrounds. These would be more relevant to use in field breeding to improve resistance to both diseases. Genomic prediction models trained on the biparental population data yielded average prediction accuracies of 0.66-0.75 for the disease traits when validated in the same population. Applying these prediction models to the association panel produced accuracies of 0.49 and 0.75 for GLS and NCLB, respectively. This research conducted in maize fields relevant to farmers in western Kenya has combined linkage and association mapping to identify new QTLs and confirm previous QTLs for GLS and NCLB resistance. Overall, our findings imply that genetic gain can be improved in maize breeding for resistance to multiple diseases including GLS and NCLB by using genomic selection.
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Affiliation(s)
- Dennis O. Omondi
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
| | - Mathews M. Dida
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
| | - Dave K. Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yoseph Beyene
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - David L. Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Collins Juma
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Suresh L. Mahabaleswara
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Manje Gowda
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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Thatcher S, Leonard A, Lauer M, Panangipalli G, Norman B, Hou Z, Llaca V, Hu WN, Qi X, Jaqueth J, Severns D, Whitaker D, Wilson B, Tabor G, Li B. The northern corn leaf blight resistance gene Ht1 encodes an nucleotide-binding, leucine-rich repeat immune receptor. MOLECULAR PLANT PATHOLOGY 2023; 24:758-767. [PMID: 36180934 DOI: 10.1111/mpp.13267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/11/2023]
Abstract
Northern corn leaf blight, caused by the fungal pathogen Exserohilum turcicum, is a major disease of maize. The first major locus conferring resistance to E. turcicum race 0, Ht1, was identified over 50 years ago, but the underlying gene has remained unknown. We employed a map-based cloning strategy to identify the Ht1 causal gene, which was found to be a coiled-coil nucleotide-binding, leucine-rich repeat (NLR) gene, which we named PH4GP-Ht1. Transgenic testing confirmed that introducing the native PH4GP-Ht1 sequence to a susceptible maize variety resulted in resistance to E. turcicum race 0. A survey of the maize nested association mapping genomes revealed that susceptible Ht1 alleles had very low to no expression of the gene. Overexpression of the susceptible B73 allele, however, did not result in resistant plants, indicating that sequence variations may underlie the difference between resistant and susceptible phenotypes. Modelling of the PH4GP-Ht1 protein indicated that it has structural homology to the Arabidopsis NLR resistance gene ZAR1, and probably forms a similar homopentamer structure following activation. RNA sequencing data from an infection time course revealed that 1 week after inoculation there was a threefold reduction in fungal biomass in the PH4GP-Ht1 transgenic plants compared to wild-type plants. Furthermore, PH4GP-Ht1 transgenics had significantly more inoculation-responsive differentially expressed genes than wild-type plants, with enrichment seen in genes associated with both defence and photosynthesis. These results demonstrate that the NLR PH4GP-Ht1 is the causal gene underlying Ht1, which represents a different mode of action compared to the previously reported wall-associated kinase northern corn leaf blight resistance gene Htn1/Ht2/Ht3.
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Affiliation(s)
- Shawn Thatcher
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - April Leonard
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Marianna Lauer
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
- Oxford, Pennsylvania, USA
| | | | - Bret Norman
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Zhenglin Hou
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Victor Llaca
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Wang-Nan Hu
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
- Kissimmee, Florida, USA
| | - Xiuli Qi
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Jennifer Jaqueth
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Dina Severns
- Department of Seed Product Development, Corteva Agriscience, Windfall, Indiana, USA
| | - David Whitaker
- Department of Seed Product Development, Corteva Agriscience, New Holland, Pennsylvania, USA
| | - Bill Wilson
- Department of Seed Product Development, Corteva Agriscience, Windfall, Indiana, USA
| | - Girma Tabor
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
| | - Bailin Li
- Department of Biotechnology, Corteva Agriscience, Johnston, Iowa, USA
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Wang L, Yang Y, Yang Z, Li W, Hu D, Yu H, Li X, Cheng H, Kan G, Che Z, Zhang D, Zhang H, Wang H, Huang F, Yu D. GmFtsH25 overexpression increases soybean seed yield by enhancing photosynthesis and photosynthates. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1026-1040. [PMID: 36349957 DOI: 10.1111/jipb.13405] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Increasing plant photosynthetic capacity is a promising approach to boost yields, but it is particularly challenging in C3 crops, such as soybean (Glycine max (L.) Merr.). Here, we identified GmFtsH25, encoding a member of the filamentation temperature-sensitive protein H protease family, as a major gene involved in soybean photosynthesis, using linkage mapping and a genome-wide association study. Overexpressing GmFtsH25 resulted in more grana thylakoid stacks in chloroplasts and increased photosynthetic efficiency and starch content, while knocking out GmFtsH25 produced the opposite phenotypes. GmFtsH25 interacted with photosystem I light harvesting complex 2 (GmLHCa2), and this interaction may contribute to the observed enhanced photosynthesis. GmFtsH25 overexpression lines had superior yield traits, such as yield per plant, compared to the wild type and knockout lines. Additionally, we identified an elite haplotype of GmFtsH25, generated by natural mutations, which appears to have been selected during soybean domestication. Our study sheds light on the molecular mechanism by which GmFtsH25 modulates photosynthesis and provides a promising strategy for improving the yields of soybean and other crops.
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Affiliation(s)
- Li Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongyi Yang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenlong Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dezhou Hu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huilian Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhijun Che
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Hengyou Zhang
- Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, the Chinese Academy of Sciences, Harbin, 150081, China
| | - Hui Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Huang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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Rashid Z, Babu V, Sharma SS, Singh PK, Nair SK. Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4549-4563. [PMID: 36271945 PMCID: PMC9734215 DOI: 10.1007/s00122-022-04239-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/15/2022] [Indexed: 06/16/2023]
Abstract
A key genomic region was identified for resistance to FSR at 168 Mb on chromosome 6 in GWAS and haplotype regression analysis, which was validated by QTL mapping in two populations. Fusarium stalk rot (FSR) of maize is an economically important post-flowering stalk rot (PFSR) disease caused by Fusarium verticillioides. The pathogen invades the plant individually, or in combination with other stalk rot pathogens or secondary colonizers, thereby making it difficult to make accurate selection for resistance. For identification and validation of genomic regions associated with FSR resistance, a genome-wide association study (GWAS) was conducted with 342 maize lines. The panel was screened for FSR in three environments using standard artificial inoculation methodology. GWAS using the mixed linear model corrected for population structure and kinship was done, in which 290,626 SNPs from genotyping-by-sequencing were used. A total of 7 SNPs, five on chromosome 6 showing strong LD at 168 Mb, were identified to be associated with FSR. Haplotype regression analysis identified 32 haplotypes with a significant effect on the trait. In a QTL mapping experiment in two populations for validating the identified variants, QTLs were identified with confidence intervals having overlapped physical coordinates in both the populations on chromosome 6, which was closely located to the GWAS-identified variants on chromosome 6. It makes this genomic region a crucial one to further investigate the possibility of developing trait markers for deployment in breeding pipelines. It was noted that previously reported QTLs for other stalk rots in maize mapped within the same physical intervals of several haplotypes identified for FSR resistance in this study. The possibility of QTLs controlling broad-spectrum resistance for PFSR in general requires further investigation.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
| | - Veerendra Babu
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
| | - Shyam Sundar Sharma
- Maharana Pratap University of Agriculture and Technology (MPUAT), Udaipur, 313001, Rajasthan, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India
- Corteva Agriscience Seeds India Pvt Ltd., Madhapur, Hyderabad, 500081, Telangana, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater, Hyderabad, 502324, Telangana, India.
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Wang D, Li M, Yuan C, Fang Y, Zhang Z. Guaiacol as a natural melanin biosynthesis inhibitor to control northern corn leaf blight. PEST MANAGEMENT SCIENCE 2022; 78:4557-4568. [PMID: 35833811 DOI: 10.1002/ps.7075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/04/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The natural 1,8-dihydroxynaphthalene (DHN) melanin biosynthesis inhibitors (MBIs) are one of the promising approaches to the integrated management of plant diseases but have received scarce attention until now. Herein, to explore the natural DHN MBIs used in the control of northern corn leaf blight (NCLB), a library of 53 essential oil compounds was used to screen the MBIs against Exserohilum turcicum, the causal pathogen of NCLB, using tricyclazole as a reference compound. RESULTS The results of morphological change in the colony, thermogravimetric analysis, ultraviolet-visible spectroscopy, and transmission electron microscopy confirmed that guaiacol could effectively inhibit the melanin production at 50 μg/mL under in vitro conditions. The in vitro bioassay results indicated that this inhibition effect was concentration-dependent and the minimum inhibition concentration of guaiacol was 50 μg/mL. The in vivo experimental results demonstrated that guaiacol significantly inhibited appressorium formation and penetration on corn leaf sheaths at the concentration of 500 μg/mL. The pot experiment results revealed that there were no differences between guaiacol (500 μg/mL) and tricyclazole (100 μg/mL) in control efficacy. The enzymatic assay suggested that guaiacol might exert the activity through inhibiting DHN polymerization to form melanins, which was distinct from tricyclazole. CONCLUSIONS Taken together, this study screened out guaiacol as a natural MBI from 53 essential oil compounds and verified its effectiveness in the control of NCLB at 500 μg/mL. Above all, this research opened an avenue for exploring natural DHN MBIs in the integrated management of plant diseases. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Delong Wang
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Min Li
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Chunxia Yuan
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Yali Fang
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Zhijia Zhang
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
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Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers. Genes (Basel) 2022; 13:genes13040618. [PMID: 35456424 PMCID: PMC9030036 DOI: 10.3390/genes13040618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 12/04/2022] Open
Abstract
Maize is an important cereal crop in the world for feed, food, fodder, and raw materials of industries. Turcicum leaf blight (TLB) is a major foliar disease that can cause more than 50% yield losses in maize. Considering this, the molecular diversity, population structure, and genome-wide association study (GWAS) for TLB resistance were studied in 288 diverse inbred lines genotyped using 89 polymorphic simple sequence repeats (SSR) markers. These lines werescreened for TLB disease at two hot-spot locations under artificially inoculated conditions. The average percent disease incidence (PDI) calculated for each genotype ranged from 17 (UMI 1201) to 78% (IML 12-22) with an overall mean of 40%. The numbers of alleles detected at a locus ranged from twoto nine, with a total of 388 alleles. The polymorphic information content (PIC) of each marker ranged between 0.04 and 0.86. Out of 89 markers, 47 markers were highly polymorphic (PIC ≥ 0.60). This indicated that the SSR markers used were very informative and suitable for genetic diversity, population structure, and marker-trait association studies.The overall observed homozygosity for highly polymorphic markers was 0.98, which indicated that lines used were genetically pure. Neighbor-joining clustering, factorial analysis, and population structure studies clustered the 288 lines into 3–5 groups. The patterns of grouping were in agreement with the origin and pedigree records of the genotypesto a greater extent.A total of 94.10% lines were successfully assigned to one or another group at a membership probability of ≥0.60. An analysis of molecular variance (AMOVA) revealed highly significant differences among populations and within individuals. Linkage disequilibrium for r2 and D′ between loci ranged from 0 to 0.77 and 0 to 1, respectively. A marker trait association analysis carried out using a general linear model (GLM) and mixed linear model (MLM), identified 15 SSRs markers significantly associated with TLB resistance.These 15 markers were located on almost all chromosomes (Chr) except 7, 8, and 9. The phenotypic variation explained by these loci ranged from 6% (umc1367) to 26% (nc130, phi085). Maximum 7 associated markers were located together on Chr 2 and 5. The selected regions identified on Chr 2 and 5 corroborated the previous studies carried out in the Indian maize germplasm. Further, 11 candidate genes were identified to be associated with significant markers. The identified sources for TLB resistance and associated markers may be utilized in molecular breeding for the development of suitable genotypes.
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Back to the wild: mining maize (Zea mays L.) disease resistance using advanced breeding tools. Mol Biol Rep 2022; 49:5787-5803. [PMID: 35064401 DOI: 10.1007/s11033-021-06815-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/06/2021] [Indexed: 10/19/2022]
Abstract
Cultivated modern maize (Zea mays L.) originated through the continuous process of domestication from its wild progenitors. Today, maize is considered as the most important cereal crop which is extensively cultivated in all parts of the world. Maize shows remarkable genotypic and phenotypic diversity which makes it an ideal model species for crop genetic research. However, intensive breeding and artificial selection of desired agronomic traits greatly narrow down the genetic bases of maize. This reduction in genetic diversity among cultivated maize led to increase the chance of more attack of biotic stress as climate changes hampering the maize grain production globally. Maize germplasm requires to integrate both durable multiple-diseases and multiple insect-pathogen resistance through tapping the unexplored resources of maize landraces. Revisiting the landraces seed banks will provide effective opportunities to transfer the resistant genes into the modern cultivars. Here, we describe the maize domestication process and discuss the unique genes from wild progenitors which potentially can be utilized for disease resistant in maize. We also focus on the genetics and disease resistance mechanism of various genes against maize biotic stresses and then considered the different molecular breeding tools for gene transfer and advanced high resolution mapping for gene pyramiding in maize lines. At last, we provide an insight for targeting identified key genes through CRISPR/Cas9 genome editing system to enhance the maize resilience towards biotic stress.
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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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Rashid Z, Kaur H, Babu V, Singh PK, Harlapur SI, Nair SK. Identification and Validation of Genomic Regions Associated With Charcoal Rot Resistance in Tropical Maize by Genome-Wide Association and Linkage Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:726767. [PMID: 34691105 PMCID: PMC8531636 DOI: 10.3389/fpls.2021.726767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 06/01/2023]
Abstract
Charcoal rot is a post-flowering stalk rot (PFSR) disease of maize caused by the fungal pathogen, Macrophomina phaseolina. It is a serious concern for smallholder maize cultivation, due to significant yield loss and plant lodging at harvest, and this disease is expected to surge with climate change effects like drought and high soil temperature. For identification and validation of genomic variants associated with charcoal rot resistance, a genome-wide association study (GWAS) was conducted on CIMMYT Asia association mapping panel comprising 396 tropical-adapted lines, especially to Asian environments. The panel was phenotyped for disease severity across two locations with high disease prevalence in India. A subset of 296,497 high-quality SNPs filtered from genotyping by sequencing was correcting for population structure and kinship matrices for single locus mixed linear model (MLM) of GWAS analysis. A total of 19 SNPs were identified to be associated with charcoal rot resistance with P-value ranging from 5.88 × 10-06 to 4.80 × 10-05. Haplotype regression analysis identified 21 significant haplotypes for the trait with Bonferroni corrected P ≤ 0.05. For validating the associated variants and identifying novel QTLs, QTL mapping was conducted using two F2:3 populations. Two QTLs with overlapping physical intervals, qMSR6 and qFMSR6 on chromosome 6, identified from two different mapping populations and contributed by two different resistant parents, were co-located with the SNPs and haplotypes identified at 103.51 Mb on chromosome 6. Similarly, several SNPs/haplotypes identified on chromosomes 3, 6 and 8 were also found to be physically co-located within QTL intervals detected in one of the two mapping populations. The study also noted that several SNPs/haplotypes for resistance to charcoal rot were located within physical intervals of previously reported QTLs for Gibberella stalk rot resistance, which opens up a new possibility for common disease resistance mechanisms for multiple stalk rots.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Harleen Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Veerendra Babu
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
| | | | - Sudha K. Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Hyderabad, India
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