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Bi Y, Jiang F, Yin X, Shaw RK, Guo R, Wang J, Fan X. Identification of candidate gene associated with maize northern leaf blight resistance in a multi-parent population. PLANT CELL REPORTS 2024; 43:189. [PMID: 38960996 PMCID: PMC11222180 DOI: 10.1007/s00299-024-03269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
KEY MESSAGE QTL mapping combined with genome-wide association studies, revealed a potential candidate gene for resistance to northern leaf blight in the tropical CATETO-related maize line YML226, providing a basis for marker-assisted selection of maize varieties Northern leaf blight (NLB) is a foliar disease that can cause severe yield losses in maize. Identifying and utilizing NLB-resistant genes is the most effective way to prevent and control this disease. In this study, five important inbred lines of maize were used as parental lines to construct a multi-parent population for the identification of NLB-resistant loci. QTL mapping and GWAS analysis revealed that QTL qtl_YML226_1, which had the largest phenotypic variance explanation (PVE) of 9.28%, and SNP 5-49,193,921 were co-located in the CATETO-related line YML226. This locus was associated with the candidate gene Zm00001d014471, which encodes a pentatricopeptide repeat (PPR) protein. In the coding region of Zm00001d014471, YML226 had more specific SNPs than the other parental lines. qRT-PCR showed that the relative expressions of Zm00001d014471 in inoculated and uninoculated leaves of YML226 were significantly higher, indicating that the expression of the candidate gene was correlated with NLB resistance. The analysis showed that the higher expression level in YML226 might be caused by SNP mutations. This study identified NLB resistance candidate loci and genes in the tropical maize inbred line YML226 derived from the CATETO germplasm, thereby providing a theoretical basis for using modern marker-assisted breeding techniques to select genetic resources resistant to NLB.
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Affiliation(s)
- Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xingfu Yin
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ranjan K Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jing Wang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China.
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Wang Z, Guo L, Tan X, Deng J, Gong S, Li D, Zhang J, Ruan C, Sun W, Peng Z, Hu Y. Development of Loop-Mediated Isothermal Amplification Assays for the Rapid and Accurate Diagnosis of Exserohilum turcicum for Field Applications. PLANT DISEASE 2024; 108:1461-1469. [PMID: 38240714 DOI: 10.1094/pdis-10-23-2101-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Northern corn leaf blight (NCLB), caused by Exserohilum turcicum, is one of the most devastating foliar diseases of maize. Rapid and accurate diagnosis for this disease is urgently needed but still limited. Here, we establish a field-deployable diagnostic method to detect E. turcicum based on loop-mediated isothermal amplification (LAMP) assays. A software application called K-mer Elimination by Cross-reference was used to search for the specific sequences belonging to E. turcicum by comparing the whole genome sequence between E. turcicum and other known maize pathogens. Five LAMP primer sets were designed based on specific and single-copy fragments of E. turcicum. Post-LAMP analyses indicated that only the primer set, Et9468_set1, was the most suitable, producing a ladder-like amplification pattern in the agarose gel electrophoresis and a strong fluorescence signal in the presence of SYBR Green I. The LAMP assay using Et9468_set1 primers demonstrated a high level of specificity in distinguishing E. turcicum from six other common fungal pathogens of maize, as well as 12 more fungal and oomycete strains including the epiphytic fungi from maize leaves and other crop pathogens. Moreover, it exhibited remarkable sensitivity by detecting five copies per reaction, which was approximately 104 times more sensitive compared with conventional PCR. The LAMP assay successfully detected E. turcicum in field maize leaves without DNA extraction, demonstrating its suitability for rapid on-spot detection of NCLB. Our study provides a direct LAMP diagnostic method to detect E. turcicum, which enables on-site pathogen detection in the field and the development of preventive strategies for NCLB management.
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Affiliation(s)
- Zhenan Wang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Lifang Guo
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xiaoshan Tan
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Jili Deng
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shengjie Gong
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Dayong Li
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Junjie Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Changchun Ruan
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Wenxian Sun
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Zhao Peng
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Ying Hu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
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3
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Navarro BL, Streit S, Nogueira Júnior AF, von Tiedemann A. Photosynthetic Costs and Impact on Epidemiological Parameters Associated with Ht Resistance Genes in Maize Lines Infected with Exserohilum turcicum. PHYTOPATHOLOGY 2024; 114:760-769. [PMID: 37889164 DOI: 10.1094/phyto-07-23-0247-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Northern corn leaf blight, caused by Exserohilum turcicum, is mainly controlled by the use of resistant cultivars. Maize lines carrying individual resistance genes B37Ht1, B37Ht2, B37Ht3, and B37Htn1 express different defense symptoms having an impact on the photosynthetic activity, the accumulation of reactive oxygen species, and epidemiological parameters. Plants were inoculated with a race 0 isolate of E. turcicum conferring a compatible interaction with B37 and incompatible interactions with plants carrying resistance genes. Five days postinoculation (dpi), the resistant lines displayed a reduction in leaf CO2 assimilation of 30 to 80% compared with healthy plants. At 14 dpi, inoculated plants of B37Ht1 showed a significant decrease in leaf CO2 assimilation, similar to B37 (up to 94%). The instantaneous carboxylation efficiency was significantly reduced on inoculated plants of the lines B37Ht2, B37Ht3, and B37Htn1 (54 to 81%) at 5 dpi. Curiously, the reduction in carboxylation efficiency for B37 and B37Ht1 (up to 95%) was higher at 14 dpi than at 5 dpi (up to 81%). At 6 dpi, low levels of H2O2 were detected in B37Ht1, in contrast to B37Htn1, where a high H2O2 level and peroxidase activity were observed. The sporulation rate on B37Ht1, B37Ht3, and B37Htn1 decreased by 92% compared with the susceptible control, whereas strong sporulation occurred in lesions on line B37Ht2. The resistance in maize to E. turcicum conferred by Ht resistance genes is associated with photosynthetic costs and may have quite contrasting effects on host physiology and major epidemiological parameters, such as sporulation, which contributes inoculum for secondary infections.
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Affiliation(s)
- Barbara Ludwig Navarro
- Georg-August-Universität Göttingen, Department of Crop Sciences, Division of Plant Pathology and Crop Protection, Göttingen, Germany
| | - Sebastian Streit
- Georg-August-Universität Göttingen, Department of Crop Sciences, Division of Plant Pathology and Crop Protection, Göttingen, Germany
| | | | - Andreas von Tiedemann
- Georg-August-Universität Göttingen, Department of Crop Sciences, Division of Plant Pathology and Crop Protection, Göttingen, Germany
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Qiao L, Gao X, Jia Z, Liu X, Wang H, Kong Y, Qin P, Yang B. Identification of adult resistant genes to stripe rust in wheat from southwestern China based on GWAS and WGCNA analysis. PLANT CELL REPORTS 2024; 43:67. [PMID: 38341832 DOI: 10.1007/s00299-024-03148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/13/2024]
Abstract
KEY MESSAGE In this study, genome-wide association studies combined with transcriptome data analysis were utilized to reveal potential candidate genes for stripe rust resistance in wheat, providing a basis for screening wheat varieties for stripe rust resistance. Wheat stripe rust, which is caused by the wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) is one of the world's most devastating diseases of wheat. Genetic resistance is the most effective strategy for controlling diseases. Although wheat stripe rust resistance genes have been identified to date, only a few of them confer strong and broad-spectrum resistance. Here, the resistance of 335 wheat germplasm resources (mainly wheat landraces) from southwestern China to wheat stripe rust was evaluated at the adult stage. Combined genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) based on RNA sequencing from stripe rust resistant accession Y0337 and susceptible accession Y0402, five candidate resistance genes to wheat stripe rust (TraesCS1B02G170200, TraesCS2D02G181000, TraesCS4B02G117200, TraesCS6A02G189300, and TraesCS3A02G122300) were identified. The transcription level analyses showed that these five genes were significantly differentially expressed between resistant and susceptible accessions post inoculation with Pst at different times. These candidate genes could be experimentally transformed to validate and manipulate fungal resistance, which is beneficial for the development of the wheat cultivars resistant to stripe rust.
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Affiliation(s)
- Liang Qiao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xue Gao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhiqiang Jia
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xingchen Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Huiyutang Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Yixi Kong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Baoju Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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Nowak B, Tomkowiak A, Sobiech A, Bocianowski J, Kowalczewski PŁ, Spychała J, Jamruszka T. Identification and Analysis of Candidate Genes Associated with Yield Structure Traits and Maize Yield Using Next-Generation Sequencing Technology. Genes (Basel) 2023; 15:56. [PMID: 38254946 PMCID: PMC10815399 DOI: 10.3390/genes15010056] [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: 12/08/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
The main challenge of agriculture in the 21st century is the continuous increase in food production. In addition to ensuring food security, the goal of modern agriculture is the continued development and production of plant-derived biomaterials. Conventional plant breeding methods do not allow breeders to achieve satisfactory results in obtaining new varieties in a short time. Currently, advanced molecular biology tools play a significant role worldwide, markedly contributing to biological progress. The aim of this study was to identify new markers linked to candidate genes determining grain yield. Next-generation sequencing, gene association, and physical mapping were used to identify markers. An additional goal was to also optimize diagnostic procedures to identify molecular markers on reference materials. As a result of the conducted research, 19 SNP markers significantly associated with yield structure traits in maize were identified. Five of these markers (28629, 28625, 28640, 28649, and 29294) are located within genes that can be considered candidate genes associated with yield traits. For two markers (28639 and 29294), different amplification products were obtained on the electrophorograms. For marker 28629, a specific product of 189 bp was observed for genotypes 1, 4, and 10. For marker 29294, a specific product of 189 bp was observed for genotypes 1 and 10. Both markers can be used for the preliminary selection of well-yielding genotypes.
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Affiliation(s)
- Bartosz Nowak
- Smolice Plant Breeding Ltd., IHAR Group, Smolice 146, 63-740 Kobylin, Poland;
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (J.S.); (T.J.)
| | - Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (J.S.); (T.J.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland;
| | - Przemysław Łukasz Kowalczewski
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland;
| | - Julia Spychała
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (J.S.); (T.J.)
| | - Tomasz Jamruszka
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (A.S.); (J.S.); (T.J.)
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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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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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Poonam, Sharma R, Sharma P, Sharma NC, Kumar K, Singh KN, Bhardwaj V, Negi N, Chauhan N. Exploring genetic diversity and ascertaining genetic loci associated with important fruit quality traits in apple ( Malus × domestica Borkh.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1693-1716. [PMID: 38162921 PMCID: PMC10754789 DOI: 10.1007/s12298-023-01382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Genetic diversity is the primary source of variability in any crop improvement program, and the diverse germplasm of any crop species represents an important genetic resource for gene or allele mining to meet future needs. Huge genetic and phenotypic diversity is present in the apple gene pool, even though, breeding programs have been mainly focused on a few traits of interests, which have resulted in the reduction of the diversity in the cultivated lines of apple. Therefore, the present study was carried out on 70 diverse apple genotypes with the objective of analyzing the genetic diversity and to identify the genetic loci associated with important fruit quality traits. A total of 140 SSR primers were used to characterize the 70 genotypes of apples, out of which only 88 SSRs were found to be polymorphic. The PIC values varied from 0.03 to 0.75. The value of MI, EMR, and RP varied from 0.03 to 3.5, 0.5 to 5.0, and 1.89 to 6.74, respectively. The dendrogram and structure analysis divided all the genotypes into two main groups. In addition to this, large phenotypic variability was observed for the fruit quality traits under study indicated the suitability of the genotypes for association studies. Altogether 71 novel MTAs were identified for 10 fruit quality traits, of which 15 for fruit length, 15 for fruit diameter, 12 for fruit weight, 2 for total sugar, 2 for TSS, 4 for reducing sugar, 5 for non-reducing sugar, 5 for fruit firmness, 5 for fruit acidity and 6 for anthocyanin, respectively. Consistent with the physicochemical evaluation of traits, there was a significant correlation coefficient among different fruit quality characters, and many common markers were found to be associated with these traits (fruit diameter, length, TSS, total sugar, acidity and anthocyanin, respectively) by using the different modeling techniques (GLM, MLM). The inferred genetic structure, diversity pattern and the identified MTAs will be serving as resourceful grounds for better predictions and understanding of apple genome towards efficient conservation and utilization of apple germplasm for facilitating genetic improvement of fruit quality traits. Furthermore, these findings also suggested that association mapping could be a viable alternative to the conventional QTL mapping approach in apple. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01382-w.
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Affiliation(s)
- Poonam
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
- School of Bioengineering & Food Technology, Shoolini University, Solan, HP, 173 229, India
| | - Rajnish Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Parul Sharma
- Department of Biotechnology, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Naveen C. Sharma
- Department of Fruit Science, Dr YS Parmar University of Horticulture & Forestry, Solan, HP 173 230 India
| | - Kuldeep Kumar
- ICAR-Indian Institute of Pulses Research, Kanpur, UP 208 024 India
| | - Krishna Nand Singh
- Department of Botany, University of Delhi, North Campus, New Delhi, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP 171 004 India
| | - Narender Negi
- ICAR-NBPGR Regional Station, Phagli, Shimla, HP 171 004 India
| | - Neena Chauhan
- RHR&TS, Dr YS Parmar University of Horticulture & Forestry, Mashobra, Shimla, HP, 171 007 India
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9
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Hou M, Cao Y, Zhang X, Zhang S, Jia T, Yang J, Han S, Wang L, Li J, Wang H, Zhang L, Wu X, Duan C, Li H. Genome-wide association study of maize resistance to Pythium aristosporum stalk rot. FRONTIERS IN PLANT SCIENCE 2023; 14:1239635. [PMID: 37662167 PMCID: PMC10470045 DOI: 10.3389/fpls.2023.1239635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize's antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.
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Affiliation(s)
- Mengwei Hou
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingrui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shulin Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tengjiao Jia
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiwei Yang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shengbo Han
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lifeng Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jingjing Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hao Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lili Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaolin Wu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiyong Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
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10
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Petroli CD, Subbarao GV, Burgueño JA, Yoshihashi T, Li H, Franco Duran J, Pixley KV. Genetic variation among elite inbred lines suggests potential to breed for BNI-capacity in maize. Sci Rep 2023; 13:13422. [PMID: 37591891 PMCID: PMC10435450 DOI: 10.1038/s41598-023-39720-3] [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: 10/06/2022] [Accepted: 07/29/2023] [Indexed: 08/19/2023] Open
Abstract
Biological nitrification inhibition (BNI) is a plant function where root systems release antibiotic compounds (BNIs) specifically aimed at suppressing nitrifiers to limit soil-nitrate formation in the root zone. Little is known about BNI-activity in maize (Zea mays L.), the most important food, feed, and energy crop. Two categories of BNIs are released from maize roots; hydrophobic and hydrophilic BNIs, that determine BNI-capacity in root systems. Zeanone is a recently discovered hydrophobic compound with BNI-activity, released from maize roots. The objectives of this study were to understand/quantify the relationship between zeanone activity and hydrophobic BNI-capacity. We assessed genetic variability among 250 CIMMYT maize lines (CMLs) characterized for hydrophobic BNI-capacity and zeanone activity, towards developing genetic markers linked to this trait in maize. CMLs with high BNI-capacity and ability to release zeanone from roots were identified. GWAS was performed using 27,085 SNPs (with unique positions on the B73v.4 reference genome, and false discovery rate = 10), and phenotypic information for BNI-capacity and zeanone production from root systems. Eighteen significant markers were identified; three associated with specific BNI-activity (SBNI), four with BNI-activity per plant (BNIPP), another ten were common between SBNI and BNIPP, and one with zeanone release. Further, 30 annotated genes were associated with the significant SNPs; most of these genes are involved in pathways of "biological process", and one (AMT5) in ammonium regulation in maize roots. Although the inbred lines in this study were not developed for BNI-traits, the identification of markers associated with BNI-capacity suggests the possibility of using these genomic tools in marker-assisted selection to improve hydrophobic BNI-capacity in maize.
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Affiliation(s)
- César D Petroli
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, Texcoco, C.P. 56237, Mexico.
| | - Guntur V Subbarao
- Japan International Research Center for Agricultural Science, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Juan A Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, Texcoco, C.P. 56237, Mexico
| | - Tadashi Yoshihashi
- Japan International Research Center for Agricultural Science, 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Huihui Li
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, Texcoco, C.P. 56237, Mexico
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), No 12 Zhongguancun South Street, Beijing, 10081, China
| | - Jorge Franco Duran
- Departamento de Biometría y Estadística, Facultad de Agronomía, Universidad de la República, Ruta 3, Km 363, C.P. 60000, Paysandú, Uruguay
| | - Kevin V Pixley
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz, Km. 45, El Batán, Texcoco, C.P. 56237, Mexico
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11
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Nowak B, Tomkowiak A, Bocianowski J, Sobiech A, Bobrowska R, Kowalczewski PŁ, Bocianowska M. The Use of DArTseq Technology to Identify Markers Linked to Genes Responsible for Seed Germination and Seed Vigor in Maize. Int J Mol Sci 2022; 23:ijms232314865. [PMID: 36499196 PMCID: PMC9736657 DOI: 10.3390/ijms232314865] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Seed vigor and seed germination are very important traits, determined by several factors including genetic and physical purity, mechanical damage, and physiological condition, characterized by maintaining a high seed vigor and stable content after storage. The search for molecular markers related to improvement in seed vigor under adverse condition is an important issue in maize breeding currently. Higher sowing quality of seeds is necessary for the development of the agriculture production and better ability to resist all kinds of adversity in the seeds’ storage. Condition is a very important factor affecting the yield of plants, thanks to the construction of their vitality. Identification of molecular markers associated with seed germination and seed vigor may prove to be very important in the selection of high-yielding maize varieties. The aim of this study was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the seed germination and seed vigor in inbred lines of maize (Zea mays L.). The plant material used for the research was 152 inbred maize lines. The seed germination and seed vigor were analyzed. For identification of SNP and SilicoDArT markers related to the seed germination and seed vigor, the SilicoDarT technique developed by Diversity Arrays Technology was used. The analysis of variance indicated a statistically significant differentiation between genotypes for both observed traits. Positive (r = 0.41) correlation (p < 0.001) between seed germination and seed vigor was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNP) were selected as a result of association mapping, which showed them to be significantly related to the analyzed traits. The 890 molecular markers were associated with seed vigor, and 1323 with seed germination. Fifty-six markers (47 SilicoDArT and nine SNP) were significant for both traits. Of these 56 markers, the 20 most significant were selected (five of these markers were significant at the level of 0.001 for seed vigor and at the level of 0.05 for seed germination, another five markers were significant at the level of 0.001 for seed germination and at the level of 0.05 for seed vigor, five markers significant at the level of 0.001 only for seed vigor and five significant at the level of 0.001 only for seed germination also selected). These markers were used for physical mapping to determine their location on the genetic map. Finally, it was found that six of these markers (five silicoDArT—2,435,784, 4,772,587, 4,776,334, 2,507,310, 25,981,291, and one SNP—2,386,217) are located inside genes, the action of which may affect both seed germination and seed vigor. These markers can be used to select genotypes with high vigor and good seed germination.
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Affiliation(s)
- Bartosz Nowak
- Smolice Plant Breeding Sp. z o. o. IHAR Group, Smolice 146, 63-740 Kobylin, Poland
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
- Correspondence:
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Przemysław Łukasz Kowalczewski
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, 31 Wojska Polskiego St., 60-624 Poznań, Poland
| | - Marianna Bocianowska
- Faculty of Chemical Technology, Poznań University of Technology, Piotrowo 3A, 60-965 Poznań, Poland
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12
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Zhu M, Ma J, Liu X, Guo Y, Qi X, Gong X, Zhu Y, Wang Y, Jiang M. High-resolution mapping reveals a Ht3-like locus against northern corn leaf blight. FRONTIERS IN PLANT SCIENCE 2022; 13:968924. [PMID: 36160951 PMCID: PMC9506542 DOI: 10.3389/fpls.2022.968924] [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: 06/14/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Northern corn leaf blight (NCLB), caused by the fungal pathogen Exserohilum turcicum, poses a grave threat to maize production worldwide. The resistance gene in A619Ht3, discovered decades ago, is an important genetic resource for NCLB control. By using a pair of near-isogenic lines (NILs) A619Ht3 and A619, together with the resistant and susceptible bulks derived from the cross of A619Ht3 and L3162 lines, we initially detected a Ht3-like (Ht3L) locus in bin 8.06 that was closely associated with NCLB resistance. We then performed five rounds of fine-mapping, which ultimately delimited the Ht3L locus to a 577-kb interval flanked by SNP markers KA002081 and KA002084. Plants homozygous for the Ht3L/Ht3L genotype exhibited an average reduction in diseased leaf area (DLA) by 16.5% compared to plants lacking Ht3L locus. The Ht3L locus showed extensive variation in genomic architecture among different maize lines and did not appear to contain any genes encoding canonical cell wall-associated kinases against NCLB. Moreover, the Ht3L locus was located ∼2.7 Mb away from the known Htn1 locus. We speculate that the Ht3L locus may contain a bona fide Ht3 gene or a novel NCLB resistance gene closely linked to Ht3. In practice, the Ht3L locus is a valuable resource for improving maize resistance to NCLB.
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Affiliation(s)
- Mang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jun Ma
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xinfang Liu
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanling Guo
- Liaoning Dongya Agricultural Development Co., Ltd., Shenyang, China
| | - Xin Qi
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Xue Gong
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Yanbin Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- Liaoning Dongya Agricultural Development Co., Ltd., Shenyang, China
| | - Yanbo Wang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Min Jiang
- Liaoning Academy of Agricultural Sciences, Shenyang, China
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13
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Qu Z, Wu Y, Hu D, Li T, Liang H, Ye F, Xue J, Xu S. Genome-Wide Association Analysis for Candidate Genes Contributing to Kernel-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:872292. [PMID: 35685022 PMCID: PMC9171146 DOI: 10.3389/fpls.2022.872292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with p < 1 × 10-4 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
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Affiliation(s)
- Zhibo Qu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Ting Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, China
- Maize Engineering Technology Research Centre, Yangling, China
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14
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The Use of DArTseq Technology to Identify New SNP and SilicoDArT Markers Related to the Yield-Related Traits Components in Maize. Genes (Basel) 2022; 13:genes13050848. [PMID: 35627233 PMCID: PMC9142088 DOI: 10.3390/genes13050848] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/04/2023] Open
Abstract
In the last decade, many scientists have used molecular biology methods in their research to locate the grain-yield-determining loci and yield structure characteristics in maize. Large-scale molecular analyses in maize do not only focus on the identification of new markers and quantitative trait locus (QTL) regions. DNA analysis in the selection of parental components for heterotic crosses is a very important tool for breeders. The aim of this research was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the size of the yield components in maize. The plant material used for the research was 186 inbred maize lines. The field experiment was established in twolocations. The yield and six yield components were analyzed. For identification of SNP and SilicoDArT markers related to the yield and yield components, next-generation sequencing was used. As a result of the biometric measurements analysis, differentiation in the average elevation of the analyzed traits for the lines in both locations was found. The above-mentioned results indicate the existence of genotype–environment interactions. The analysis of variance for the observed quality between genotypes indicated a statistically significant differentiation between genotypes and a statistically significant differentiation for all the observed properties betweenlocations. A canonical variable analysis was applied to present a multi-trait assessment of the similarity of the tested maize genotypes in a lower number of dimensions with the lowest possible loss of information. No grouping of lines due to the analyzed was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. The genetic distance between the analyzed lines was estimated on the basis of these markers. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNPs) significantly related to the analyzed yield components were selected as a result of association mapping. The greatest numbers of molecular markers were associated with cob length (1203), cob diameter (1759), core length (1201) and core diameter (2326). From 15,409 markers significantly related to the analyzed traits of the yield components, 18 DArT markers were selected, which were significant for the same four traits (cob length, cob diameter, core length, core diameter) in both Kobierzyce and Smolice. These markers were used for physical mapping. As a result of the analyses, it was found that 6 out of 18 (1818; 14,506; 2317; 3233; 11,657; 12,812) identified markers are located inside genes. These markers are located on chromosomes 8, 9, 7, 3, 5, and 1, respectively.
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15
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Ma Z, Hui H, Huang Y, Yao Y, Sun Y, Liu B, Gao Z. Evaluation of Maize Hybrids for Identifying Resistance to Northern Corn Leaf Blight in Northeast China. PLANT DISEASE 2022; 106:1003-1008. [PMID: 34735284 DOI: 10.1094/pdis-09-21-1914-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Northern corn leaf blight (NCLB) caused by Setosphaeria turcica is one of the most devastating foliar diseases in maize (Zea mays L.), resulting in great economic losses worldwide. The mutation of the pathogen exacerbates the occurrence and harmfulness of NCLB in China. Therefore, there is an urgent need for evaluating and cultivating resistant hybrids. Here, the response of 239 maize hybrids approved in Northeast China to NCLB was evaluated during 2019 and 2020. The results showed that 92 (38.49%) and 75 (31.38%) hybrids were rated as moderately resistant and resistant, respectively, which together constituted the predominant resistant categories. We observed that maize hybrids from different certified sources had different levels of resistance to NCLB, whose disease parameter values varied significantly (P < 0.05) among 52 main cultivated hybrids. In 2019 and 2020, the average size of the lesions increased from 21.02 to 21.06 cm2, the average lesion density decreased from 1.36 to 1.33 lesions/100 cm2, and more than 30% of the hybrids registered final disease severity scores between 10 and 30%. The area under the disease progress curve of the main cultivated hybrids ranged from 57.96 to 986.86 cm2 in 2019 and from 50.75 to 1,028.65 cm2 in 2020. Correlation analysis revealed a significant relationship (P < 0.0001) among four disease parameters. Current research has shown that many maize hybrids in Northeast China are resistant to NCLB, suggesting that the large-scale cultivation of susceptible hybrids has led to the occurrence and prevalence of the disease. This study should assist growers in purposefully selecting resistant commercial hybrids to contribute to the management of NCLB.
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Affiliation(s)
- Zhoujie Ma
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Hongyan Hui
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Yufei Huang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yuan Yao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Yangqiu Sun
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Bo Liu
- College of Life Sciences, Yan'an University, Yan'an 716000, Shaanxi, China
| | - Zenggui Gao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
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16
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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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17
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Adak A, Murray SC, Anderson SL, Popescu SC, Malambo L, Romay MC, de Leon N. Unoccupied aerial systems discovered overlooked loci capturing the variation of entire growing period in maize. THE PLANT GENOME 2021; 14:e20102. [PMID: 34009740 DOI: 10.1002/tpg2.20102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Traditional phenotyping methods, coupled with genetic mapping in segregating populations, have identified loci governing complex traits in many crops. Unoccupied aerial systems (UAS)-based phenotyping has helped to reveal a more novel and dynamic relationship between time-specific associated loci with complex traits previously unable to be evaluated. Over 1,500 maize (Zea mays L.) hybrid row plots containing 280 different replicated maize hybrids from the Genomes to Fields (G2F) project were evaluated agronomically and using UAS in 2017. Weekly UAS flights captured variation in plant heights during the growing season under three different management conditions each year: optimal planting with irrigation (G2FI), optimal dryland planting without irrigation (G2FD), and a stressed late planting (G2LA). Plant height of different flights were ranked based on importance for yield using a random forest (RF) algorithm. Plant heights captured by early flights in G2FI trials had higher importance (based on Gini scores) for predicting maize grain yield (GY) but also higher accuracies in genomic predictions which fluctuated for G2FD (-0.06∼0.73), G2FI (0.33∼0.76), and G2LA (0.26∼0.78) trials. A genome-wide association analysis discovered 52 significant single nucleotide polymorphisms (SNPs), seven were found consistently in more than one flights or trial; 45 were flight or trial specific. Total cumulative marker effects for each chromosome's contributions to plant height also changed depending on flight. Using UAS phenotyping, this study showed that many candidate genes putatively play a role in the regulation of plant architecture even in relatively early stages of maize growth and development.
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Affiliation(s)
- Alper Adak
- Dept. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843-2474, USA
| | - Seth C Murray
- Dept. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843-2474, USA
| | - Steven L Anderson
- Dept. of Environmental Hort., Institute of Food and Agricultural Sciences, Mid-Florida Research and Education Center, University of Florida, Apopka, FL, USA
| | - Sorin C Popescu
- Dept. of Ecosystem Science and Management, Texas A&M Univ., College Station, TX, 77843-2120, USA
| | - Lonesome Malambo
- Dept. of Ecosystem Science and Management, Texas A&M Univ., College Station, TX, 77843-2120, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI, 53706, USA
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18
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Gowda M, Makumbi D, Das B, Nyaga C, Kosgei T, Crossa J, Beyene Y, Montesinos-López OA, Olsen MS, Prasanna BM. Genetic dissection of Striga hermonthica (Del.) Benth. resistance via genome-wide association and genomic prediction in tropical maize germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:941-958. [PMID: 33388884 PMCID: PMC7925482 DOI: 10.1007/s00122-020-03744-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 12/02/2020] [Indexed: 06/01/2023]
Abstract
KEY MESSAGE Genome-wide association revealed that resistance to Striga hermonthica is influenced by multiple genomic regions with moderate effects. It is possible to increase genetic gains from selection for Striga resistance using genomic prediction. Striga hermonthica (Del.) Benth., commonly known as the purple witchweed or giant witchweed, is a serious problem for maize-dependent smallholder farmers in sub-Saharan Africa. Breeding for Striga resistance in maize is complicated due to limited genetic variation, complexity of resistance and challenges with phenotyping. This study was conducted to (i) evaluate a set of diverse tropical maize lines for their responses to Striga under artificial infestation in three environments in Kenya; (ii) detect quantitative trait loci associated with Striga resistance through genome-wide association study (GWAS); and (iii) evaluate the effectiveness of genomic prediction (GP) of Striga-related traits. An association mapping panel of 380 inbred lines was evaluated in three environments under artificial Striga infestation in replicated trials and genotyped with 278,810 single-nucleotide polymorphism (SNP) markers. Genotypic and genotype x environment variations were significant for measured traits associated with Striga resistance. Heritability estimates were moderate (0.42) to high (0.92) for measured traits. GWAS revealed 57 SNPs significantly associated with Striga resistance indicator traits and grain yield (GY) under artificial Striga infestation with low to moderate effect. A set of 32 candidate genes physically near the significant SNPs with roles in plant defense against biotic stresses were identified. GP with different cross-validations revealed that prediction of performance of lines in new environments is better than prediction of performance of new lines for all traits. Predictions across environments revealed high accuracy for all the traits, while inclusion of GWAS-detected SNPs led to slight increase in the accuracy. The item-based collaborative filtering approach that incorporates related traits evaluated in different environments to predict GY and Striga-related traits outperformed GP for Striga resistance indicator traits. The results demonstrated the polygenic nature of resistance to S. hermonthica, and that implementation of GP in Striga resistance breeding could potentially aid in increasing genetic gain for this important trait.
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Affiliation(s)
- Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya.
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Christine Nyaga
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Titus Kosgei
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
- Moi University, P. O. Box 3900-30100, Eldoret, Kenya
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, D.F, Mexico
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | | | - Michael S Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, 00621, Nairobi, Kenya
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Lu X, Wang J, Wang Y, Wen W, Zhang Y, Du J, Zhao Y, Guo X. Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage. Front Genet 2021; 11:571236. [PMID: 33519889 PMCID: PMC7838602 DOI: 10.3389/fgene.2020.571236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value < 1.28e-6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.
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Affiliation(s)
- Xianju Lu
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjian Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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20
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Zang Z, Wang Z, Zhao F, Yang W, Ci J, Ren X, Jiang L, Yang W. Maize Ethylene Response Factor ZmERF061 Is Required for Resistance to Exserohilum turcicum. FRONTIERS IN PLANT SCIENCE 2021; 12:630413. [PMID: 33767717 PMCID: PMC7985547 DOI: 10.3389/fpls.2021.630413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/14/2021] [Indexed: 05/09/2023]
Abstract
Plants have evolved a series of sophisticated defense mechanisms to help them from harm. Ethylene Response Factor (ERF) plays pivotal roles in plant immune reactions, however, its underlying mechanism in maize with a defensive function to Exserohilum turcicum (E. turcicum) remains poorly understood. Here, we isolated and characterized a novel ERF transcription factor, designated ZmERF061, from maize. Phylogenetic analysis revealed that ZmERF061 is a member of B3 group in the ERF family. qRT-PCR assays showed that the expression of ZmERF061 is significantly induced by E. turcicum inoculation and hormone treatments with salicylic acid (SA) and methyl jasmonate (MeJA). ZmERF061 was proved to function as a nucleus-localized transcription activator and specifically bind to the GCC-box element. zmerf061 mutant lines resulted in enhanced susceptibility to E. turcicum via decreasing the expression of ZmPR10.1 and ZmPR10.2 and the activity of antioxidant defense system. zmerf061 mutant lines increased the expression of the SA signaling-related gene ZmPR1a and decreased the expression of the jasmonic acid (JA) signaling-related gene ZmLox1 after infection with E. turcicum. In addition, ZmERF061 could interact with ZmMPK6-1. These results suggested that ZmERF061 plays an important role in response to E. turcicum and may be useful in genetic engineering breeding.
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Affiliation(s)
- Zhenyuan Zang
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Zhen Wang
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Fuxing Zhao
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Wei Yang
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Jiabin Ci
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Xuejiao Ren
- College of Agriculture, Jilin Agricultural University, Changchun, China
| | - Liangyu Jiang
- College of Agriculture, Jilin Agricultural University, Changchun, China
- Crop Science Post-doctoral Station, Jilin Agricultural University, Changchun, China
- *Correspondence: Liangyu Jiang,
| | - Weiguang Yang
- College of Agriculture, Jilin Agricultural University, Changchun, China
- Weiguang Yang,
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Galiano-Carneiro AL, Kessel B, Presterl T, Miedaner T. Intercontinental trials reveal stable QTL for Northern corn leaf blight resistance in Europe and in Brazil. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:63-79. [PMID: 32995900 PMCID: PMC7813747 DOI: 10.1007/s00122-020-03682-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE NCLB is the most devastating leaf disease in European maize, and the introduction of Brazilian resistance donors can efficiently increase the resistance levels of European maize germplasm. Northern corn leaf blight (NCLB) is one of the most devastating leaf pathogens in maize (Zea mays L.). Maize cultivars need to be equipped with broad and stable NCLB resistance to cope with production intensification and climate change. Brazilian germplasm is a great source to increase low NCLB resistance levels in European materials, but little is known about their effect in European environments. To investigate the usefulness of Brazilian germplasm as NCLB resistance donors, we conducted multi-parent QTL mapping, evaluated the potential of marker-assisted selection as well as genome-wide selection of 742 F1-derived DH lines. The line per se performance was evaluated in one location in Brazil and six location-by-year combinations (= environments) in Europe, while testcrosses were assessed in two locations in Brazil and further 10 environments in Europe. Jointly, we identified 17 QTL for NCLB resistance explaining 3.57-30.98% of the genotypic variance each. Two of these QTL were detected in both Brazilian and European environments indicating the stability of these QTL in contrasting ecosystems. We observed moderate to high genomic prediction accuracies between 0.58 and 0.83 depending on population and continent. Collectively, our study illustrates the potential use of tropical resistance sources to increase NCLB resistance level in applied European maize breeding programs.
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Affiliation(s)
| | - Bettina Kessel
- Kleinwanzlebener Saatzucht (KWS) KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Thomas Presterl
- Kleinwanzlebener Saatzucht (KWS) KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany.
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Miedaner T, Boeven ALGC, Gaikpa DS, Kistner MB, Grote CP. Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize. Int J Mol Sci 2020; 21:E9717. [PMID: 33352763 PMCID: PMC7766114 DOI: 10.3390/ijms21249717] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Generating genomics-driven knowledge opens a way to accelerate the resistance breeding process by family or population mapping and genomic selection. Important prerequisites are large populations that are genomically analyzed by medium- to high-density marker arrays and extensive phenotyping across locations and years of the same populations. The latter is important to train a genomic model that is used to predict genomic estimated breeding values of phenotypically untested genotypes. After reviewing the specific features of quantitative resistances and the basic genomic techniques, the possibilities for genomics-assisted breeding are evaluated for six pathosystems with hemi-biotrophic fungi: Small-grain cereals/Fusarium head blight (FHB), wheat/Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB), maize/Gibberella ear rot (GER) and Fusarium ear rot (FER), maize/Northern corn leaf blight (NCLB). Typically, all quantitative disease resistances are caused by hundreds of QTL scattered across the whole genome, but often available in hotspots as exemplified for NCLB resistance in maize. Because all crops are suffering from many diseases, multi-disease resistance (MDR) is an attractive aim that can be selected by specific MDR QTL. Finally, the integration of genomic data in the breeding process for introgression of genetic resources and for the improvement within elite materials is discussed.
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Affiliation(s)
- Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
| | - Ana Luisa Galiano-Carneiro Boeven
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
- Kleinwanzlebener Saatzucht (KWS) SAAT SE & Co. KGaA, 37574 Einbeck, Germany
| | - David Sewodor Gaikpa
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
| | - Maria Belén Kistner
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
- Estación Experimental Pergamino, Instituto Nacional de Tecnología Agropecuaria (INTA), CC31, B2700WAA Pergamino, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, C1425FQB Buenos Aires, Argentina
| | - Cathérine Pauline Grote
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany; (A.L.G.-C.B.); (D.S.G.); (M.B.K.); (C.P.G.)
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23
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Rashid Z, Sofi M, Harlapur SI, Kachapur RM, Dar ZA, Singh PK, Zaidi PH, Vivek BS, Nair SK. Genome-wide association studies in tropical maize germplasm reveal novel and known genomic regions for resistance to Northern corn leaf blight. Sci Rep 2020; 10:21949. [PMID: 33319847 PMCID: PMC7738672 DOI: 10.1038/s41598-020-78928-5] [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: 07/15/2020] [Accepted: 11/26/2020] [Indexed: 02/08/2023] Open
Abstract
Northern Corn Leaf Blight (NCLB) caused by Setosphaeria turcica, is one of the most important diseases of maize world-wide, and one of the major reasons behind yield losses in maize crop in Asia. In the present investigation, a high-resolution genome wide association study (GWAS) was conducted for NCLB resistance in three association mapping panels, predominantly consisting of tropical lines adapted to different agro-ecologies. These panels were phenotyped for disease severity across three locations with high disease prevalence in India. High density SNPs from Genotyping-by-sequencing were used in GWAS, after controlling for population structure and kinship matrices, based on single locus mixed linear model (MLM). Twenty-two SNPs were identified, that revealed a significant association with NCLB in the three mapping panels. Haplotype regression analysis revealed association of 17 significant haplotypes at FDR ≤ 0.05, with two common haplotypes across three maize panels. Several of the significantly associated SNPs/haplotypes were found to be co-located in chromosomal bins previously reported for major genes like Ht2, Ht3 and Htn1 and QTL for NCLB resistance and multiple foliar disease resistance. Phenotypic variance explained by these significant SNPs/haplotypes ranged from low to moderate, suggesting a breeding strategy of combining multiple resistance alleles towards resistance for NCLB.
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Affiliation(s)
- Zerka Rashid
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Mehrajuddin Sofi
- High Mountain Arid Agricultural Research Institute (HMAARI) Stakna, SKUAST-Kashmir, Leh, 194101, India
| | - Sharanappa I Harlapur
- University of Agricultural Sciences, Krishi Nagar, Dharwad, Karnataka, 580005, India
| | | | - Zahoor Ahmed Dar
- Sher-E-Kashmir University of Agriculture Sciences and Technology (SKUAST), Srinagar, Jammu and Kashmir, 190001, India
| | - Pradeep Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Pervez Haider Zaidi
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Bindiganavile Sampath Vivek
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India
| | - Sudha Krishnan Nair
- International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad Telangana, 502324, India.
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Yang Y, He R, Zheng J, Hu Z, Wu J, Leng P. Development of EST-SSR markers and association mapping with floral traits in Syringa oblata. BMC PLANT BIOLOGY 2020; 20:436. [PMID: 32957917 PMCID: PMC7507607 DOI: 10.1186/s12870-020-02652-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata. RESULTS In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait. CONCLUSION The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.
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Affiliation(s)
- Yunyao Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruiqing He
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
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25
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Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm. Int J Mol Sci 2020; 21:ijms21186518. [PMID: 32899999 PMCID: PMC7555316 DOI: 10.3390/ijms21186518] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 12/27/2022] Open
Abstract
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37-0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6-10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14-40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize.
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Xia H, Gao W, Qu J, Dai L, Gao Y, Lu S, Zhang M, Wang P, Wang T. Genetic mapping of northern corn leaf blight-resistant quantitative trait loci in maize. Medicine (Baltimore) 2020; 99:e21326. [PMID: 32756117 PMCID: PMC7402768 DOI: 10.1097/md.0000000000021326] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Northern corn leaf blight (NCLB), a corn disease infected by Exserohilum turcicum, can cause loss of harvest and economy. Identification or evaluation of NCLB-resistant quantitative trait loci (QTL) and genes could improve maize breeds. This study aimed to identify novel QTLs for NCLB-resistance.Two maize strains (BB and BC) were utilized to generate B73 × B97 and B73 × CML322 and constructed the genetic linkage using high-throughput single nucleotide polymorphism (SNP) linkage map analysis of 170 (BB) and 163(BC) recombinant inbred line (RIL) genomic DNA samples. NCLB-resistant QTL was associated with phenotypic data from the field trial of 170 BB and 163 BC strains over two years using these 1100 SNPs to identify high-density NCLB-resistant QTLs.In BB, QTL of the NCLB resistance was on chromosome 1 and 3 (LOD scores between 2.74 and 5.44); in BC, QTL of NCLB resistance was on chromosome 1, 2, 4, 8, and 9 (LOD scores between 2.52 and 8.53). A number of genes or genetic information related to NCLB resistance in both BB and BC were identified with the maximum number of genes/NCLB resistance-related QTL on chromosome 3 for BB and on chromosome 1 for BC.This study successfully mapped and identified NCLB-resistant QTL and genes for these 2 different maize strains, which provides insightful information for future study of NCLB-resistance and selection of NCLB-resistant maize variants.
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Affiliation(s)
- Haifeng Xia
- Tonghua Academy of Agricultural Sciences, Tonghua
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Wei Gao
- Tonghua Academy of Agricultural Sciences, Tonghua
| | - Jing Qu
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Liqiang Dai
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Yan Gao
- Tonghua Academy of Agricultural Sciences, Tonghua
| | - Shi Lu
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Mo Zhang
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Piwu Wang
- College of Agronomy, Jilin Agricultural University, Changchun
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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27
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Zhang X, Fernandes SB, Kaiser C, Adhikari P, Brown PJ, Mideros SX, Jamann TM. Conserved defense responses between maize and sorghum to Exserohilum turcicum. BMC PLANT BIOLOGY 2020; 20:67. [PMID: 32041528 PMCID: PMC7011368 DOI: 10.1186/s12870-020-2275-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/03/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Exserohilum turcicum is an important pathogen of both sorghum and maize, causing sorghum leaf blight and northern corn leaf blight. Because the same pathogen can infect and cause major losses for two of the most important grain crops, it is an ideal pathosystem to study plant-pathogen evolution and investigate shared resistance mechanisms between the two plant species. To identify sorghum genes involved in the E. turcicum response, we conducted a genome-wide association study (GWAS). RESULTS Using the sorghum conversion panel evaluated across three environments, we identified a total of 216 significant markers. Based on physical linkage with the significant markers, we detected a total of 113 unique candidate genes, some with known roles in plant defense. Also, we compared maize genes known to play a role in resistance to E. turcicum with the association mapping results and found evidence of genes conferring resistance in both crops, providing evidence of shared resistance between maize and sorghum. CONCLUSIONS Using a genetics approach, we identified shared genetic regions conferring resistance to E. turcicum in both maize and sorghum. We identified several promising candidate genes for resistance to leaf blight in sorghum, including genes related to R-gene mediated resistance. We present significant advancements in the understanding of host resistance to E. turcicum, which is crucial to reduce losses due to this important pathogen.
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Affiliation(s)
- Xiaoyue Zhang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samuel B Fernandes
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Christopher Kaiser
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pragya Adhikari
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Patrick J Brown
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Santiago X Mideros
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Tiffany M Jamann
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Liu J, Fernie AR, Yan J. The Past, Present, and Future of Maize Improvement: Domestication, Genomics, and Functional Genomic Routes toward Crop Enhancement. PLANT COMMUNICATIONS 2020; 1:100010. [PMID: 33404535 PMCID: PMC7747985 DOI: 10.1016/j.xplc.2019.100010] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 05/14/2023]
Abstract
After being domesticated from teosinte, cultivated maize (Zea mays ssp. mays) spread worldwide and now is one of the most important staple crops. Due to its tremendous phenotypic and genotypic diversity, maize also becomes to be one of the most widely used model plant species for fundamental research, with many important discoveries reported by maize researchers. Here, we provide an overview of the history of maize domestication and key genes controlling major domestication-related traits, review the currently available resources for functional genomics studies in maize, and discuss the functions of most of the maize genes that have been positionally cloned and can be used for crop improvement. Finally, we provide some perspectives on future directions regarding functional genomics research and the breeding of maize and other crops.
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Affiliation(s)
- Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
| | - Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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Heuermann MC, Rosso MG, Mascher M, Brandt R, Tschiersch H, Altschmied L, Altmann T. Combining next-generation sequencing and progeny testing for rapid identification of induced recessive and dominant mutations in maize M 2 individuals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:851-862. [PMID: 31169333 PMCID: PMC6899793 DOI: 10.1111/tpj.14431] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 05/31/2023]
Abstract
Molecular identification of mutant alleles responsible for certain phenotypic alterations is a central goal of genetic analyses. In this study we describe a rapid procedure suitable for the identification of induced recessive and dominant mutations applied to two Zea mays mutants expressing a dwarf and a pale green phenotype, respectively, which were obtained through pollen ethyl methanesulfonate (EMS) mutagenesis. First, without prior backcrossing, induced mutations (single nucleotide polymorphisms, SNPs) segregating in a (M2 ) family derived from a heterozygous (M1 ) parent were identified using whole-genome shotgun (WGS) sequencing of a small number of (M2 ) individuals with mutant and wild-type phenotypes. Second, the state of zygosity of the mutation causing the phenotype was determined for each sequenced individual by phenotypic segregation analysis of the self-pollinated (M3 ) offspring. Finally, we filtered for segregating EMS-induced SNPs whose state of zygosity matched the determined state of zygosity of the mutant locus in each sequenced (M2 ) individuals. Through this procedure, combining sequencing of individuals and Mendelian inheritance, three and four SNPs in linkage passed our zygosity filter for the homozygous dwarf and heterozygous pale green mutation, respectively. The dwarf mutation was found to be allelic to the an1 locus and caused by an insertion in the largest exon of the AN1 gene. The pale green mutation affected the nuclear W2 gene and was caused by a non-synonymous amino acid exchange in encoded chloroplast DNA polymerase with a predicted deleterious effect. This coincided with lower cpDNA levels in pale green plants.
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Affiliation(s)
- Marc C. Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Mario G. Rosso
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Ronny Brandt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
- Max Planck‐Genome‐Centre CologneMax Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829KölnGermany
| | - Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenCorrensstrasse 306466Seeland OT GaterslebenGermany
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Natural variation in ZmFBL41 confers banded leaf and sheath blight resistance in maize. Nat Genet 2019; 51:1540-1548. [DOI: 10.1038/s41588-019-0503-y] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 08/19/2019] [Indexed: 11/08/2022]
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Sitonik C, Suresh LM, Beyene Y, Olsen MS, Makumbi D, Oliver K, Das B, Bright JM, Mugo S, Crossa J, Tarekegne A, Prasanna BM, Gowda M. Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2381-2399. [PMID: 31098757 PMCID: PMC6647133 DOI: 10.1007/s00122-019-03360-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/08/2019] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE Analysis of the genetic architecture of MCMV and MLN resistance in maize doubled-haploid populations revealed QTLs with major effects on chromosomes 3 and 6 that were consistent across genetic backgrounds and environments. Two major-effect QTLs, qMCMV3-108/qMLN3-108 and qMCMV6-17/qMLN6-17, were identified as conferring resistance to both MCMV and MLN. Maize lethal necrosis (MLN) is a serious threat to the food security of maize-growing smallholders in sub-Saharan Africa. The ability of the maize chlorotic mottle virus (MCMV) to interact with other members of the Potyviridae causes severe yield losses in the form of MLN. The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkage association mapping (JLAM) revealed 18 and 21 main-effect QTLs for MCMV and MLN resistance, respectively. Another major-effect QTL, qMCMV6-17/qMLN6-17, was detected for both MCMV and MLN resistance. The GWAS revealed a total of 54 SNPs (MCMV-13 and MLN-41) significantly associated (P ≤ 5.60 × 10-05) with MCMV and MLN resistance. Most of the GWAS-identified SNPs were within or adjacent to the QTLs detected through linkage mapping. The prediction accuracy for within populations as well as the combined populations is promising; however, the accuracy was low across populations. Overall, MCMV resistance is controlled by a few major and many minor-effect loci and seems more complex than the genetic architecture for MLN resistance.
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Affiliation(s)
- Chelang'at Sitonik
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
- Department of Plant Breeding and Biotechnology, University of Eldoret (UoE), P.O. Box 1125, Eldoret, 30100, Kenya
| | - L M Suresh
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Michael S Olsen
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Kiplagat Oliver
- Department of Plant Breeding and Biotechnology, University of Eldoret (UoE), P.O. Box 1125, Eldoret, 30100, Kenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Jumbo M Bright
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Stephen Mugo
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, DF, Mexico
| | - Amsal Tarekegne
- International Maize and Wheat Improvement Center (CIMMYT), 12.5 km Peg Mazowe Road, Mount Pleasant, P.O. Box MP163, Harare, Zimbabwe
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya.
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041-00621, Village Market, Nairobi, 00621, Kenya.
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SNP-based mixed model association of growth- and yield-related traits in popcorn. PLoS One 2019; 14:e0218552. [PMID: 31237892 PMCID: PMC6592533 DOI: 10.1371/journal.pone.0218552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/04/2019] [Indexed: 12/26/2022] Open
Abstract
The identification of the genes responsible for complex traits is highly promising to accelerate crop breeding, but such information is still limited for popcorn. Thus, in the present study, a mixed linear model-based association analysis (MLMA) was applied for six important popcorn traits: plant and ear height, 100-grain weight, popping expansion, grain yield and expanded popcorn volume per hectare. To this end, 196 plants of the open-pollinated popcorn population UENF-14 were sampled, selfed (S1), and then genotyped with a panel of 10,507 single nucleotide polymorphisms (SNPs) markers distributed throughout the genome. The six traits were studied under two environments [Campos dos Goytacazes-RJ (ENV1) and Itaocara-RJ (ENV2)] in an incomplete block design. Based on the phenotypic data of the S1 progenies and on the genetic characteristics of the parents, the MLMA was performed. Thereafter, genes annotated in the MaizeGDB platform were screened for potential linkage disequilibrium with the SNPs associated to the six evaluated traits. Overall, seven and eight genes were identified as associated with the traits in ENV1 and ENV2, respectively, and proteins encoded by these genes were evaluated for their function. The results obtained here contribute to increase knowledge on the genetic architecture of the six evaluated traits and might be used for marker-assisted selection in breeding programs.
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Yuan Y, Cairns JE, Babu R, Gowda M, Makumbi D, Magorokosho C, Zhang A, Liu Y, Wang N, Hao Z, San Vicente F, Olsen MS, Prasanna BM, Lu Y, Zhang X. Genome-Wide Association Mapping and Genomic Prediction Analyses Reveal the Genetic Architecture of Grain Yield and Flowering Time Under Drought and Heat Stress Conditions in Maize. FRONTIERS IN PLANT SCIENCE 2019; 9:1919. [PMID: 30761177 PMCID: PMC6363715 DOI: 10.3389/fpls.2018.01919] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/10/2018] [Indexed: 05/20/2023]
Abstract
Drought stress (DS) is a major constraint to maize yield production. Heat stress (HS) alone and in combination with DS are likely to become the increasing constraints. Association mapping and genomic prediction (GP) analyses were conducted in a collection of 300 tropical and subtropical maize inbred lines to reveal the genetic architecture of grain yield and flowering time under well-watered (WW), DS, HS, and combined DS and HS conditions. Out of the 381,165 genotyping-by-sequencing SNPs, 1549 SNPs were significantly associated with all the 12 trait-environment combinations, the average PVE (phenotypic variation explained) by these SNPs was 4.33%, and 541 of them had a PVE value greater than 5%. These significant associations were clustered into 446 genomic regions with a window size of 20 Mb per region, and 673 candidate genes containing the significantly associated SNPs were identified. In addition, 33 hotspots were identified for 12 trait-environment combinations and most were located on chromosomes 1 and 8. Compared with single SNP-based association mapping, the haplotype-based associated mapping detected fewer number of significant associations and candidate genes with higher PVE values. All the 688 candidate genes were enriched into 15 gene ontology terms, and 46 candidate genes showed significant differential expression under the WW and DS conditions. Association mapping results identified few overlapped significant markers and candidate genes for the same traits evaluated under different managements, indicating the genetic divergence between the individual stress tolerance and the combined drought and HS tolerance. The GP accuracies obtained from the marker-trait associated SNPs were relatively higher than those obtained from the genome-wide SNPs for most of the target traits. The genetic architecture information of the grain yield and flowering time revealed in this study, and the genomic regions identified for the different trait-environment combinations are useful in accelerating the efforts on rapid development of the stress-tolerant maize germplasm through marker-assisted selection and/or genomic selection.
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Affiliation(s)
- Yibing Yuan
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Jill E. Cairns
- International Maize and Wheat Improvement Center, Harare, Zimbabwe
| | - Raman Babu
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Manje Gowda
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | | | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yubo Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Nan Wang
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhuanfang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Michael S. Olsen
- International Maize and Wheat Improvement Center, Nairobi, Kenya
| | | | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center, Texcoco, Mexico
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Lamara M, Parent GJ, Giguère I, Beaulieu J, Bousquet J, MacKay JJ. Association genetics of acetophenone defence against spruce budworm in mature white spruce. BMC PLANT BIOLOGY 2018; 18:231. [PMID: 30309315 PMCID: PMC6182838 DOI: 10.1186/s12870-018-1434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 09/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Outbreaks of spruce budworm (SBW, Choristoneura fumiferana Clem.) cause major recurrent damage in boreal conifers such as white spruce (Picea glauca [Moench] Voss) and large losses of forest biomass in North America. Although defensive phenolic compounds have recently been linked to chemical resistance against SBW, their genetic basis remains poorly understood in forest trees, especially in conifers. Here, we used diverse association genetics approaches to discover genes and their variants that may control the accumulation of acetophenones, and dissect the genetic architecture of these defence compounds against SBW in white spruce mature trees. RESULTS Out of 4747 single nucleotide polymorphisms (SNPs) from 2312 genes genotyped in a population of 211 unrelated individuals, genetic association analyses identified 35 SNPs in 33 different genes that were significantly associated with the defence traits by using single-locus, multi-locus and multi-trait approaches. The multi-locus approach was particularly effective at detecting SNP-trait associations that explained a large fraction of the phenotypic variance (from 20 to 43%). Significant genes were regulatory including the NAC transcription factor, or they were involved in carbohydrate metabolism, falling into the binding, catalytic or transporter activity functional classes. Most of them were highly expressed in foliage. Weak positive phenotypic correlations were observed between defence and growth traits, indicating little or no evidence of defence-growth trade-offs. CONCLUSIONS This study provides new insights on the genetic architecture of tree defence traits, contributing to our understanding of the physiology of resistance mechanisms to biotic factors and providing a basis for the genetic improvement of the constitutive defence of white spruce against SBW.
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Affiliation(s)
- Mebarek Lamara
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | | | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Beaulieu
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
| | - John J. MacKay
- Forest Research Centre and Institute for Systems and Integrative Biology, Département des sciences du bois et de la forêt, Université Laval, Qc, Québec, G1V 0A6 Canada
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
- Canada Research Chair in Forest Genomics, Université Laval, Qc, Québec, G1V 0A6 Canada
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Increased experimental conditions and marker densities identified more genetic loci associated with southern and northern leaf blight resistance in maize. Sci Rep 2018; 8:6848. [PMID: 29717181 PMCID: PMC5931595 DOI: 10.1038/s41598-018-25304-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
Southern leaf blight (SLB) and northern leaf blight (NLB) are the two major foliar diseases limiting maize production worldwide. Upon previous study with the nested association mapping (NAM) population, which consist of 5,000 recombinant inbred lines from 25 parents crossed with B73, we expanded the phenotyping environments from the United States (US) to China, and increased the marker densities from 1106 to 7386 SNPs for linkage mapping, and from 1.6 to 28.5 million markers for association mapping. We identified 49 SLB and 48 NLB resistance-related unique QTLs in linkage mapping, and multiple loci in association mapping with candidate genes involved in known plant disease-resistance pathways. Furthermore, an independent natural population with 282 diversified inbred lines were sequenced for four candidate genes selected based on their biological functions. Three of them demonstrated significant associations with disease resistance. These findings provided valuable resources for further implementations to develop varieties with superior resistance for NLB and SLB.
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Galiano-Carneiro AL, Miedaner T. Genetics of Resistance and Pathogenicity in the Maize/ Setosphaeria turcica Pathosystem and Implications for Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:1490. [PMID: 28900437 PMCID: PMC5581881 DOI: 10.3389/fpls.2017.01490] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/11/2017] [Indexed: 05/24/2023]
Abstract
Northern corn leaf blight (NCLB), the most devastating leaf pathogen in maize (Zea mays L.), is caused by the heterothallic ascomycete Setosphaeria turcica. The pathogen population shows an extremely high genetic diversity in tropical and subtropical regions. Varietal resistance is the most efficient technique to control NCLB. Host resistance can be qualitative based on race-specific Ht genes or quantitative controlled by many genes with small effects. Quantitative resistance is moderately to highly effective and should be more durable combatting all races of the pathogen. Quantitative resistance must, however, be analyzed in many environments (= location × year combinations) to select stable resistances. In the tropical and subtropical environments, quantitative resistance is the preferred option to manage NCLB epidemics. Resistance level can be increased in practical breeding programs by several recurrent selection cycles based on disease severity rating and/or by genomic selection. This review aims to address two important aspects of the NCLB pathosystem: the genetics of the fungus S. turcica and the modes of inheritance of the host plant maize, including successful breeding strategies regarding NCLB resistance. Both drivers of this pathosystem, pathogen, and host, must be taken into account to result in more durable resistance.
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Affiliation(s)
- Ana L. Galiano-Carneiro
- State Plant Breeding Institute, University of HohenheimStuttgart, Germany
- Kleinwanzlebener Saatzucht (KWS) SAAT SEEinbeck, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of HohenheimStuttgart, Germany
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Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K. Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 2017; 109:475-484. [PMID: 28751185 DOI: 10.1016/j.ygeno.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022]
Abstract
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.
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Affiliation(s)
- Vipavee Chanroj
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Ratchanee Rattanawong
- Nong Khai Rubber Research Center, Rubber Research Institute of Thailand, Rattanawapi District, Nong Khai, 43120, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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Wang X, Luo G, Yang W, Li Y, Sun J, Zhan K, Liu D, Zhang A. Genetic diversity, population structure and marker-trait associations for agronomic and grain traits in wild diploid wheat Triticum urartu. BMC PLANT BIOLOGY 2017; 17:112. [PMID: 28668082 PMCID: PMC5494140 DOI: 10.1186/s12870-017-1058-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/14/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND Wild diploid wheat, Triticum urartu (T. urartu) is the progenitor of bread wheat, and understanding its genetic diversity and genome function will provide considerable reference for dissecting genomic information of common wheat. RESULTS In this study, we investigated the morphological and genetic diversity and population structure of 238 T. urartu accessions collected from different geographic regions. This collection had 19.37 alleles per SSR locus and its polymorphic information content (PIC) value was 0.76, and the PIC and Nei's gene diversity (GD) of high-molecular-weight glutenin subunits (HMW-GSs) were 0.86 and 0.88, respectively. UPGMA clustering analysis indicated that the 238 T. urartu accessions could be classified into two subpopulations, of which Cluster I contained accessions from Eastern Mediterranean coast and those from Mesopotamia and Transcaucasia belonged to Cluster II. The wide range of genetic diversity along with the manageable number of accessions makes it one of the best collections for mining valuable genes based on marker-trait association. Significant associations were observed between simple sequence repeats (SSR) or HMW-GSs and six morphological traits: heading date (HD), plant height (PH), spike length (SPL), spikelet number per spike (SPLN), tiller angle (TA) and grain length (GL). CONCLUSIONS Our data demonstrated that SSRs and HMW-GSs were useful markers for identification of beneficial genes controlling important traits in T. urartu, and subsequently for their conservation and future utilization, which may be useful for genetic improvement of the cultivated hexaploid wheat.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Guangbin Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Kehui Zhan
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Chaoyang District, Beijing, 100101 China
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, 450002 China
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Ju M, Zhou Z, Mu C, Zhang X, Gao J, Liang Y, Chen J, Wu Y, Li X, Wang S, Wen J, Yang L, Wu J. Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis. Sci Rep 2017; 7:46446. [PMID: 28422143 PMCID: PMC5396065 DOI: 10.1038/srep46446] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 03/17/2017] [Indexed: 01/22/2023] Open
Abstract
Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.
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Affiliation(s)
- Ming Ju
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zijian Zhou
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Cong Mu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuecai Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingyang Gao
- College of Life sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yakun Liang
- College of Life sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiafa Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yabin Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaopeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Shiwei Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingjing Wen
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianyu Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
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Xiao Y, Liu H, Wu L, Warburton M, Yan J. Genome-wide Association Studies in Maize: Praise and Stargaze. MOLECULAR PLANT 2017; 10:359-374. [PMID: 28039028 DOI: 10.1016/j.molp.2016.12.008] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/02/2016] [Accepted: 12/20/2016] [Indexed: 05/18/2023]
Abstract
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.
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Affiliation(s)
- Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Liuji Wu
- Synergetic Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Marilyn Warburton
- United States of Department of Agriculture, Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, MS 39762, Mississippi, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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Chen L, An Y, Li YX, Li C, Shi Y, Song Y, Zhang D, Wang T, Li Y. Candidate Loci for Yield-Related Traits in Maize Revealed by a Combination of MetaQTL Analysis and Regional Association Mapping. FRONTIERS IN PLANT SCIENCE 2017; 8:2190. [PMID: 29312420 PMCID: PMC5744402 DOI: 10.3389/fpls.2017.02190] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/12/2017] [Indexed: 05/05/2023]
Abstract
Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci.
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Chen J, Shrestha R, Ding J, Zheng H, Mu C, Wu J, Mahuku G. Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm. G3 (BETHESDA, MD.) 2016; 6:3803-3815. [PMID: 27742723 PMCID: PMC5144952 DOI: 10.1534/g3.116.034561] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/25/2016] [Indexed: 11/18/2022]
Abstract
Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1-4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.
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Affiliation(s)
- Jiafa Chen
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Rosemary Shrestha
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
| | - Junqiang Ding
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongjian Zheng
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shangai 201403 China
| | - Chunhua Mu
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jianyu Wu
- College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - George Mahuku
- International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico
- International Institute of Tropical Agriculture, 34441 Dar es Salaam, Tanzania
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Wu J, Cheng F, Cai C, Zhong Y, Jie X. Association mapping for floral traits in cultivated Paeonia rockii based on SSR markers. Mol Genet Genomics 2016; 292:187-200. [PMID: 27807670 DOI: 10.1007/s00438-016-1266-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 10/25/2016] [Indexed: 01/29/2023]
Abstract
Tree peony (Paeonia Sect. Moutan) is an economically important ornamental plant, but little is known about the genetic architecture of important ornamental traits. To effectively improve ornamental value, we require a better understanding of genetic architecture in the complex traits of the tree peony. Association mapping is a powerful tool for detection of variation associated with traits. Thus, we examined the genetic diversity and the population structure of 462 unrelated cultivated P. rockii individuals, then performed association mapping to identify simple sequence repeat (SSR) markers associated with 12 floral traits. We observed a moderate level of genetic diversity (PIC = 0.459) and low linkage disequilibrium (LD) between markers, demonstrating that the potential value of an LD approach in elucidating the molecular basis of the quantitative variation in this species. An analysis of population structure revealed three subgroups in the association population. Subsequent single-marker association analysis identified 46 significant associations, involving the 11 traits with 37 SSRs. These loci explained a small proportion of the phenotypic variance, ranging from 2.68 to 23.97% (mean 5.50%). We also validated 15 of the 46 associations in a linkage mapping population of 159 individuals. Finally, five associations were further confirmed in the linkage mapping population, involving the four traits with four SSRs. These results can serve as a foundation for further analyses of the genetic architecture of floral traits, and the SSRs associated in this work have potential applications in marker-assisted breeding in tree peony.
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Affiliation(s)
- Jing Wu
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Fangyun Cheng
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
| | - Changfu Cai
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Yuan Zhong
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Xiao Jie
- National Flower Engineering Research Centre, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, College of Landscape Architecture, Beijing Forestry University, Beijing, China
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Li K, Wang H, Hu X, Liu Z, Wu Y, Huang C. Genome-Wide Association Study Reveals the Genetic Basis of Stalk Cell Wall Components in Maize. PLoS One 2016; 11:e0158906. [PMID: 27479588 PMCID: PMC4968789 DOI: 10.1371/journal.pone.0158906] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/23/2016] [Indexed: 12/03/2022] Open
Abstract
Lignin, cellulose and hemicellulose are the three main components of the plant cell wall and can impact stalk quality by affecting cell wall structure and strength. In this study, we evaluated the lignin (LIG), cellulose (CEL) and hemicellulose (HC) contents in maize using an association mapping panel that included 368 inbred lines in seven environments. A genome-wide association study using approximately 0.56 million SNPs with a minor allele frequency of 0.05 identified 22, 18 and 24 loci significantly associated with LIG, CEL and HC at P < 1.0×10−4, respectively. The allelic variation of each significant association contributed 4 to 7% of the phenotypic variation. Candidate genes identified by GWAS mainly encode enzymes involved in cell wall metabolism, transcription factors, protein kinase and protein related to other biological processes. Among the association signals, six candidate genes had pleiotropic effects on lignin and cellulose content. These results provide valuable information for better understanding the genetic basis of stalk cell wall components in maize.
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Affiliation(s)
- Kun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwu Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojiao Hu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhifang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yujin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changling Huang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- * E-mail:
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Liu S, Fan C, Li J, Cai G, Yang Q, Wu J, Yi X, Zhang C, Zhou Y. A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1203-15. [PMID: 26912143 DOI: 10.1007/s00122-016-2697-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 02/02/2016] [Indexed: 05/04/2023]
Abstract
A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping. Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson-Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5-1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.
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Affiliation(s)
- Sheng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Guangqin Cai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingyong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinqi Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Wang J, Chu S, Zhang H, Zhu Y, Cheng H, Yu D. Development and application of a novel genome-wide SNP array reveals domestication history in soybean. Sci Rep 2016; 6:20728. [PMID: 26856884 PMCID: PMC4746597 DOI: 10.1038/srep20728] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 01/11/2016] [Indexed: 11/24/2022] Open
Abstract
Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean.
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Affiliation(s)
- Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shanshan Chu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huairen Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Zhu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hao Cheng
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
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