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Li J, Zhai S, Xu X, Su Y, Yu J, Gao Y, Yang J, Zheng Z, Li B, Sun Q, Xie C, Ma J. Dissecting the genetic basis of Fusarium crown rot resistance in wheat by genome wide association study. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:43. [PMID: 38321245 DOI: 10.1007/s00122-024-04553-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
KEY MESSAGE A locus conferring Fusarium crown rot resistance was identified on chromosome arm 3DL through genome wide association study and further validated in two recombinant inbred lines populations. Fusarium crown rot (FCR) is a severe soil borne disease in many wheat growing regions of the world. In this study, we attempted to detect loci conferring FCR resistance through a new seedling inoculation assay. A total of 223 wheat accessions from different geography origins were used to assemble an association panel for GWAS analysis. Four genotypes including Heng 4332, Luwanmai, Pingan 998 and Yannong 24 showed stable resistance to FCR. A total of 54 SNPs associated with FCR resistance were identified. Among the 10 putative QTLs represented by these SNPs, seven QTLs on chromosome 2B, 3A, 3D, 4A, 7A and 7B were novel and were consistently detected in at least two of the three trials conducted. Qfcr.cau.3D-3, which was targeted by 38 SNPs clustered within a genomic region of approximately 5.57 Mb (609.12-614.69 Mb) on chromosome arm 3DL, was consistently detected in all the three trials. The effects of Qfcr.cau.3D-3 were further validated in two recombinant inbred line populations. The presence of this locus reduced FCR severity up to 21.55%. Interestingly, the collinear positions of sequences containing the four SNPs associated with two FCR loci (Qfcr.cau.3A and Qfcr.cau.3B) were within the regions of Qfcr.cau.3D-3, suggesting that genes underlying these three loci may be homologous. Our results provide useful information for improving FCR resistance in wheat.
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Affiliation(s)
- Jinlong Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shanshan Zhai
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiangru Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuqing Su
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiazheng Yu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiatian Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Baoyun Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Li Q, Hao X, Guo Z, Qu K, Gao M, Song G, Yin Z, Yuan Y, Dong C, Niu J, Yin G. Screening and Resistance Locus Identification of the Mutant fcrZ22 Resistant to Crown Rot Caused by Fusarium pseudograminearum. PLANT DISEASE 2024; 108:426-433. [PMID: 37578361 DOI: 10.1094/pdis-06-23-1195-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Crown rot caused by Fusarium pseudograminearum is a devastating wheat disease worldwide. In addition to yield losses, the fungi causing Fusarium crown rot (FCR) also deteriorate the quality and safety of food because of the production of mycotoxins. Planting resistant cultivars is an effective way to control FCR. However, most wheat cultivars are susceptible to FCR. Therefore, development of new sources and detection of loci for FCR resistance are necessary. In the present study, a resistant mutant, fcrZ22, was identified from an ethyl methane sulfonate (EMS)-mutagenized population of the cultivar Zhoumai 22, and then fcrZ22 was crossed with the wild type to produce an F2 population. Genetic analysis of the F2 population was carried out by the mixed inheritance model of major genes plus polygenes, and 20 resistant and 20 susceptible plants were selected to assemble mixed pools. Combining 660K SNP arrays, the resistance loci were detected by bulked segregant analysis. The resistance to FCR caused by F. pseudograminearum in the F2 population was in accordance with the "mixed model with two major genes of additive-epistasis effect + additive-dominant polygenes," and the heritability of the major gene was 0.92. Twenty-one loci were detected, which were located on 10 chromosomes, namely, 1B (1), 1D (1), 2A (3), 1B (1), 3A (3), 3B (3), 4A (2), 5A (2), 7A (3), and 7B (2). Among the 21 loci, eight were new loci for FCR resistance. This is the first report of detecting loci for FCR resistance from a mutant. The results of the present study provided excellent germplasm resources for breeding wheat cultivars with FCR resistance and laid the foundation for fine mapping of FCR resistance loci.
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Affiliation(s)
- Qiaoyun Li
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Xiaopeng Hao
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Zhenfeng Guo
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Kefei Qu
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Mingshuang Gao
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Gaili Song
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Zhao Yin
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Yuhao Yuan
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Chunhao Dong
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jishan Niu
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Guihong Yin
- National Engineering Research Center for Wheat, College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, P.R. China
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Zhou J, Liu Q, Tian R, Chen H, Wang J, Yang Y, Zhao C, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, Tang L, Ren Y, Zheng Z, Liu C, Zheng Y, He Y, Wei Y, Ma J. A co-located QTL for seven spike architecture-related traits shows promising breeding use potential in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:31. [PMID: 38267732 DOI: 10.1007/s00122-023-04536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
KEY MESSAGE A co-located novel QTL for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs with potential of improving wheat yield was identified and validated. Spike-related traits, including fertile florets per spike (FFS), kernel weight per spike (KWS), total florets per spike (TFS), florets per spikelet (FPs), florets in the middle spikelet (FMs), fertile florets per spikelet (FFPs), and kernel weight per spikelet (KWPs), are key traits in improving wheat yield. In the present study, quantitative trait loci (QTL) for these traits evaluated under various environments were detected in a recombinant inbred line population (msf/Chuannong 16) mainly genotyped using the 16 K SNP array. Ultimately, we identified 60 QTL, but only QFFS.sau-MC-1A for FFS was a major and stably expressed QTL. It was located on chromosome arm 1AS, where loci for TFS, FPs, FMs, FFS, FFPs, KWS, and KWPs were also simultaneously co-mapped. The effect of QFFS.sau-MC-1A was further validated in three independent segregating populations using a Kompetitive Allele-Specific PCR marker. For the co-located QTL, QFFS.sau-MC-1A, the presence of a positive allele from msf was associate with increases for all traits: + 12.29% TFS, + 10.15% FPs, + 13.97% FMs, + 17.12% FFS, + 14.75% FFPs, + 22.17% KWS, and + 19.42% KWPs. Furthermore, pleiotropy analysis showed that the positive allele at QFFS.sau-MC-1A simultaneously increased the spike length, spikelet number per spike, and thousand-kernel weight. QFFS.sau-MC-1A represents a novel QTL for marker-assisted selection with the potential for improving wheat yield. Four genes, TraesCS1A03G0012700, TraesCS1A03G0015700, TraesCS1A03G0016000, and TraesCS1A03G0016300, which may affect spike development, were predicted in the physical interval harboring QFFS.sau-MC-1A. Our results will help in further fine mapping QFFS.sau-MC-1A and be useful for improving wheat yield.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huangxin Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China.
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Channale S, Thompson JP, Varshney RK, Thudi M, Zwart RS. Multi-locus genome-wide association study of chickpea reference set identifies genetic determinants of Pratylenchus thornei resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1139574. [PMID: 37035083 PMCID: PMC10080060 DOI: 10.3389/fpls.2023.1139574] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
Pratylenchus thornei is an economically important species of root-lesion nematode adversely affecting chickpea (Cicer arietinum) yields globally. Integration of resistant crops in farming systems is recognised as the most effective and sustainable management strategy for plant-parasitic nematodes. However, breeding for P. thornei resistance in chickpea is limited by the lack of genetic diversity. We deployed a genome-wide association approach to identify genomic regions and candidate genes associated with P. thornei resistance in 285 genetically diverse chickpea accessions. Chickpea accessions were phenotyped for P. thornei resistance in replicated glasshouse experiments performed for two years (2018 and 2020). Whole genome sequencing data comprising 492,849 SNPs were used to implement six multi-locus GWAS models. Fourteen chickpea genotypes were found to be resistant to P. thornei. Of the six multi-locus GWAS methods deployed, FASTmrMLM was found to be the best performing model. In all, 24 significant quantitative trait nucleotides (QTNs) were identified, of which 13 QTNs were associated with lower nematode population density and 11 QTNs with higher nematode population density. These QTNs were distributed across all of the chickpea chromosomes, except chromosome 8. We identified, receptor-linked kinases (RLKs) on chromosomes 1, 4 and 6, GDSL-like Lipase/Acylhydrolase on chromosome 3, Aspartic proteinase-like and Thaumatin-like protein on chromosome 4, AT-hook DNA-binding and HSPRO2 on chromosome 6 as candidate genes for P. thornei resistance in the chickpea reference set. New sources of P. thornei resistant genotypes were identified that can be harnessed into breeding programs and putative candidate P. thornei resistant genes were identified that can be explored further to develop molecular markers and accelerate the incorporation of improved P. thornei resistance into elite chickpea cultivars.
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Affiliation(s)
- Sonal Channale
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - John P. Thompson
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Rajeev K. Varshney
- Centre for Crop & Food Innovation, Murdoch University, Perth, WA, Australia
| | - Mahendar Thudi
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, India
| | - Rebecca S. Zwart
- Centre for Crop Health, Institute for Life Sciences and the Environment, University of Southern Queensland, Toowoomba, QLD, Australia
- School of Agriculture and Environmental Science, Faculty of Health, Engineering and Science, University of Southern Queensland, Toowoomba, QLD, Australia
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