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Zhao K, Li Z, Ke Y, Ren R, Cao Z, Li Z, Wang K, Wang X, Wang J, Ma Q, Cao D, Zhao K, Li Y, Hu S, Qiu D, Gong F, Ma X, Zhang X, Fan G, Liang Z, Yin D. Dynamic N 6 -methyladenosine RNA modification regulates peanut resistance to bacterial wilt. THE NEW PHYTOLOGIST 2024; 242:231-246. [PMID: 38326943 DOI: 10.1111/nph.19568] [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: 08/27/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
N6 -methyladenosine (m6 A) is the most abundant mRNA modification in eukaryotes and is an important regulator of gene expression as well as many other critical biological processes. However, the characteristics and functions of m6 A in peanut (Arachis hypogea L.) resistance to bacterial wilt (BW) remain unknown. Here, we analyzed the dynamic of m6 A during infection of resistant (H108) and susceptible (H107) peanut accessions with Ralstonia solanacearum (R. solanacearum), the causative agent of BW. Throughout the transcriptome, we identified 'URUAY' as a highly conserved motif for m6 A in peanut. The majority of differential m6 A located within the 3' untranslated region (UTR) of the transcript, with fewer in the exons. Integrative analysis of RNA-Seq and m6 A methylomes suggests the correlation between m6 A and gene expression in peanut R. solanacearum infection, and functional analysis reveals that m6 A-associated genes were related to plant-pathogen interaction. Our experimental analysis suggests that AhALKBH15 is an m6 A demethylase in peanut, leading to decreased m6 A levels and upregulation of the resistance gene AhCQ2G6Y. The upregulation of AhCQ2G6Y expression appears to promote BW resistance in the H108 accession.
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Affiliation(s)
- Kai Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhongfeng Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yunzhuo Ke
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Ren
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zenghui Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhan Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kuopeng Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaoxuan Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jinzhi Wang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qian Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Di Cao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Kunkun Zhao
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yaoyao Li
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Sasa Hu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Ding Qiu
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fangping Gong
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xingli Ma
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xingguo Zhang
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dongmei Yin
- College of Agronomy & Peanut Functional Genome and Molecular Breeding Engineering, Henan Agricultural University, Zhengzhou, 450046, China
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Wang X, Qi F, Sun Z, Liu H, Wu Y, Wu X, Xu J, Liu H, Qin L, Wang Z, Sang S, Dong W, Huang B, Zheng Z, Zhang X. Transcriptome sequencing and expression analysis in peanut reveal the potential mechanism response to Ralstonia solanacearum infection. BMC PLANT BIOLOGY 2024; 24:207. [PMID: 38515036 PMCID: PMC10956345 DOI: 10.1186/s12870-024-04877-0] [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: 07/28/2023] [Accepted: 03/03/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND Bacterial wilt caused by Ralstonia solanacearum severely affects peanut (Arachis hypogaea L.) yields. The breeding of resistant cultivars is an efficient means of controlling plant diseases. Therefore, identification of resistance genes effective against bacterial wilt is a matter of urgency. The lack of a reference genome for a resistant genotype severely hinders the process of identification of resistance genes in peanut. In addition, limited information is available on disease resistance-related pathways in peanut. RESULTS Full-length transcriptome data were used to generate wilt-resistant and -susceptible transcript pools. In total, 253,869 transcripts were retained to form a reference transcriptome for RNA-sequencing data analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes revealed the plant-pathogen interaction pathway to be the main resistance-related pathway for peanut to prevent bacterial invasion and calcium plays an important role in this pathway. Glutathione metabolism was enriched in wilt-susceptible genotypes, which would promote glutathione synthesis in the early stages of pathogen invasion. Based on our previous quantitative trait locus (QTL) mapping results, the genes arahy.V6I7WA and arahy.MXY2PU, which encode nucleotide-binding site-leucine-rich repeat receptor proteins, were indicated to be associated with resistance to bacterial wilt. CONCLUSIONS This study identified several pathways associated with resistance to bacterial wilt and identified candidate genes for bacterial wilt resistance in a major QTL region. These findings lay a foundation for investigation of the mechanism of resistance to bacterial wilt in peanut.
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Affiliation(s)
- Xiao Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, China
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Feiyan Qi
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ziqi Sun
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Hongfei Liu
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Yue Wu
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Xiaohui Wu
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jing Xu
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Hua Liu
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Li Qin
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zhenyu Wang
- Henan Academy of Agricultural Sciences, Institute of Plant Protection, Zhengzhou, 450002, China
| | - Suling Sang
- Henan Academy of Agricultural Sciences, Institute of Plant Protection, Zhengzhou, 450002, China
| | - Wenzhao Dong
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zheng Zheng
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
| | - Xinyou Zhang
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, China.
- The Shennong Laboratory, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, National Innovation Centre for Bio-Breeding Industry, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China.
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Raza A, Chen H, Zhang C, Zhuang Y, Sharif Y, Cai T, Yang Q, Soni P, Pandey MK, Varshney RK, Zhuang W. Designing future peanut: the power of genomics-assisted breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:66. [PMID: 38438591 DOI: 10.1007/s00122-024-04575-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 02/03/2024] [Indexed: 03/06/2024]
Abstract
KEY MESSAGE Integrating GAB methods with high-throughput phenotyping, genome editing, and speed breeding hold great potential in designing future smart peanut cultivars to meet market and food supply demands. Cultivated peanut (Arachis hypogaea L.), a legume crop greatly valued for its nourishing food, cooking oil, and fodder, is extensively grown worldwide. Despite decades of classical breeding efforts, the actual on-farm yield of peanut remains below its potential productivity due to the complicated interplay of genotype, environment, and management factors, as well as their intricate interactions. Integrating modern genomics tools into crop breeding is necessary to fast-track breeding efficiency and rapid progress. When combined with speed breeding methods, this integration can substantially accelerate the breeding process, leading to faster access of improved varieties to farmers. Availability of high-quality reference genomes for wild diploid progenitors and cultivated peanuts has accelerated the process of gene/quantitative locus discovery, developing markers and genotyping assays as well as a few molecular breeding products with improved resistance and oil quality. The use of new breeding tools, e.g., genomic selection, haplotype-based breeding, speed breeding, high-throughput phenotyping, and genome editing, is probable to boost genetic gains in peanut. Moreover, renewed attention to efficient selection and exploitation of targeted genetic resources is also needed to design high-quality and high-yielding peanut cultivars with main adaptation attributes. In this context, the combination of genomics-assisted breeding (GAB), genome editing, and speed breeding hold great potential in designing future improved peanut cultivars to meet market and food supply demands.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Yasir Sharif
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Tiecheng Cai
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Qiang Yang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China
| | - Pooja Soni
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Manish K Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, India
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 350002, China.
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Miao P, Meng X, Li Z, Sun S, Chen CY, Yang X. Mapping Quantitative Trait Loci (QTLs) for Hundred-Pod and Hundred-Seed Weight under Seven Environments in a Recombinant Inbred Line Population of Cultivated Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1792. [PMID: 37761932 PMCID: PMC10531390 DOI: 10.3390/genes14091792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a recombinant inbred line (RIL) population with 188 individuals was developed from a cross between JH5 (JH5, large pod and seed weight) and M130 (small pod and seed weight), and was utilized to identify QTLs for HPW and HSW. An integrated genetic linkage map was constructed by using SSR, AhTE, SRAP, TRAP and SNP markers. This map consisted of 3130 genetic markers, which were assigned to 20 chromosomes, and covered 1998.95 cM with an average distance 0.64 cM. On this basis, 31 QTLs for HPW and HSW were located on seven chromosomes, with each QTL accounting for 3.7-10.8% of phenotypic variance explained (PVE). Among these, seven QTLs were detected under multiple environments, and two major QTLs were found on B04 and B08. Notably, a QTL hotspot on chromosome A08 contained seven QTLs over a 2.74 cM genetic interval with an 0.36 Mb physical map, including 18 candidate genes. Of these, Arahy.D52S1Z, Arahy.IBM9RL, Arahy.W18Y25, Arahy.CPLC2W and Arahy.14EF4H might play a role in modulating peanut pod and seed weight. These findings could facilitate further research into the genetic mechanisms influencing pod and seed weight in cultivated peanut.
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Affiliation(s)
- Penghui Miao
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Xinhao Meng
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Zeren Li
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Sainan Sun
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xinlei Yang
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
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Deng Q, Liu H, Lu Q, Gangurde SS, Du P, Li H, Li S, Liu H, Wang R, Huang L, Chen R, Fan C, Liang X, Chen X, Hong Y. Silicon Application for the Modulation of Rhizosphere Soil Bacterial Community Structures and Metabolite Profiles in Peanut under Ralstonia solanacearum Inoculation. Int J Mol Sci 2023; 24:ijms24043268. [PMID: 36834682 PMCID: PMC9960962 DOI: 10.3390/ijms24043268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Silicon (Si) has been shown to promote peanut growth and yield, but whether Si can enhance the resistance against peanut bacterial wilt (PBW) caused by Ralstonia solanacearum, identified as a soil-borne pathogen, is still unclear. A question regarding whether Si enhances the resistance of PBW is still unclear. Here, an in vitro R. solanacearum inoculation experiment was conducted to study the effects of Si application on the disease severity and phenotype of peanuts, as well as the microbial ecology of the rhizosphere. Results revealed that Si treatment significantly reduced the disease rate, with a decrement PBW severity of 37.50% as compared to non-Si treatment. The soil available Si (ASi) significantly increased by 13.62-44.87%, and catalase activity improved by 3.01-3.10%, which displayed obvious discrimination between non-Si and Si treatments. Furthermore, the rhizosphere soil bacterial community structures and metabolite profiles dramatically changed under Si treatment. Three significantly changed bacterial taxa were observed, which showed significant abundance under Si treatment, whereas the genus Ralstonia genus was significantly suppressed by Si. Similarly, nine differential metabolites were identified to involve into unsaturated fatty acids via a biosynthesis pathway. Significant correlations were also displayed between soil physiochemical properties and enzymes, the bacterial community, and the differential metabolites by pairwise comparisons. Overall, this study reports that Si application mediated the evolution of soil physicochemical properties, the bacterial community, and metabolite profiles in the soil rhizosphere, which significantly affects the colonization of the Ralstonia genus and provides a new theoretical basis for Si application in PBW prevention.
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Affiliation(s)
- Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA 30602, USA
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Shaoxiong Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Haiyan Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Runfeng Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lu Huang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Ronghua Chen
- Institute of Agricultural Sciences in Ganzhou, Ganzhou 341000, China
| | - Chenggen Fan
- Institute of Agricultural Sciences in Ganzhou, Ganzhou 341000, China
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (X.C.); (Y.H.)
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (X.C.); (Y.H.)
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Zhao C, Gangurde SS, Xin X, Varshney RK. Editorial: Creation and utilization of crop germplasm resources. FRONTIERS IN PLANT SCIENCE 2023; 14:1140037. [PMID: 36760642 PMCID: PMC9905828 DOI: 10.3389/fpls.2023.1140037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Sunil S. Gangurde
- Crop Protection and Management Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, GA, United States
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Xia Xin
- National Crop GeneBank, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Xiao XO, Lin W, Feng E, Ou X. Transcriptome and metabolome response of eggplant against Ralstonia solanacearum infection. PeerJ 2023; 11:e14658. [PMID: 36647448 PMCID: PMC9840387 DOI: 10.7717/peerj.14658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Bacterial wilt is a soil-borne disease that represents ubiquitous threat to Solanaceae crops. The whole-root transcriptomes and metabolomes of bacterial wilt-resistant eggplant were studied to understand the response of eggplant to bacterial wilt. A total of 2,896 differentially expressed genes and 63 differences in metabolites were identified after inoculation with Ralstonia solanacearum. Further analysis showed that the biosynthesis pathways for phytohormones, phenylpropanoids, and flavonoids were altered in eggplant after inoculation with R. solanacearum. The results of metabolomes also showed that phytohormones played a key role in eggplant response to bacterial wilt. Integrated analyses of the transcriptomic and metabolic datasets indicated that jasmonic acid (JA) content and gene involved in the JA signaling pathway increased in response to bacterial wilt. These findings remarkably improve our understanding of the mechanisms of induced defense response in eggplant and will provide insights intothe development of disease-resistant varieties of eggplant.
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Affiliation(s)
- Xi Ou Xiao
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
| | - Wenqiu Lin
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
| | - Enyou Feng
- Zhanjiang Academy of Agricultural Sciences, Zhanjiang, Guangdong, China
| | - Xiongchang Ou
- South Subtropical Crop Research Institute Chinese Academy of Tropical Agricultural Sciences (CATAS), Zhanjiang, Guangdong, China,Key Laboratory of Hainan Province for Postharvest Physiology and Technology of Tropical Horticultural Products, Zhanjiang, Guagndong, China,Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, Zhanjiang, Guangdong, China
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Song H, Guo Z, Zhang X, Sui J. De novo genes in Arachis hypogaea cv. Tifrunner: systematic identification, molecular evolution, and potential contributions to cultivated peanut. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1081-1095. [PMID: 35748398 DOI: 10.1111/tpj.15875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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9
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Zia B, Shi A, Olaoye D, Xiong H, Ravelombola W, Gepts P, Schwartz HF, Brick MA, Otto K, Ogg B, Chen S. Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean ( Phaseolus vulgaris) Core Collection. Front Genet 2022; 13:853114. [PMID: 35711938 PMCID: PMC9197503 DOI: 10.3389/fgene.2022.853114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.
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Affiliation(s)
- Bazgha Zia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Waltram Ravelombola
- Organic & Specialty Crop Breeding, Texas A&M AgriLife Research, Vernon, TX, United States
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, Davis, CA, United States
| | - Howard F Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kristen Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Barry Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Senyu Chen
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, United States
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10
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Han S, Zhou X, Shi L, Zhang H, Geng Y, Fang Y, Xia H, Liu H, Li P, Zhao S, Miao L, Hou L, Zhang Z, Xu J, Ma C, Wang Z, Li H, Zheng Z, Huang B, Dong W, Zhang J, Tang F, Li S, Gao M, Zhang X, Zhao C, Wang X. AhNPR3 regulates the expression of WRKY and PR genes, and mediates the immune response of the peanut (Arachis hypogaea L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:735-747. [PMID: 35124871 DOI: 10.1111/tpj.15700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Systemic acquired resistance is an essential immune response that triggers a broad-spectrum disease resistance throughout the plant. In the present study, we identified a peanut lesion mimic mutant m14 derived from an ethyl methane sulfonate-mutagenized mutant pool of peanut cultivar "Yuanza9102." Brown lesions were observed in the leaves of an m14 mutant from seedling stage to maturity. Using MutMap together with bulked segregation RNA analysis approaches, a G-to-A point mutation was identified in the exon region of candidate gene Arahy.R60CUW, which is the homolog of AtNPR3 (Nonexpresser of PR genes) in Arabidopsis. This point mutation caused a transition from Gly to Arg within the C-terminal transactivation domain of AhNPR3A. The mutation of AhNPR3A showed no effect in the induction of PR genes when treated with salicylic acid. Instead, the mutation resulted in upregulation of WRKY genes and several PR genes, including pathogenesis-related thaumatin- and chitinase-encoding genes, which is consistent with the resistant phenotype of m14 to leaf spot disease. Further study on the AhNPR3A gene will provide valuable insights into understanding the molecular mechanism of systemic acquired resistance in peanut. Moreover, our results indicated that a combination of MutMap and bulked segregation RNA analysis is an effective method for identifying genes from peanut mutants.
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Affiliation(s)
- Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Ximeng Zhou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lei Shi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Huayang Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Yun Geng
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
| | - Yuanjin Fang
- Kaifeng Academy of Agriculture and Forestry, Kaifeng, 475000, China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Hua Liu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Lijuan Miao
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhongxin Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jing Xu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Changle Ma
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Hongyan Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Zheng Zheng
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Jun Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Fengshou Tang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Shaojian Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
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11
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Qi F, Sun Z, Liu H, Zheng Z, Qin L, Shi L, Chen Q, Liu H, Lin X, Miao L, Tian M, Wang X, Huang B, Dong W, Zhang X. QTL identification, fine mapping, and marker development for breeding peanut (Arachis hypogaea L.) resistant to bacterial wilt. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1319-1330. [PMID: 35059781 PMCID: PMC9033696 DOI: 10.1007/s00122-022-04033-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 12/31/2021] [Indexed: 05/26/2023]
Abstract
A major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt. Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 521 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5120 SNP markers, covered a length of 3179 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, with LOD score of 32.8-66.0 and PVE of 31.2-44.8%, was stably detected in all four development stages investigated over the 3 trial years. Additionally, qBWA12 spanned a 2.7 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt.
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Affiliation(s)
- Feiyan Qi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Ziqi Sun
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Hua Liu
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Zheng Zheng
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Li Qin
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Lei Shi
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Qingzheng Chen
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Haidong Liu
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Xiufang Lin
- Hezhou Academy of Agricultural Science, Hezhou, 542899, Guangxi, China
| | - Lijuan Miao
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Mengdi Tian
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Xiao Wang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crop Improvement, Zhengzhou, 450002, Henan, China.
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12
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Luo H, Guo J, Yu B, Chen W, Zhang H, Zhou X, Chen Y, Huang L, Liu N, Ren X, Yan L, Huai D, Lei Y, Liao B, Jiang H. Construction of ddRADseq-Based High-Density Genetic Map and Identification of Quantitative Trait Loci for Trans-resveratrol Content in Peanut Seeds. FRONTIERS IN PLANT SCIENCE 2021; 12:644402. [PMID: 33868342 PMCID: PMC8044979 DOI: 10.3389/fpls.2021.644402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Resveratrol (trans-3,4',5-trihydroxystilbene) is a natural stilbene phytoalexin which is also found to be good for human health. Cultivated peanut (Arachis hypogaea L.), a worldwide important legume crop, is one of the few sources of human's dietary intake of resveratrol. Although the variations of resveratrol contents among peanut varieties were observed, the variations across environments and its underlying genetic basis were poorly investigated. In this study, the resveratrol content in seeds of a recombination inbred line (RIL) population (Zhonghua 6 × Xuhua 13, 186 progenies) were quantified by high performance liquid chromatography (HPLC) method across four environments. Genotypes, environments and genotype × environment interactions significantly influenced the resveratrol contents in the RIL population. A total of 8,114 high-quality single nucleotide polymorphisms (SNPs) were identified based on double-digest restriction-site-associated DNA sequencing (ddRADseq) reads. These SNPs were clustered into bins using a reference-based method, which facilitated the construction of high-density genetic map (2,183 loci with a total length of 2,063.55 cM) and the discovery of several chromosome translocations. Through composite interval mapping (CIM), nine additive quantitative trait loci (QTL) for resveratrol contents were identified on chromosomes A01, A07, A08, B04, B05, B06, B07, and B10 with 5.07-8.19% phenotypic variations explained (PVE). Putative genes within their confidential intervals might play roles in diverse primary and secondary metabolic processes. These results laid a foundation for the further genetic dissection of resveratrol content as well as the breeding and production of high-resveratrol peanuts.
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13
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Chavarro C, Chu Y, Holbrook C, Isleib T, Bertioli D, Hovav R, Butts C, Lamb M, Sorensen R, A Jackson S, Ozias-Akins P. Pod and Seed Trait QTL Identification To Assist Breeding for Peanut Market Preferences. G3 (BETHESDA, MD.) 2020; 10:2297-2315. [PMID: 32398236 PMCID: PMC7341151 DOI: 10.1534/g3.120.401147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/01/2020] [Indexed: 12/20/2022]
Abstract
Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explore the distribution of recombination and potential chromosomal rearrangements. This linkage map was then used to identify Quantitative Trait Loci (QTL) for seed and pod traits that were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.
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Affiliation(s)
- Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793
| | - Corley Holbrook
- USDA- Agricultural Research Service, Crop Genetics and Breeding Research Unit, Tifton, GA 31793
| | - Thomas Isleib
- Department of Crop Science, North Carolina State University, P.O. Box 7629, Raleigh, NC 27695
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ran Hovav
- Department of Field and Vegetable Crops, Plant Sciences Institute, ARO (Volcani Center), Bet Dagan, Israel, and
| | - Christopher Butts
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Marshall Lamb
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Ronald Sorensen
- USDA- Agricultural Research Service, National Peanut Research Laboratory, Dawson, GA 39842
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Peggy Ozias-Akins
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Tifton, GA 31793,
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14
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Liu H, Sun Z, Zhang X, Qin L, Qi F, Wang Z, Du P, Xu J, Zhang Z, Han S, Li S, Gao M, Zhang L, Cheng Y, Zheng Z, Huang B, Dong W. QTL mapping of web blotch resistance in peanut by high-throughput genome-wide sequencing. BMC PLANT BIOLOGY 2020; 20:249. [PMID: 32493219 PMCID: PMC7268717 DOI: 10.1186/s12870-020-02455-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/21/2020] [Indexed: 06/08/2023]
Abstract
BACKGROUND Web blotch is one of the most important foliar diseases worldwide in peanut (Arachis hypogaea L.). The identification of quantitative trait loci (QTLs) for peanut web blotch resistance represents the basis for gene mining and the application of molecular breeding technologies. RESULTS In this study, a peanut recombinant inbred line (RIL) population was used to map QTLs for web blotch resistance based on high-throughput genome-wide sequencing. Frequency distributions of disease grade and disease index in five environments indicated wide phenotypic variations in response to web blotch among RILs. A high-density genetic map was constructed, containing 3634 bin markers distributed on 20 peanut linkage groups (LGs) with an average genetic distance of 0.5 cM. In total, eight QTLs were detected for peanut web blotch resistance in at least two environments, explaining from 2.8 to 15.1% of phenotypic variance. Two major QTLs qWBRA04 and qWBRA14 were detected in all five environments and were linked to 40 candidate genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) or other proteins related to disease resistances. CONCLUSIONS The results of this study provide a basis for breeding peanut cultivars with web blotch resistance.
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Affiliation(s)
- Hua Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, PR China
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Ziqi Sun
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Xinyou Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China.
| | - Li Qin
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Feiyan Qi
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, PR China
| | - Pei Du
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Jing Xu
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Zhongxin Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Suoyi Han
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Shaojian Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, PR China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, PR China
| | - Lina Zhang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Yujie Cheng
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Zheng Zheng
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Bingyan Huang
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
| | - Wenzhao Dong
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences / Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture and Rural Affairs / Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, 450002, PR China
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15
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Luo H, Pandey MK, Zhi Y, Zhang H, Xu S, Guo J, Wu B, Chen H, Ren X, Zhou X, Chen Y, Chen W, Huang L, Liu N, Sudini HK, Varshney RK, Lei Y, Liao B, Jiang H. Discovery of two novel and adjacent QTLs on chromosome B02 controlling resistance against bacterial wilt in peanut variety Zhonghua 6. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1133-1148. [PMID: 31980836 PMCID: PMC7064456 DOI: 10.1007/s00122-020-03537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/03/2020] [Indexed: 05/09/2023]
Abstract
Two novel and adjacent genomics and candidate genes for bacterial wilt resistance were identified on chromosome B02 in peanut variety Zhonghua 6 using both traditional QTL mapping and QTL-seq methods. Peanut (Arachis hypogaea) is an important oilseed crop worldwide. Utilization of genetic resistance is the most economic and effective approach to control bacterial wilt, one of the most devastating plant diseases, in peanut production. To accelerate the genetic improvement of bacterial wilt resistance (BWR) in peanut breeding programs, quantitative trait locus (QTL) mapping has been conducted for two resistant varieties. In this context, we deployed linkage mapping as well as sequencing-based mapping approach, QTL-seq, to identify genomic regions and candidate genes for BWR in another highly resistant variety Zhonghua 6. The recombination inbred line population (268 progenies) from the cross Xuhua 13 × Zhonghua 6 was used in BWR evaluation across five environments. QTL mapping using both SSR- and SNP-based genetic maps identified a stable QTL (qBWRB02-1) on chromosome B02 with 37.79-78.86% phenotypic variation explained (PVE) across five environments. The QTL-seq facilitated further dissection of qBWRB02-1 into two adjacent genomic regions, qBWRB02-1-1 (2.81-4.24 Mb) and qBWRB02-1-2 (6.54-8.75 Mb). Mapping of newly developed Kompetitive allele-specific PCR (KASP) markers on the genetic map confirmed their stable expressions across five environments. The effects of qBWRB02-1-1 (49.43-68.86% PVE) were much higher than qBWRB02-1-2 (3.96-6.48% PVE) and other previously reported QTLs. Nineteen putative candidate genes affected by 49 non-synonymous SNPs were identified for qBWRB02-1-1, and ten of them were predicted to code for disease resistance proteins. The major and stable QTL qBWRB02-1-1 and validated KASP markers could be deployed in genomics-assisted breeding (GAB) to develop improved peanut varieties with enhanced BWR.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Ye Zhi
- Angel Yeast Co., Ltd, Yichang, 443003, Hubei, China
| | - Huan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Siliang Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Haiwen Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Hari K Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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16
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Identification of Two Novel Peanut Genotypes Resistant to Aflatoxin Production and Their SNP Markers Associated with Resistance. Toxins (Basel) 2020; 12:toxins12030156. [PMID: 32121605 PMCID: PMC7150746 DOI: 10.3390/toxins12030156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 02/20/2020] [Accepted: 02/28/2020] [Indexed: 12/25/2022] Open
Abstract
Aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) are the most common aflatoxins produced by Aspergillus flavus in peanuts, with high carcinogenicity and teratogenicity. Identification of DNA markers associated with resistance to aflatoxin production is likely to offer breeders efficient tools to develop resistant cultivars through molecular breeding. In this study, seeds of 99 accessions of a Chinese peanut mini-mini core collection were investigated for their reaction to aflatoxin production by a laboratory kernel inoculation assay. Two resistant accessions (Zh.h0551 and Zh.h2150) were identified, with their aflatoxin content being 8.11%-18.90% of the susceptible control. The 99 peanut accessions were also genotyped by restriction site-associated DNA sequencing (RAD-Seq) for a genome-wide association study (GWAS). A total of 60 SNP (single nucleotide polymorphism) markers associated with aflatoxin production were detected, and they explained 16.87%-31.70% of phenotypic variation (PVE), with SNP02686 and SNP19994 possessing 31.70% and 28.91% PVE, respectively. Aflatoxin contents of accessions with "AG" (existed in Zh.h0551 and Zh.h2150) and "GG" genotypes of either SNP19994 or SNP02686 were significantly lower than that of "AA" genotypes in the mean value of a three-year assay. The resistant accessions and molecular markers identified in this study are likely to be helpful for deployment in aflatoxin resistance breeding in peanuts.
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Luo H, Pandey MK, Khan AW, Wu B, Guo J, Ren X, Zhou X, Chen Y, Chen W, Huang L, Liu N, Lei Y, Liao B, Varshney RK, Jiang H. Next-generation sequencing identified genomic region and diagnostic markers for resistance to bacterial wilt on chromosome B02 in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2356-2369. [PMID: 31087470 PMCID: PMC6835129 DOI: 10.1111/pbi.13153] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/01/2019] [Accepted: 05/12/2019] [Indexed: 05/24/2023]
Abstract
Bacterial wilt, caused by Ralstonia solanacearum, is a devastating disease affecting over 350 plant species. A few peanut cultivars were found to possess stable and durable bacterial wilt resistance (BWR). Genomics-assisted breeding can accelerate the process of developing resistant cultivars by using diagnostic markers. Here, we deployed sequencing-based trait mapping approach, QTL-seq, to discover genomic regions, candidate genes and diagnostic markers for BWR in a recombination inbred line population (195 progenies) of peanut. The QTL-seq analysis identified one candidate genomic region on chromosome B02 significantly associated with BWR. Mapping of newly developed single nucleotide polymorphism (SNP) markers narrowed down the region to 2.07 Mb and confirmed its major effects and stable expressions across three environments. This candidate genomic region had 49 nonsynonymous SNPs affecting 19 putative candidate genes including seven putative resistance genes (R-genes). Two diagnostic markers were successfully validated in diverse breeding lines and cultivars and could be deployed in genomics-assisted breeding of varieties with enhanced BWR.
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Affiliation(s)
- Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Xiaoping Ren
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)WuhanChina
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