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Lu Q, Huang L, Liu H, Garg V, Gangurde SS, Li H, Chitikineni A, Guo D, Pandey MK, Li S, Liu H, Wang R, Deng Q, Du P, Varshney RK, Liang X, Hong Y, Chen X. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits. Nat Genet 2024; 56:530-540. [PMID: 38378864 DOI: 10.1038/s41588-024-01660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
Peanut (Arachis hypogaea L.) is an important allotetraploid oil and food legume crop. China is one of the world's largest peanut producers and consumers. However, genomic variations underlying the migration and divergence of peanuts in China remain unclear. Here we reported a genome-wide variation map based on the resequencing of 390 peanut accessions, suggesting that peanuts might have been introduced into southern and northern China separately, forming two cultivation centers. Selective sweep analysis highlights asymmetric selection between the two subgenomes during peanut improvement. A classical pedigree from South China offers a context for the examination of the impact of artificial selection on peanut genome. Genome-wide association studies identified 22,309 significant associations with 28 agronomic traits, including candidate genes for plant architecture and oil biosynthesis. Our findings shed light on peanut migration and diversity in China and provide valuable genomic resources for peanut improvement.
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Affiliation(s)
- Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Lu Huang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Annapurna Chitikineni
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Dandan Guo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shaoxiong Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Haiyan Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Runfeng Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Quanqing Deng
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Puxuan Du
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Centre of National Centre of Oilseed Crops Improvement, Guangzhou, China.
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Song H, Guo Z, Duan Z, Li M, Zhang J. WRKY transcription factors in Arachis hypogaea and its donors: From identification to function prediction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108131. [PMID: 37897893 DOI: 10.1016/j.plaphy.2023.108131] [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: 08/09/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
WRKY transcription factors (TFs) play important roles in plant growth and development and responses to abiotic and biotic stresses. Since the initial isolation of a WRKY TF in Ipomoea batatas in 1994, WRKY TFs have been identified in plants, protozoa, and fungi. Peanut (Arachis hypogaea) is a key oil and protein crop for humans and a forage source for animal consumption. Several Arachis genomes have been sequenced and genome-wide WRKY TFs have been identified. In this review, we summarized WRKY TFs and their functions in A. hypogaea and its donors. We also standardized the nomenclature for Arachis WRKY TFs to ensure uniformity. We determined the evolutionary relationships between Arachis and Arabidopsis thaliana WRKY (AtWRKY) TFs using a phylogenetic analysis. Biological functions and regulatory networks of Arachis WRKY TFs were predicted using AtWRKY TFs. Thus, this review paves the way for studies of Arachis WRKY TFs.
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Affiliation(s)
- Hui Song
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhonglong Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhenquan Duan
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Meiran Li
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China; Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
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Liang B, Bai Y, Zang C, Pei X, Xie J, Lin Y, Liu X, Ahsan T, Liang C. Overexpression of the First Peanut-Susceptible Gene, AhS5H1 or AhS5H2, Enhanced Susceptibility to Pst DC3000 in Arabidopsis. Int J Mol Sci 2023; 24:14210. [PMID: 37762513 PMCID: PMC10531710 DOI: 10.3390/ijms241814210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Salicylic acid (SA) serves as a pivotal plant hormone involved in regulating plant defense mechanisms against biotic stresses, but the extent of its biological significance in relation to peanut resistance is currently lacking. This study elucidated the involvement of salicylic acid (SA) in conferring broad-spectrum disease resistance in peanuts through the experimental approach of inoculating SA-treated leaves. In several other plants, the salicylate hydroxylase genes are the typical susceptible genes (S genes). Here, we characterized two SA hydroxylase genes (AhS5H1 and AhS5H2) as the first S genes in peanut. Recombinant AhS5H proteins catalyzed SA in vitro, and showed SA 5-ydroxylase (S5H) activity. Overexpression of AhS5H1 or AhS5H2 decreased SA content and increased 2,5-DHBA levels in Arabidopsis, suggesting that both enzymes had a similar role in planta. Moreover, overexpression of each AhS5H gene increased susceptibility to Pst DC3000. Analysis of the transcript levels of defense-related genes indicated that the expression of AhS5H genes, AhNPR1 and AhPR10 was simultaneously induced by chitin. Overexpression of each AhS5H in Arabidopsis abolished the induction of AtPR1 or AtPR2 upon chitin treatment. Eventually, AhS5H2 expression levels were highly correlated with SA content in different tissues of peanut. Hence, the expression of AhS5H1 and AhS5H2 was tissue-specific.
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Affiliation(s)
- Bingbing Liang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Yuanjun Bai
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
- Institute of Rice Research, Liaoning Academy of Agricultural Sciences, Shenyang 110101, China
| | - Chaoqun Zang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Xue Pei
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Jinhui Xie
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Ying Lin
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Xiaozhou Liu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Taswar Ahsan
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
| | - Chunhao Liang
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China; (B.L.)
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Chen H, Yang X, Xu R, Chen X, Zhong H, Liu N, Huang L, Luo H, Huai D, Liu W, Chen Y, Chen J, Jiang H. Genetic mapping of AhVt1, a novel genetic locus that confers the variegated testa color in cultivated peanut ( Arachis hypogaea L.) and its utilization for marker-assisted selection. FRONTIERS IN PLANT SCIENCE 2023; 14:1145098. [PMID: 37021305 PMCID: PMC10067746 DOI: 10.3389/fpls.2023.1145098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Peanut (Arachis hypogaea L.) is an important cash crop worldwide. Compared with the ordinary peanut with pure pink testa, peanut with variegated testa color has attractive appearance and a higher market value. In addition, the variegated testa represents a distinct regulation pattern of anthocyanin accumulation in integument cells. METHODS In order to identify the genetic locus underlying variegated testa color in peanut, two populations were constructed from the crosses between Fuhua 8 (pure-pink testa) and Wucai (red on white variegated testa), Quanhonghua 1 (pure-red testa) and Wucai, respectively. Genetic analysis and bulked sergeant analysis sequencing were applied to detect and identify the genetic locus for variegated testa color. Marker-assisted selection was used to develop new variegated testa peanut lines. RESULTS As a result, all the seeds harvested from the F1 individuals of both populations showed the variegated testa type with white trace. Genetic analysis revealed that the pigmentation of colored region in red on white variegated testa was controlled by a previous reported gene AhRt1, while the formation of white region (un-pigmented region) in variegated testa was controlled by another single genetic locus. This locus, named as AhVt1 (Arachis hypogaea Variegated Testa 1), was preliminary mapped on chromosome 08 through bulked sergeant analysis sequencing. Using a secondary mapping population derived from the cross between Fuhua 8 and Wucai, AhVt1 was further mapped to a 1.89-Mb genomic interval by linkage analysis, and several potential genes associated with the uneven distribution of anthocyanin, such as MADS-box, MYB, and Chalcone synthase-like protein, were harbored in the region. Moreover, the molecular markers closely linked to the AhVt1 were developed, and the new variegated testa peanut lines were obtained with the help of marker-assisted selection. CONCLUSION Our findings will accelerate the breeding program for developing new peanut varieties with "colorful" testa colors and laid a foundation for map-based cloning of gene responsible for variegated testa.
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Affiliation(s)
- Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Xinlei Yang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory for Crop Germplasm Resources of Hebei, Hebei Agricultural University, Baoding, China
| | - Rirong Xu
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Xiangyu Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Haifeng Zhong
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Li Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Huaiyong Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Dongxin Huai
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
| | - Wenjing Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fujian Key Laboratory of Agro-products Quality and Safety, Fuzhou, China
| | - Yuhua Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fujian Research Station of Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Fujian Engineering Research Center for Characteristic Upland Crops Breeding, Fujian Engineering Laboratory of Crop Molecular Breeding, Fuzhou, China
| | - Jianhong Chen
- R&D Center for Oil Crops, Quanzhou Institute of Agricultural Sciences, Jinjiang, China
| | - Huifang Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs of People’s Republic of China, Wuhan, China
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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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Guo J, Qi F, Qin L, Zhang M, Sun Z, Li H, Cui M, Zhang M, Li C, Li X, Zhao Q, Luo D, Tian M, Liu H, Xu J, Miao L, Huang B, Dong W, Han S, Zhang X. Mapping of a QTL associated with sucrose content in peanut kernels using BSA-seq. Front Genet 2023; 13:1089389. [PMID: 36685909 PMCID: PMC9845247 DOI: 10.3389/fgene.2022.1089389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
As an important factor affecting the edible quality of peanut kernels, sucrose content is a complex quantitative trait regulated by multiple factors. In this study, an F2 segregating population and a recombinant inbred line (RIL) population, derived from a cross between the high sucrose content variety Jihuatian 1 and the low sucrose content line PI478819, were used as materials to map a quantitative trait locus (QTL) associated with sucrose content in peanut kernels. Four QTLs were initially located on chromosomes A03 and A06 based on BSA-seq technology, and multiple kompetitive allele-specific PCR markers were developed based on single-nucleotide polymorphisms (SNPs) in the intervals. The markers were genotyped in the RIL population and finely mapped to a stable QTL, qSUCA06, located on chromosome A06 within a 0.29-Mb physical genomic interval (112367085-112662675 bp), which accounted for 31.95%-41.05% of the phenotypic variance explained. SNP and insertion/deletion annotations were performed on genes in the candidate interval, and having screened out those genes with mutations in exons, candidate genes were verified by qRT-PCR. The results revealed that Arahy.Y2LWD9 may be the main gene regulating sucrose content. The QTL identified in this study will not only contribute to marker-assisted breeding for improvement of peanut sucrose content but also paves the way for identifying gene function.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Suoyi Han
- *Correspondence: Xinyou Zhang, ; Suoyi Han,
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