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Zheng Z, Sun Z, Qi F, Fang Y, Lin K, Pavan S, Huang B, Dong W, Du P, Tian M, Shi L, Xu J, Han S, Liu H, Qin L, Zhang Z, Dai X, Miao L, Zhao R, Wang J, Liao Y, Li A, Ruan J, Delvento C, Aiese Cigliano R, Maliepaard C, Bai Y, Visser RGF, Zhang X. Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts. Nat Genet 2024; 56:1975-1984. [PMID: 39138385 PMCID: PMC11387195 DOI: 10.1038/s41588-024-01876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Cultivated peanut (Arachis hypogaea L.) is a widely grown oilseed crop worldwide; however, the events leading to its origin and diversification are not fully understood. Here by combining chloroplast and whole-genome sequence data from a large germplasm collection, we show that the two subspecies of A. hypogaea (hypogaea and fastigiata) likely arose from distinct allopolyploidization and domestication events. Peanut genetic clusters were then differentiated in relation to dissemination routes and breeding efforts. A combination of linkage mapping and genome-wide association studies allowed us to characterize genes and genomic regions related to main peanut morpho-agronomic traits, namely flowering pattern, inner tegument color, growth habit, pod/seed weight and oil content. Together, our findings shed light on the evolutionary history and phenotypic diversification of peanuts and might be of broad interest to plant breeders.
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Affiliation(s)
- Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China.
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China.
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China.
- The Shennong Laboratory, Zhengzhou, China.
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Yuanjin Fang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Ke Lin
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Stefano Pavan
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Pei Du
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Mengdi Tian
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Lei Shi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Jing Xu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Suoyi Han
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Hua Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Li Qin
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Zhongxin Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Xiaodong Dai
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Lijuan Miao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Ruifang Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Juan Wang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
| | - Yanlin Liao
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China
- The Shennong Laboratory, Zhengzhou, China
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Alun Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Chiara Delvento
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | | | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Yuling Bai
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou, China.
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Zhengzhou, China.
- National Innovation Centre for Bio-breeding Industry, Xinxiang, China.
- The Shennong Laboratory, Zhengzhou, China.
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Wang Z, Lei Y, Liao B. Omics-driven advances in the understanding of regulatory landscape of peanut seed development. FRONTIERS IN PLANT SCIENCE 2024; 15:1393438. [PMID: 38766472 PMCID: PMC11099219 DOI: 10.3389/fpls.2024.1393438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Peanuts (Arachis hypogaea) are an essential oilseed crop known for their unique developmental process, characterized by aerial flowering followed by subterranean fruit development. This crop is polyploid, consisting of A and B subgenomes, which complicates its genetic analysis. The advent and progression of omics technologies-encompassing genomics, transcriptomics, proteomics, epigenomics, and metabolomics-have significantly advanced our understanding of peanut biology, particularly in the context of seed development and the regulation of seed-associated traits. Following the completion of the peanut reference genome, research has utilized omics data to elucidate the quantitative trait loci (QTL) associated with seed weight, oil content, protein content, fatty acid composition, sucrose content, and seed coat color as well as the regulatory mechanisms governing seed development. This review aims to summarize the advancements in peanut seed development regulation and trait analysis based on reference genome-guided omics studies. It provides an overview of the significant progress made in understanding the molecular basis of peanut seed development, offering insights into the complex genetic and epigenetic mechanisms that influence key agronomic traits. These studies highlight the significance of omics data in profoundly elucidating the regulatory mechanisms of peanut seed development. Furthermore, they lay a foundational basis for future research on trait-related functional genes, highlighting the pivotal role of comprehensive genomic analysis in advancing our understanding of plant biology.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
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Wang Z, Zhang Y, Huai D, Chen Y, Wang X, Kang Y, Yan L, Jiang H, Liu K, Lei Y, Liao B. Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:61. [PMID: 38411751 DOI: 10.1007/s00122-024-04549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024]
Abstract
KEY MESSAGE We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, 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 and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, 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 and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, 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 and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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Zhou M, Li Y, Cheng Z, Zheng X, Cai C, Wang H, Lu K, Zhu C, Ding Y. Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15895-15907. [PMID: 37862148 DOI: 10.1021/acs.jafc.3c03560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.
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Affiliation(s)
- Mei Zhou
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yakun Li
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhuowei Cheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyu Zheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Chong Cai
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Huizhen Wang
- Huangshan Institute of Product Quality Inspection, Huangshan 242700, China
| | - Kaixing Lu
- Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Ningbo 315000, China
| | - Cheng Zhu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yanfei Ding
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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Sun Z, Zheng Z, Qi F, Wang J, Wang M, Zhao R, Liu H, Xu J, Qin L, Dong W, Huang B, Han S, Zhang X. Development and evaluation of the utility of GenoBaits Peanut 40K for a peanut MAGIC population. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:72. [PMID: 37786866 PMCID: PMC10542084 DOI: 10.1007/s11032-023-01417-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Population and genotype data are essential for genetic mapping. The multi-parent advanced generation intercross (MAGIC) population is a permanent mapping population used for precisely mapping quantitative trait loci. Moreover, genotyping-by-target sequencing (GBTS) is a robust high-throughput genotyping technology characterized by its low cost, flexibility, and limited requirements for information management and support. In this study, an 8-way MAGIC population was constructed using eight elite founder lines. In addition, GenoBaits Peanut 40K was developed and utilized for the constructed MAGIC population. A subset (297 lines) of the MAGIC population at the S2 stage was genotyped using GenoBaits Peanut 40K. Furthermore, these lines and the eight parents were analyzed in terms of pod length, width, area, and perimeter. A total of 27 single nucleotide polymorphisms (SNPs) were revealed to be significantly associated with peanut pod size-related traits according to a genome-wide association study. The GenoBaits Peanut 40K provided herein and the constructed MAGIC population will be applicable for future research to identify the key genes responsible for important peanut traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01417-w.
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Affiliation(s)
- Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Juan Wang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Mengmeng Wang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Ruifang Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Hua Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Jing Xu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Li Qin
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Suoyi Han
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/The Shennong Laboratory/State Industrial Innovation Center of Biological Breeding/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, Henan China
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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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7
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Jiang Y, Luo H, Yu B, Ding Y, Kang Y, Huang L, Zhou X, Liu N, Chen W, Guo J, Huai D, Lei Y, Jiang H, Yan L, Liao B. High-Density Genetic Linkage Map Construction Using Whole-Genome Resequencing for Mapping QTLs of Resistance to Aspergillus flavus Infection in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:745408. [PMID: 34745176 PMCID: PMC8566722 DOI: 10.3389/fpls.2021.745408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/20/2021] [Indexed: 06/08/2023]
Abstract
The cultivated peanut (Arachis hypogaea L.), which is rich in edible oil and protein, is widely planted around the world as an oil and cash crop. However, aflatoxin contamination seriously affects the quality safety of peanuts, hindering the development of the peanut industry and threatening the health of consumers. Breeding peanut varieties with resistance to Aspergillus flavus infection is important for the control of aflatoxin contamination, and understanding the genetic basis of resistance is vital to its genetic enhancement. In this study, we reported the quantitative trait locus (QTL) mapping of resistance to A. flavus infection of a well-known resistant variety, J11. A mapping population consisting of 200 recombinant inbred lines (RILs) was constructed by crossing a susceptible variety, Zhonghua 16, with J11. Through whole-genome resequencing, a genetic linkage map was constructed with 2,802 recombination bins and an average inter-bin distance of 0.58 cM. Combined with phenotypic data of an infection index in 4 consecutive years, six novel resistant QTLs with 5.03-10.87% phenotypic variances explained (PVE) were identified on chromosomes A05, A08, B01, B03, and B10. The favorable alleles of five QTLs were from J11, while that of one QTL was from Zhonghua 16. The combination of these favorable alleles significantly improved resistance to A. flavus infection. These results could contribute greatly to the understanding of the genetic basis of A. flavus resistance and could be meaningful in the improvement of further resistance in peanuts.
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