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Luo D, Shi L, Sun Z, Qi F, Liu H, Xue L, Li X, Liu H, Qu P, Zhao H, Dai X, Dong W, Zheng Z, Huang B, Fu L, Zhang X. Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut ( Arachis hypogaea L.). Genes (Basel) 2024; 15:160. [PMID: 38397150 PMCID: PMC10887910 DOI: 10.3390/genes15020160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The capability of embryogenic callus induction is a prerequisite for in vitro plant regeneration. However, embryogenic callus induction is strongly genotype-dependent, thus hindering the development of in vitro plant genetic engineering technology. In this study, to examine the genetic variation in embryogenic callus induction rate (CIR) in peanut (Arachis hypogaea L.) at the seventh, eighth, and ninth subcultures (T7, T8, and T9, respectively), we performed genome-wide association studies (GWAS) for CIR in a population of 353 peanut accessions. The coefficient of variation of CIR among the genotypes was high in the T7, T8, and T9 subcultures (33.06%, 34.18%, and 35.54%, respectively), and the average CIR ranged from 1.58 to 1.66. A total of 53 significant single-nucleotide polymorphisms (SNPs) were detected (based on the threshold value -log10(p) = 4.5). Among these SNPs, SNPB03-83801701 showed high phenotypic variance and neared a gene that encodes a peroxisomal ABC transporter 1. SNPA05-94095749, representing a nonsynonymous mutation, was located in the Arahy.MIX90M locus (encoding an auxin response factor 19 protein) at T8, which was associated with callus formation. These results provide guidance for future elucidation of the regulatory mechanism of embryogenic callus induction in peanut.
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Affiliation(s)
- Dandan Luo
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Shi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Ziqi Sun
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feiyan Qi
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Hongfei Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lulu Xue
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaona Li
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Han Liu
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Pengyu Qu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Huanhuan Zhao
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiaodong Dai
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Wenzhao Dong
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Zheng Zheng
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Bingyan Huang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
| | - Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xinyou Zhang
- Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Zhengzhou 450002, China
- Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- National Innovation Center for Bio-Breeding Industry, Xinxiang 453500, China
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