Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.)
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...
| Main Authors: | , , , , , , , , , , , , , , , |
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MDPI AG
2024-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/15/2/160 |
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| author | Dandan Luo Lei Shi Ziqi Sun Feiyan Qi Hongfei Liu Lulu Xue Xiaona Li Han Liu Pengyu Qu Huanhuan Zhao Xiaodong Dai Wenzhao Dong Zheng Zheng Bingyan Huang Liuyang Fu Xinyou Zhang |
| author_facet | Dandan Luo Lei Shi Ziqi Sun Feiyan Qi Hongfei Liu Lulu Xue Xiaona Li Han Liu Pengyu Qu Huanhuan Zhao Xiaodong Dai Wenzhao Dong Zheng Zheng Bingyan Huang Liuyang Fu Xinyou Zhang |
| author_sort | Dandan Luo |
| collection | DOAJ |
| description | 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 (<i>Arachis hypogaea</i> 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 −log<sub>10</sub>(<i>p</i>) = 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 <i>Arahy.MIX90M</i> 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. |
| first_indexed | 2024-03-07T22:31:24Z |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-07T22:31:24Z |
| publishDate | 2024-01-01 |
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| series | Genes |
| spelling | doaj.art-2f2677bf21ae42809eb3178b4a2412832024-02-23T15:17:41ZengMDPI AGGenes2073-44252024-01-0115216010.3390/genes15020160Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.)Dandan Luo0Lei Shi1Ziqi Sun2Feiyan Qi3Hongfei Liu4Lulu Xue5Xiaona Li6Han Liu7Pengyu Qu8Huanhuan Zhao9Xiaodong Dai10Wenzhao Dong11Zheng Zheng12Bingyan Huang13Liuyang Fu14Xinyou Zhang15School of Life Sciences, Zhengzhou University, Zhengzhou 450001, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaSchool of Life Sciences, Zhengzhou University, Zhengzhou 450001, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaSchool of Life Sciences, Zhengzhou University, Zhengzhou 450001, ChinaInstitute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaThe 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 (<i>Arachis hypogaea</i> 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 −log<sub>10</sub>(<i>p</i>) = 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 <i>Arahy.MIX90M</i> 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.https://www.mdpi.com/2073-4425/15/2/160peanutCIRGWAScandidate gene |
| spellingShingle | Dandan Luo Lei Shi Ziqi Sun Feiyan Qi Hongfei Liu Lulu Xue Xiaona Li Han Liu Pengyu Qu Huanhuan Zhao Xiaodong Dai Wenzhao Dong Zheng Zheng Bingyan Huang Liuyang Fu Xinyou Zhang Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) Genes peanut CIR GWAS candidate gene |
| title | Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) |
| title_full | Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) |
| title_fullStr | Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) |
| title_full_unstemmed | Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) |
| title_short | Genome-Wide Association Studies of Embryogenic Callus Induction Rate in Peanut (<i>Arachis hypogaea</i> L.) |
| title_sort | genome wide association studies of embryogenic callus induction rate in peanut i arachis hypogaea i l |
| topic | peanut CIR GWAS candidate gene |
| url | https://www.mdpi.com/2073-4425/15/2/160 |
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