<i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd
Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (<i>McAPRR2</i>) controlling pericarp color via a genome-wide associatio...
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| Format: | Article |
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MDPI AG
2023-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/20/3585 |
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| author | Shouwei Tian Jingjing Yang Yiqian Fu Xiaofei Zhang Jian Zhang Hong Zhao Qi Hu Pangyuan Liu Weiming He Xiangyang Han Changlong Wen |
| author_facet | Shouwei Tian Jingjing Yang Yiqian Fu Xiaofei Zhang Jian Zhang Hong Zhao Qi Hu Pangyuan Liu Weiming He Xiangyang Han Changlong Wen |
| author_sort | Shouwei Tian |
| collection | DOAJ |
| description | Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (<i>McAPRR2</i>) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. <i>McAPRR2</i> exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The <i>McAPRR2</i> haplotype is significantly correlated with both pericarp color and ecological type. Importantly, <i>McAPRR2</i> with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the <i>McAPRR2</i> gene and its promoter. High π<sub>wild/SEA</sub> and π<sub>SA/SEA</sub> values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the <i>McAPRR2</i> gene. The haplotypes, phylogenetic tree, and nucleotide diversity of <i>McAPRR2</i> suggest that <i>McAPRR2</i> has undergone domestication selection. This study identifies <i>McAPRR2</i> as the key gene determining pericarp color in bitter gourds and introduces a novel insight that <i>McAPRR2</i> is subject to domestication selection. |
| first_indexed | 2024-03-10T20:56:40Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T20:56:40Z |
| publishDate | 2023-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-70314468d64f4d55a18adbcda1ac08252023-11-19T17:49:07ZengMDPI AGPlants2223-77472023-10-011220358510.3390/plants12203585<i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter GourdShouwei Tian0Jingjing Yang1Yiqian Fu2Xiaofei Zhang3Jian Zhang4Hong Zhao5Qi Hu6Pangyuan Liu7Weiming He8Xiangyang Han9Changlong Wen10Beijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaBeijing Key Laboratory of Vegetable Germplasms Improvement, Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, ChinaPericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (<i>McAPRR2</i>) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. <i>McAPRR2</i> exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The <i>McAPRR2</i> haplotype is significantly correlated with both pericarp color and ecological type. Importantly, <i>McAPRR2</i> with the light green pericarp demonstrated premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the <i>McAPRR2</i> gene and its promoter. High π<sub>wild/SEA</sub> and π<sub>SA/SEA</sub> values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the <i>McAPRR2</i> gene. The haplotypes, phylogenetic tree, and nucleotide diversity of <i>McAPRR2</i> suggest that <i>McAPRR2</i> has undergone domestication selection. This study identifies <i>McAPRR2</i> as the key gene determining pericarp color in bitter gourds and introduces a novel insight that <i>McAPRR2</i> is subject to domestication selection.https://www.mdpi.com/2223-7747/12/20/3585<i>Momordica charantia</i><i>McAPRR2</i>pericarp colorhaplotypedomestication |
| spellingShingle | Shouwei Tian Jingjing Yang Yiqian Fu Xiaofei Zhang Jian Zhang Hong Zhao Qi Hu Pangyuan Liu Weiming He Xiangyang Han Changlong Wen <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd Plants <i>Momordica charantia</i> <i>McAPRR2</i> pericarp color haplotype domestication |
| title | <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd |
| title_full | <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd |
| title_fullStr | <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd |
| title_full_unstemmed | <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd |
| title_short | <i>McAPRR2</i>: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd |
| title_sort | i mcaprr2 i the key regulator of domesticated pericarp color in bitter gourd |
| topic | <i>Momordica charantia</i> <i>McAPRR2</i> pericarp color haplotype domestication |
| url | https://www.mdpi.com/2223-7747/12/20/3585 |
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