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Chen Z, Wang P, Bai W, Deng Y, Cheng Z, Su L, Nong L, Liu T, Yang W, Yang X, Liu Z. Quantitative Trait Loci Sequencing and Genetic Mapping Reveal Two Main Regulatory Genes for Stem Color in Wax Gourds. PLANTS (BASEL, SWITZERLAND) 2024; 13:1804. [PMID: 38999643 PMCID: PMC11244448 DOI: 10.3390/plants13131804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024]
Abstract
Stem color is an important agronomic trait of wax gourds. However, its regulatory genes have not been identified. In this study, 105 inbred lines constructed from two parents (GX-71 and MY-1) were sequenced and quantitative trait loci sequencing was used to mine the genes that regulate stem color in wax gourds. The results identified two quantitative trait loci related to stem color, qSC5 and qSC12, located on Chr05 (11,134,567-16,459,268) and Chr12 (74,618,168-75,712,335), respectively. The qSC5 had a phenotypic variation rate of 36.9% and a maximum limit of detection of 16.9. And the qSC12 had a phenotypic variation rate of 20.9%, and a maximum limit of detection of 11.2. Bch05G003950 (named BchAPRR2) and Bch12G020400 were identified as candidate genes involved in stem color regulation in wax gourds. The chlorophyll content and expression of BchAPRR2 and Bch12G020400 were significantly higher in green-stemmed wax gourds than in white-stemmed ones. Therefore, BchAPRR2 and Bch12G020400 were considered the main and secondary regulatory genes for wax gourd stem color, respectively. Finally, InDel markers closely linked to BchAPRR2 were developed to validate the prediction of wax gourd stem color traits in 55 germplasm lines, with an accuracy of 81.8%. These findings lay the foundation for exploring the genetic regulation of wax gourd stem color and future research on wax gourd breeding.
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Affiliation(s)
- Zhihao Chen
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Peng Wang
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Wenhui Bai
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Yan Deng
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Zhikui Cheng
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Liwen Su
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Lifeng Nong
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Ting Liu
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Wenrui Yang
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Xiping Yang
- College of Agriculture, Guangxi University, Nanning 530000, China
| | - Zhengguo Liu
- College of Agriculture, Guangxi University, Nanning 530000, China
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Ding W, Luo Y, Li W, Chen F, Wang C, Xu W, Wang Y, Qu S. Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini (Cucurbita pepo). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:167. [PMID: 38909110 DOI: 10.1007/s00122-024-04676-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024]
Abstract
KEY MESSAGE A large fragment deletion of CpAPRR2, encoding a two-component response regulator-like protein, which influences immature white rind color formation in zucchini (Cucurbita pepo). Fruit rind color is an important agronomic trait that affects commodity quality and consumer choice in zucchini (Cucurbita pepo). However, the molecular mechanism controlling rind color is unclear. We characterized two zucchini inbred lines: '19' (dark green rind) and '113' (white rind). Genetic analysis revealed white immature fruit rind color to be controlled by a dominant locus (CpW). Combining bulked segregant analysis sequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) markers, we mapped the CpW locus to a 100.4 kb region on chromosome 5 and then narrow down the candidate region to 37.5 kb using linkage analysis of 532 BC1 and 1613 F2 individuals, including 6 coding genes. Among them, Cp4.1LG05g02070 (CpAPRR2), encoding a two-component response regulator-like protein, was regarded to be a promising candidate gene. The expression level of CpAPRR2 in dark green rind was significantly higher than that in white rind and was induced by light. A deletion of 2227 bp at the 5' end of CpAPRR2 in '113' might explain the white phenotype. Further analysis of allelic diversity in zucchini germplasm resources revealed rind color to be associated with the deletion of CpAPRR2. Subcellular localization analysis indicated that CpAPRR2 was a nuclear protein. Transcriptome analysis using near-isogenic lines with dark green (DG) and white (W) rind indicated that genes involved in photosynthesis and porphyrin metabolism pathways were enriched in DG compared with W. Additionally, chlorophyll synthesis-related genes were upregulated in DG. These results identify mechanisms of zucchini rind color and provide genetic resources for breeding.
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Affiliation(s)
- Wenqi Ding
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wenling Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Fangyuan Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, 150030, China.
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Zhang B, Wu Y, Li S, Ren W, Yang L, Zhuang M, Lv H, Wang Y, Ji J, Hou X, Zhang Y. Chloroplast C-to-U editing, regulated by a PPR protein BoYgl-2, is important for chlorophyll biosynthesis in cabbage. HORTICULTURE RESEARCH 2024; 11:uhae006. [PMID: 38559470 PMCID: PMC10980974 DOI: 10.1093/hr/uhae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/30/2023] [Indexed: 04/04/2024]
Abstract
Leaf color is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the detailed mechanism underlying leaf color formation remains unclear. In this study, we characterized a Brassica oleracea yellow-green leaf 2 (BoYgl-2) mutant 4036Y, which has significantly reduced chlorophyll content and abnormal chloroplasts during early leaf development. Genetic analysis revealed that the yellow-green leaf trait is controlled by a single recessive gene. Map-based cloning revealed that BoYgl-2 encodes a novel nuclear-targeted P-type PPR protein, which is absent in the 4036Y mutant. Functional complementation showed that BoYgl-2 from the normal-green leaf 4036G can rescue the yellow-green leaf phenotype of 4036Y. The C-to-U editing efficiency and expression levels of atpF, rps14, petL and ndhD were significantly reduced in 4036Y than that in 4036G, and significantly increased in BoYgl-2 overexpression lines than that in 4036Y. The expression levels of many plastid- and nuclear-encoded genes associated with chloroplast development in BoYgl-2 mutant were also significantly altered. These results suggest that BoYgl-2 participates in chloroplast C-to-U editing and development, which provides rare insight into the molecular mechanism underlying leaf color formation in cabbage.
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Affiliation(s)
- Bin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuankang Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shoufan Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjing Ren
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limei Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mu Zhuang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Honghao Lv
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yong Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Ji
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yangyong Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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McLeod L, Barchi L, Tumino G, Tripodi P, Salinier J, Gros C, Boyaci HF, Ozalp R, Borovsky Y, Schafleitner R, Barchenger D, Finkers R, Brouwer M, Stein N, Rabanus-Wallace MT, Giuliano G, Voorrips R, Paran I, Lefebvre V. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1508-1528. [PMID: 37602679 DOI: 10.1111/tpj.16425] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.
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Affiliation(s)
- Louis McLeod
- INRAE, GAFL, Montfavet, France
- INRAE, A2M, Montfavet, France
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Giorgio Tumino
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), Pontecagnano Faiano, Italy
| | | | | | | | - Ramazan Ozalp
- Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye
| | - Yelena Borovsky
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
| | - Roland Schafleitner
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Derek Barchenger
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Corre, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | | | - Giovanni Giuliano
- Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ENEA), Rome, Italy
| | - Roeland Voorrips
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Ilan Paran
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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Zhan J, Zhong J, Cheng J, Wang Y, Hu K. Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd ( Momordica charantia). FRONTIERS IN PLANT SCIENCE 2023; 14:1128926. [PMID: 37235005 PMCID: PMC10208069 DOI: 10.3389/fpls.2023.1128926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/20/2023] [Indexed: 05/28/2023]
Abstract
Bitter gourd is an economically important vegetable and medicinal crop distinguished by its bitter fruits. Its stigma color is widely used to assess the distinctiveness, uniformity, and stability of bitter gourd varieties. However, limited researches have been dedicated to genetic basis of its stigma color. In this study, we employed bulked segregant analysis (BSA) sequencing to identify a single dominant locus McSTC1 located on pseudochromosome 6 through genetic mapping of an F2 population (n =241) derived from the cross between green and yellow stigma parental lines. An F2-derived F3 segregation population (n = 847) was further adopted for fine mapping, which delimited the McSTC1 locus to a 13.87 kb region containing one predicted gene McAPRR2 (Mc06g1638), a homolog of the Arabidopsis two-component response regulator-like gene AtAPRR2. Sequence alignment analysis of McAPRR2 revealed that a 15 bp insertion at exon 9 results in a truncated GLK domain of its encoded protein, which existed in 19 bitter gourd varieties with yellow stigma. A genome-wide synteny search of the bitter gourd McAPRR2 genes in Cucurbitaceae family revealed its close relationship with other cucurbits APRR2 genes that are corresponding to white or light green fruit skin. Our findings provide insights into the molecular marker-assisted breeding of bitter gourd stigma color and the mechanism of gene regulation for stigma color.
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Affiliation(s)
- Jinyi Zhan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jian Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiaowen Cheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yuhui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Kailin Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
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Huo Y, Zhang G, Yu W, Liu Z, Shen M, Zhao R, Hu S, Zheng X, Wang P, Yang Y. Forward genetic studies reveal LsAPRR2 as a key gene in regulating the green color of pericarp in bottle gourd ( Lagenaria siceraria). FRONTIERS IN PLANT SCIENCE 2023; 14:1130669. [PMID: 36875578 PMCID: PMC9975725 DOI: 10.3389/fpls.2023.1130669] [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: 12/23/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
The fruit peel color is an important factor that affects its quality. However, genes involved in regulating pericarp color in bottle gourd (Lagenaria siceraria) have not been explored to date. Genetic analysis of color traits in bottle gourd peel through a genetic population of six generations demonstrated that the green color of peels is inherited as a single gene dominant trait. Combined phenotype-genotype analysis of recombinant plants using BSA-seq mapped the candidate gene to a 22.645 Kb interval at the head end of chromosome 1. We observed that the final interval contained only one gene, LsAPRR2 (HG_GLEAN_10010973). Sequence and spatiotemporal expression analyses of LsAPRR2 unraveled two nonsynonymous mutations (A→G) and (G→C) in the parental CDS sequences. Further, LsAPRR2 expression was higher in all green-skinned bottle gourds (H16) at various stages of fruit development than in white-skinned bottle gourds (H06). Cloning and sequence comparison of the two parental LsAPRR2 promoter regions indicated 11 bases insertion and 8 SNPs mutations in the region -991~-1033, upstream of the start codon in white bottle gourd. Proof of GUS reporting system, Genetic variation in this fragment significantly reduced the expression of LsAPRR2 in the pericarp of white bottle gourd. In addition, we developed a tightly linked (accuracy 93.88%) InDel marker for the promoter variant segment. Overall, the current study provides a theoretical basis for comprehensive elucidation of the regulatory mechanisms underlying the determination of bottle gourd pericarp color. This would further help in the directed molecular design breeding of bottle gourd pericarp.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peng Wang
- *Correspondence: Yanjuan Yang, ; Peng Wang,
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