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Gebretsadik K, Chen W, Duan Y, Sun Y, He Y, Liao Q, Wang C, Bo K. Map-based cloning reveals Cpgp gene encoding an APRR2 protein to regulate the green fruit peel formation in Cucurbita pepo. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:53. [PMID: 39130616 PMCID: PMC11315825 DOI: 10.1007/s11032-024-01492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
Fruit peel color is a major factor that influences fruit quality and customers' demand. However, the molecular mechanisms underlying the green fruit peel color trait of Cucurbita pepo L. remain unknown. Two parental lines, RP16 and RP38, were used to study the fruit peel color trait in C. pepo. The parental line RP16 shows white peel color, whereas RP38 exhibits green peel color. 384 F2 populations were used to identify the inheritance pattern associated with green fruit and white fruit peel in Cucurbita pepo L. 293 F2 individuals were white, and 91 F2 individuals were green, resulting in a ratio of 3:1. Hence, white peel is dominant over the green fruit peel trait, and a single recessive green peel gene (Cpgp) controls the green fruit peel. The fruit chlorophyll (Chll) content decreases as fruit matures in the RP16 line. In contrast, Chll increases during the fruit growing periods on fruit peels of the RP38 line. The BSA-sequence analysis revealed the Cpgp locus on Chr5, within a 2.3 Mb region. Subsequent fine-mapping analysis, using 699 F2 plants, narrowed down this region to 23.90 kb on the same chromosome. Within this region, two annotated genes, namely Cp4.1LG05g02070 and Cp4.1LG05g02060, are present. These genes are predicted to encode a two-component Arabidopsis Pseudo-Response Regulator 2-like protein (APRR2), which may be involved in green pigmentation processes in plants. Consequently, sequence alignment and gene expression analyses at various fruit development stages supported that Cp4.1LG05g02070 may be the primary candidate gene responsible for regulating the green fruit peel color trait in Cucurbita pepo L. This study may provide a basis for further study on the basic mechanisms that control the fruit peel colors in Cucurbita spp. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01492-7.
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Affiliation(s)
- Kiros Gebretsadik
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
- Department of Plant Sciences, Aksum University Shire Campus, Shire, Ethiopia
| | - Wanlu Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Ying Duan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yapei Sun
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yadi He
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Qinggui Liao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Changlin Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Kailiang Bo
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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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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Gao Y, Peng J, Qiao Y, Wang G. Natural Allelic Variations of Bch10G006400 Controlling Seed Size in Chieh-qua ( Benincasa hispida Cogn. var. Chieh-qua How). Int J Mol Sci 2024; 25:4236. [PMID: 38673826 PMCID: PMC11050567 DOI: 10.3390/ijms25084236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/17/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Seeds are the most important reproductive organs of higher plants, the beginning and end of a plant's lifecycle. They are very important to plant growth and development, and also an important factor affecting yield. In this study, genetic analysis and BSA-seq of the F2 population crossed with the large-seeded material 'J16' and small-seeded material 'FJ5' were carried out, and the seed size locus was initially located within the 1.31 Mb region on chr10. In addition, 2281 F2 plants were used to further reduce the candidate interval to 48.8 Kb. This region contains only one gene encoding the N-acetyltransferase (NAT) protein (Bch10G006400). Transcriptome and expression analysis revealed that the gene was significantly more highly expressed in 'J16' than in 'FJ5'. Variation analysis of Bch10G006400 among parents and 50 chieh-qua germplasms revealed that as well as a nonsynonymous mutation (SNP_314) between parents, two mutations (SNP_400 and InDel_551) were detected in other materials. Combining these three mutations completely distinguished the seed size of the chieh-qua. GO and KEGG enrichment analyses revealed that DGEs played the most important roles in carbohydrate metabolism and plant hormone signal transduction, respectively. The results of this study provide important information for molecular marker-assisted breeding and help to reveal the molecular mechanism of seed size.
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Affiliation(s)
- Yin Gao
- Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou 510335, China;
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jiazhu Peng
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
| | - Yanchun Qiao
- Guangzhou Academy of Agricultural and Rural Sciences, Guangzhou 510335, China;
- Guangzhou Academy of Agricultural Sciences, Guangzhou 510308, China;
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Guo J, Han X, Wu T, Wang R, Zhao J, Wang R, Tan D, Yan S, Gao J, Huang W, Zhang H, Zhang C. Potential locus W and candidate gene McPRR2 associated with pericarp pigment accumulation in bitter gourd (Momordica charantia L.) revealed via BSA-seq analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108515. [PMID: 38484681 DOI: 10.1016/j.plaphy.2024.108515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 04/02/2024]
Abstract
Pericarp color is a prominent agronomic trait that exerts a significant impact on consumer and breeder preferences. Genetic analysis has revealed that the pericarp color of bitter gourd is a quantitative trait. However, the underlying mechanism for this trait in bitter gourd remains largely unknown. In the present study, we employed bulked segregant analysis (BSA) to identify the candidate genes responsible for bitter gourd pericarp color (specifically, dark green versus white) within F2 segregation populations resulting from the crossing of B07 (dark green pericarp) and A06 (white pericarp). Through genomic variation, genetic mapping, and expression analysis, we identified a candidate gene named McPRR2, which was a homolog of Arabidopsis pseudo response regulator 2 (APRR2) encoded by LOC111023472. Sequence alignment of the candidate gene between the two parental lines revealed a 15-bp nucleotide insertion in the coding region of LOC111023472, leading to a premature stop codon and potentially causing a loss-of-function mutation. qRT-PCR analysis demonstrated that the expression of McPRR2 was significantly higher in B07 compared to A06, and it was primarily expressed in the immature fruit pericarp. Moreover, overexpression of McPRR2 in tomato could enhance the green color of immature fruit pericarp by increasing the chlorophyll content. Consequently, McPRR2 emerged as a strong candidate gene regulating the bitter gourd pericarp color by influencing chlorophyll accumulation. Finally, we developed a molecular marker linked to pericarp color, enabling the identification of genotypes in breeding populations. These findings provided valuable insights into the genetic improvement of bitter gourd pericarp color.
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Affiliation(s)
- Jinju Guo
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Xin Han
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Tingquan Wu
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Rui Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Junhong Zhao
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Rufang Wang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Delong Tan
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Shijuan Yan
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Jie Gao
- Environment Horticulture Research Institute/Guangdong Provincial Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Wenjie Huang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Huiyao Zhang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Changyuan Zhang
- Institute of Facility Agriculture, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, 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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Liu W, Wang M, Zhong M, Luo C, Shi S, Qian Y, Kang Y, Jiang B. Genome-wide identification of bZIP gene family and expression analysis of BhbZIP58 under heat stress in wax gourd. BMC PLANT BIOLOGY 2023; 23:598. [PMID: 38017380 PMCID: PMC10685590 DOI: 10.1186/s12870-023-04580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 11/03/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor family is one of the most abundant and evolutionarily conserved gene families in plants. It assumes crucial functions in the life cycle of plants, including pathogen defense, secondary metabolism, stress response, seed maturation, and flower development. Although the genome of wax gourd has been published, little is known about the functions, evolutionary background, and gene expression patterns of the bZIP gene family, which limits its utilization. RESULTS A total of 61 bZIP genes (BhbZIPs) were identified from wax gourd (Benincasa hispida) genome and divided into 12 subgroups. Whole-genome duplication (WGD) and dispersed duplication (DSD) were the main driving forces of bZIP gene family expansion in wax gourd, and this family may have undergone intense purifying selection pressure during the evolutionary process. We selected BhbZIP58, only one in the member of subgroup B, to study its expression patterns under different stresses, including heat, salt, drought, cold stress, and ABA treatment. Surprisingly, BhbZIP58 had a dramatic response under heat stress. BhbZIP58 showed the highest expression level in the root compared with leaves, stem, stamen, pistil, and ovary. In addition, BhbZIP58 protein was located in the nucleus and had transcriptional activation activity. Overexpression of BhbZIP58 in Arabidopsis enhanced their heat tolerance. CONCLUSIONS In this study, bZIP gene family is systematically bioinformatically in wax gourd for the first time. Particularly, BhbZIP58 may have an important role in heat stress. It will facilitate further research on the bZIP gene family regarding their evolutionary history and biological functions.
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Affiliation(s)
- Wei Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Min Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Min Zhong
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Chen Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Shaoqi Shi
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Yulei Qian
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China
| | - Yunyan Kang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Biao Jiang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510640, Guangdong, China.
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8
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Tian S, Yang J, Fu Y, Zhang X, Zhang J, Zhao H, Hu Q, Liu P, He W, Han X, Wen C. McAPRR2: The Key Regulator of Domesticated Pericarp Color in Bitter Gourd. PLANTS (BASEL, SWITZERLAND) 2023; 12:3585. [PMID: 37896048 PMCID: PMC10610206 DOI: 10.3390/plants12203585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023]
Abstract
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 (McAPRR2) controlling pericarp color via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 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 McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 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 McAPRR2 gene and its promoter. High πwild/SEA and πSA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Changlong Wen
- Beijing 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, China (J.Y.); (J.Z.); (H.Z.)
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9
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Yang W, Wang P, Liu T, Nong L, Cheng Z, Su L, Bai W, Deng Y, Chen Z, Liu Z. Fine mapping of the major gene BhHLS1 controlling seed size in wax gourd ( Benincasa hispida). FRONTIERS IN PLANT SCIENCE 2023; 14:1266796. [PMID: 37841615 PMCID: PMC10570438 DOI: 10.3389/fpls.2023.1266796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Introduction/Background The seed size of wax gourds is an important agronomic trait; however, the associated genes have not yet been reported. Methods In this study, we used a high-density genetic map constructed based on F8 recombinant inbred line populations derived from a cross between MY-1 (large seed) and GX-71 (small seed) strains to detect quantitative trait locis (QTLs) for seed-size-related traits in wax gourd over a two-year period. Results Two stable QTLs (qSL10 and qSW10) for seed length (SL) and seed width (SW) on chromosome 10 were repeatedly detected over two years (2021-2022). qSL10 had a phenotypic variation rate of 75.30% and 80.80% in 2021 and 2022, respectively. Whereas, qSW10 had a phenotypic variation rate of 66.60% and 73.80% in 2021 and 2022, respectively. Further, a single nucleotide polymorphism mutation was found to cause early termination of Bch10G006400 (BhHLS1) translation in GX-71 through sequencing analysis of candidate genes. Based on gene functional annotation and quantitative real-time PCR analyses, BhHLS1 encoded a probable N-acetyltransferase HLS1-like protein and its expression level was significantly different between parents. Therefore, BhHLS1 is a major candidate gene associated with a one-factor polymorphism regulating the SL and SW of wax gourds. Finally, based on variation in the BhHLS1 sequence, a cleaved amplified polymorphic sequence marker was developed for the molecular marker-assisted breeding of wax gourds. Discussion Overall, this study is of great significance for the genetic improvement of seed size, verification of gene functions, and cultivation of specific germplasm resources for wax gourds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Zhengguo Liu
- College of Agriculture, Guangxi University, Nanning, China
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10
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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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11
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Fu H, Wei X, Chen Q, Yong S, Liu Q, Dang J, Wu D, Liang G, Guo Q. Comparative transcriptome analysis of molecular mechanisms underlying adventitious root developments in Huangshan Bitter tea ( Camellia gymnogyna Chang) under red light quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1154169. [PMID: 37025148 PMCID: PMC10070859 DOI: 10.3389/fpls.2023.1154169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
As the formation of adventitious roots (AR) is an important component of in vitro regeneration of tea plants, the propagation and preservation of Huangshan Bitter tea (Camellia gymnogyna Chang) cuttings have been hindered due to its lower rooting rate. As light is a crucial environmental factor that affects AR formation, this study aimed to investigate the special role of red light (RL) in the formation of AR in Huangshan Bitter tea plants, which has not been well understood. Huangshan Bitter tea plants were induced with white light (control, WL) and red light (660 nm, RL) qualities 36 days after induced treatment (DAI) to investigate dynamic AR formation and development, anatomical observation, hormones content change, and weighted gene co-expression network analysis (WGCNA) of the transcriptome. Results showed that RL promoted the rooting rate and root characteristics compared to WL. Anatomical observations demonstrated that root primordium was induced earlier by RL at the 4 DAI. RL positively affected IAA, ZT and GA3 content and negatively influenced ABA from the 4 to 16 DAI. RNA-seq and analysis of differential expression genes (DEGs) exhibited extensive variation in gene expression profiles between RL and WL. Meanwhile, the results of WGCNA and correlation analysis identified three highly correlated modules and hub genes mainly participated in 'response to hormone', 'cellular glucan metabolic progress', and 'response to auxin'. Furthermore, the proportion of transcription factors (TFs) such as ethylene response factor (ERF), myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WRKYGQK (WRKY) were the top four in DEGs. These results suggested that the AR-promoting potential of red light was due to complex hormone interactions in tea plants by regulating the expression of related genes. This study provided an important reference to shorten breeding cycles and accelerate superiority in tea plant propagation and preservation.
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Affiliation(s)
- Hao Fu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Xu Wei
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Qian Chen
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Shunyuan Yong
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
| | - Qinjin Liu
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Di Wu
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
- Chongqing Institute of Ancient Tea Plant and Product, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing, China
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12
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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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13
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Fine Mapping and Identification of SmAPRR2 Regulating Rind Color in Eggplant ( Solanum melongena L.). Int J Mol Sci 2023; 24:ijms24043059. [PMID: 36834473 PMCID: PMC9964064 DOI: 10.3390/ijms24043059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Rind color is an economically important agronomic trait in eggplant that impacts consumer preferences. In this study, bulked segregant analysis and competitive allele-specific PCR were employed to identify the candidate gene for eggplant rind color through constructing a 2794 F2 population generated from a cross between "BL01" (green pericarp) and "B1" (white pericarp). Genetic analysis of rind color revealed that a single dominant gene controls green color of eggplant peel. Pigment content measurement and cytological observations demonstrated that chlorophyll content and chloroplast number in BL01 were higher than in B1. A candidate gene (EGP19168.1) was fine-mapped to a 20.36 Kb interval on chromosome 8, which was predicted to encode the two-component response regulator-like protein Arabidopsis pseudo-response regulator2 (APRR2). Subsequently, allelic sequence analysis revealed that a SNP deletion (ACT→AT) in white-skinned eggplant led to a premature termination codon. Genotypic validation of 113 breeding lines using the Indel marker closely linked to SmAPRR2 could predict the skin color (green/white) trait with an accuracy of 92.9%. This study will be valuable for molecular marker-assisted selection in eggplant breeding and provides theoretical foundation for analyzing the formation mechanism of eggplant peel color.
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14
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Niu J, Chen Q, Lu X, Wang X, Tang Z, Liu Q, Lei F, Xu X. Fine mapping and identifying candidate gene of Y underlying yellow peel in Cucurbita pepo. FRONTIERS IN PLANT SCIENCE 2023; 14:1159937. [PMID: 37152148 PMCID: PMC10160447 DOI: 10.3389/fpls.2023.1159937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
As a conspicuous trait, peel color is one of the most important characteristics that affects commodity quality and consumer preferences. The locus Y underlying yellow peel in Cucurbita pepo (zucchini) was first reported in 1922; however, its molecular mechanism is still unknown. In this study, a genetic analysis revealed that yellow peel is controlled by a single dominant genetic factor. Furthermore, Y was mapped in a ~170 kb region on chromosome 10 by bulked segregated analysis (BSA) and fine mapping in F2 and BC1 segregating populations. The candidate region harbors fifteen annotated genes, among which Cp4.1LG10g11560 (CpCHLH) is regarded as a promising candidate gene. CpCHLH encodes a magnesium chelatase H subunit involved in chlorophyll biosynthesis, and its mutation can result in a reduction in chlorophyll content and yellow phenotype. Interestingly, a large fragment (~15 kb) duplication containing incomplete CpCHLH was inserted in the candidate interval, resulting in two reformed CpCHLH proteins in the yellow parental line. It is most likely that the reformed CpCHLH proteins act as a malfunctional competitor of the normal CpCHLH protein to interrupt the formation of chlorophyll. Overall, the isolation of Y will shed light on the molecular mechanism of the peel color regulation of zucchini and lay a foundation for breeding.
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Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
| | - Qiong Chen
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
| | - Xiaonan Lu
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | | | - Zhongli Tang
- College of Horticulture, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Qinghua Liu
- Cotton Research Institute, Shanxi Agricultural University, Yuncheng, Shanxi, China
| | - Fengjin Lei
- Cotton Research Institute, Shanxi Agricultural University, Yuncheng, Shanxi, China
- *Correspondence: Fengjin Lei, ; Xiaoyong Xu,
| | - Xiaoyong Xu
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
- *Correspondence: Fengjin Lei, ; Xiaoyong Xu,
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15
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Cai J, Yang S, Liu W, Yan J, Jiang B, Xie D. A transcriptome analysis of Benincasa hispida revealed the pathways and genes involved in response to Phytophthora melonis infection. FRONTIERS IN PLANT SCIENCE 2022; 13:1106123. [PMID: 36618646 PMCID: PMC9815465 DOI: 10.3389/fpls.2022.1106123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Wilt disease caused by Phytophthora melonis infection is one of the most serious threats to Benincasa hispida production. However, the mechanism of the response of B. hispida to a P. melonis infection remains largely unknown. In the present study, two B. hispida cultivars with different degrees of resistance to P. melonis were identified: B488 (a moderately resistant cultivar) and B214 (a moderately susceptible cultivar). RNA-seq was performed on P. melonis-infected B488 and B214 12 hours post infection (hpi). Compared with the control, 680 and 988 DEGs were respectively detected in B488 and B214. A KEGG pathway analysis combined with a cluster analysis revealed that phenylpropanoid biosynthesis, plant-pathogen interaction, the MAPK signaling pathway-plant, and plant hormone signal transduction were the most relevant pathways during the response of both B488 and B214 to P. melonis infection, as well as the differentially expressed genes in the two cultivars. In addition, a cluster analysis of transcription factor genes in DEGs identified four genes upregulated in B488 but not in B214 at 6 hpi and 12 hpi, which was confirmed by qRT-PCR. These were candidate genes for elucidating the mechanism of the B. hispida response to P. melonis infection and laying the foundation for the improvement of B. hispida.
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Affiliation(s)
- Jinsen Cai
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wenrui Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jinqiang Yan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Biao Jiang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dasen Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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16
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Luo C, Yan J, He C, Liu W, Xie D, Jiang B. Genome-Wide Identification of the SAUR Gene Family in Wax Gourd ( Benincasa hispida) and Functional Characterization of BhSAUR60 during Fruit Development. Int J Mol Sci 2022; 23:ijms232214021. [PMID: 36430500 PMCID: PMC9694812 DOI: 10.3390/ijms232214021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
The wax gourd (Benincasa hispida) is an important vegetable crop whose fruits contain nutrients and metabolites. Small auxin upregulated RNA (SAUR) genes constitute the largest early auxin-responsive gene family and regulate various biological processes in plants, although this gene family has not been studied in the wax gourd. Here, we performed genome-wide identification of the SAUR gene family in wax gourds and analyzed their syntenic and phylogenetic relationships, gene structures, conserved motifs, cis-acting elements, and expression patterns. A total of 68 SAUR (BhSAUR) genes were identified, which were distributed on nine chromosomes with 41 genes in two clusters. More than half of the BhSAUR genes were derived from tandem duplication events. The BhSAUR proteins were classified into seven subfamilies. BhSAUR gene promoters contained cis-acting elements involved in plant hormone and environmental signal responses. Further expression profiles showed that BhSAUR genes displayed different expression patterns. BhSAUR60 was highly expressed in fruits, and overexpression led to longer fruits in Arabidopsis. In addition, the plants with overexpression displayed longer floral organs and wavy stems. In conclusion, our results provide a systematic analysis of the wax gourd SAUR gene family and facilitate the functional study of BhSAUR60 during wax gourd fruit development.
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Affiliation(s)
- Chen Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Changxia He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
- Correspondence: ; Tel.: +86-020-38469441
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Huang X, Wu W, Su L, Lv H, Cheng Z, Yang W, Nong L, Liu T, Chen Y, Wang P, Liu Z. Development and Application of InDel Markers Linked to Fruit-Shape and Peel-Colour Genes in Wax Gourd. Genes (Basel) 2022; 13:genes13091567. [PMID: 36140735 PMCID: PMC9498789 DOI: 10.3390/genes13091567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 12/03/2022] Open
Abstract
The wax gourd is commonly grown in many countries because of its high nutritional and economic value. While the genes for the fruit shape and peel colour of wax gourd have been reported, the InDel markers linked to these genes remain undeveloped. In this study, the InDel markers linked to fruit-shape (Bch02G016830) and peel-colour (Bch05G003950) genes were developed from resequenced data. We used 120 inbred lines, 536 isolated populations, and 4 commercial hybrids to evaluate the validity and application value of the InDel markers. The accuracy rates of nine pairs of fruit-shape InDel markers (GX1-GX9) were 84.16–91.66% in 120 inbred lines. The accuracy rates of 27 pairs of peel-colour InDel markers (PS1-PS27) within approximately 3.0 Mb upstream and 3.0 Mb downstream of the peel-colour gene were 100% and those of 6 pairs of peel-colour InDel markers (PS28-PS33) within 3.0–20 Mb upstream and downstream of the peel-colour gene were 55.83–90% in 120 inbred lines. The purity of four commercial hybrids determined using GX1, GX2, PS13, and PS14 was highly consistent with the field results for purity determination. Our results provide important information for genetic linkage map construction, molecular-marker-assisted selective breeding, and purity determination of wax gourd hybrids.
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Affiliation(s)
- Xiaochun Huang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenting Wu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Liwen Su
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Haixuan Lv
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Zhikui Cheng
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Wenrui Yang
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Lifeng Nong
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Ting Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
| | - Yong Chen
- Institute for New Rural Development, Guangxi University, Nanning 530004, China
| | - Peng Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning 530004, China
| | - Zhengguo Liu
- College of Agricultural, Guangxi University, Nanning 530004, China
- Correspondence:
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18
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Fine Mapping and Functional Analysis of Major Regulatory Genes of Soluble Solids Content in Wax Gourd (Benincasa hispida). Int J Mol Sci 2022; 23:ijms23136999. [PMID: 35806004 PMCID: PMC9266771 DOI: 10.3390/ijms23136999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Soluble solids content (SSC) is an important quality trait of wax gourd, but reports about its regulatory genes are scarce. In this study, the SSC regulatory gene BhSSC2.1 in wax gourd was mined via quantitative trait locus (QTL) mapping based on high-density genetic mapping containing 12 linkage groups (LG) and bulked segregant analysis (BSA)-seq. QTL mapping and BSA-seq revealed for the first time that the SSC QTL (107.658–108.176 cM) of wax gourd was on Chr2 (LG2). The interpretable phenotypic variation rate and maximum LOD were 16.033% and 6.454, respectively. The QTL interval contained 13 genes. Real-time fluorescence quantitative expression analysis, functional annotation, and sequence analysis suggested that Bch02G016960, named BhSSC2.1, was a candidate regulatory gene of the SSC in wax gourd. Functional annotation of this gene showed that it codes for a NADP-dependent malic enzyme. According to BhSSC2.1 sequence variation, an InDel marker was developed for molecular marker-assisted breeding of wax gourd. This study will lay the foundation for future studies regarding breeding and understanding genetic mechanisms of wax gourd.
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Huang H, Yang Q, Zhang L, Kong W, Wang H, Wei A, Du S, Yang R, Li J, Lin T, Geng X, Li Y. Genome-wide association analysis reveals a novel QTL CsPC1 for pericarp color in cucumber. BMC Genomics 2022; 23:383. [PMID: 35590237 PMCID: PMC9121586 DOI: 10.1186/s12864-022-08606-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cucumber is an important melon crop in the world, with different pericarp colors. However, the candidate genes and the underlying genetic mechanism for such an important trait in cucumber are unknown. In this study, a locus controlling pericarp color was found on chromosome 3 of cucumber genome. RESULTS In this study, the light green inbred line G35 and the dark green inbred line Q51 were crossed to produce one F2 population. Consequently, we identified a major locus CsPC1 (Pericarp color 1). Next, we mapped the CsPC1 locus to a 94-kb region chromosome 3 which contains 15 genes. Among these genes, Csa3G912920, which encodes a GATA transcription factor, was expressed at a higher level in the pericarp of the NIL-1334 line (with light-green pericarp) than in that of the NIL-1325 line (with dark-green pericarp). This study provides a new allele for the improvement of cucumber pericarp color. CONCLUSION A major QTL that controls pericarp color in cucumber, CsPC1, was identified in a 94-kb region that harbors the strong candidate gene CsGATA1.
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Affiliation(s)
- Hongyu Huang
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192, China
| | - Qinqin Yang
- China Agricultural University College of Horticulture, Beijing, 100193, China
| | - Lidong Zhang
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192, China
| | - Weiliang Kong
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192, China
| | - Huizhe Wang
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Aimin Wei
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Shengli Du
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Ruihuan Yang
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Jiawang Li
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin Kernel Cucumber Research Institute, Tianjin, 300192, China
| | - Tao Lin
- China Agricultural University College of Horticulture, Beijing, 100193, China
| | - Xiaolin Geng
- China Agricultural University College of Horticulture, Beijing, 100193, China.
| | - Yuhe Li
- Institute of Cucumber Research, Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China.
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