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Wang Y, Fang Y, Ning S, Xia L, Zhan J, Yang Z, Cheng C, Lou Q, Li J, Chen J. QTL Mapping for Ovary- and Fruit-Related Traits in Cucumis sativus-C. hystrix Introgression Line IL52. Genes (Basel) 2023; 14:1133. [PMID: 37372313 DOI: 10.3390/genes14061133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
IL52 is a valuable introgression line obtained from interspecific hybridization between cultivated cucumber (Cucumis sativus L., 2n = 14) and the wild relative species C. hystrix Chakr. (2n = 24). IL52 exhibits high resistance to a number of diseases, including downy mildew, powdery mildew, and angular leaf spot. However, the ovary- and fruit-related traits of IL52 have not been thoroughly investigated. Here, we conducted quantitative trait loci (QTL) mapping for 11 traits related to ovary size, fruit size, and flowering time using a previously developed 155 F7:8 RIL population derived from a cross between CCMC and IL52. In total, 27 QTL associated with the 11 traits were detected, distributed on seven chromosomes. These QTL explained 3.61% to 43.98% of the phenotypic variance. Notably, we identified a major-effect QTL (qOHN4.1) on chromosome 4 associated with the ovary hypanthium neck width and further delimited it into a 114-kb candidate region harboring 13 candidate genes. Furthermore, the QTL qOHN4.1 is co-localized with the QTL detected for ovary length, mature fruit length, and fruit neck length, all residing within the consensus QTL FS4.1, suggesting a plausible pleiotropic effect.
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Affiliation(s)
- Yuhui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Yu Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Shixiong Ning
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Lei Xia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Jinyi Zhan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Zhilong Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
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Li C, Dong S, Beckles DM, Liu X, Guan J, Gu X, Miao H, Zhang S. GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1116214. [PMID: 37235012 PMCID: PMC10208356 DOI: 10.3389/fpls.2023.1116214] [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: 12/05/2022] [Accepted: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.
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Affiliation(s)
- Caixia Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Grumet R, Lin YC, Rett-Cadman S, Malik A. Morphological and Genetic Diversity of Cucumber ( Cucumis sativus L.) Fruit Development. PLANTS (BASEL, SWITZERLAND) 2022; 12:23. [PMID: 36616152 PMCID: PMC9824707 DOI: 10.3390/plants12010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 06/03/2023]
Abstract
Cucumber (Cucumis sativus L.) fruits, which are eaten at an immature stage of development, can vary extensively in morphological features such as size, shape, waxiness, spines, warts, and flesh thickness. Different types of cucumbers that vary in these morphological traits are preferred throughout the world. Numerous studies in recent years have added greatly to our understanding of cucumber fruit development and have identified a variety of genetic factors leading to extensive diversity. Candidate genes influencing floral organ establishment, cell division and cell cycle regulation, hormone biosynthesis and response, sugar transport, trichome development, and cutin, wax, and pigment biosynthesis have all been identified as factors influencing cucumber fruit morphology. The identified genes demonstrate complex interplay between structural genes, transcription factors, and hormone signaling. Identification of genetic factors controlling these traits will facilitate breeding for desired characteristics to increase productivity, improve shipping, handling, and storage traits, and enhance consumer-desired qualities. The following review examines our current understanding of developmental and genetic factors driving diversity of cucumber fruit morphology.
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Affiliation(s)
- Rebecca Grumet
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ying-Chen Lin
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Stephanie Rett-Cadman
- Graduate Program in Plant Breeding, Genetics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Ajaz Malik
- Department of Horticulture-Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar 190 025, India
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Yang Y, Dong S, Miao H, Liu X, Dai Z, Li X, Gu X, Zhang S. Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber ( Cucumis sativus L.). Genes (Basel) 2022; 13:genes13061095. [PMID: 35741858 PMCID: PMC9222855 DOI: 10.3390/genes13061095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development.
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Liu X, Yang X, Xie Q, Miao H, Bo K, Dong S, Xin T, Gu X, Sun J, Zhang S. NS encodes an auxin transporter that regulates the 'numerous spines' trait in cucumber (Cucumis sativus) fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:325-336. [PMID: 35181968 DOI: 10.1111/tpj.15710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Fruit spine is an important agronomic trait in cucumber and the "numerous spines (ns)" cucumber varieties are popular in Europe and West Asia. Although the classical genetic locus of ns was reported more than two decades ago, the NS gene has not been cloned yet. In this study, nine genetic loci for the different densities of fruit spines were identified by a genome-wide association study. Among the nine loci, fsdG2.1 was closely associated with the classical genetic locus ns, which harbors a candidate gene Csa2G264590. Overexpression of Csa2G264590 resulted in lower fruit spine density, and the knockout mutant generated by CRISPR/Cas9 displayed an increased spine density, demonstrating that the Csa2G264590 gene is NS. NS is specifically expressed in the fruit peel and spine. Genetic analysis showed that NS regulates fruit spine development independently of the tuberculate gene, Tu, which regulates spine development on tubercules; the cucumber glabrous mutants csgl1 and csgl3 are epistatic to ns. Furthermore, we found that auxin levels in the fruit peel and spine were significantly lower in the knockout mutant ns-cr. Moreover, RNA-sequencing showed that the plant hormone signal transduction pathway was enriched. Notably, most of the auxin responsive Aux/IAA family genes were downregulated in ns-cr. Haplotype analysis showed that the non-functional haplotype of NS exists exclusively in the Eurasian cucumber backgrounds. Taken together, the cloning of NS gene provides new insights into the regulatory network of fruit spine development.
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Affiliation(s)
- Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyong Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qing Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tongxu Xin
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Gebretsadik K, Qiu X, Dong S, Miao H, Bo K. Molecular research progress and improvement approach of fruit quality traits in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3535-3552. [PMID: 34181057 DOI: 10.1007/s00122-021-03895-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/21/2021] [Indexed: 05/10/2023]
Abstract
Recent molecular studies revealed new opportunities to improve cucumber fruit quality. However, the fruit color and spine traits molecular basis remain vague despite the vast sources of genetic diversity. Cucumber is agriculturally, economically and nutritionally important vegetable crop. China produces three-fourths of the world's total cucumber production. Cucumber fruit quality depends on a number of traits such as the fruit color (peel and flesh color), spine (density, size and color), fruit shape, fruit size, defects, texture, firmness, taste, maturity stage and nutritional composition. Fruit color and spine traits determine critical quality attributes and have been the interest of researchers at the molecular level. Evaluating the molecular mechanisms of fruit quality traits is important to improve production and quality of cucumber varieties. Genes and qualitative trait locus (QTL) that are responsible for cucumber fruit color and fruit spine have been identified. The purpose of this paper is to reveal the molecular research progress of fruit color and spines as key quality traits of cucumber. The markers and genes identified so far could help for marker-assisted selection of the fruit color and spine trait in cucumber breeding and its associated nutritional improvement. Based on the previous studies, peel color and spine density as examples, we proposed a comprehensive approach for cucumber fruit quality traits improvement. Moreover, the markers and genes can be useful to facilitate cloning-mediated genetic breeding in cucumber. However, in the era of climate change, increased human population and high-quality demand of consumers, studies on molecular mechanisms of cucumber fruit quality traits are limited.
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Affiliation(s)
- Kiros Gebretsadik
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Science, Aksum University, Shire Campus, Shire, Ethiopia
| | - Xiyan Qiu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Zhang Y, Shen J, Bartholomew ES, Dong M, Chen S, Yin S, Zhai X, Feng Z, Ren H, Liu X. TINY BRANCHED HAIR functions in multicellular trichome development through an ethylene pathway in Cucumis sativus L. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:753-765. [PMID: 33577109 DOI: 10.1111/tpj.15198] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 01/19/2021] [Accepted: 02/05/2021] [Indexed: 05/24/2023]
Abstract
The fruit trichomes of Cucurbitaceae are widely desired in many Asian countries and have been a key determinant of cucumber (Cucumis sativus L.) cultivar selection for commercial production and breeding. However, our understanding of the initiation and development of cucumber trichomes is still limited. Here, we found that the cucumber TINY BRANCHED HAIR (TBH) gene is preferentially expressed in multicellular trichomes. Overexpression of CsTBH in tbh mutants restored the trichome phenotype and increased the percentage of female flowers, whereas silencing of CsTBH in wild-type plants resulted in stunted trichomes with a lower rate of female flowers. Furthermore, we provide evidence that CsTBH can directly bind to the promoters of cucumber 1-Aminocyclopropane-1-Carboxylate Synthase (CsACS) genes and regulate their expression, which affects multicellular trichome development, ethylene accumulation, and sex expression. Two cucumber acs mutants with different trichome morphology and sex morphs compared with their near-isogenic line further support our findings. Collectively, our study provides new information on the molecular mechanism of CsTBH in regulating multicellular trichome development and sex expression through an ethylene pathway.
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Affiliation(s)
- Yaqi Zhang
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Junjun Shen
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Ezra S Bartholomew
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Mingming Dong
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Shuying Chen
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Shuai Yin
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Xuling Zhai
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Zhongxuan Feng
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Huazhong Ren
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
| | - Xingwang Liu
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry on Education, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
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Identification of Quantitative Trait Loci Controlling High-Temperature Tolerance in Cucumber ( Cucumis sativus L.) Seedlings. PLANTS 2020; 9:plants9091155. [PMID: 32906664 PMCID: PMC7570005 DOI: 10.3390/plants9091155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 12/23/2022]
Abstract
High temperature is one of the major abiotic stresses that affect cucumber growth and development. Heat stress often leads to metabolic malfunction, dehydration, wilting and death, which has a great impact on the yield and fruit quality. In this study, genetic analysis and quantitative trait loci (QTL) mapping for thermotolerance in cucumber seedlings was investigated using a recombinant inbred line (RILs; HR) population and a doubled haploid (DH; HP) population derived from two parental lines ‘65G’ (heat-sensitive) and ‘02245′ (heat-tolerant). Inheritance analysis suggested that both short-term extreme and long-term mild thermotolerance in cucumber seedlings were determined by multiple genes. Six QTLs for heat tolerance including qHT3.1, qHT3.2, qHT3.3, qHT4.1, qHT4.2, and qHT6.1 were detected. Among them, the major QTL, qHT3.2, was repeatedly detected for three times in HR and HP at different environments, explained 28.3% of the phenotypic variability. The 481.2 kb region harbored 79 genes, nine of which might involve in heat stress response. This study provides a basis for further identifying thermotolerant genes and helps understanding the molecular mechanism underlying thermotolerance in cucumber seedlings.
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Aguado E, García A, Iglesias-Moya J, Romero J, Wehner TC, Gómez-Guillamón ML, Picó B, Garcés-Claver A, Martínez C, Jamilena M. Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches. FRONTIERS IN PLANT SCIENCE 2020; 11:1243. [PMID: 32973825 PMCID: PMC7466658 DOI: 10.3389/fpls.2020.01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/29/2020] [Indexed: 05/11/2023]
Abstract
The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.
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Affiliation(s)
- Encarnación Aguado
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Alicia García
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jessica Iglesias-Moya
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Jonathan Romero
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Todd C. Wehner
- Departament of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | | | - Belén Picó
- COMAV—Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Cecilia Martínez
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
| | - Manuel Jamilena
- Department of Biology and Geology, Research Centers CIAIMBITAL and CeiA3, University of Almería, Almería, Spain
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Wang Y, Bo K, Gu X, Pan J, Li Y, Chen J, Wen C, Ren Z, Ren H, Chen X, Grumet R, Weng Y. Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. HORTICULTURE RESEARCH 2020; 7:3. [PMID: 31908806 PMCID: PMC6938495 DOI: 10.1038/s41438-019-0226-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/05/2019] [Accepted: 11/08/2019] [Indexed: 05/06/2023]
Abstract
Cucumber, Cucumis sativus L. (2n = 2x = 14), is an important vegetable crop worldwide. It was the first specialty crop with a publicly available draft genome. Its relatively small, diploid genome, short life cycle, and self-compatible mating system offers advantages for genetic studies. In recent years, significant progress has been made in molecular mapping, and identification of genes and QTL responsible for key phenotypic traits, but a systematic review of the work is lacking. Here, we conducted an extensive literature review on mutants, genes and QTL that have been molecularly mapped or characterized in cucumber. We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped. For each gene, detailed information was compiled including chromosome locations, allelic variants and associated polymorphisms, predicted functions, and diagnostic markers that could be used for marker-assisted selection in cucumber breeding. We also documented 322 QTL for 42 quantitative traits, including 109 for disease resistances against seven pathogens. By alignment of these QTL on the latest version of cucumber draft genomes, consensus QTL across multiple studies were inferred, which provided insights into heritable correlations among different traits. Through collaborative efforts among public and private cucumber researchers, we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber. This is the first attempt to systematically summarize, analyze and inventory cucumber mutants, cloned or mapped genes and QTL, which should be a useful resource for the cucurbit research community.
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Affiliation(s)
- Yuhui Wang
- Department of Horticulture, University of Wisconsin, Madison, WI 53706 USA
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Junsong Pan
- Department of Plant Sciences, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yuhong Li
- Horticulture College, Northwest A&F University, Yangling, 712100 China
| | - Jinfeng Chen
- Horticulture College, Nanjing Agricultural University, Nanjing, 210095 China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097 China
| | - Zhonghai Ren
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, 271018 China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Xuehao Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin, Madison, WI 53706 USA
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI 53706 USA
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Dong S, Wang W, Bo K, Miao H, Song Z, Wei S, Zhang S, Gu X. Quantitative Trait Loci Mapping and Candidate Gene Analysis of Low Temperature Tolerance in Cucumber Seedlings. FRONTIERS IN PLANT SCIENCE 2019; 10:1620. [PMID: 31921263 PMCID: PMC6917663 DOI: 10.3389/fpls.2019.01620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 11/18/2019] [Indexed: 05/27/2023]
Abstract
Cucumber (Cucumis sativus L.) is an economically important vegetable crop worldwide, but it is sensitive to low temperatures. Cucumber seedlings exposed to long-term low temperature stress (LT), i.e., below 20°C during the day, and 8°C at night, exhibit leaf yellowing, accelerated senescence, and reduced yield, therefore posing a threat to cucumber production. Studying the underlying mechanisms involved in LT tolerance in cucumber seedlings, and developing germplasm with improved LT-tolerance could provide fundamental solutions to the problem. In this study, an F2 population was generated from two parental lines, "CG104" (LT-tolerant inbred line) and "CG37" (LT-sensitive inbred line), to identify loci that are responsible for LT tolerance in cucumber seedlings. Replicated phenotypic analysis of the F2-derived F3 family using a low-temperature injury index (LTII) suggested that the LT tolerance of cucumber seedlings is controlled by multiple genes. A genetic map of 990.8 cM was constructed, with an average interval between markers of 5.2 cM. One quantitative trait loci (QTL) named qLTT5.1 on chromosome 5, and two QTLs named qLTT6.1 and qLTT6.2 on chromosome 6 were detected. Among them, qLTT6.2 accounted for 26.8 and 24.1% of the phenotypic variation in two different experiments. Single-nucleotide polymorphism (SNP) variations within the region of qLTT6.2 were analyzed using two contrasting in silico bulks generated from the cucumber core germplasm. Result showed that 214 SNPs were distributed within the 42-kb interval, containing three candidate genes. Real-time quantitative reverse transcription PCR and sequence analysis suggested that two genes Csa6G445210, an auxin response factor, and Csa6G445230, an ethylene-responsive transmembrane protein, might be candidate genes responsible for LT tolerance in cucumber seedlings. This study furthers the understanding of the molecular mechanism underlying LT tolerance in cucumber seedlings, and provides new markers for molecular breeding.
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Affiliation(s)
| | | | | | | | | | | | | | - Xingfang Gu
- *Correspondence: Xingfang Gu, ; Shengping Zhang,
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Bo K, Wei S, Wang W, Miao H, Dong S, Zhang S, Gu X. QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber. BMC PLANT BIOLOGY 2019; 19:243. [PMID: 31174472 PMCID: PMC6556036 DOI: 10.1186/s12870-019-1835-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/15/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. The genetic network regulating green flesh formation has been studied in tomato, melon and watermelon. However, little is known about the inheritance and molecular basis of green flesh in cucumber. This study sought to determine the main genomic regions associated with green flesh. Three F2 and two BC1 populations derived from the 9110Gt (cultivated cucumber, green flesh color) and PI183967 (wild cucumber, white flesh color) were used for the green flesh genetic analysis. Two F2 populations of them were further employed to do the map construction and quantitative trait loci (QTL) study. Also, a core cucumber germplasms population was used to do the GWAS analysis. RESULTS We identified three indexes, flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in three environments. Genetic analysis indicated that green flesh color in 9110Gt is controlled by a major-effect QTL. We developed two genetic maps with 192 and 174 microsatellite markers respectively. Two novel inversions in Chr1 were identified between cultivated and wild cucumbers. The major-effect QTL, qgf5.1, was identified using FC, FEC and FCC index in all different environments used. In addition, the same qgf5.1, together with qgf3.1, was identified via GWAS. Further investigation of two candidate regions using pairwise LD correlations, combined with genetic diversity of qgf5.1 in natural populations, it was found that Csa5G021320 is the candidate gene of qgf5.1. Geographical distribution revealed that green flesh color formation could be due to the high latitude, which has longer day time to produce the photosynthesis and chlorophyll synthesis during cucumber domestication and evolution. CONCLUSIONS We first reported the cucumber green flesh color is a quantitative trait. We detected two novel loci qgf5.1 and qgf3.1, which regulate the green flesh formation in cucumber. The QTL mapping and GWAS approaches identified several candidate genes for further validation using functional genomics or forward genetics approaches. Findings from the present study provide a new insight into the genetic control of green flesh in cucumber.
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Affiliation(s)
- Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shuang Wei
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Weiping Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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