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Sun J, Nie J, Xiao T, Guo C, Lv D, Zhang K, He HL, Pan J, Cai R, Wang G. CsPM5.2, a phosphate transporter protein-like gene, promotes powdery mildew resistance in cucumber. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1487-1502. [PMID: 38048475 DOI: 10.1111/tpj.16576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/06/2023]
Abstract
Powdery mildew (PM) is one of the most serious fungal diseases affecting cucumbers (Cucumis sativus L.). The mechanism of PM resistance in cucumber is intricate and remains fragmentary as it is controlled by several genes. In this study, we detected the major-effect Quantitative Trait Locus (QTL), PM5.2, involved in PM resistance by QTL mapping. Through fine mapping, the dominant PM resistance gene, CsPM5.2, was cloned and its function was confirmed by transgenic complementation and natural variation identification. In cultivar 9930, a dysfunctional CsPM5.2 mutant resulted from a single nucleotide polymorphism in the coding region and endowed susceptibility to PM. CsPM5.2 encodes a phosphate transporter-like protein PHO1; H3. The expression of CsPM5.2 is ubiquitous and induced by the PM pathogen. In cucumber, both CsPM5.2 and Cspm5.1 (Csmlo1) are required for PM resistance. Transcriptome analysis suggested that the salicylic acid (SA) pathway may play an important role in CsPM5.2-mediated PM resistance. Our findings help parse the mechanisms of PM resistance and provide strategies for breeding PM-resistant cucumber cultivars.
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Affiliation(s)
- Jingxian Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, China
| | - Jingtao Nie
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Tingting Xiao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Chunli Guo
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Duo Lv
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Keyan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- School of Agriculture and Biology, Shanghai Jiao Tong University/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai, 200240, China
| | - Junsong Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- School of Agriculture and Biology, Shanghai Jiao Tong University/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai, 200240, China
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- School of Agriculture and Biology, Shanghai Jiao Tong University/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai, 200240, China
| | - Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
- School of Agriculture and Biology, Shanghai Jiao Tong University/Shanghai Collaborative Innovation Center of Agri-Seeds, Shanghai, 200240, China
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Dong S, Liu X, Han J, Miao H, Beckles DM, Bai Y, Liu X, Guan J, Yang R, Gu X, Sun J, Yang X, Zhang S. CsMLO8/11 are required for full susceptibility of cucumber stem to powdery mildew and interact with CsCRK2 and CsRbohD. HORTICULTURE RESEARCH 2024; 11:uhad295. [PMID: 38404593 PMCID: PMC10894460 DOI: 10.1093/hr/uhad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/20/2023] [Indexed: 02/27/2024]
Abstract
Powdery mildew (PM) is one of the most destructive diseases that threaten cucumber production globally. Efficient breeding of novel PM-resistant cultivars will require a robust understanding of the molecular mechanisms of cucumber resistance against PM. Using a genome-wide association study, we detected a locus significantly correlated with PM resistance in cucumber stem, pm-s5.1. A 1449-bp insertion in the CsMLO8 coding region at the pm-s5.1 locus resulted in enhanced stem PM resistance. Knockout mutants of CsMLO8 and CsMLO11 generated by CRISPR/Cas9 both showed improved PM resistance in the stem, hypocotyl, and leaves, and the double mutant mlo8mlo11 displayed even stronger resistance. We found that reactive oxygen species (ROS) accumulation was higher in the stem of these mutants. Protein interaction assays suggested that CsMLO8 and CsMLO11 could physically interact with CsRbohD and CsCRK2, respectively. Further, we showed that CsMLO8 and CsCRK2 competitively interact with the C-terminus of CsRbohD to affect CsCRK2-CsRbohD module-mediated ROS production during PM defense. These findings provide new insights into the understanding of CsMLO proteins during PM defense responses.
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Affiliation(s)
- Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Xin Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jianan Han
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Diane M Beckles
- Department of Plant Sciences, University of California Davis, One Shield Avenue, Davis, CA 95616, USA
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Ruizhen Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xueyong Yang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing China
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Mahmood U, Li X, Fan Y, Chang W, Niu Y, Li J, Qu C, Lu K. Multi-omics revolution to promote plant breeding efficiency. FRONTIERS IN PLANT SCIENCE 2022; 13:1062952. [PMID: 36570904 PMCID: PMC9773847 DOI: 10.3389/fpls.2022.1062952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Crop production is the primary goal of agricultural activities, which is always taken into consideration. However, global agricultural systems are coming under increasing pressure from the rising food demand of the rapidly growing world population and changing climate. To address these issues, improving high-yield and climate-resilient related-traits in crop breeding is an effective strategy. In recent years, advances in omics techniques, including genomics, transcriptomics, proteomics, and metabolomics, paved the way for accelerating plant/crop breeding to cope with the changing climate and enhance food production. Optimized omics and phenotypic plasticity platform integration, exploited by evolving machine learning algorithms will aid in the development of biological interpretations for complex crop traits. The precise and progressive assembly of desire alleles using precise genome editing approaches and enhanced breeding strategies would enable future crops to excel in combating the changing climates. Furthermore, plant breeding and genetic engineering ensures an exclusive approach to developing nutrient sufficient and climate-resilient crops, the productivity of which can sustainably and adequately meet the world's food, nutrition, and energy needs. This review provides an overview of how the integration of omics approaches could be exploited to select crop varieties with desired traits.
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Affiliation(s)
- Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xiaodong Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Chang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yue Niu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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Tan J, Wang Y, Dymerski R, Wu Z, Weng Y. Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4197-4215. [PMID: 36094614 DOI: 10.1007/s00122-022-04212-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
The dm5.3 major-effect QTL in cucumber encodes a homolog of Arabidopsis sigma factor binding protein 1 (CsSIB1). CsSIB1 positively regulates defense responses against downy mildew in cucumber through the salicylic acid (SA) biosynthesis/signaling pathway. Downy mildew (DM) caused by the oomycete pathogen Pseudoperonospora cubensis is an important disease of cucumber and other cucurbits. Our knowledge on molecular mechanisms of DM resistance is still limited. In this study, we reported identification and functional characterization of the candidate gene for the major-effect QTL, dm5.3 for DM resistance originated from PI 197088. The dm5.3 QTL was Modelized through marker-assisted development of near isogenic lines (NILs). NIL-derived segregating populations were used for fine mapping which narrowed the dm5.3 locus down to a 144 kb region. Based on multiple lines of evidence, we show that CsSIB1 (CsGy5G027140) that encodes the VQ motif-containing sigma factor binding protein 1 as the most likely candidate for dm5.3. Local association analysis identified a haplotype consisting of 7 SNPs inside the coding and promoter region of CsSIB1 that was associated with DM resistance. Expression of CsSIB1 was up-regulated with P. cubensis infection. Transcriptome profiling of NILs in response to P. cubensis inoculation revealed key players and associated gene networks in which increased expression of CsSIB1 antagonistically promoted salicylic acid (SA) but suppressed jasmonic acid (JA) biosynthesis/signaling pathways. Our work provides novel insights into the function of CsSIB1/dm5.3 as a disease resistance (R) gene. The roles of sigma factor binding protein genes in pathogen defense in cucumber were also discussed.
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Affiliation(s)
- Junyi Tan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Ronald Dymerski
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Zhiming Wu
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Institute of Cash Crops, Hebei Academy of Agriculture & Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53706, USA.
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Bartholomew ES, Xu S, Zhang Y, Yin S, Feng Z, Chen S, Sun L, Yang S, Wang Y, Liu P, Ren H, Liu X. A chitinase CsChi23 promoter polymorphism underlies cucumber resistance against Fusarium oxysporum f. sp. cucumerinum. THE NEW PHYTOLOGIST 2022; 236:1471-1486. [PMID: 36068958 DOI: 10.1111/nph.18463] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Fusarium wilt disease, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), leads to widespread yield loss and quality decline in cucumber. However, the molecular mechanisms underlying Foc resistance remain poorly understood. We report the mapping and functional characterisation of CsChi23, encoding a cucumber class I chitinase with antifungal properties. We assessed sequence variations at CsChi23 and the associated defence response against Foc. We functionally characterised CsChi23 using transgenic assay and expression analysis. The mechanism regulating CsChi23 expression was assessed by genetic and molecular approaches. CsChi23 was induced by Foc infection, which led to rapid upregulation in resistant cucumber lines. Overexpressing CsChi23 enhanced fusarium wilt resistance and reduced fungal biomass accumulation, whereas silencing CsChi23 causes loss of resistance. CsHB15, a homeodomain leucine zipper (HD-Zip) III transcription factor, was found to bind to the CsChi23 promoter region and activate its expression. Furthermore, silencing of CsHB15 reduces CsChi23 expression. A single-nucleotide polymorphism variation -400 bp upstream of CsChi23 abolished the HD-Zip III binding site in a susceptible cucumber line. Collectively, our study indicates that CsChi23 is sufficient to enhance fusarium wilt resistance and reveals a novel function of an HD-Zip III transcription factor in regulating chitinase expression in cucumber defence against fusarium wilt.
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Affiliation(s)
- Ezra S Bartholomew
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuo Xu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Yaqi Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuai Yin
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhongxuan Feng
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Shuyinq Chen
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Lei Sun
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Songlin Yang
- College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Wang
- Heze Agricultural and Rural Bureau, No. 1021 Shuanghe Road, Mudan District, Heze City, Shandong, 274000, China
| | - Peng Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Huazhong Ren
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry of National Education, Beijing, 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Beijing, 100193, China
| | - Xingwang Liu
- College of Horticulture, China Agricultural University, Beijing, 100193, China
- Engineering Research Center of Breeding and Propagation of Horticultural Crops, Ministry of National Education, Beijing, 100193, China
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Beijing, 100193, China
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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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Nyirahabimana F, Shimira F, Zahid G, Solmaz I. Recent status of Genotyping by Sequencing (GBS) Technology in cucumber (Cucumis sativus L.): a review. Mol Biol Rep 2022; 49:5547-5554. [PMID: 35596053 DOI: 10.1007/s11033-022-07469-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023]
Abstract
Current and advanced breeding tools are being used to improve economically important horticultural crops to meet the consumers' needs and preferences. Genotyping-by-sequencing (GBS) is an extremely useful tool in the investigation and analysis of the genetic diversity of different cultivars. Based on a broad range of genetic backgrounds like single nucleotide polymorphism (SNPs), GBS is known as a novel technique to facilitate the detection of quantitative trait loci (QTL) regions robustly linked with interested traits compared to genome-wide association study (GWAS) and QTL. GBS has gained popularity among breeders in recent years and it is also employed in cucumber breeding programs. Cucumbers (C. sativus L.) are monoecious, gynoecious and some of them are parthenocarpic species. Cucumber is one of the most economical and essential crops in the Cucurbitaceae family. For time immemorial, cucumber has been produced and consumed all over the world like other cucurbits. To a large extent, cultivated cucurbits are beneficial to human health for providing necessary minerals and fibers.Therefore, this review portrays the current status of advances made by using GBS and its combination with other tools in various studies of cucumber such as the use of GBS and single nucleotide polymorphism (SNP) markers, GBS and GWAS, also with QTL and marker-assisted selection (MAS) are applied to display and detect explicit genetic architecture complex traits in crops and chromosome rearrangements.Cucumber breeding programs have undoubtedly benefited from genotyping-by-sequencing. Using the GBS method, research discovered lots of new candidate genes that control various traits including spine color, fruit stalk-end color, and disease resistance in cucumber lines.
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Affiliation(s)
- Fildaus Nyirahabimana
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey.
| | - Flavien Shimira
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Ghassan Zahid
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey
| | - Ilknur Solmaz
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
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He Y, Wei M, Yan Y, Yu C, Cheng S, Sun Y, Zhu X, Wei L, Wang H, Miao L. Research Advances in Genetic Mechanisms of Major Cucumber Diseases Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:862486. [PMID: 35665153 PMCID: PMC9161162 DOI: 10.3389/fpls.2022.862486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 06/15/2023]
Abstract
Cucumber (Cucumis sativus L.) is an important economic vegetable crop worldwide that is susceptible to various common pathogens, including powdery mildew (PM), downy mildew (DM), and Fusarium wilt (FM). In cucumber breeding programs, identifying disease resistance and related molecular markers is generally a top priority. PM, DM, and FW are the major diseases of cucumber in China that cause severe yield losses and the genetic-based cucumber resistance against these diseases has been developed over the last decade. Still, the molecular mechanisms of cucumber disease resistance remain unclear. In this review, we summarize recent findings on the inheritance, molecular markers, and quantitative trait locus mapping of cucumber PM, DM, and FM resistance. In addition, several candidate genes, such as PM, DM, and FM resistance genes, with or without functional verification are reviewed. The data help to reveal the molecular mechanisms of cucumber disease resistance and provide exciting new opportunities for further resistance breeding.
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Affiliation(s)
- Yujin He
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Mingming Wei
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resource Utilization of Rubber Tree, State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Yanyan Yan
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Chao Yu
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Siqi Cheng
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yihan Sun
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xiangtao Zhu
- College of Jiyang, Zhejiang Agriculture and Forestry University, Zhuji, China
| | - Lingling Wei
- Institute of Ecological Civilization, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Huasen Wang
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Ministry of Agriculture Key Laboratory of Biology and Genetic Resource Utilization of Rubber Tree, State Key Laboratory Breeding Base of Cultivation and Physiology for Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Li Miao
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
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9
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Zhang D, Wu S, Li N, Gao J, Liu S, Zhu S, Li Z, Ren G, Kuai B. Chemical induction of leaf senescence and powdery mildew resistance involves ethylene-mediated chlorophyll degradation and ROS metabolism in cucumber. HORTICULTURE RESEARCH 2022; 9:uhac101. [PMID: 35795391 PMCID: PMC9250653 DOI: 10.1093/hr/uhac101] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Timely initiation of leaf senescence is an integral part of plant development and, importantly, an adaptive strategy by which plants cope with various stresses, e.g. to limit the spread of pathogens. Powdery mildew is a major cucumber disease that promotes the initiation/progression of leaf senescence and reduces leaf photosynthesis, resulting in severe losses of yield and quality. However, how powdery mildew induces leaf senescence and how cucumber plants respond to enhance their resistance remain unclear. Here, with established agrochemical induction and pathogen inoculation systems, we demonstrate that both probenazole (PBZ) and powdery mildew activate ethylene (ET) biosynthesis and signal transduction, consequently promoting leaf senescence and enhancing plant resistance to powdery mildew through CsEIN3 to directly upregulate the expression of CsCCGs and CsRBOHs. Our analysis convincingly suggests that the regulation of leaf senescence and powdery mildew resistance is interconnected and mediated mainly by ET in cucumber.
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Affiliation(s)
| | - Shengdong Wu
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | | | - Jiong Gao
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shihui Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Shuai Zhu
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zilin Li
- State Key Laboratory of Genetic Engineering and Fudan Center for Genetic Diversity and Designing Agriculture, School of Life Sciences, Fudan University, Shanghai 200438, China
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Parvathi MS, Antony PD, Kutty MS. Multiple Stressors in Vegetable Production: Insights for Trait-Based Crop Improvement in Cucurbits. FRONTIERS IN PLANT SCIENCE 2022; 13:861637. [PMID: 35592574 PMCID: PMC9111534 DOI: 10.3389/fpls.2022.861637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
Vegetable production is a key determinant of contribution from the agricultural sector toward national Gross Domestic Product in a country like India, the second largest producer of fresh vegetables in the world. This calls for a careful scrutiny of the threats to vegetable farming in the event of climate extremes, environmental degradation and incidence of plant pests/diseases. Cucurbits are a vast group of vegetables grown almost throughout the world, which contribute to the daily diet on a global scale. Increasing food supply to cater to the ever-increasing world population, calls for intensive, off-season and year-round cultivation of cucurbits. Current situation predisposes these crops to a multitude of stressors, often simultaneously, under field conditions. This scenario warrants a systematic understanding of the different stress specific traits/mechanisms/pathways and their crosstalk that have been examined in cucurbits and identification of gaps and formulation of perspectives on prospective research directions. The careful dissection of plant responses under specific production environments will help in trait identification for genotype selection, germplasm screens to identify superior donors or for direct genetic manipulation by modern tools for crop improvement. Cucurbits exhibit a wide range of acclimatory responses to both biotic and abiotic stresses, among which a few like morphological characters like waxiness of cuticle; primary and secondary metabolic adjustments; membrane thermostability, osmoregulation and, protein and reactive oxygen species homeostasis and turnover contributing to cellular tolerance, appear to be common and involved in cross talk under combinatorial stress exposures. This is assumed to have profound influence in triggering system level acclimation responses that safeguard growth and metabolism. The possible strategies attempted such as grafting initiatives, molecular breeding, novel genetic manipulation avenues like gene editing and ameliorative stress mitigation approaches, have paved way to unravel the prospects for combined stress tolerance. The advent of next generation sequencing technologies and big data management of the omics output generated have added to the mettle of such emanated concepts and ideas. In this review, we attempt to compile the progress made in deciphering the biotic and abiotic stress responses of cucurbits and their associated traits, both individually and in combination.
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Affiliation(s)
- M. S. Parvathi
- Department of Plant Physiology, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - P. Deepthy Antony
- Centre for Intellectual Property Rights, Technology Management and Trade, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
| | - M. Sangeeta Kutty
- Department of Vegetable Science, College of Agriculture Vellanikkara, Kerala Agricultural University, Thrissur, India
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11
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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12
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Wu L, Fredua-Agyeman R, Strelkov SE, Chang KF, Hwang SF. Identification of Quantitative Trait Loci Associated With Partial Resistance to Fusarium Root Rot and Wilt Caused by Fusarium graminearum in Field Pea. FRONTIERS IN PLANT SCIENCE 2022; 12:784593. [PMID: 35126415 PMCID: PMC8812527 DOI: 10.3389/fpls.2021.784593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Fusarium root rot, caused by a complex of Fusarium spp., is a major disease of field pea (Pisum sativum). The development of genetic resistance is the most promising approach to manage the disease, but no pea germplasm has been identified that is completely resistant to root rot. The aim of this study was to detect quantitative trait loci (QTL) conferring partial resistance to root rot and wilting, caused by five fungal isolates representing Fusarium solani, F. avenaceum, F. acuminatum, F. proliferatum, and F. graminearum. Evaluation of the root rot-tolerant cultivar "00-2067" and susceptible cultivar "Reward" was carried out with the five species. There was a significant difference (p < 0.001) between the mean root rot values of the two cultivars inoculated with the F. avenaceum (F4A) and F. graminearum (FG2) isolates. Therefore, in the QTL study, the F8 recombinant inbred line (RIL) population derived from "Reward" × "00-2067" was inoculated in the greenhouse (4 ×) with only F4A and FG2. The parents and F8 population were genotyped using 13.2K single nucleotide polymorphisms (SNPs) and 222 simple sequence repeat (SSR) markers. A significant genotypic effect (p < 0.05) and high heritability (79% to 92.1%) were observed for disease severity, vigor, and plant height following inoculation with F4A and FG2. Significant correlation coefficients were detected among and within all traits. This suggested that a high proportion of the genetic variance was transmitted from the parents to the progeny. However, no significant QTL (LOD > 3) were detected for the RILs inoculated with F4A. In the case of the RILs inoculated with FG2, 5 QTL for root rot severity and 3 QTL each for vigor and plant height were detected. The most stable QTL for plant height (Hgt-Ps3.1) was detected on Chrom5/LGIII. The two most stable QTL for partial resistance to FG2, Fg-Ps4.1, and Fg-Ps4.2 were located in a 15.1-cM and 11.2-cM genomic region, respectively, on Chrom4/LGIV. The most stable QTL for vigor (Vig-Ps4.1) was found in the same region. Twenty-five major and moderate effect digenic epistatic interactions were detected. The identified region on chrom4/LGIV could be important for resistance breeding and marker development.
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Affiliation(s)
| | | | | | | | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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13
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Nie J, Wang H, Zhang W, Teng X, Yu C, Cai R, Wu G. Characterization of lncRNAs and mRNAs Involved in Powdery Mildew Resistance in Cucumber. PHYTOPATHOLOGY 2021; 111:1613-1624. [PMID: 33522835 DOI: 10.1094/phyto-11-20-0521-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Powdery mildew (PM) is a severe fungal disease of cucumber worldwide. Identification of genetic factors resistant to PM is of great importance for marker-assisted breeding to ensure cucumber production. Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) have been shown to play important roles in plant development and immunity; however, whether they have a role in PM response in cucurbit crops remains unknown. We performed strand-specific RNA sequencing and miRNA sequencing using RNA from cucumber leaves of two near-isogenic lines (NILs), S1003 and NIL (Pm5.1) infected with PM, and systematically characterized the profiles of cucumber lncRNAs and messenger RNA (mRNAs) responsive to PM. In total, we identified 12,903 lncRNAs and 25,598 mRNAs responsive to PM. Differential expression (DE) analysis showed that 119 lncRNAs and 136 mRNAs correlated with PM resistance. Functional analysis of these DE lncRNAs and DE mRNAs revealed that they are significantly associated with phenylpropanoid biosynthesis, phenylalanine metabolism, ubiquinone and other terpenoid-quinone biosynthesis, and endocytosis. Particularly, two lncRNAs, LNC_006805 and LNC_012667, might play important roles in PM resistance. In addition, we also predicted mature miRNAs and competing endogenous RNA (ceRNA) networks of lncRNA-miRNA-mRNA involved in PM resistance. A total of 49 DE lncRNAs could potentially act as target mimics for 106 miRNAs. Taken together, our results provide an abundant resource for further exploration of cucumber lncRNAs, mRNAs, miRNAs, and ceRNAs in PM resistance, and will facilitate the molecular breeding for PM-resistant varieties to control this severe disease in cucumber.
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Affiliation(s)
- Jingtao Nie
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Huasen Wang
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Wanlu Zhang
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xue Teng
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Chao Yu
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Wu
- The Laboratory of Plant Molecular and Developmental Biology, College of Agriculture and Food Sciences, Zhejiang Agriculture and Forestry University, Hangzhou, China
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14
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Cai H, Wang Q, Gao J, Li C, Du X, Ding B, Yang T. Construction of a high-density genetic linkage map and QTL analysis of morphological traits in an F1 Malusdomestica × Malus baccata hybrid. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1997-2007. [PMID: 34629774 PMCID: PMC8484404 DOI: 10.1007/s12298-021-01069-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Apple is considered the most commonly grown fruit crop in temperate regions that brings great economic profits to fruit growers. Dwarfing rootstocks have been extensively used in apple breeding as well as commercial orchards, but the molecular and genetic basis of scion dwarfing and other morphological traits induced by them is still unclear. At present, we report a genetic map of Malusdomestica × Malus baccata with high density. The F1 population was sequenced by a specific length amplified fragment (SLAF). In the genetic map, 5064 SLAF markers spanning 17 linkage groups (LG) were included. Dwarf-related and other phenotypic traits of the scion were evaluated over a 3-year growth period. Based on quantitative trait loci (QTL) evaluation of plant height and trunk diameter, two QTL clusters were found on LG 11, which exhibited remarkable influences on dwarfing of the scion. In this analysis, QTL DW2, which was previously reported as a locus that controls dwarfing, was confirmed. Moreover, three novel QTLs for total flower number and branching flower number were detected on LG2 and LG4, exhibited the phenotypic variation that has been explained by QTL ranging from 8.80% to 34.80%. The findings of the present study are helpful to find scion dwarfing and other phenotypes induced by rootstock in the apple. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01069-0.
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Affiliation(s)
- Huacheng Cai
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Qian Wang
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Jingdong Gao
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Chunyan Li
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Xuemei Du
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
| | - Baopeng Ding
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- College of Forestry, Shanxi Agricultural University, Taigu, 030801 Shanxi China
| | - Tingzhen Yang
- Pomology Institute, Shanxi Agricultural University, Taigu, 030801 Shanxi China
- Shanxi Key Laboratory of Germplasm Improvement and Utilization in Pomology, Taiyuan, 030031 Shanxi China
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15
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Grumet R, McCreight JD, McGregor C, Weng Y, Mazourek M, Reitsma K, Labate J, Davis A, Fei Z. Genetic Resources and Vulnerabilities of Major Cucurbit Crops. Genes (Basel) 2021; 12:1222. [PMID: 34440396 PMCID: PMC8392200 DOI: 10.3390/genes12081222] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The Cucurbitaceae family provides numerous important crops including watermelons (Citrullus lanatus), melons (Cucumis melo), cucumbers (Cucumis sativus), and pumpkins and squashes (Cucurbita spp.). Centers of domestication in Africa, Asia, and the Americas were followed by distribution throughout the world and the evolution of secondary centers of diversity. Each of these crops is challenged by multiple fungal, oomycete, bacterial, and viral diseases and insects that vector disease and cause feeding damage. Cultivated varieties are constrained by market demands, the necessity for climatic adaptations, domestication bottlenecks, and in most cases, limited capacity for interspecific hybridization, creating narrow genetic bases for crop improvement. This analysis of crop vulnerabilities examines the four major cucurbit crops, their uses, challenges, and genetic resources. ex situ germplasm banks, the primary strategy to preserve genetic diversity, have been extensively utilized by cucurbit breeders, especially for resistances to biotic and abiotic stresses. Recent genomic efforts have documented genetic diversity, population structure, and genetic relationships among accessions within collections. Collection size and accessibility are impacted by historical collections, current ability to collect, and ability to store and maintain collections. The biology of cucurbits, with insect-pollinated, outcrossing plants, and large, spreading vines, pose additional challenges for regeneration and maintenance. Our ability to address ongoing and future cucurbit crop vulnerabilities will require a combination of investment, agricultural, and conservation policies, and technological advances to facilitate collection, preservation, and access to critical Cucurbitaceae diversity.
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Affiliation(s)
- Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - James D. McCreight
- USDA, ARS, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA;
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706, USA;
| | - Michael Mazourek
- School of Integrative Plant Science, Plant Breeding & Genetics Section, Cornell University, Ithaca, NY 14853, USA;
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA 50014, USA;
| | - Joanne Labate
- Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, Geneva, NY 14456, USA;
| | - Angela Davis
- Sakata Seed America, Inc., Woodland, CA 95776, USA;
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA;
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16
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Toporek SM, Branham SE, Katawczik ML, Keinath AP, Patrick Wechter W. QTL mapping of resistance to Pseudoperonospora cubensis clade 1, mating type A2, in Cucumis melo. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2577-2586. [PMID: 33950283 DOI: 10.1007/s00122-021-03843-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
This is the first identification of QTLs underlying resistance to Pseudoperonospora cubensis in Cucumis melo using a genetically characterized isolate. Pseudoperonospora cubensis, causal organism of cucurbit downy mildew (CDM), is one of the largest threats to cucurbit production in the eastern USA. Currently, no Cucumis melo (melon) cultivars have significant levels of resistance. Additionally, little is understood about the genetic basis of resistance in C. melo. Recombinant inbred lines (RILs; N = 169) generated from a cross between the resistant melon breeding line MR-1 and susceptible cultivar Ananas Yok'neam were phenotyped for CDM resistance in both greenhouse and growth chamber studies. A high-density genetic linkage map with 5,663 binned SNPs created from the RIL population was utilized for QTL mapping. Nine QTLs, including two major QTLs, were associated with CDM resistance. Of the major QTLs, qPcub-10.1 was stable across growth chamber and greenhouse tests, whereas qPcub-8.2 was detected only in growth chamber tests. qPcub-10.1 co-located with an MLO-like protein coding gene, which has been shown to confer resistance to powdery mildew and Phytophthora in other plants. This is the first screening of C. melo germplasm with a genetically characterized P. cubensis isolate.
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Affiliation(s)
- Sean M Toporek
- Department of Plant and Environmental Sciences, Coastal Research and Education Center, Clemson University, Charleston, SC, 29414, USA
| | - Sandra E Branham
- Department of Plant and Environmental Sciences, Coastal Research and Education Center, Clemson University, Charleston, SC, 29414, USA
| | - Melanie L Katawczik
- US Vegetable Laboratory, USDA, ARS, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Anthony P Keinath
- Department of Plant and Environmental Sciences, Coastal Research and Education Center, Clemson University, Charleston, SC, 29414, USA
| | - W Patrick Wechter
- US Vegetable Laboratory, USDA, ARS, 2700 Savannah Highway, Charleston, SC, 29414, USA.
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17
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Shaw RK, Shen Y, Zhao Z, Sheng X, Wang J, Yu H, Gu H. Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower ( Brassica oleracea var. botrytis L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667757. [PMID: 34354719 PMCID: PMC8329456 DOI: 10.3389/fpls.2021.667757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis L.) is one of the important, nutritious and healthy vegetable crops grown and consumed worldwide. But its production is constrained by several destructive fungal diseases and most importantly, downy mildew leading to severe yield and quality losses. For sustainable cauliflower production, developing resistant varieties/hybrids with durable resistance against broad-spectrum of pathogens is the best strategy for a long term and reliable solution. Identification of novel resistant resources, knowledge of the genetics of resistance, mapping and cloning of resistance QTLs and identification of candidate genes would facilitate molecular breeding for disease resistance in cauliflower. Advent of next-generation sequencing technologies (NGS) and publishing of draft genome sequence of cauliflower has opened the flood gate for new possibilities to develop enormous amount of genomic resources leading to mapping and cloning of resistance QTLs. In cauliflower, several molecular breeding approaches such as QTL mapping, marker-assisted backcrossing, gene pyramiding have been carried out to develop new resistant cultivars. Marker-assisted selection (MAS) would be beneficial in improving the precision in the selection of improved cultivars against multiple pathogens. This comprehensive review emphasizes the fascinating recent advances made in the application of molecular breeding approach for resistance against an important pathogen; Downy Mildew (Hyaloperonospora parasitica) affecting cauliflower and Brassica oleracea crops and highlights the QTLs identified imparting resistance against this pathogen. We have also emphasized the critical research areas as future perspectives to bridge the gap between availability of genomic resources and its utility in identifying resistance genes/QTLs to breed downy mildew resistant cultivars. Additionally, we have also discussed the challenges and the way forward to realize the full potential of molecular breeding for downy mildew resistance by integrating marker technology with conventional breeding in the post-genomics era. All this information will undoubtedly provide new insights to the researchers in formulating future breeding strategies in cauliflower to develop durable resistant cultivars against the major pathogens in general and downy mildew in particular.
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Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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18
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Shimomura K, Sugiyama M, Kawazu Y, Yoshioka Y. Identification of quantitative trait loci for powdery mildew resistance in highly resistant cucumber ( Cucumis sativus L.) using ddRAD-seq analysis. BREEDING SCIENCE 2021; 71:326-333. [PMID: 34776739 PMCID: PMC8573554 DOI: 10.1270/jsbbs.20141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew, caused by Podosphaera xanthii (syn. Sphaerotheca fuliginea ex Fr. Poll.), is one of the most economically important foliar diseases in cucumber (Cucumis sativus L.). Cucumber parental line 'Kyuri Chukanbohon Nou 5 Go', developed from weedy cucumber line CS-PMR1, is highly resistant to powdery mildew and is promising breeding material. We performed quantitative trait locus (QTL) analysis using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in a population from a cross between 'Kyuri Chukanbohon Nou 5 Go' and the Japanese native cultivar 'Kaga-aonaga-fushinari', which is susceptible to powdery mildew. The resistance of the population and its parents was evaluated using leaf disc assays and image analysis. We detected one major QTL on Chr. 5 that was effective at both 20°C and 25°C and one minor QTL on Chr. 1 effective at 20°C. We detected two additional QTLs in subpopulation: one on Chr. 3 effective at 20°C and one on Chr. 5 effective at both 20°C and 25°C in a position different from the major QTL. The resistance alleles at all four QTLs were contributed by 'Kyuri Chukanbohon Nou 5 Go'. The results of this study can be used to develop practical DNA markers tightly linked to genes for powdery mildew resistance.
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Affiliation(s)
- Koichiro Shimomura
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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19
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Berg JA, Hermans FWK, Beenders F, Abedinpour H, Vriezen WH, Visser RGF, Bai Y, Schouten HJ. The amino acid permease (AAP) genes CsAAP2A and SlAAP5A/B are required for oomycete susceptibility in cucumber and tomato. MOLECULAR PLANT PATHOLOGY 2021; 22:658-672. [PMID: 33934492 PMCID: PMC8126186 DOI: 10.1111/mpp.13052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/13/2021] [Accepted: 02/16/2021] [Indexed: 05/16/2023]
Abstract
Cucurbit downy mildew (DM), caused by the obligate biotroph Pseudoperonospora cubensis, is a destructive disease in cucumber. A valuable source of DM resistance is the Indian cucumber accession PI 197088, which harbours several quantitative trait loci (QTLs) contributing to quantitatively inherited DM resistance. With a combination of fine-mapping and transcriptomics, we identified Amino Acid Permease 2A (CsAAP2A) as a candidate gene for QTL DM4.1.3. Whole-genome and Sanger sequencing revealed the insertion of a Cucumis Mu-like element (CUMULE) transposon in the allele of the resistant near-isogenic line DM4.1.3. To confirm whether loss of CsAAP2A contributes to partial DM resistance, we performed targeting induced local lesions in genomes on a DM-susceptible cucumber genotype to identify an additional csaap2a mutant, which indeed was partially DM resistant. In view of the loss of the putative function as amino acid transporter, we measured amino acids in leaves. We found that DM-inoculated leaves of line DM4.1.3 (with the csaap2a mutation) contained significantly fewer amino acids than wild-type cucumber. The decreased flow of amino acids towards infected leaves in csaap2a plants compared to the wild type might explain the resistant phenotype of the mutant, as this would limit the available nutrients for the pathogen and thereby its fitness. To examine whether AAP genes play a conserved role as susceptibility factors in plant-oomycete interactions, we made targeted mutations in two AAP genes from tomato and studied the effect on susceptibility to Phytophthora infestans. We conclude that not only CsAAP2A but also SlAAP5A/SlAAP5B are susceptibility genes for oomycete pathogens.
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Affiliation(s)
- Jeroen A. Berg
- Plant BreedingWageningen University & ResearchWageningenNetherlands
| | | | | | | | | | | | - Yuling Bai
- Plant BreedingWageningen University & ResearchWageningenNetherlands
| | - Henk J. Schouten
- Plant BreedingWageningen University & ResearchWageningenNetherlands
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20
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Liu X, Gu X, Lu H, Liu P, Miao H, Bai Y, Zhang S. Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm. Genes (Basel) 2021; 12:genes12040584. [PMID: 33923788 PMCID: PMC8072792 DOI: 10.3390/genes12040584] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/04/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022] Open
Abstract
Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding.
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Affiliation(s)
- Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
| | - Hongwei Lu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
| | - Panna Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Correspondence: (Y.B.); (S.Z.); Tel.: +86-10-82105952 (Y.B.); Fax: +86-10-62174123 (Y.B.)
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (X.G.); (H.L.); (P.L.); (H.M.)
- Correspondence: (Y.B.); (S.Z.); Tel.: +86-10-82105952 (Y.B.); Fax: +86-10-62174123 (Y.B.)
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Zheng L, Zhang M, Zhuo Z, Wang Y, Gao X, Li Y, Liu W, Zhang W. Transcriptome profiling analysis reveals distinct resistance response of cucumber leaves infected with powdery mildew. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:327-340. [PMID: 33176053 DOI: 10.1111/plb.13213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Powdery mildew is the main disease affecting cucumber cultivation and causes severe economic loss. So far, research on cucumber resistance to powdery mildew has not yielded feasible solutions. This study selected two inbred cucumber lines, XY09-118 (resistant) and Q10 (susceptible) and investigated their responses to powdery mildew infection (harvested 24 and 48 h after inoculation) using RNA sequencing. More than 20,000 genes were detected in cucumber leaves both with and without powdery mildew infection at the above two time points. Among these, 5478 genes were identified as differently expressed genes (DEGs) between XY09-118 and Q10. Based on the databases GO and KEGG, the functions of DEGs were analysed. Moreover, the complex regulatory network for powdery mildew resistance was assessed, which involves plant hormone signal transduction, phenylpropanoid biosynthesis, plant-pathogen interaction and the MAPK signalling pathway. In particular, genes encoding WRKY, NAC and TCP were highlighted. In addition, genes involved in plant hormone biosynthesis, metabolism and signal transduction, pathogen resistance and abiotic stress response were analysed. Co-expression analysis indicated that the transcription factors correlated with plant hormone signal pathway and metabolism, defence and abiotic response. The expression of several genes was validated by qRT-PCR. The pathogen resistance regulatory network was identified by comparing resistant and susceptible inbred lines infected with powdery mildew. The transcriptome data provide novel insights into cucumber response to powdery mildew infection and the identified pathogen resistance genes will be highly useful for breeding efforts to enhance the resistance of cucumber to powdery mildew.
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Affiliation(s)
- L Zheng
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
- College of Life and Environment Sciences, Huanshan University, Huangshan, China
| | - M Zhang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
| | - Z Zhuo
- College of Forestry, Hainan University, Haikou, China
| | - Y Wang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
| | - X Gao
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
| | - Y Li
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
| | - W Liu
- College of Agricultural Sciences and Technology, Shandong Agriculture and Engineering University, Jinan, China
| | - W Zhang
- Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Shandong Academy of Agricultural Sciences, Institute of Vegetables and Flowers, Jinan, China
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Zhang C, Badri Anarjan M, Win KT, Begum S, Lee S. QTL-seq analysis of powdery mildew resistance in a Korean cucumber inbred line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:435-451. [PMID: 33070226 DOI: 10.1007/s00122-020-03705-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/08/2020] [Indexed: 06/11/2023]
Abstract
QTL mapping and RT-PCR analyses identified the CsGy5G015660 as a strong powdery mildew resistance candidate gene and natural variation of CsGy5G015660 allele was observed using 115 core germplasm. Powdery mildew (PM) is among the most serious fungal diseases encountered in the cultivation of cucurbits. The development of PM-resistant inbred lines is thus of considerable significance for cucumber breeding programs. In this study, we applied bulked segregant analysis combined with QTL-seq to identify PM resistance loci using F2 population derived from a cross between two Korean cucumber inbred lines, PM-R (resistant) and PM-S (susceptible). Genome-wide SNP profiling using bulks of the two extreme phenotypes identified two QTLs on chromosomes 5 and 6, designated pm5.2 and pm6.1, respectively. The two PM resistance loci were validated using molecular marker-based classical QTL analysis: pm5.2 (30% R2 at LOD 11) and pm6.1 (11% R2 at LOD 3.2). Furthermore, reverse transcriptase-PCR analyses, using genes found to be polymorphic between PM-R and PM-S, were conducted to identify the candidate gene(s) responsible for PM resistance. We found that transcripts of the gene CsGy5G015660, encoding a putative leucine-rich repeat receptor-like serine/threonine-protein kinase (RPK2), showed specific accumulation in PM-R prior to the appearance of disease symptoms, and was accordingly considered a strong candidate gene for PM resistance. In addition, cleaved amplified polymorphic sequence markers from CsGy5G015660 were developed and used to screen 35 inbred lines. Natural variation in the CsGy5G015660 allele was also observed based on analysis of a core collection of 115 cucumber accessions. Our results provide new genetic insights for gaining a better understanding of the genetic basis of PM resistance in cucumber, and pave the way for further utilization in cucumber PM resistance breeding programs.
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Affiliation(s)
- Chunying Zhang
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
- Department of Integrated Bioindustry, Graduate School of Hanseo University, 46 hanseo 1-ro, Haemi-myun, Seosan-si, Chungcheongnam-do, 31962, Republic of Korea
| | - Mahdi Badri Anarjan
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Khin Thanda Win
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Shahida Begum
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea
| | - Sanghyeob Lee
- Plant Genomics Laboratory, Department of Bio-Resource Engineering, College of Life Sciences, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea.
- Plant Engineering Research Institute, Sejong University, 209 Neungdong-ro, Gwanjing-gu, Seoul, 05006, Republic of Korea.
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Zhang P, Zhu Y, Zhou S. Comparative analysis of powdery mildew resistant and susceptible cultivated cucumber (Cucumis sativus L.) varieties to reveal the metabolic responses to Sphaerotheca fuliginea infection. BMC PLANT BIOLOGY 2021; 21:24. [PMID: 33413112 PMCID: PMC7791650 DOI: 10.1186/s12870-020-02797-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/14/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Cucumber (Cucumis sativus L.) is a widely planted vegetable crop that suffers from various pathogen infections. Powdery mildew (PM) is typical disease caused by Sphaerotheca fuliginea infection and destroys the production of cucumber. However, the metabolic responses to S. fuliginea infection are largely unknown. RESULTS In our study, a PM resistant variety 'BK2' and a susceptible variety 'H136' were used to screen differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) under S. fuliginea infection. Most of DEGs and DAMs were enriched in several primary and secondary metabolic pathways, including flavonoid, hormone, fatty acid and diterpenoid metabolisms. Our data showed that many flavonoid-related metabolites were significantly accumulated in BK2 rather than H136, suggesting an essential role of flavonoids in formation of resistant quality. Changes in expression of CYP73A, CYP81E1, CHS, F3H, HCT and F3'M genes provided a probable explanation for the differential accumulation of flavonoid-related metabolites. Interestingly, more hormone-related DEGs were detected in BK2 compared to H136, suggesting a violent response of hormone signaling pathways in the PM-resistant variety. The number of fatty acid metabolism-related DAMs in H136 was larger than that in BK2, indicating an active fatty acid metabolism in the PM-susceptible variety. CONCLUSIONS Many differentially expressed transcription factor genes were identified under S. fuliginea infection, providing some potential regulators for the improvement of PM resistance. PM resistance of cucumber was controlled by a complex network consisting of various hormonal and metabolic pathways.
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Affiliation(s)
- Peng Zhang
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
| | - Yuqiang Zhu
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
| | - Shengjun Zhou
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
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Wang Y, Jiang B, Dymerski R, Xu X, Weng Y. Quantitative trait loci for horticulturally important traits defining the Sikkim cucumber, Cucumis sativus var. sikkimensis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:229-247. [PMID: 32997165 DOI: 10.1007/s00122-020-03693-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
QTL mapping identified simply inherited genes and quantitative trait loci underlying morphologically characteristic traits of the Sikkim cucumber, which reveals their genetic basis during crop evolution. The data suggest the Sikkim cucumber as an ecotype of cultivated cucumber not worthy of formal taxonomic recognition. The Sikkim cucumber, Cucumis sativus var. sikkimensis, is featured with some morphological traits like black spine, brown fruit with fine and heavy netting, as well as large hollow in mature fruit. Despite its establishment as a botanical variety ~ 150 years ago, and its wide use as an important source of disease resistances in cucumber breeding, little is known about its taxonomic status and genetic basis of those characteristic traits. Here we reported QTL mapping with segregating populations derived from two Sikkim-type inbred lines, WI7088D and WI7120, and identification of 48 QTL underlying phenotypic variation for 18 horticulturally important traits. We found that the fruit spine and skin colors in the two populations were controlled by the previously cloned pleiotropic B (black spine) locus. The fruit netting in WI7088D and WI7120 was controlled by the well-known H (Heavy netting) and a novel Rs (Russet skin) locus, which was delimited to a 271-kb region on Chr5 and ~ 736-kb region on Chr1, respectively. A single major-effect QTL was detected for flowering time in each population (ft1.1 for WI7088D and ft6.2 for WI7120). Fifteen, six and five QTL were identified for fruit size, hollow size and flesh thickness variation in the two populations, respectively. No major structural changes were found between the Sikkim and cultivated cucumbers. Except for the rare allele at the Rs locus, there seem no private QTL/alleles identified from this study supporting the Sikkim cucumber as an ecotype of C. sativus, not worthy of formal taxonomic recognition.
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Affiliation(s)
- Yuhui Wang
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Biao Jiang
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ronald Dymerski
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Xuewen Xu
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin - Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA.
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Liu X, Lu H, Liu P, Miao H, Bai Y, Gu X, Zhang S. Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS. PLANTS 2020; 9:plants9121659. [PMID: 33260843 PMCID: PMC7768435 DOI: 10.3390/plants9121659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM.
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Affiliation(s)
- Xiaoping Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
| | - Hongwei Lu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
| | - Panna Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Correspondence: (Y.B.); (X.G.); (S.Z.)
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
- Correspondence: (Y.B.); (X.G.); (S.Z.)
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (H.L.); (P.L.); (H.M.)
- Correspondence: (Y.B.); (X.G.); (S.Z.)
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Berg JA, Hermans FWK, Beenders F, Lou L, Vriezen WH, Visser RGF, Bai Y, Schouten HJ. Analysis of QTL DM4.1 for Downy Mildew Resistance in Cucumber Reveals Multiple subQTL: A Novel RLK as Candidate Gene for the Most Important subQTL. FRONTIERS IN PLANT SCIENCE 2020; 11:569876. [PMID: 33193500 PMCID: PMC7649820 DOI: 10.3389/fpls.2020.569876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/28/2020] [Indexed: 05/28/2023]
Abstract
One of the biggest problems in cucumber cultivation is cucurbit downy mildew (DM), caused by the obligate biotroph Pseudoperonospora cubensis. Whereas DM in cucumber was previously efficiently controlled by the dm-1 gene from Indian cucumber accession PI 197087, this resistance was broken by new DM strains, prompting the search for novel sources of resistance. A promising source of resistance is the wild cucumber accession PI 197088. It was previously shown that DM resistance in this genotype inherits polygenically. In this paper, we put the focus on one of the QTL, DM4.1 that is located on chromosome 4. QTL DM4.1 was shown to consist of three subQTL: DM4.1.1 affected pathogen-induced necrosis, DM4.1.2 was shown to have an additive effect on sporulation, and DM4.1.3 had a recessive effect on chlorosis as well as an effect on sporulation. Near-isogenic lines (NILs) were produced by introgressing the subQTLs into a susceptible cucumber line (HS279) with good horticultural traits. Transcriptomic analysis revealed that many genes in general, and defense pathway genes in particular, were differentially expressed in NIL DM4.1.1/.2 compared to NIL DM4.1.3 and the susceptible parent HS279. This indicates that the resistance from subQTL DM4.1.1 and/or subQTL DM4.1.2 likely involves defense signaling pathways, whereas resistance due to subQTL DM4.1.3 is more likely to be independent of known defense pathways. Based on fine-mapping data, we identified the RLK gene CsLRK10L2 as a likely candidate for subQTL DM4.1.2, as this gene was found to have a loss-of-function mutation in the susceptible parent HS279, and was strongly upregulated by P. cubensis inoculation in NIL DM4.1.1/.2. Heterologous expression of this gene triggered necrosis, providing further evidence that this gene is indeed causal for subQTL DM4.1.2.
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Affiliation(s)
- Jeroen A. Berg
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | | | | | - Lina Lou
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | | | | | - Yuling Bai
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Henk J. Schouten
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Pan Y, Wen C, Han Y, Wang Y, Li Y, Li S, Cheng X, Weng Y. QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2271-2290. [PMID: 32306094 DOI: 10.1007/s00122-020-03596-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/05/2020] [Indexed: 06/11/2023]
Abstract
The legendary cucumber inbred line WI2757 possesses a rare combination of resistances against nine pathogens, which is an important germplasm for cucumber breeding. However, WI2757 flowers late and does not perform well under field conditions. The genetic basis for horticulturally important traits other than disease resistances in WI2757 is largely unknown. In this study, we conducted QTL mapping using F2 and recombinant inbred line (RIL) populations from the WI2757 × True Lemon cross that were segregating for multiple traits. Phenotypic data were collected in replicated field trials across multiple years for seven traits including fruit carpel number (CN) and sex expression. A high-density SNP-based genetic map was developed with genotyping by sequencing of the RIL population, which revealed a region on chromosome 1 with strong recombination suppression. The reduced recombination in this region was due to a ~ 10-Mbp paracentric inversion in WI2757 that was confirmed with additional segregation and cytological (FISH) analyses. Thirty-six QTL were detected for flowering time, fruit length (FL), fruit diameter (FD), fruit shape (LD), fruit number (FN), CN, and powdery mildew resistance. Five moderate- or major-effect QTL for FL, FD, LD, and FN inside the inversion are likely the pleiotropic effects of the andromonoecy (m), or the cn locus. The major-effect flowering time QTL ft1.1 was also mapped inside the inversion, which seems to be different from the previously assigned delayed flowering in WI2757. Implications of these findings on the use of WI2757 in cucumber breeding are discussed.
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Affiliation(s)
- Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Changlong Wen
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Yonghua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yuhui Wang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sen Li
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Horticulture College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiaomao Cheng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yiqun Weng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, 1575 Linden Dr., Madison, WI, 53706, USA.
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Zhang P, Zhu Y, Zhou S. Comparative transcriptomic analyses of powdery mildew resistant and susceptible cultivated cucumber ( Cucumis sativus L.) varieties to identify the genes involved in the resistance to Sphaerotheca fuliginea infection. PeerJ 2020; 8:e8250. [PMID: 32337096 PMCID: PMC7169966 DOI: 10.7717/peerj.8250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/20/2019] [Indexed: 11/20/2022] Open
Abstract
Background Cucumber (Cucumis sativus L.) is a widely cultivated vegetable crop, and its yield and quality are greatly affected by various pathogen infections. Sphaerotheca fuliginea is a pathogen that causes powdery mildew (PM) disease in cucumber. However, the genes involved in the resistance to PM in cucumber are largely unknown. Methods In our study, a cucumber PM resistant cultivated variety “BK2” and a susceptible cultivated variety “H136” were used to screen and identify differential expressed genes (DEGs) under the S. fuliginea infection. Results There were only 97 DEGs between BK2 and H136 under the control condition, suggesting a similarity in the basal gene expression between the resistant and susceptible cultivated varieties. A large number of hormone signaling-related DEGs (9.2% of all DEGs) between resistant and susceptible varieties were identified, suggesting an involvement of hormone signaling pathways in the resistance to PM. In our study, the defense-related DEGs belonging to Class I were only induced in susceptible cultivated variety and the defense-related DEGs belonging to Class II were only induced in resistant cultivated variety. The peroxidase, NBS, glucanase and chitinase genes that were grouped into Class I and II might contribute to production of the resistance to PM in resistant cultivated variety. Furthermore, several members of Pathogen Response-2 family, such as glucanases and chitinases, were identified as DEGs, suggesting that cucumber might enhance the resistance to PM by accelerating the degradation of the pathogen cell walls. Our data allowed us to identify and analyze more potential genes related to PM resistance.
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Affiliation(s)
- Peng Zhang
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
| | - Yuqiang Zhu
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
| | - Shengjun Zhou
- Institute of Vegetable, Zhejiang Academy of Agriculture Sciences, Hangzhou, China
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Genome-Wide Identification of QTLs for Grain Protein Content Based on Genotyping-by-Resequencing and Verification of qGPC1-1 in Rice. Int J Mol Sci 2020; 21:ijms21020408. [PMID: 31936451 PMCID: PMC7014352 DOI: 10.3390/ijms21020408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/27/2023] Open
Abstract
To clarify the genetic mechanism underlying grain protein content (GPC) and to improve rice grain qualities, the mapping and cloning of quantitative trait loci (QTLs) controlling the natural variation of GPC are very important. Based on genotyping-by-resequencing, a total of 14 QTLs were detected with the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population in 2016 and 2017. Seven of the fourteen QTLs were repeatedly identified across two years. Using three residual heterozygote-derived populations, a stably inherited QTL named as qGPC1-1 was validated and delimited to a ~862 kb marker interval JD1006–JD1075 on the short arm of chromosome 1. Comparing the GPC values of the RIL population determined by near infrared reflectance spectroscopy (NIRS) and Kjeldahl nitrogen determination (KND) methods, high correlation coefficients (0.966 and 0.983) were observed in 2016 and 2017. Furthermore, 12 of the 14 QTLs were identically identified with the GPC measured by the two methods. These results indicated that instead of the traditional KND method, the rapid and easy-to-operate NIRS was suitable for analyzing a massive number of samples in mapping and cloning QTLs for GPC. Using the gel-based low-density map consisted of 208 simple sequence repeat (SSR) and insert/deletion (InDel) markers, the same number of QTLs (fourteen) were identified in the same HHZ/JZ1560 RIL population, and three QTLs were repeatedly detected across two years. More stably expressed QTLs were identified based on the genome resequencing, which might be attributed to the high-density map, increasing the detection power of minor QTLs. Our results are helpful in dissecting the genetic basis of GPC and improving rice grain qualities through molecular assisted selection.
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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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Wei J, Chen Y, Wang W. A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach ( Paramisgurnus dabryanus). Front Genet 2019; 10:1023. [PMID: 31708968 PMCID: PMC6823184 DOI: 10.3389/fgene.2019.01023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022] Open
Abstract
Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.
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Affiliation(s)
- Jin Wei
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yuanyuan Chen
- Key Lab of Agricultural Animal Genetics, College of Fisheries, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Weimin Wang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
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Keinath AP. Integrated Management of Downy Mildew on Slicing Cucumber With Fungicides and Host Resistance But Not Trellising. PLANT DISEASE 2019; 103:2592-2598. [PMID: 31347987 DOI: 10.1094/pdis-02-19-0323-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The objective of this study was to evaluate fungicide applications, host resistance, and trellising, alone and in combination, as management practices for downy mildew on slicing cucumber. A split-split plot experimental design was used with three and four replications in spring and fall 2017, respectively. The whole-plot treatment was fungicide, four applications of chlorothalonil (Bravo Weather Stik 6SC) alternated with three applications of cyazofamid (Ranman 400SC), or water. Split plots were nontrellised or trellised with four strings supported by stakes. Split-split plots were cultivar Bristol, which is intermediately resistant to downy mildew, or cultivar Speedway, which is susceptible to downy mildew with similar parentage as Bristol. In both seasons, area under the disease progress curve (AUDPC) values were lower with fungicides than water for both cultivars. In the spring, AUDPC for Bristol was lower than for Speedway regardless of fungicide treatment. In the fall, Bristol had a lower AUDPC than Speedway with fungicides, but the AUDPC did not differ between the two cultivars with water. The mean AUDPC for trellised plants (376.2) was lower than for nontrellised plants (434.0; P = 0.007). Fungicide applications increased marketable and total fruit weights in both seasons (P ≤ 0.0002). Marketable weight with fungicides was almost double (93% greater) the marketable weight with water. Marketable weight was 55% greater for Bristol than for Speedway in spring, but yields did not differ between cultivars in fall (season-by-cultivar interaction, P ≤ 0.0003). Because trellising had no effect on marketable yields (P = 0.11), trellising is not recommended for managing downy mildew on slicing cucumber. Of the three management techniques examined, fungicides had the largest effects on disease and yields, followed by cultivar resistance.
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Affiliation(s)
- Anthony P Keinath
- Department of Plant and Environmental Sciences, Coastal Research and Education Center, Clemson University, Charleston, SC 29414
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Wang Y, Tan J, Wu Z, VandenLangenberg K, Wehner TC, Wen C, Zheng X, Owens K, Thornton A, Bang HH, Hoeft E, Kraan PAG, Suelmann J, Pan J, Weng Y. STAYGREEN, STAY HEALTHY: a loss-of-susceptibility mutation in the STAYGREEN gene provides durable, broad-spectrum disease resistances for over 50 years of US cucumber production. THE NEW PHYTOLOGIST 2019; 221:415-430. [PMID: 30022503 DOI: 10.1111/nph.15353] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/13/2018] [Indexed: 05/22/2023]
Abstract
The Gy14 cucumber (Cucumis sativus) is resistant to oomyceteous downy mildew (DM), bacterial angular leaf spot (ALS) and fungal anthracnose (AR) pathogens, but the underlying molecular mechanisms are unknown. Quantitative trait locus (QTL) mapping for the disease resistances in Gy14 and further map-based cloning identified a candidate gene for the resistant loci, which was validated and functionally characterized by spatial-temporal gene expression profiling, allelic diversity and phylogenetic analysis, as well as local association studies. We showed that the triple-disease resistances in Gy14 were controlled by the cucumber STAYGREEN (CsSGR) gene. A single nucleotide polymorphism (SNP) in the coding region resulted in a nonsynonymous amino acid substitution in the CsSGR protein, and thus disease resistance. Genes in the chlorophyll degradation pathway showed differential expression between resistant and susceptible lines in response to pathogen inoculation. The causal SNP was significantly associated with disease resistances in natural and breeding populations. The resistance allele has undergone selection in cucumber breeding. The durable, broad-spectrum disease resistance is caused by a loss-of-susceptibility mutation of CsSGR. Probably, this is achieved through the inhibition of reactive oxygen species over-accumulation and phytotoxic catabolite over-buildup in the chlorophyll degradation pathway. The CsSGR-mediated host resistance represents a novel function of this highly conserved gene in plants.
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Affiliation(s)
- Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Junyi Tan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Zhiming Wu
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Institute of Cash Crops, Hebei Academy of Agriculture & Forestry Sciences, Shijiazhuang, Hebei, 050051, China
| | - Kyle VandenLangenberg
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Todd C Wehner
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | | | - Ken Owens
- Magnum Seeds Inc., Dixon, CA, 95620, USA
| | | | | | - Eric Hoeft
- HM Clause Seed Company, Davis, CA, 95618, USA
| | | | - Jos Suelmann
- Bayer Vegetable Seeds, 6083 AB, Nunhem, the Netherlands
| | - Junsong Pan
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200241, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA
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Paudel L, Clevenger J, McGregor C. Chromosomal Locations and Interactions of Four Loci Associated With Seed Coat Color in Watermelon. FRONTIERS IN PLANT SCIENCE 2019; 10:788. [PMID: 31293604 PMCID: PMC6603093 DOI: 10.3389/fpls.2019.00788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/29/2019] [Indexed: 05/13/2023]
Abstract
Different species of edible seed watermelons (Citrullus spp.) are cultivated in Asia and Africa for their colorful nutritious seeds. Consumer preference varies for watermelon seed coat color. Therefore, it is an important consideration for watermelon breeders. In 1940s, a genetic model of four genes, R, T, W and D, was proposed to elucidate the inheritance of seed coat color in watermelon. In this study, we developed three segregating F2 populations: Sugar Baby (dotted black seed, RRTTWW) × plant introduction (PI) 482379 (green seed, rrTTWW), Charleston Gray (dotted black seed, RRTTWW) × PI 189225 (red seed, rrttWW), and Charleston Gray (dotted black seed, RRTTWWdd) × UGA147 (clump seed, RRTTwwDD) to re-examine the four-gene model and to map the four genes. In the dotted black × green population, the dotted black seed coat color (R_) is dominant to green seed coat color (rr). In the dotted black × red population, the dominant dotted black seed coat color and the recessive red seed coat color segregate for the R and T genes, where the R gene is dominantly epistatic to the T gene. However, the inheritance of the T locus did not fit the four-gene model, thus we named it T1 . In the dotted black × clump population, the clump seed coat color and the dotted black seed coat color segregate for W and D, where D is recessively epistatic to W. The R, T1 , W, and D loci were mapped on chromosomes 3, 5, 6, and 8, respectively, using QTL-seq and genotyping-by-sequencing (GBS). Kompetitive Allele Specific PCR (KASP™) assays and SNP markers linked to the four loci were developed to facilitate maker-assisted selection (MAS) for watermelon seed coat color.
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Affiliation(s)
- Lucky Paudel
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Josh Clevenger
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Cecilia McGregor
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- *Correspondence: Cecilia McGregor,
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Xu X, Liu X, Yan Y, Wang W, Gebretsadik K, Qi X, Xu Q, Chen X. Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent. HORTICULTURE RESEARCH 2019; 6:115. [PMID: 31645969 PMCID: PMC6804742 DOI: 10.1038/s41438-019-0198-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/04/2019] [Accepted: 08/27/2019] [Indexed: 05/04/2023]
Abstract
Powdery mildew (PM) is considered a major cause of yield losses and reduced quality in cucumber worldwide, but the molecular basis of PM resistance remains poorly understood. A segment substitution line, namely, SSL508-28, was developed with dominant PM resistance in the genetic background of PM-susceptible cucumber inbred line D8. The substituted segment contains 860 genes. An iTRAQ-based comparative proteomic technology was used to map the proteomes of PM-inoculated and untreated (control) D8 and SSL508-28. The number of differentially regulated proteins (DRPs) in SSL508-28 was almost three times higher than that in D8. Fourteen DRPs were located in the substituted segment interval. Comparative gene expression analysis revealed that nodulin-related protein 1 (NRP1) may be a good candidate for PM resistance. Gene Ontology enrichment analysis showed that DRPs functioning in tetrapyrrole biosynthetic process, sulfur metabolic process and cell redox homeostasis were specifically enriched in the resistant line SSL508-28. DRPs categorized in the KEGG term photosynthesis increased in both lines upon PM infection, suggesting that the strategies used by cucumber may be different from those used by other crops to react to PM attacks at the initial stage. The measurement of hydrogen peroxide and superoxide anion production and net photosynthetic rate were consistent with the changes in protein abundance, suggesting that the proteomic results were reliable. There was a poor correlation between DRPs measured by iTRAQ and the corresponding gene expression changes measured by RNA-seq with the same experimental design. Taken together, these findings improve the understanding of the molecular mechanisms underlying the response of cucumber to PM infection.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xueli Liu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Yali Yan
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Wei Wang
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Kiros Gebretsadik
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
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Wang X, Bao K, Reddy UK, Bai Y, Hammar SA, Jiao C, Wehner TC, Ramírez-Madera AO, Weng Y, Grumet R, Fei Z. The USDA cucumber ( Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development. HORTICULTURE RESEARCH 2018; 5:64. [PMID: 30302260 PMCID: PMC6165849 DOI: 10.1038/s41438-018-0080-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 05/19/2023]
Abstract
Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement. Optimal collection, preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection. Here we use the high-throughput genotyping-by-sequencing (GBS) technology to characterize the United States National Plant Germplasm System (NPGS) collection of cucumber (Cucumis sativus L.). The GBS data, derived from 1234 cucumber accessions, provided more than 23 K high-quality single-nucleotide polymorphisms (SNPs) that are well distributed at high density in the genome (~1 SNP/10.6 kb). The SNP markers were used to characterize genetic diversity, population structure, phylogenetic relationships, linkage disequilibrium, and population differentiation of the NPGS cucumber collection. These results, providing detailed genetic analysis of the U.S. cucumber collection, complement NPGS descriptive information regarding geographic origin and phenotypic characterization. We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies (GWAS). Finally, we developed a molecularly informed, publicly accessible core collection of 395 accessions that represents at least 96% of the genetic variation present in the NPGS. Collectively, the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection, and will provide a valuable resource for genetic analyses, gene discovery, crop improvement, and germplasm preservation.
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Affiliation(s)
- Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, Virginia, WV 25112 USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Sue A. Hammar
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Todd C. Wehner
- Horticultural Science Department, North Carolina State University, Raleigh, NC 27695 USA
| | | | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706 USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706 USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
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Zhang K, Wang X, Zhu W, Qin X, Xu J, Cheng C, Lou Q, Li J, Chen J. Complete resistance to powdery mildew and partial resistance to downy mildew in a Cucumis hystrix introgression line of cucumber were controlled by a co-localized locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2229-2243. [PMID: 30078164 DOI: 10.1007/s00122-018-3150-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/23/2018] [Indexed: 05/16/2023]
Abstract
Key message A single recessive gene for complete resistance to powdery mildew and a major-effect QTL for partial resistance to downy mildew were co-localized in a Cucumis hystrix introgression line of cucumber. Downy mildew (DM) and powdery mildew (PM) are two major foliar diseases in cucumber. DM resistance (DMR) and PM resistance (PMR) may share common components; however, the genetic relationship between them remains unclear. IL52, a Cucumis hystrix introgression line of cucumber which has been reported to possess DMR, was recently identified to exhibit PMR as well. In this study, a single recessive gene pm for PMR was mapped to an approximately 468-kb region on chromosome 5 with 155 recombinant inbred lines (RILs) and 193 F2 plants derived from the cross between a susceptible line 'changchunmici' and IL52. Interestingly, pm was co-localized with the major-effect DMR QTL dm5.2 confirmed by combining linkage analysis and BSA-seq, which was consistent with the observed linkage of DMR and PMR in IL52. Further, phenotype-genotype correlation analysis of DMR and PMR in the RILs indicated that the co-localized locus pm/dm5.2 confers complete resistance to PM and partial resistance to DM. Seven candidate genes for DMR were identified within dm5.2 by BSA-seq analysis, of which Csa5M622800.1, Csa5M622830.1 and Csa5M623490.1 were also the same candidate genes for PMR. A single nucleotide polymorphism that is present in the 3' untranslated region (3'UTR) of Csa5M622830.1 co-segregated perfectly with PMR. The GATA transcriptional factor gene Csa5M622830.1 may be a likely candidate gene for DMR and PMR. This study has provided a clear evidence for the relationship between DMR and PMR in IL52 and sheds new light on the potential value of IL52 for cucumber DMR and PMR breeding program.
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Affiliation(s)
- Kaijing Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Xing Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Wenwei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Jian Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No. 1, Nanjing, 210095, China.
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38
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Słomnicka R, Olczak-Woltman H, Korzeniewska A, Gozdowski D, Niemirowicz-Szczytt K, Bartoszewski G. Genetic mapping of psl locus and quantitative trait loci for angular leaf spot resistance in cucumber ( Cucumis sativus L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:111. [PMID: 30174539 PMCID: PMC6105252 DOI: 10.1007/s11032-018-0866-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 08/06/2018] [Indexed: 05/16/2023]
Abstract
One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.
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Affiliation(s)
- Renata Słomnicka
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Helena Olczak-Woltman
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Aleksandra Korzeniewska
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Dariusz Gozdowski
- Department of Experimental Design and Bioinformatics, Faculty of Agriculture and Biology, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Katarzyna Niemirowicz-Szczytt
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics Breeding and Biotechnology, Faculty of Horticulture Biotechnology and Landscape Architecture, Warsaw University of Life Sciences–SGGW, Warsaw, Poland
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