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Wang X, Ando K, Wu S, Reddy UK, Tamang P, Bao K, Hammar SA, Grumet R, McCreight JD, Fei Z. Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection. Mol Hortic 2021; 1:11. [PMID: 37789496 PMCID: PMC10515074 DOI: 10.1186/s43897-021-00014-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/25/2021] [Indexed: 09/28/2023]
Abstract
Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide. The melon collection in the U.S. National Plant Germplasm System (NPGS) is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding. Here we use the genotyping-by-sequencing (GBS) technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist. Population structure and genetic diversity analyses suggested that C. melo ssp. melo was firstly introduced from the centers of origin, Indian and Pakistan, to Central and West Asia, and then brought to Europe and Americas. C. melo ssp. melo from East Asia was likely derived from C. melo ssp. agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp. melo accessions from other geographic regions. We developed a core collection of 383 accessions capturing more than 98% of genetic variation in the germplasm, providing a publicly accessible collection for future research and genomics-assisted breeding of melon. Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection. Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits. This study provides insights into melon origin and domestication, and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.
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Affiliation(s)
- Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA
- Nunhems USA, Inc, Acampo, CA, 95220, USA
| | - Shan Wu
- 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, WV, 25112, USA
| | - Prabin Tamang
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA
- U.S. Department of Agriculture-Agricultural Research Service, Natural Products Utilization Research Unit, Thad Cochran Research Center, P.O. Box 1848, Oxford, MS, 38677, USA
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Sue A Hammar
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, 93905, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2020; 47:D1128-D1136. [PMID: 30321383 PMCID: PMC6324010 DOI: 10.1093/nar/gky944] [Citation(s) in RCA: 111] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a ‘SyntenyViewer’ to view genome synteny between different cucurbit species and an ‘RNA-Seq’ module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA.,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain.,Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA.,U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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4
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Zheng Y, Wu S, Bai Y, Sun H, Jiao C, Guo S, Zhao K, Blanca J, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, K Reddy U, Ando K, McCreight JD, Schaffer AA, Burger J, Tadmor Y, Katzir N, Tang X, Liu Y, Giovannoni JJ, Ling KS, Wechter WP, Levi A, Garcia-Mas J, Grumet R, Fei Z. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Res 2019; 47:D1128-D1136. [PMID: 30321383 DOI: 10.1093/nar/gky944s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 05/20/2023] Open
Abstract
The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.org) using the Tripal toolkit. The database currently contains all available genome and expressed sequence tag (EST) sequences, genetic maps, and transcriptome profiles for cucurbit species, as well as sequence annotations, biochemical pathways and comparative genomic analysis results such as synteny blocks and homologous gene pairs between different cucurbit species. A set of analysis and visualization tools and user-friendly query interfaces have been implemented in the database to facilitate the usage of these large-scale data by the community. In particular, two new tools have been developed in the database, a 'SyntenyViewer' to view genome synteny between different cucurbit species and an 'RNA-Seq' module to analyze and visualize gene expression profiles. Both tools have been packed as Tripal extension modules that can be adopted in other genomics databases developed using the Tripal system.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Bai
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Shaogui Guo
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Kun Zhao
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Jose Blanca
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Valencia 46022, Spain
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sanwen Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Umesh K Reddy
- Department of Biology, West Virginia State University, Institute, WV 25112, USA
| | - Kaori Ando
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James D McCreight
- U.S. Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - Arthur A Schaffer
- Plant Science Institute, Agricultural Research Organization, The Volcani Center, P.O.B. 6, Bet-Dagan 50250, Israel
| | - Joseph Burger
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Yaakov Tadmor
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Nurit Katzir
- Plant Science Institute, Agricultural Research Organization, Newe Yaar Research Center, Ramat Yishai 30095, Israel
| | - Xuemei Tang
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
| | - Yang Liu
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - James J Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona 08193, Spain
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
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Sabanadzovic S, Wintermantel WM, Valverde RA, McCreight JD, Aboughanem-Sabanadzovic N. Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host. Virus Res 2016; 214:49-58. [DOI: 10.1016/j.virusres.2016.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/03/2016] [Indexed: 01/30/2023]
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Wintermantel WM, Gilbertson RL, McCreight JD, Natwick ET. Host-Specific Relationship Between Virus Titer and Whitefly Transmission of Cucurbit yellow stunting disorder virus. Plant Dis 2016; 100:92-98. [PMID: 30688566 DOI: 10.1094/pdis-11-14-1119-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, family Closteroviridae) was identified in the melon (Cucumis melo) production regions of the desert southwestern United States in fall 2006. It is now well established in the region, where it is transmitted efficiently by the sweet potato whitefly, Bemisia tabaci biotype B (MEAM1). In order to evaluate the spread and establishment of the virus, nearly all spring and fall cucurbit fields planted in the Imperial Valley of California from 2007 to 2009 were surveyed and representative plants were tested for CYSDV infection. Incidence of CYSDV in spring melon fields was initially low and limited to a small number of fields in 2007 but increased to 63% of fields by spring 2009. Virus incidence in fall melon fields was 100% in each year. These results suggested that the virus had become established in native vegetation, weeds, and other crop species, and represented an increasing threat to melon production in the southwestern United States. Therefore, a select set of weed and crop species which grow or are cultivated in the Imperial Valley were evaluated as CYSDV reservoir hosts. For each species, we determined the capacity of CYSDV to accumulate, the relationship between virus titer in these source plants and transmission by whiteflies, as well as subsequent accumulation in inoculated cucurbit plants. Among these hosts, there was considerable variation in virus accumulation and transmission rates. Cucurbit hosts had the highest CYSDV titers, were efficient sources for virus acquisition, and showed a positive correlation between titer in source plants and transmission. Noncucurbit hosts had significantly lower CYSDV titers and varied in their capacity to serve as sources for transmission. CYSDV titers in some noncucurbit source plants, specifically common bean (Phaseolus vulgaris) and shepherd's purse (Capsella bursa-pastoris), were not positively correlated with transmission, demonstrating that additional environmental, physical, or biochemical factors were involved. These results demonstrate that multiple factors influence the efficiency with which a host plant species will be a reservoir for vector transmission of virus to crops.
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Affiliation(s)
- William M Wintermantel
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, CA 93905
| | | | | | - Eric T Natwick
- University of California Cooperative Extension Imperial County, Holtville 92250
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7
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Nimmakayala P, Tomason YR, Abburi VL, Alvarado A, Saminathan T, Vajja VG, Salazar G, Panicker GK, Levi A, Wechter WP, McCreight JD, Korol AB, Ronin Y, Garcia-Mas J, Reddy UK. Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. Front Plant Sci 2016; 7:1437. [PMID: 27713759 PMCID: PMC5031849 DOI: 10.3389/fpls.2016.01437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/08/2016] [Indexed: 05/06/2023]
Abstract
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19-0.53 and between inodorus and agrestis accessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.
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Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Yan R. Tomason
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- Department of Selection and Seed Production, Dnepropetrovsk State Agrarian and Economic UniversityDnepropetrovsk, Ukraine
| | - Venkata L. Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Alejandra Alvarado
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Venkata G. Vajja
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Germania Salazar
- Department of Agriculture, Alcorn State UniversityLorman, MS, USA
| | | | - Amnon Levi
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | - William P. Wechter
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | | | - Abraham B. Korol
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Yefim Ronin
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institute for Food and Agricultural Research and Technology-Universitat Autònoma de Barcelona-Universitat de BarcelonaBarcelona, Spain
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- *Correspondence: Umesh K. Reddy
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Cuevas HE, Staub JE, Simon PW, Zalapa JE, McCreight JD. Mapping of genetic loci that regulate quantity of beta-carotene in fruit of US Western Shipping melon (Cucumis melo L.). Theor Appl Genet 2008; 117:1345-59. [PMID: 18773190 DOI: 10.1007/s00122-008-0868-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Accepted: 08/12/2008] [Indexed: 05/03/2023]
Abstract
Melon (Cucumis melo L.) is highly nutritious vegetable species and an important source of beta-carotene (Vitamin A), which is an important nutrient in the human diet. A previously developed set of 81 recombinant inbred lines (RIL) derived from Group Cantalupensis US Western Shipper market type germplasm was examined in two locations [Wisconsin (WI) and California (CA), USA] over 2 years to identify quantitative trait loci (QTL) associated with quantity of beta-carotene (QbetaC) in mature fruit. A moderately saturated 256-point RIL-based map [104 SSR, 7 CAPS, 4 SNP in putative carotenoid candidate genes, 140 dominant markers and one morphological trait (a) spanning 12 linkage groups (LG)] was used for QbetaC-QTL analysis. Eight QTL were detected in this evaluation that were distributed across four LG that explained a significant portion of the associated phenotypic variation for QbetaC (R (2) = 8 to 31.0%). Broad sense heritabilities for QbetaC obtained from RIL grown in WI. and CA were 0.56 and 0.68, respectively, and 0.62 over combined locations. The consistence of QbetaC in high/low RIL within location across years was confirmed in experiments conducted over 2 years. QTL map positions were not uniformly associated with putative carotenoid genes, although one QTL (beta-car6.1) interval was located 10 cM from a beta-carotene hydroxylase gene. These results suggest that accumulation of beta-carotene in melon is under complex genetic control. This study provides the initial step for defining the genetic control of QbetaC in melon leading to the development of varieties with enhanced beta-carotene content.
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Affiliation(s)
- H E Cuevas
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706, USA,
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Zalapa JE, Staub JE, McCreight JD, Chung SM, Cuevas H. Detection of QTL for yield-related traits using recombinant inbred lines derived from exotic and elite US Western Shipping melon germplasm. Theor Appl Genet 2007; 114:1185-201. [PMID: 17294163 DOI: 10.1007/s00122-007-0510-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Accepted: 01/12/2007] [Indexed: 05/06/2023]
Abstract
The inheritance of yield-related traits in melon (Cucumis melo L.; 2n = 2x = 24) is poorly understood, and the mapping of quantitative trait loci (QTL) for such traits has not been reported. Therefore, a set of 81 recombinant inbred lines (RIL) was developed from a cross between the monoecious, highly branched line USDA 846-1 and a standard vining, andromonoecious cultivar, 'Top Mark'. The RIL, parental lines, and three control cultivars ('Esteem', 'Sol Dorado', and 'Hales Best Jumbo') were grown at Hancock, WI and El Centro, CA in 2002, and evaluated for primary branch number (PB), fruit number per plant (FN), fruit weight per plant (FW), average weight per fruit (AWF), and percentage of mature fruit per plot (PMF). A 190-point genetic map was constructed using 114 RAPD, 43 SSR, 32 AFLP markers, and one phenotypic trait. Fifteen linkage groups spanned 1,116 cM with a mean marker interval of 5.9 cM. A total of 37 QTL were detected in both locations (PB = 6, FN = 9, FW = 12, AWF = 5, and PMF = 5). QTL analyses revealed four location-independent factors for PB (pb1.1, pb1.2, pb2.3, and pb10.5), five for FN (fn1.1, fn1.2, fn1.3, fn2.4, and fn8.8), four for FW (fw5.8, fw6.10, fw8.11, and fw8.12), two for AWF (awf1.3 and awf8.5), and one for PMF (pmf10.4). The significant (P </= 0.05) positive phenotypic correlations observed among PB, FN, and FW, and negative phenotypic correlations between PB and AWF and between FN and AWF were consistent with the genomic locations and effects (negative vs. positive) of the QTL detected. Results indicate that genes resident in highly branched melon types have potential for increasing yield in US Western Shipping type germplasm via marker-assisted selection.
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Affiliation(s)
- J E Zalapa
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Unit, Department of Horticulture, University of Wisconsin, 1575 Linden Dr., Madison, WI 53706, USA.
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Liu YB, McCreight JD. Responses of Nasonovia ribisnigri (Homoptera: Aphididae) to susceptible and resistant lettuce. J Econ Entomol 2006; 99:972-8. [PMID: 16813339 DOI: 10.1603/0022-0493-99.3.972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nymphs and alates of aphid Nasonovia ribisnigri (Mosley) (Homoptera: Aphididae) were tested on 10 lettuce cultivars with N. ribisnigri resistance gene Nr and 18 cultivars without the resistance gene in various bioassays. Bioassays used whole plants, leaf discs, or leaf cages to determine susceptibility of commercial lettuce cultivars to N. ribisnigri infestation and to evaluate screening methods for breeding lettuce resistance to N. ribisnigri. Resistant and susceptible plants were separated in 3 d when using whole plant bioassays. Long-term (> or =7 d) no-choice tests using leaf cages or whole plants resulted in no survival of N. ribisnigri on resistant plants, indicating great promise of the Nr gene for management of N. ribisnigri. Effective screening was achieved in both no-choice tests where resistant or susceptible intact plants were tested separately in groups or individually and in choice tests where susceptible and resistant plants were intermixed. Leaf discs bioassays were not suitable for resistance screening. All lettuce cultivars without the resistance gene were suitable hosts for N. ribisnigri, indicating the great importance of this pest to lettuce production and the urgency in developing resistant lettuce cultivars to manage N. ribisnigri.
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Affiliation(s)
- Yong-Biao Liu
- USDA-ARS, U.S. Agricultural Research Station, 1636 E. Alisal Street, Salinas, CA 93905, USA
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Matheron ME, McCreight JD, Tickes BR. Effect of Planting Date, Cultivar, and Stage of Plant Development on Incidence of Fusarium Wilt of Lettuce in Desert Production Fields. Plant Dis 2005; 89:565-570. [PMID: 30795379 DOI: 10.1094/pd-89-0565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium wilt of lettuce, first recognized in Japan in 1955, has since been discovered in the United States (California in 1990, Arizona in 2001), Iran (1995), Taiwan (1998), and Italy (2001). In Arizona, the causal agent, Fusarium oxysporum f. sp. lactucae, has been recovered from lettuce plants in 27 different lettuce fields during the 2001 to 2003 production seasons. Studies were initiated to examine the impact of planting date, cultivar, and stage of plant development on the incidence of disease in the field. In 2002 and 2003, tested lettuce cultivars were sown in at least one of the following planting windows; early-season (September), mid-season (October), and late-season (December). Within each planting window, significant differences in disease incidence among lettuce cultivars were noted at plant maturity. The mean incidence of Fusarium wilt on cultivars sown in September, October, and December was 92.3, 15.1, and 2.0%, respectively, in 2002 and 74.2, 5.1, and 0.7%, respectively, in 2003. The mean soil temperatures at the10-cm depth during the September, October, and December plantings for both years were 26, 14, and 14°C, respectively. Initial symptoms of Fusarium wilt were apparent as early as 14 days after seeding, with increasing incidence of disease noted as the crop developed and reached maturity. Among all lettuce cultivars planted in September, only one and two cultivars of romaine in 2002 and 2003, respectively, reached maturity with ≤5% incidence of Fusarium wilt, whereas the lowest incidence of disease among crisphead, green leaf, red leaf, or butterhead cultivars was 73.7, 27.0, 20.2, and 65.7%, respectively, in 2002 and 62.1, 29.0, 100, and 100%, respectively, in 2003. For October plantings, all romaine cultivars had ≤5% incidence of Fusarium wilt at maturity, whereas disease incidence among tested cultivars of crisphead lettuce in 2002 and 2003 ranged from 0.8 to 66.8% and 0.3 to 43.3%, respectively. When planted in December, 82 and 88% of tested cultivars, including all romaine entries, reached maturity with ≤1% incidence of Fusarium wilt. Selection of appropriate lettuce cultivars and planting times should allow successful production of lettuce in the southwestern Arizona production region with minimal or no incidence of disease in fields infested with F. oxysporum f. sp. lactucae. On the other hand, successful production of lettuce in infested fields when temperatures favor disease development will not be possible until lettuce cultivars are developed that possess high tolerance or resistance to the pathogen.
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Affiliation(s)
- Michael E Matheron
- The University of Arizona, Yuma Agricultural Center, 6425 West Eighth Street, Yuma 85364
| | - James D McCreight
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, 1636 East Alisal Street, Salinas, CA
| | - Barry R Tickes
- The University of Arizona, Yuma Agricultural Center, 6425 West Eighth Street, Yuma 85364
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Abstract
Plant virus inclusion bodies can be stained specifically with established staining methods for light microscopy. The procedure can be augmented by a short microwave treatment to provide better staining intensity and reduced staining time. The method is useful for preliminary sampling prior to collection for electron microscopy and for plant pathologists, plant breeders, and diagnosticians as a rapid means of plant virus characterization.
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Affiliation(s)
- L L Hoefert
- USDA, Agricultural Research Station, Salinas, CA 93905
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