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Fu G, Yu S, Wu K, Yang M, Altaf MA, Wu Z, Deng Q, Lu X, Fu H, Wang Z, Cheng S. Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. Sci Rep 2024; 14:14691. [PMID: 38926509 PMCID: PMC11208541 DOI: 10.1038/s41598-024-65332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.
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Affiliation(s)
- Genying Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shuang Yu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Kun Wu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Mengxian Yang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhuo Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Qin Deng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Xu Lu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Huizhen Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China.
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
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McLeod L, Barchi L, Tumino G, Tripodi P, Salinier J, Gros C, Boyaci HF, Ozalp R, Borovsky Y, Schafleitner R, Barchenger D, Finkers R, Brouwer M, Stein N, Rabanus-Wallace MT, Giuliano G, Voorrips R, Paran I, Lefebvre V. Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1508-1528. [PMID: 37602679 DOI: 10.1111/tpj.16425] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.
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Affiliation(s)
- Louis McLeod
- INRAE, GAFL, Montfavet, France
- INRAE, A2M, Montfavet, France
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Giorgio Tumino
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), Pontecagnano Faiano, Italy
| | | | | | | | - Ramazan Ozalp
- Bati Akdeniz Agricultural Research Institute (BATEM), Antalya, Türkiye
| | - Yelena Borovsky
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
| | - Roland Schafleitner
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Derek Barchenger
- Vegetable Diversity and Improvement, World Vegetable Center, Shanhua, Taiwan
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Corre, Gatersleben, Germany
- Department of Crop Sciences, Center for Integrated Breeding Research, Georg-August-University, Göttingen, Germany
| | | | - Giovanni Giuliano
- Casaccia Research Centre, Italian National Agency for New Technologies, Energy, and Sustainable Economic Development (ENEA), Rome, Italy
| | - Roeland Voorrips
- Plant Breeding, Wageningen University and Research (WUR), Wageningen, The Netherlands
| | - Ilan Paran
- The Volcani Center, Institute of Plant Sciences, Agricultural Research Organization (ARO), Rishon LeZion, Israel
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Goldman IL, Wang Y, Alfaro AV, Brainard S, Oravec MW, McGregor CE, van der Knaap E. Form and contour: breeding and genetics of organ shape from wild relatives to modern vegetable crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1257707. [PMID: 37841632 PMCID: PMC10568141 DOI: 10.3389/fpls.2023.1257707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 10/17/2023]
Abstract
Shape is a primary determinant of consumer preference for many horticultural crops and it is also associated with many aspects of marketing, harvest mechanics, and postharvest handling. Perceptions of quality and preference often map to specific shapes of fruits, tubers, leaves, flowers, roots, and other plant organs. As a result, humans have greatly expanded the palette of shapes available for horticultural crops, in many cases creating a series of market classes where particular shapes predominate. Crop wild relatives possess organs shaped by natural selection, while domesticated species possess organs shaped by human desires. Selection for visually-pleasing shapes in vegetable crops resulted from a number of opportunistic factors, including modification of supernumerary cambia, allelic variation at loci that control fundamental processes such as cell division, cell elongation, transposon-mediated variation, and partitioning of photosynthate. Genes that control cell division patterning may be universal shape regulators in horticultural crops, influencing the form of fruits, tubers, and grains in disparate species. Crop wild relatives are often considered less relevant for modern breeding efforts when it comes to characteristics such as shape, however this view may be unnecessarily limiting. Useful allelic variation in wild species may not have been examined or exploited with respect to shape modifications, and newly emergent information on key genes and proteins may provide additional opportunities to regulate the form and contour of vegetable crops.
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Affiliation(s)
- Irwin L. Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Yanbing Wang
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Andrey Vega Alfaro
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Scott Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Madeline W. Oravec
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Cecilia Elizabeth McGregor
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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Choi H, Back S, Kim GW, Lee K, Venkatesh J, Lee HB, Kwon JK, Kang BC. Development of a speed breeding protocol with flowering gene investigation in pepper ( Capsicum annuum). FRONTIERS IN PLANT SCIENCE 2023; 14:1151765. [PMID: 37841628 PMCID: PMC10569693 DOI: 10.3389/fpls.2023.1151765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 08/14/2023] [Indexed: 10/17/2023]
Abstract
Pepper (Capsicum spp.) is a vegetable and spice crop in the Solanaceae family with many nutritional benefits for human health. During several decades, horticultural traits, including disease resistance, yield, and fruit quality, have been improved through conventional breeding methods. Nevertheless, cultivar development is a time-consuming process because of the long generation time of pepper. Recently, speed breeding has been introduced as a solution for shorting the breeding cycle in long-day or day-neutral field crops, but there have been only a few studies on speed breeding in vegetable crops. In this study, a speed breeding protocol for pepper was developed by controlling the photoperiod and light quality. Under the condition of a low red (R) to far-red (FR) ratio of 0.3 with an extended photoperiod (Epp) of 20 h (95 ± 0 DAT), the time to first harvest was shortened by 75 days after transplant (DAT) compared to that of the control treatment (170 ± 2 DAT), suggesting that Epp with FR light is an essential factor for flowering in pepper. In addition, we established the speed breeding system in a greenhouse with a 20 h photoperiod and a 3.8 R:FR ratio and promoted the breeding cycle of C. annuum for 110 days from seed to seed. To explain the accelerated flowering response to the Epp and supplemented FR light, genome-wide association study (GWAS) and gene expression analysis were performed. As a result of the GWAS, we identified a new flowering gene locus for pepper and suggested four candidate genes for flowering (APETALA2 (AP2), WUSCHEL-RELATED HOMEOBOX4 (WOX4), FLOWERING LOCUS T (FT), and GIGANTEA (GI)). Through expression analysis with the candidate genes, it appeared that Epp and FR induced flowering by up-regulating the flowering-promoting gene GI and down-regulating FT. The results demonstrate the effect of a combination of Epp and FR light by genetic analysis of flowering gene expression. This is the first study that verifies gene expression patterns associated with the flowering responses of pepper in a speed breeding system. Overall, this study demonstrates that speed breeding can shorten the breeding cycle and accelerate genetic research in pepper through reduced generation time.
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Affiliation(s)
| | | | | | | | | | | | | | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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Liu F, Zhao J, Sun H, Xiong C, Sun X, Wang X, Wang Z, Jarret R, Wang J, Tang B, Xu H, Hu B, Suo H, Yang B, Ou L, Li X, Zhou S, Yang S, Liu Z, Yuan F, Pei Z, Ma Y, Dai X, Wu S, Fei Z, Zou X. Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nat Commun 2023; 14:5487. [PMID: 37679363 PMCID: PMC10484947 DOI: 10.1038/s41467-023-41251-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
Pepper (Capsicum spp.) is one of the earliest cultivated crops and includes five domesticated species, C. annuum var. annuum, C. chinense, C. frutescens, C. baccatum var. pendulum and C. pubescens. Here, we report a pepper graph pan-genome and a genome variation map of 500 accessions from the five domesticated Capsicum species and close wild relatives. We identify highly differentiated genomic regions among the domesticated peppers that underlie their natural variations in flowering time, characteristic flavors, and unique resistances to biotic and abiotic stresses. Domestication sweeps detected in C. annuum var. annuum and C. baccatum var. pendulum are mostly different, and the common domestication traits, including fruit size, shape and pungency, are achieved mainly through the selection of distinct genomic regions between these two cultivated species. Introgressions from C. baccatum into C. chinense and C. frutescens are detected, including those providing genetic sources for various biotic and abiotic stress tolerances.
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Affiliation(s)
- Feng Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Jiantao Zhao
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Cheng Xiong
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuepeng Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xin Wang
- Boyce Thompson Institute, Ithaca, NY, USA
- Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Zhongyi Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Robert Jarret
- U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Jin Wang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bingqian Tang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Hao Xu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bowen Hu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Huan Suo
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Bozhi Yang
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Lijun Ou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuefeng Li
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Shudong Zhou
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Sha Yang
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhoubing Liu
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Fang Yuan
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Zhenming Pei
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Yanqing Ma
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xiongze Dai
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, USA.
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA.
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Xuexiao Zou
- Engineering Research Center for Germplasm Innovation and New Varieties Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha, China.
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Lopez-Moreno H, Basurto-Garduño AC, Torres-Meraz MA, Diaz-Valenzuela E, Arellano-Arciniega S, Zalapa J, Sawers RJH, Cibrián-Jaramillo A, Diaz-Garcia L. Genetic analysis and QTL mapping of domestication-related traits in chili pepper ( Capsicum annuum L .). Front Genet 2023; 14:1101401. [PMID: 37255716 PMCID: PMC10225550 DOI: 10.3389/fgene.2023.1101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 06/01/2023] Open
Abstract
Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
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Affiliation(s)
- Hector Lopez-Moreno
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Ana Celia Basurto-Garduño
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | | | - Eric Diaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Sergio Arellano-Arciniega
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
| | - Juan Zalapa
- Department of Horticulture, University of WI-Madison, Madison, WI, United States
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture University of WI-Madison, Madison, WI, United States
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, United States
| | - Angelica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
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Rosa-Martínez E, Bovy A, Plazas M, Tikunov Y, Prohens J, Pereira-Dias L. Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits. FRONTIERS IN PLANT SCIENCE 2023; 14:1135237. [PMID: 37025131 PMCID: PMC10070870 DOI: 10.3389/fpls.2023.1135237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.
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Affiliation(s)
- Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Arnaud Bovy
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Cao Y, Zhang K, Yu H, Chen S, Xu D, Zhao H, Zhang Z, Yang Y, Gu X, Liu X, Wang H, Jing Y, Mei Y, Wang X, Lefebvre V, Zhang W, Jin Y, An D, Wang R, Bosland P, Li X, Paran I, Zhang B, Giuliano G, Wang L, Cheng F. Pepper variome reveals the history and key loci associated with fruit domestication and diversification. MOLECULAR PLANT 2022; 15:1744-1758. [PMID: 36176193 DOI: 10.1016/j.molp.2022.09.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
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Affiliation(s)
- Yacong Cao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kang Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hailong Yu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Shumin Chen
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Donghui Xu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hong Zhao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhenghai Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yinqing Yang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaozhen Gu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xinyan Liu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Haiping Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yaxin Jing
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yajie Mei
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiang Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Véronique Lefebvre
- INRAE, GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, 84140 Montfavet, France
| | - Weili Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Jin
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Dongliang An
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Risheng Wang
- Institute of Vegetables, Academy of Agricultural Sciences of Guangxi, 174 Daxue East Road, Nanning 53007, P. R. China
| | - Paul Bosland
- Department of Plant and Environmental Sciences, NMSU, Las Cruces, NM 88003, USA
| | - Xixiang Li
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ilan Paran
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Baoxi Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Giovanni Giuliano
- Biotechnology and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese, 301-00123 Roma, Italy.
| | - Lihao Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Feng Cheng
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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Borovsky Y, Raz A, Doron-Faigenboim A, Zemach H, Karavani E, Paran I. Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20. FRONTIERS IN PLANT SCIENCE 2022; 12:815589. [PMID: 35058962 PMCID: PMC8763684 DOI: 10.3389/fpls.2021.815589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 05/28/2023]
Abstract
Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.
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Jha TB, Bhowmick BK. Conservation of floral, fruit and chromosomal diversity: a review on diploid and polyploid Capsicum annuum complex in India. Mol Biol Rep 2021; 48:5587-5605. [PMID: 34235618 DOI: 10.1007/s11033-021-06355-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/12/2021] [Indexed: 11/25/2022]
Abstract
Capsicum as a spice crop, has wild and cultivated forms admired globally, including Indian subcontinent with vast climatic ranges. Systematic representation of the Indian Capsicum is required to address species relationships and sustainable agriculture, in face of unpredictable climatic conditions. We have updated the catalogue of Indian 'C. annuum complex' with 28 landraces and populations from different agro-climatic regions. The agro-climatic influence on the origin of stable chili landraces in India is remarkable, especially in the North East. The floral and fruit morphotype standards and chromosomal attributes have been considered for four distinct 'C. annuum complex' members under three species. The highlights of study are: (1) comparative profiling of Indian Capsicum species revealing less infraspecific variation within C. frutescens and C. chinense than C. annuum, at par with cultivation status, (2) karyotype analysis of some unique diploid landraces of C. annuum, (3) karyotypic confirmation of the polyploid Dalle Khursani landraces exclusive to India. To obtain more information, we attempted to correlate diversity of fruit and floral morphotype with chromosomal diversity. Existence of elite and rare germplasm found in the regional pockets offer great scope for enriching the agricultural tradition. The present dataset may serve as a template to be continuously upgraded by taxonomists, genomicists and breeders.
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Affiliation(s)
- Timir Baran Jha
- Department of Botany, Maulana Azad College, Rafi Ahmed Kidwai Road, Kolkata, West Bengal, 700113, India
| | - Biplab Kumar Bhowmick
- Department of Botany, Scottish Church College, 1 and 3, Urquhart Square, Kolkata, West Bengal, 700006, India.
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12
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Lee HY, Jang S, Yu CR, Kang BC, Chin JH, Song K. Population Structure and Genetic Diversity of Cucurbita moschata Based on Genome-Wide High-Quality SNPs. PLANTS 2020; 10:plants10010056. [PMID: 33383787 PMCID: PMC7823833 DOI: 10.3390/plants10010056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/30/2022]
Abstract
Pumpkins (Cucurbita moschata) are one of the most important economic crops in genus Cucurbita worldwide. They are a popular food resource and an important rootstock resource for various Cucurbitaceae. Especially, C. moschata is widely used as a rootstock for the commercial production of bloomless cucumbers in East Asia. Since the genetic diversity of the commercial rootstock varieties is narrow, there has been an increasing demand for the trait development of abiotic and biotic stress tolerance breeding. In this study, 2071 high-quality SNPs that were distributed evenly across 20 chromosomes of pumpkins were discovered through the genotyping-by-sequencing (GBS) analysis of 610 accessions of C. moschata germplasm with a global origin. Using these SNPs, various analyses of the genetic diversity and the population structure were performed. Three subgroups were clustered from the germplasm collection, which included East Asia, Africa, and America, and these areas were included the most in each subgroup. Among those groups, accessions from Africa and South Asia showed the highest genetic diversity, which was followed by the Mexico accessions. This result reflected that large gene pools that consist of various native landraces have been conserved in those of countries. Based on the genetic diversity, we finally constructed the C. moschata core collection, which included 67 representative accessions from the 610 germplasms. Five morphological traits that are important in commercial grafting and rootstock seed production, which include the cotyledon length, the cotyledon width, the hypocotyl length, the internode length, and the number of female flowers, were investigated for three years and used to confirm the validity of the core collection selection. The results are expected to provide valuable information about the genetic structure of the worldwide C. moschata germplasm and help to create new gene pools to develop genetically diverse rootstock breeding materials.
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Affiliation(s)
- Hea-Young Lee
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (S.J.); (B.-C.K.)
| | - Chea-Rin Yu
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (S.J.); (B.-C.K.)
| | - Joong-Hyoun Chin
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
| | - Kihwan Song
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea; (H.-Y.L.); (C.-R.Y.); (J.-H.C.)
- Correspondence: ; Tel.: +82-2-3408-2905
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