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Pérez-Martínez AL, Eguiarte LE, Mercer KL, Martínez-Ainsworth NE, McHale L, van der Knaap E, Jardón-Barbolla L. Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico. AMERICAN JOURNAL OF BOTANY 2022; 109:1157-1176. [PMID: 35694731 DOI: 10.1002/ajb2.16019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. METHODS We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. RESULTS Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. CONCLUSIONS Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.
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Affiliation(s)
- Ana L Pérez-Martínez
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México; Circuito exterior s/n anexo al Jardín Botánico. C.P. 04510. Ciudad Universitaria, Ciudad de México, México
| | - Kristin L Mercer
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Natalia E Martínez-Ainsworth
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
| | - Leah McHale
- Department of Horticulture and Crop Science, Ohio State University, Columbus, OH, 43210, USA
| | - Esther van der Knaap
- Department of Horticulture, Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Lev Jardón-Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Torre II de Humanidades 4°, 5° y 6° pisos, Circuito Interior, C.P. 04510, Ciudad Universitaria, Ciudad de México, México
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Christov NK, Tsonev S, Todorova V, Todorovska EG. Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan Capsicum annuum germplasm. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1946428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
| | - Stefan Tsonev
- Department of Functional Genetics, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | - Velichka Todorova
- Department of Breeding, Maritsa Vegetable Crops Research Institute, Agricultural Academy, Plovdiv, Bulgaria
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Konishi A, Furutani N, Minamiyama Y, Ohyama A. Detection of quantitative trait loci for capsanthin content in pepper ( Capsicum annuum L.) at different fruit ripening stages. BREEDING SCIENCE 2019; 69:30-39. [PMID: 31086481 PMCID: PMC6507717 DOI: 10.1270/jsbbs.18070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/04/2018] [Indexed: 05/10/2023]
Abstract
Capsanthin, the main carotenoid of red pepper fruits, is beneficial for human health. To breed pepper (Capsicum annuum L.) with high capsanthin content by marker-assisted selection, we constructed a linkage map of doubled-haploid (DH) lines derived from a cross of two pure lines of C. annuum ('S3586' × 'Kyoto-Manganji No. 2'). The map, designated as the SM-DH map, consisted of 15 linkage groups and the total map distance was 1403.8 cM. Mapping of quantitative trait loci (QTLs) for capsanthin content detected one QTL on linkage group (LG) 13 at 90 days after flowering (DAF) and one on LG 15 at 45 DAF; they were designated Cst13.1 and Cst15.1, respectively. Cst13.1 explained 17.0% of phenotypic variance and Cst15.1 explained 16.1%. We grouped DH lines according to the genotypes of markers adjacent to Cst13.1 and Cst15.1 on both sides. The DH lines with the alleles of both QTLs derived from 'S3586' showed higher capsanthin content at 45 and 90 DAF than the other lines. This is the first identification of QTLs for capsanthin content in any plant species. The data obtained here will be useful in marker-assisted selection for pepper breeding for high capsanthin content.
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Affiliation(s)
- Ayako Konishi
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Research Center,
74 Oji, Kitainayazuma, Seika, Soraku, Kyoto 619-0244,
Japan
- Corresponding author (e-mail: )
| | - Noriyuki Furutani
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Research Center,
74 Oji, Kitainayazuma, Seika, Soraku, Kyoto 619-0244,
Japan
| | - Yasuhiro Minamiyama
- Kyoto University of Education, Center for Environmental Education,
112 Echigoyashiki, Fukakusa, Fushimi, Kyoto 612-8431,
Japan
| | - Akio Ohyama
- National Agriculture and Food Research Organization (NARO), Institute of Vegetable and Floriculture Science (NIVFS),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8519,
Japan
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Kenig S, Baruca-Arbeiter A, Mohorko N, Stubelj M, Černelič-Bizjak M, Bandelj D, Jenko-Pražnikar Z, Petelin A. Moderate but not high daily intake of chili pepper sauce improves serum glucose and cholesterol levels. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Cheng J, Zhao Z, Li B, Qin C, Wu Z, Trejo-Saavedra DL, Luo X, Cui J, Rivera-Bustamante RF, Li S, Hu K. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep 2016; 6:18919. [PMID: 26739748 PMCID: PMC4703971 DOI: 10.1038/srep18919] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/30/2015] [Indexed: 02/05/2023] Open
Abstract
The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zicheng Zhao
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Bo Li
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Cheng Qin
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Diana L. Trejo-Saavedra
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Xirong Luo
- Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China
| | - Junjie Cui
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Rafael F. Rivera-Bustamante
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Hulse-Kemp AM, Ashrafi H, Plieske J, Lemm J, Stoffel K, Hill T, Luerssen H, Pethiyagoda CL, Lawley CT, Ganal MW, Van Deynze A. A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. HORTICULTURE RESEARCH 2016; 3:16036. [PMID: 27602231 PMCID: PMC4962762 DOI: 10.1038/hortres.2016.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 05/18/2023]
Abstract
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hamid Ashrafi
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Jana Lemm
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Kevin Stoffel
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hartmut Luerssen
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | | | - Cindy T Lawley
- Illumina Incorporated, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Allen Van Deynze
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
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Tan S, Cheng JW, Zhang L, Qin C, Nong DG, Li WP, Tang X, Wu ZM, Hu KL. Construction of an interspecific genetic map based on InDel and SSR for mapping the QTLs affecting the initiation of flower primordia in pepper (Capsicum spp.). PLoS One 2015; 10:e0119389. [PMID: 25781878 PMCID: PMC4363154 DOI: 10.1371/journal.pone.0119389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/30/2015] [Indexed: 01/18/2023] Open
Abstract
Re-sequencing permits the mining of genome-wide variations on a large scale and provides excellent resources for the research community. To accelerate the development and application of molecular markers and identify the QTLs affecting the flowering time-related trait in pepper, a total of 1,038 pairs of InDel and 674 SSR primers from different sources were used for genetic mapping using the F2 population (n = 154) derived from a cross between BA3 (C. annuum) and YNXML (C. frutescens). Of these, a total of 224 simple PCR-based markers, including 129 InDels and 95 SSRs, were validated and integrated into a map, which was designated as the BY map. The BY map consisted of 13 linkage groups (LGs) and spanned a total genetic distance of 1,249.77 cM with an average marker distance of 5.60 cM. Comparative analysis of the genetic and physical map based on the anchored markers showed that the BY map covered nearly the whole pepper genome. Based on the BY map, one major and five minor QTLs affecting the number of leaves on the primary axis (Nle) were detected on chromosomes P2, P7, P10 and P11 in 2012. The major QTL on P2 was confirmed based on another subset of the same F2 population (n = 147) in 2014 with selective genotyping of markers from the BY map. With the accomplishment of pepper whole genome sequencing and annotations (release 2.0), 153 candidate genes were predicted to embed in the Nle2.2 region, of which 12 important flowering related genes were obtained. The InDel/SSR-based interspecific genetic map, QTLs and candidate genes obtained by the present study will be useful for the downstream isolation of flowering time-related gene and other genetic applications for pepper.
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Affiliation(s)
- Shu Tan
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jiao-Wen Cheng
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Li Zhang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Cheng Qin
- College of Horticulture, South China Agricultural University, Guangzhou, China; Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou, China; Maize Research Institute of Sichuan Agricultural University / Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, China
| | - Ding-Guo Nong
- College of Agriculture, Guangxi University, Nanning, China
| | - Wei-Peng Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Xin Tang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zhi-Ming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Kai-Lin Hu
- College of Horticulture, South China Agricultural University, Guangzhou, China
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González-Pérez S, Garcés-Claver A, Mallor C, Sáenz de Miera LE, Fayos O, Pomar F, Merino F, Silvar C. New insights into Capsicum spp relatedness and the diversification process of Capsicum annuum in Spain. PLoS One 2014; 9:e116276. [PMID: 25545628 PMCID: PMC4278865 DOI: 10.1371/journal.pone.0116276] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
The successful exploitation of germplasm banks, harbouring plant genetic resources indispensable for plant breeding, will depend on our ability to characterize their genetic diversity. The Vegetable Germplasm Bank of Zaragoza (BGHZ) (Spain) holds an important Capsicum annuum collection, where most of the Spanish pepper variability is represented, as well as several accessions of other domesticated and non-domesticated Capsicum spp from all over the five continents. In the present work, a total of 51 C. annuum landraces (mainly from Spain) and 51 accessions from nine Capsicum species maintained at the BGHZ were evaluated using 39 microsatellite (SSR) markers spanning the whole genome. The 39 polymorphic markers allowed the detection of 381 alleles, with an average of 9.8 alleles per locus. A sizeable proportion of alleles (41.2%) were recorded as specific alleles and the majority of these were present at very low frequencies (rare alleles). Multivariate and model-based analyses partitioned the collection in seven clusters comprising the ten different Capsicum spp analysed: C. annuum, C. chinense, C. frutescens, C. pubescens, C. bacatum, C. chacoense and C. eximium. The data clearly showed the close relationships between C. chinense and C. frutescens. C. cardenasii and C. eximium were indistinguishable as a single, morphologically variable species. Moreover, C. chacoense was placed between C. baccatum and C. pubescens complexes. The C. annuum group was structured into three main clusters, mostly according to the pepper fruit shape, size and potential pungency. Results suggest that the diversification of C. annuum in Spain may occur from a rather limited gene pool, still represented by few landraces with ancestral traits. This ancient population would suffer from local selection at the distinct geographical regions of Spain, giving way to pungent and elongated fruited peppers in the South and Center, while sweet blocky and triangular types in Northern Spain.
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Affiliation(s)
- Susana González-Pérez
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain
| | - Ana Garcés-Claver
- Agrifood Research and Technology Centre of Aragón (CITA), Zaragoza, Spain
| | - Cristina Mallor
- Agrifood Research and Technology Centre of Aragón (CITA), Zaragoza, Spain
| | | | - Oreto Fayos
- Agrifood Research and Technology Centre of Aragón (CITA), Zaragoza, Spain
| | - Federico Pomar
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain
| | - Fuencisla Merino
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain
| | - Cristina Silvar
- Department of Ecology, Plant and Animal Biology, University of Coruña, A Coruña, Spain
- * E-mail:
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Quenouille J, Paulhiac E, Moury B, Palloix A. Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants. Heredity (Edinb) 2014; 112:579-87. [PMID: 24569635 DOI: 10.1038/hdy.2013.138] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/06/2013] [Accepted: 11/08/2013] [Indexed: 11/09/2022] Open
Abstract
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.
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Affiliation(s)
- J Quenouille
- 1] INRA, UR1052 GAFL, Montfavet Cedex, France [2] INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - E Paulhiac
- INRA, UR1052 GAFL, Montfavet Cedex, France
| | - B Moury
- INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - A Palloix
- INRA, UR1052 GAFL, Montfavet Cedex, France
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Miranda FDD, Gontijo ABPL, Santiliano FC, Favoreto FC, Soares TCB. Transferability and characterization of microsatellite markers in five Bromeliaceae species belonging to the subfamilies Pitcairnioideae and Bromelioideae. BIOTA NEOTROPICA 2012. [DOI: 10.1590/s1676-06032012000300032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite markers previously developed for Pitcairnia albiflos Herb. and Pitcairnia geysksii L.B.Sm. were used in cross-amplification tests of five other Bromeliaceae species. Ten (76.9%) out of the 13 evaluated pair of primers had positive results for some of the species tested. The number of polymorphic alleles ranged between two and four in most species. Ho values ranged between zero, in Pitcairnia flammea Lindl. (PaA05), Aechmea ramosa Mart ex Schult & Schult and Billbergia horrida Regel (PaC05), and one in Billbergia euphemiae E. Morren (PaA05, PaA10, PaC05 and PaD07). This study showed that microsatellite markers developed for P. albiflos and P. geysksii effectively amplified the DNA samples of Pitcairnia flammea, Aechmea nudicaulis (L.) Griseb., Aechmea ramosa, Billbergia horrida and Billbergia euphemiae, validating the transferability of these markers to species of the Pitcairnioideae and Bromelioideae subfamilies.
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Mimura Y, Inoue T, Minamiyama Y, Kubo N. An SSR-based genetic map of pepper (Capsicum annuum L.) serves as an anchor for the alignment of major pepper maps. BREEDING SCIENCE 2012; 62:93-8. [PMID: 23136519 PMCID: PMC3405950 DOI: 10.1270/jsbbs.62.93] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/08/2011] [Indexed: 05/13/2023]
Abstract
Of the Capsicum peppers (Capsicum spp.), cultivated C. annuum is the most commercially important, but has lacked an intraspecific linkage map based on sequence-specific PCR markers in accord with haploid chromosome numbers. We constructed a linkage map of pepper using a doubled haploid (DH) population derived from a cross between two C. annuum genotypes, a bell-type cultivar 'California Wonder' and a Malaysian small-fruited cultivar 'LS2341 (JP187992)', which is used as a source of resistance to bacterial wilt (Ralstonia solanacearum). A set of 253 markers (151 SSRs, 90 AFLPs, 10 CAPSs and 2 sequence-tagged sites) was on the map which we constructed, spanning 1,336 cM. This is the first SSR-based map to consist of 12 linkage groups, corresponding to the haploid chromosome number in an intraspecific cross of C. annuum. As this map has a lot of PCR-based anchor markers, it is easy to compare it to other pepper genetic maps. Therefore, this map and the newly developed markers will be useful for cultivated C. annuum breeding.
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Affiliation(s)
- Yutaka Mimura
- Agriculture and Forestry Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Centre, Amarube-cho, Kameoka, Kyoto 621-0806, Japan
- Corresponding author (e-mail: )
| | - Takahiro Inoue
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Oji, Kitainayazuma, Seika, Kyoto 619-0244, Japan
| | - Yasuhiro Minamiyama
- Faculty of Education, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Oji, Kitainayazuma, Seika, Kyoto 619-0244, Japan
- Biotechnology Research Department (KAB), Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Centre, 74 Oji, Kitainayazuma, Seika, Kyoto 619-0244, Japan
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12
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Kong Q, Zhang G, Chen W, Zhang Z, Zou X. Identification and development of polymorphic EST-SSR markers by sequence alignment in pepper, Capsicum annuum (Solanaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:e59-61. [PMID: 22282113 DOI: 10.3732/ajb.1100347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY The redundancies in expressed sequence tags (ESTs) in the National Center for Biotechnology Information sequence database were used to identify and develop polymorphic simple sequence repeat (SSR) markers for pepper (Capsicum annuum). METHODS AND RESULTS Sixty-eight polymorphic SSR loci were identified in the contigs (containing redundant ESTs) generated by assembling 118060 pepper ESTs from the public sequence database. Thirty-three SSR markers exhibited polymorphism among 31 pepper varieties, with alleles per SSR marker ranging from two to six. The mean observed and expected heterozygosity were 0.28 and 0.39, respectively. There were 18 SSR markers with a motif repeat number of less than five, accounting for 55% of the total. CONCLUSIONS We demonstrated the value of mining the redundant sequences in public sequence databases for the development of polymorphic SSR markers, which can be used for marker-assisted breeding in pepper.
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Affiliation(s)
- Qiusheng Kong
- Hunan Vegetable Research Institute, Changsha 410125, Hunan, China
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Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL. Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 2011; 12:304. [PMID: 21663628 PMCID: PMC3128069 DOI: 10.1186/1471-2164-12-304] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 06/10/2011] [Indexed: 11/10/2022] Open
Abstract
Background The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.
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Affiliation(s)
- Lorenzo Barchi
- DIVAPRA Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:973-89. [PMID: 19618162 DOI: 10.1007/s00122-009-1102-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/25/2009] [Indexed: 05/03/2023]
Abstract
Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.
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Affiliation(s)
- Sheh May Tam
- Laboratoire de Biologie Cellulaire, UR501, Institut Jean-Pierre Bourgin, INRA, 78026, Versailles Cedex, France
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Stàgel A, Portis E, Toppino L, Rotino GL, Lanteri S. Gene-based microsatellite development for mapping and phylogeny studies in eggplant. BMC Genomics 2008; 9:357. [PMID: 18667065 PMCID: PMC2527019 DOI: 10.1186/1471-2164-9-357] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 07/30/2008] [Indexed: 11/10/2022] Open
Abstract
Background Eggplant (Solanum melongena L.) is a member of the Solanaceae family. In spite of its widespread cultivation and nutritional and economic importance, its genome has not as yet been extensively investigated. Few analyses have been carried out to determine the genetic diversity of eggplant at the DNA level, and linkage relationships have not been well characterised. As for the other Solanaceae crop species (potato, tomato and pepper), the level of intra-specific polymorphism appears to be rather limited, and so it is important that an effort is made to develop more informative DNA markers to make progress in understanding the genetics of eggplant and to advance its breeding. The aim of the present work was to develop a set of functional microsatellite (SSR) markers, via an in silico analysis of publicly available DNA sequence. Results From >3,300 genic DNA sequences, 50 SSR-containing candidates suitable for primer design were recovered. Of these, 39 were functional, and were then applied to a panel of 44 accessions, of which 38 were cultivated eggplant varieties, and six were from related Solanum species. The usefulness of the SSR assays for diversity analysis and taxonomic discrimination was demonstrated by constructing a phylogeny based on SSR polymorphisms, and by the demonstration that most were also functional when tested with template from tomato, pepper and potato. As a results of BLASTN analyses, several eggplant SSRs were found to have homologous counterparts in the phylogenetically related species, which carry microsatellite motifs in the same position. Conclusion The set of eggplant EST-SSR markers was informative for phylogenetic analysis and genetic mapping. Since EST-SSRs lie within expressed sequence, they have the potential to serve as perfect markers for genes determining variation in phenotype. Their high level of transferability to other Solanaceae species can be used to provide anchoring points for the integration of genetic maps across species.
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Affiliation(s)
- Anikò Stàgel
- Di.Va.P.R.A, Plant Genetics and Breeding, University of Torino, Via L, da Vinci 44, 10095, Grugliasco, Torino, Italy.
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