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de Assis R, Gonçalves LSA, Guyot R, Vanzela ALL. Abundance of distal repetitive DNA sequences in Capsicum L. (Solanaceae) chromosomes. Genome 2023; 66:269-280. [PMID: 37364373 DOI: 10.1139/gen-2022-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Chili peppers (Solanaceae family) have great commercial value. They are commercialized in natura and used as spices and for ornamental and medicinal purposes. Although three whole genomes have been published, limited information about satellite DNA sequences, their composition, and genomic distribution has been provided. Here, we exploited the noncoding repetitive fraction, represented by satellite sequences, that tends to accumulate in blocks along chromosomes, especially near the chromosome ends of peppers. Two satellite DNA sequences were identified (CDR-1 and CDR-2), characterized and mapped in silico in three Capsicum genomes (C. annuum, C. chinense, and C. baccatum) using data from the published high-coverage sequencing and repeats finding bioinformatic tools. Localization using FISH in the chromosomes of these species and in two others (C. frutescens and C. chacoense), totaling five species, showed signals adjacent to the rDNA sites. A sequence comparison with existing Solanaceae repeats showed that CDR-1 and CDR-2 have different origins but without homology to rDNA sequences. Satellites occupied subterminal chromosomal regions, sometimes collocated with or adjacent to 35S rDNA sequences. Our results expand knowledge about the diversity of subterminal regions of Capsicum chromosomes, showing different amounts and distributions within and between karyotypes. In addition, these sequences may be useful for future phylogenetic studies.
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Affiliation(s)
- Rafael de Assis
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina 86097-570, Paraná, Brazil
| | | | - Romain Guyot
- Institute de Recherche pour le Développement, CIRAD, Université de Montpellier, UMR DIADE, Montpellier, France
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Ince AG, Karaca M. Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum. JOURNAL OF PLANT RESEARCH 2021; 134:841-855. [PMID: 33886005 DOI: 10.1007/s10265-021-01287-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Thus, this research was undertaken to study level and pattern of site-specific cytosine methylation of ITS1, 5.8S and ITS2 in nine tissues and/or developmental stage of pepper Capsicum annuum L. cultivar Demre Sivrisi. Tissues studied consisted of young and old roots at 30 and 90 days after sowing (das), mature dry seeds and seeds at 26 days of post anthesis (dpa), flowering buds at 1 day before flowering, pericarps at 3, 15 and 65 dpa. Levels and patterns of DNA cytosine methylation were identified at single base resolution using bisulfite conversion sequencing. Results of this study revealed that DNA cytosine level and pattern of ITS1, 5.8S and ITS2 were different in most tissues and/or developmental stages studied. In addition, methylation levels of CG, CHG and CHH contexts were also significantly different among the regions. Based on the findings of this study, it was concluded that high level of methylation of nrDNA sequences was relatively higher as observed in transposable element and promoter. On the other hand, its tissue-specific gene expression was effective as that of gene body and promoter methylation. Overall findings revealed that methylation levels of nrDNA could be used as biomarkers for tissue identification or age estimation in plants.
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Affiliation(s)
- Ayse Gul Ince
- Vocational School of Technical Sciences, Akdeniz University, 07059, Antalya, Turkey.
| | - Mehmet Karaca
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07059, Antalya, Turkey
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Grabiele M, Aguilera PM, Ducasse DA, Debat HJ. Molecular characterization of the 5S rDNA non-transcribed spacer and reconstruction of phylogenetic relationships in Capsicum. RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Capsicum includes ca. 41 species of chili peppers. In this original report we PCR amplified, cloned, sequenced and characterized the 5S rDNA non-transcribed spacer -NTS- in 23 taxa of nine clades of Capsicum, divergent at geographical origin and fruit and chromosome traits, and compared the NTS features throughout Solanaceae. According to GC content, inner variability and regulatory elements, the NTS organizes into three distinct structural regions; genetic variability at the NTS in Capsicum and related genus clusters into defined taxa hierarchies. Based on the reconstruction of a maximum-likelihood phylogenetic tree and phylogenetic networks, NTS sequences of Capsicum and related taxa grouped into well recognized categories -genus, section, clade, species, variety-. An evolutionary scenario arose from combined genetic and phylogenetic NTS data, in which monophyly and lineage diversification over time of Capsicum are addressed. Our analysis is original to include all domesticated species of Capsicum prevailing in germplasm collections and breeding programs, together with a large group of wild taxa that demanded further genetic characterization. The NTS set up as a double purpose marker in Capsicum, to directly evaluate genetic variability and reconstruct phylogenetic relationships to a broad extent, and constitutes a valuable tool for germplasm characterization and evolutionary studies within Solanaceae.
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Park HR, Park JE, Kim JH, Shin H, Yu SH, Son S, Yi G, Lee SS, Kim HH, Huh JH. Meiotic Chromosome Stability and Suppression of Crossover Between Non-homologous Chromosomes in x Brassicoraphanus, an Intergeneric Allotetraploid Derived From a Cross Between Brassica rapa and Raphanus sativus. FRONTIERS IN PLANT SCIENCE 2020; 11:851. [PMID: 32612629 PMCID: PMC7309133 DOI: 10.3389/fpls.2020.00851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
Hybridization and polyploidization are major driving forces in plant evolution. Allopolyploids can be occasionally formed from a cross between distantly related species but often suffer from chromosome instability and infertility. xBrassicoraphanus is an intergeneric allotetraploid (AARR; 2n = 38) derived from a cross between Brassica rapa (AA; 2n = 20) and Raphanus sativus (RR; 2n = 18). xBrassicoraphanus is fertile and genetically stable, while retaining complete sets of both B. rapa and R. sativus chromosomes. Precise control of meiotic recombination is essential for the production of balanced gametes, and crossovers (COs) must occur exclusively between homologous chromosomes. Many interspecific hybrids have problems with meiotic division at early generations, in which interactions between non-homologous chromosomes often bring about aneuploidy and unbalanced gamete formation. We analyzed meiotic chromosome behaviors in pollen mother cells (PMCs) of allotetraploid and allodiploid F1 individuals of newly synthesized xBrassicoraphanus. Allotetraploid xBrassicoraphanus PMCs showed a normal diploid-like meiotic behavior. By contrast, allodiploid xBrassicoraphanus PMCs displayed abnormal segregation of chromosomes mainly due to the absence of homologous pairs. Notably, during early stages of meiosis I many of allodiploid xBrassicoraphanus chromosomes behave independently with few interactions between B. rapa and R. sativus chromosomes, forming many univalent chromosomes before segregation. Chromosomes were randomly assorted at later stages of meiosis, and tetrads with unequal numbers of chromosomes were formed at completion of meiosis. Immunolocalization of HEI10 protein mediating meiotic recombination revealed that COs were more frequent in synthetic allotetraploid xBrassicoraphanus than in allodiploid, but less than in the stabilized line. These findings suggest that structural dissimilarity between B. rapa and R. sativus chromosomes prevents non-homologous interactions between the parental chromosomes in allotetraploid xBrassicoraphanus, allowing normal diploid-like meiosis when homologous pairing partners are present. This study also suggests that CO suppression between non-homologous chromosomes is required for correct meiotic progression in newly synthesized allopolyploids, which is important for the formation of viable gametes and reproductive success in the hybrid progeny.
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Affiliation(s)
- Hye Rang Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jeong Eun Park
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Jung Hyo Kim
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Hosub Shin
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Seung Hwa Yu
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Sehyeok Son
- Department of Plant Science, Seoul National University, Seoul, South Korea
| | - Gibum Yi
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | | | - Hyun Hee Kim
- Department of Life Science, Chromosome Research Institute, Sahmyook University, Seoul, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Zhou HC, Waminal NE, Kim HH. In silico mining and FISH mapping of a chromosome-specific satellite DNA in Capsicum annuum L. Genes Genomics 2019; 41:1001-1006. [PMID: 31134590 DOI: 10.1007/s13258-019-00832-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND A large proportion of eukaryote nuclear genomes is composed of repetitive DNA. Tracing the dynamics of repetitive elements in the genomes of related taxa can reveal important information about their phylogenic relationships as well as traits that have become distinct to a lineage. OBJECTIVE Study the genomic abundance and chromosomal location of repetitive DNA in Capsicum annuum L. to understand the repeat dynamics. METHOD We quantified repeated DNA content in the C. annuum genome using the RepeatExplorer pipeline. RESULTS About 42% of the C. annuum genome dataset comprised repetitive elements. Of these, 0.011, 0.98, 3.09, and 0.024% represented high and low confidence satellite repeats, putative long-terminal repeats (LTRs), and rDNA sequences, respectively. One novel high confidence 167-bp satellite repeat with a genomic proportion of 0.011%, Ca167TR, was identified. Furthermore, FISH with Ca167TR on metaphase chromosomes of C. annuum revealed signals in the subtelomeric regions of the short and long arms of chromosome 3 and 4, respectively. CONCLUSION Further understanding of the origin and associated functions of Ca167TR and other repeats in Capsicum will give us insights into the genomic relationships and functions of the genome.
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Affiliation(s)
- Hui Chao Zhou
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Hyun Hee Kim
- Department of Life Sciences, Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea.
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Sattler MC, Soares FAF, Silva JC, Carvalho CR, Clarindo WR. Physical Mapping of 5S rDNA in Eucalyptus dunnii Maiden and Zea mays L. by PRINS. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Carlos Roberto Carvalho
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa
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Scaldaferro MA, da Cruz MVR, Cecchini NM, Moscone EA. FISH and AgNor mapping of the 45S and 5S rRNA genes in wild and cultivated species of Capsicum (Solananceae). Genome 2016; 59:95-113. [PMID: 26853884 DOI: 10.1139/gen-2015-0099] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chromosome number and position of rDNA were studied in 12 wild and cultivated species of the genus Capsicum with chromosome numbers x = 12 and x = 13 (22 samples). For the first time in these species, the 5S and 45S rRNA loci were localized and physically mapped using two-color fluorescence in situ hybridization and AgNOR banding. We focused on the comparison of the results obtained with both methods with the aim of accurately revealing the real functional rRNA genes. The analyzes were based on a previous work that reported that the 18S-5.8S-25S loci mostly coincide with GC-rich heterochromatic regions and likely have given rise to satellite DNAs, which are not active genes. These data show the variability of rDNA within karyotypes of the genus Capsicum, providing anchor points for (comparative) genetic maps. In addition, the obtained information might be useful for studies on evolution of repetitive DNA.
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Affiliation(s)
- Marisel A Scaldaferro
- a Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina.,b Facultad de Ciencias Exactas, Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba, Av. Vélez Sarsfield 299, CP 5000, Córdoba, Argentina
| | | | - Nicolás M Cecchini
- d Molecular Genetics and Cell Biology, The University of Chicago, 929 East 57th Street GCIS Room W519P, Chicago, USA
| | - Eduardo A Moscone
- a Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
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Aguilera PM, Debat HJ, Scaldaferro MA, Martí DA, Grabiele M. FISH-mapping of the 5S rDNA locus in chili peppers (Capsicum-Solanaceae). AN ACAD BRAS CIENC 2016; 88:117-25. [PMID: 26959315 DOI: 10.1590/0001-37652301620140616] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/26/2015] [Indexed: 11/22/2022] Open
Abstract
We present here the physical mapping of the 5S rDNA locus in six wild and five cultivated taxa of Capsicum by means of a genus-specific FISH probe. In all taxa, a single 5S locus per haploid genome that persistently mapped onto the short arm of a unique metacentric chromosome pair at intercalar position, was found. 5S FISH signals of almost the same size and brightness intensity were observed in all the analyzed taxa. This is the first cytological characterization of the 5S in wild taxa of Capsicum by using a genus-derived probe, and the most exhaustive and comprehensive in the chili peppers up to now. The information provided here will aid the cytomolecular characterization of pepper germplasm to evaluate variability and can be instrumental to integrate physical, genetic and genomic maps already generated in the genus.
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Affiliation(s)
- Patricia M Aguilera
- Instituto de Biología Subtropical, Universidad Nacional de Misiones, Misiones, Argentina
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
| | - Marisel A Scaldaferro
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Dardo A Martí
- Instituto de Biología Subtropical, Universidad Nacional de Misiones, Misiones, Argentina
| | - Mauro Grabiele
- Instituto de Biología Subtropical, Universidad Nacional de Misiones, Misiones, Argentina
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9
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Cruz VP, Oliveira C, Foresti F. An intriguing model for 5S rDNA sequences dispersion in the genome of freshwater stingray Potamotrygon motoro (Chondrichthyes: Potamotrygonidae). Mol Biol 2015. [DOI: 10.1134/s0026893315030036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Jeong HJ, Kang JH, Zhao M, Kwon JK, Choi HS, Bae JH, Lee HA, Joung YH, Choi D, Kang BC. Tomato Male sterile 1035 is essential for pollen development and meiosis in anthers. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6693-709. [PMID: 25262227 PMCID: PMC4246194 DOI: 10.1093/jxb/eru389] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Male fertility in flowering plants depends on proper cellular differentiation in anthers. Meiosis and tapetum development are particularly important processes in pollen production. In this study, we showed that the tomato male sterile (ms10(35)) mutant of cultivated tomato (Solanum lycopersicum) exhibited dysfunctional meiosis and an abnormal tapetum during anther development, resulting in no pollen production. We demonstrated that Ms10(35) encodes a basic helix-loop-helix transcription factor that is specifically expressed in meiocyte and tapetal tissue from pre-meiotic to tetrad stages. Transgenic expression of the Ms10(35) gene from its native promoter complemented the male sterility of the ms10(35) mutant. In addition, RNA-sequencing-based transcriptome analysis revealed that Ms10(35) regulates 246 genes involved in anther development processes such as meiosis, tapetum development, cell-wall degradation, pollen wall formation, transport, and lipid metabolism. Our results indicate that Ms10(35) plays key roles in regulating both meiosis and programmed cell death of the tapetum during microsporogenesis.
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Affiliation(s)
- Hee-Jin Jeong
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Jin-Ho Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Meiai Zhao
- College of Life Science, Qingdao Agricultural University, Qingdao 266-109, PR China
| | - Jin-Kyung Kwon
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Hak-Soon Choi
- National Institute of Horticultural and Herbal Science, Suwon 440-310, Republic of Korea
| | - Jung Hwan Bae
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Hyun-Ah Lee
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Young-Hee Joung
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Doil Choi
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Science, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, College of Agricultural Sciences, Seoul National University, 599 Gwanak-ro Gwank-gu, Seoul 151-921, Republic of Korea
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Lu FH, Kwon SW, Yoon MY, Kim KT, Cho MC, Yoon MK, Park YJ. SNP marker integration and QTL analysis of 12 agronomic and morphological traits in F₈ RILs of pepper (Capsicum annuum L.). Mol Cells 2012; 34:25-34. [PMID: 22684870 PMCID: PMC3887781 DOI: 10.1007/s10059-012-0018-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 01/05/2023] Open
Abstract
Red pepper, Capsicum annuum L., has been attracting geneticists' and breeders' attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family.
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Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Soon-Wook Kwon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
| | - Min-Young Yoon
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
| | - Ki-Taek Kim
- The Foundation of Agricultural Technology Commercialization and Transfer, Suwon 441-100,
Korea
| | - Myeong-Cheoul Cho
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Moo-Kyung Yoon
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Suwon 441-440,
Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-702,
Korea
- Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan 340-702,
Korea
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12
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Andrade-Souza V, Costa MGC, Chen CX, Gmitter FG, Costa MA. Physical location of the carotenoid biosynthesis genes Psy and β-Lcy in Capsicum annuum (Solanaceae) using heterologous probes from Citrus sinensis (Rutaceae). GENETICS AND MOLECULAR RESEARCH 2011; 10:404-9. [PMID: 21425090 DOI: 10.4238/vol10-1gmr1025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Carotenoids are responsible for a range of fruit colors in different hot pepper (Capsicum) varieties, from white to deep red. Color traits are genetically determined by three loci, Y, C1, and C2, which are associated with carotenogenic genes. Although such genes have been localized on genetic maps of Capsicum and anchored in Lycopersicon and Solanum, physical mapping in Capsicum has been restricted to only a few clusters of some multiple copy genes. Heterologous probes from single copy genes have been rarely used. Fluorescent in situ hybridization was performed in Capsicum annuum varieties with different fruit colors, using heterologous probes of Psy and β-Lcy genes obtained from a BAC library of the sweet orange (Citrus sinensis). The probes hybridized in the terminal portion of a chromosome pair, confirming the location of these genes in genetic maps. The hybridized segments showed variation in size in both chromosomes.
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Affiliation(s)
- V Andrade-Souza
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brasil
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13
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Park M, Jo S, Kwon JK, Park J, Ahn JH, Kim S, Lee YH, Yang TJ, Hur CG, Kang BC, Kim BD, Choi D. Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements. BMC Genomics 2011; 12:85. [PMID: 21276256 PMCID: PMC3042944 DOI: 10.1186/1471-2164-12-85] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Accepted: 01/29/2011] [Indexed: 11/23/2022] Open
Abstract
Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.
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Affiliation(s)
- Minkyu Park
- Interdisciplinary Program in Agriculture Biotechnology, Seoul National University, Seoul 151-921, Korea
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14
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Chromosomal localization of rDNA genes and genomic organization of 5S rDNA in Oreochromis mossambicus, O. urolepis hornorum and their hybrid. J Genet 2010; 89:163-71. [PMID: 20861567 DOI: 10.1007/s12041-010-0022-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this study, classical and molecular cytogenetic analyses were performed in tilapia fishes, Oreochromis mossambicus (XX/XY sex determination system), O. urolepis hornorum (WZ/ZZ sex determination system) and their hybrid by crossing O. mossambicus female x O. u. hornorum male. An identical karyotype ((2n = 44, NF (total number of chromosomal arms) = 50) was obtained from three examined tilapia samples. Genomic organization analysis of 5S rDNA revealed two different types of 5S rDNA sequences, 5S type I and 5S type II. Moreover, fluorescence in situ hybridization (FISH) with 5S rDNA probes showed six positive fluorescence signals on six chromosomes of all the analysed metaphases from the three tilapia samples. Subsequently, 45S rDNA probes were also prepared, and six positive fluorescence signals were observed on three chromosome pairs in all analysed metaphases of the three tilapia samples. The correlation between 45 rDNA localization and nucleolar organizer regions (NORs) was confirmed by silver nitrate staining in tilapia fishes. Further, different chromosomal localizations of 5S rDNA and 45S rDNA were verified by two different colour FISH probes. Briefly, the current data provide an insights for hybridization projects and breeding improvement of tilapias.
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da Silva CRM, Quintas CC, Vanzela ALL. Distribution of 45S and 5S rDNA sites in 23 species of Eleocharis (Cyperaceae). Genetica 2010; 138:951-7. [PMID: 20680404 DOI: 10.1007/s10709-010-9477-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
Studies of rDNA location in holocentric chromosomes of the Cyperaceae are scarce, but a few reports have indicated the occurrence of multiple 45S rDNA sites at terminal positions, and in the decondensed state of these regions in prometaphase/metaphase. To extend our knowledge of the number 45S and 5S rDNA sites and distribution in holocentric chromosomes of the Cyperaceae, 23 Brazilian species of Eleocharis were studied. FISH showed 45S rDNA signals always located in terminal regions, which varied from two (E. bonariensis with 2n = 20) to ten (E. flavescens with 2n = 10 and E. laeviglumis with 2n = 60). 5S rDNA showed less variation, with 16 species exhibiting two sites and 7 species four sites, preferentially at terminal positions, except for four species (E. subarticulata, E. flavescens, E. sellowiana and E. geniculata) that showed interstitial sites. The results are discussed in order to understand the predominance of terminal rDNA sites, the mechanisms involved in the interstitial positioning of 5S rDNA sites in some species, and the events of amplification and dispersion of 45S rDNA terminal sites.
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16
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Kang WH, Hoang NH, Yang HB, Kwon JK, Jo SH, Seo JK, Kim KH, Choi D, Kang BC. Molecular mapping and characterization of a single dominant gene controlling CMV resistance in peppers (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1587-96. [PMID: 20180096 DOI: 10.1007/s00122-010-1278-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2009] [Accepted: 01/19/2010] [Indexed: 05/24/2023]
Abstract
Cucumber mosaic virus (CMV) is one of the most destructive viruses in the Solanaceae family. Simple inheritance of CMV resistance in peppers has not previously been documented; all previous studies have reported that resistance to this virus is mediated by several partially dominant and recessive genes. In this study, we showed that the Capsicum annuum cultivar 'Bukang' contains a single dominant resistance gene against CMV(Korean) and CMV(FNY) strains. We named this resistance gene Cmr1 (Cucumber mosaic resistance 1). Analysis of the cellular localization of CMV using a CMV green fluorescent protein construct showed that in 'Bukang,' systemic movement of the virus from the epidermal cell layer to mesophyll cells is inhibited. Genetic mapping and FISH analysis revealed that the Cmr1 gene is located at the centromeric region of LG2, a position syntenic to the ToMV resistance locus (Tm-1) in tomatoes. Three SNP markers were developed by comparative genetic mapping: one intron-based marker using a pepper homolog of Tm-1, and two SNP markers using tomato and pepper BAC sequences mapped near Cmr1. We expect that the SNP markers developed in this study will be useful for developing CMV-resistant cultivars and for fine mapping the Cmr1 gene.
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Affiliation(s)
- Won-Hee Kang
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-921, Korea
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17
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Kim HJ, Han JH, Kwon JK, Park M, Kim BD, Choi D. Fine mapping of pepper trichome locus 1 controlling trichome formation in Capsicum annuum L. CM334. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1099-106. [PMID: 20033390 DOI: 10.1007/s00122-009-1237-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 11/30/2009] [Indexed: 05/09/2023]
Abstract
Trichomes are present on nearly all land plants and protect plants against insect herbivores, drought and UV radiation. The trichome-bearing phenotype is conferred by the dominant allele of the pepper trichome locus 1 (Ptl1) in Capsicum annuum, Mexican 'Criollo de Morelos-334' (CM334). A genetic analysis using simple sequence repeats from pepper cDNA identified the HpmsE031 marker as tightly linked to Ptl1 in 653 individuals of an F(2) population derived from a cross between CM334 and Chilsungcho varieties. A bacterial artificial chromosome (BAC) library from CM334 covering 12x of the genome was screened using the HpmsE031 SSR marker as a probe and three BAC clones were identified. The Ptl1 region was covered by one 80 kb BAC clone, TT1B7. Fluorescence in situ hybridization (FISH) confirmed that TT1B7 localized to pepper chromosome 10. One co-dominant marker, Tco, and one dominant marker, Tsca, were successfully developed from the TT1B7 BAC sequence. Tco mapped 0.33 cM up from Ptl1 and Tsca mapped 0.75 cM down from Ptl1. Analysis of the BAC sequence predicts the presence of 14 open reading frames including 60S ribosomal protein L21-like protein (Solanum demissum), protein kinase 2 (Nicotiana tabacum), hypothetical proteins, and unnamed protein products. These results will provide not only useful information for map-based cloning of Ptl1 in Capsicum but also the starting points for analysis of R-gene cluster inked with Ptl1.
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Affiliation(s)
- Hyun Jung Kim
- Department of Plant Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, South Korea
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Garcia S, Garnatje T, Pellicer J, McArthur ED, Siljak-Yakovlev S, Vallès J. Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae). Genome 2009; 52:1012-24. [DOI: 10.1139/g09-077] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenus Tridentatae ( Artemisia , Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploid-polyploid species pairs. In addition, genome sizes and heterochromatin patterns were compared between these populations. The linked 5S and 35S rRNA genes are confirmed as characteristic for Artemisia, and a pattern at the diploid level of three rDNA loci located at telomeric positions proved to be typical. Loss of rDNA loci was observed in some polyploids, whereas others showed additivity with respect to their diploid relatives. Genome downsizing was observed in all polyploids. Banding patterns differed depending on the pair of species analysed, but some polyploid populations showed an increased number of heterochromatic bands. FISH and fluorochrome banding were useful in determining the systematic position of Artemisia bigelovii , for which a differential pattern was found as compared with the rest of the group. Additionally, FISH was used to detect the presence of the Arabidopsis-type telomere repeat for the first time in Artemisia.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Teresa Garnatje
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Jaume Pellicer
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - E. Durant McArthur
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Sonja Siljak-Yakovlev
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Joan Vallès
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
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