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Tasca S, Campos C, Lacerda D, Ortiz VD, Turck P, Bianchi SE, Castro ALD, Belló-Klein A, Bassani V, Araújo ASDR. Pterostilbeno Reduz o Estresse Oxidativo no Pulmão e no Ventrículo Direito Induzido por Infarto do Miocárdio Experimental. Arq Bras Cardiol 2022; 118:435-445. [PMID: 35262578 PMCID: PMC8856678 DOI: 10.36660/abc.20201155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
Fundamento O pterostilbeno (PS), um composto polifenólico natural e antioxidante, surge como uma intervenção promissora para minimizar danos do infarto agudo do miocárdio (IAM). Objetivo Este estudo teve como objetivo avaliar o desempenho do PS na promoção da homeostase redox nos pulmões e no ventrículo direito (VD) de animais infartados. Métodos Ratos Wistar machos (60 dias de idade) foram randomizados em três grupos: SHAM, IAM (infarto) e IAM+PS (IAM + pterostilbeno). Sete dias após o procedimento de IAM, os ratos foram tratados com PS (100 mg/kg/dia) por gavagem por oito dias. Os animais foram depois sacrificados e os pulmões e VD foram coletados para análise do balanço redox (diferenças foram consideradas significativas quando p<0,05). Resultados Nossos resultados mostram que o IAM desencadeia a interrupção redox no VD e nos pulmões, o que pode contribuir para danos induzido pelo IAM nesses órgãos. Consistentemente, o PS mitigou o estresse oxidativo e restaurou as defesas antioxidantes (Glutationa – GSH nos pulmões: SHAM = 0,79 ± 0,07; IAM = 0,67 ± 0,05; IAM + PS = 0,86 ± 0,14; p<0,05), indicando seu papel protetor neste cenário. Conclusão Nosso trabalho evidencia o potencial do uso de PS como abordagem terapêutica adjuvante após IAM para proteção dos tecidos pulmonares e cardíacos direitos.
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Lee J. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-319-97217-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Arjun K, Dhaliwal MS, Jindal SK, Fakrudin B. Mapping of fruit length related QTLs in interspecific cross ( Capsicum annuum L. × Capsicum galapagoense Hunz.) of chilli. BREEDING SCIENCE 2018; 68:219-226. [PMID: 29875605 PMCID: PMC5982179 DOI: 10.1270/jsbbs.17073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/24/2017] [Indexed: 06/08/2023]
Abstract
Fruit length in chilli is quantitatively inherited trait and selection based on phenotypic performance is tedious and time consuming. To detect QTLs determining fruit length in Capsicum spp., an interspecific F2 mapping population was developed from the cross of C. annuum L. cv. 'FL 201' with C. galapagoense Hunz. accession 'TC 07245'. Fruit length in this cross showed a quantitative inheritance with the population depicting a symmetric distribution in histogram. To map quantitative trait loci (QTLs) for fruit length 400 SSR markers were surveyed on the parental genotypes but only 28 markers were observed to be polymorphic indicating less genetic diversity between the two Capsicum species. Polymorphic markers were then analyzed in F2 population consisting of 210 plants and 24 of these markers were mapped on to three linkage groups (LGs): LG 1, LG 2 and LG 3. Two fruit length determining QTLs designated as paufl2.1 and paufl2.2 were identified and both the QTLs were mapped on to LG 2. The two QTLs together explained 21.78 per cent of the phenotypic variation. Apart from the two QTLs, positive alleles were detected in the small fruited parent 'TC 07245' which might be of potential use in chilli breeding programs.
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Affiliation(s)
- Konana Arjun
- Department of Vegetable Science, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Major S Dhaliwal
- Directorate of Research, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Salesh K Jindal
- Department of Vegetable Science, Punjab Agricultural University,
Ludhiana 141004,
India
| | - Bashasab Fakrudin
- Department of Biotechnology & Crop Improvement, University of Horticultural Sciences,
Bagalkot 587104,
India
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Li N, Yin Y, Wang F, Yao M. Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper ( Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:233-241. [PMID: 29875607 PMCID: PMC5982177 DOI: 10.1270/jsbbs.17063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/13/2017] [Indexed: 05/09/2023]
Abstract
Pepper (Capsicum) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance of 0.16 cM between adjacent markers. We used this map and the interval mapping (IM) and multiple QTL mapping (MQM) procedures to detect genetic regions associated with quantitative trait for CMV resistance. Three QTLs, qcmv11.1, qcmv11.2 and qcmv12.1, conferred resistance to CMV and showed trait variation of 10.2%, 19.2% and 7.3% respectively. Our results will help to develop markers linked to CMV-resistant QTLs to improve pepper resistance to CMV.
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Affiliation(s)
| | | | - Fei Wang
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
| | - Minghua Yao
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
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Maharijaya A, Vosman B, Steenhuis-Broers G, Pelgrom K, Purwito A, Visser RGF, Voorrips RE. QTL mapping of thrips resistance in pepper. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1945-56. [PMID: 26152569 PMCID: PMC4572063 DOI: 10.1007/s00122-015-2558-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 06/13/2015] [Indexed: 05/04/2023]
Abstract
A QTL for thrips resistance on pepper chromosome 6 was identified and validated. This QTL affects thrips larval development and explains 50% of the variation. Thrips is one of the most damaging pests in pepper (Capsicum). Resistance to thrips was identified in Capsicum annuum. This study was aimed at the elucidation of the genetic background of thrips resistance in Capsicum through QTL mapping. The QTL analysis was carried out for Frankliniella occidentalis resistance in an F2 population consisting of 196 plants derived from an interspecific cross between the highly resistant C. annuum AC 1979 as female parent and the highly susceptible C. chinense 4661 as male parent. Fifty-seven SSR, 109 AFLP, and 5 SNP markers were used to construct a genetic map with a total length of 1636 cM. Damage caused by larvae and the survival of first and second instar larval stages observed in a no-choice test were used as parameters of resistance. Interval mapping detected one QTL for each of these parameters, all co-localizing near the same marker on chromosome 6. Use of this marker as co-factor in a multiple-QTL mapping analysis failed to uncover any additional QTLs. This QTL explained about 50% of the genetic variation, and the resistance allele of this QTL was inherited from the resistant parent. Thrips resistance was not linked to trichome density.
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Affiliation(s)
- Awang Maharijaya
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
- Bogor Agricultural University, Jalan Raya Darmaga, 16680, Bogor, Indonesia
| | - Ben Vosman
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Greet Steenhuis-Broers
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Koen Pelgrom
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Agus Purwito
- Bogor Agricultural University, Jalan Raya Darmaga, 16680, Bogor, Indonesia
| | - Richard G F Visser
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Roeland E Voorrips
- Wageningen UR-Plant Breeding, Wageningen University and Research Center., P.O. Box 386, 6700 AJ, Wageningen, The Netherlands.
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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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Devran Z, Kahveci E, Özkaynak E, Studholme DJ, Tör M. Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:101. [PMID: 25798050 PMCID: PMC4361654 DOI: 10.1007/s11032-015-0294-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/06/2015] [Indexed: 05/13/2023]
Abstract
It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site-leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.
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Affiliation(s)
- Zübeyir Devran
- Department of Plant Protection, Faculty of Agriculture, University of Akdeniz, Antalya, Turkey
| | - Erdem Kahveci
- M.Y. Genetic Agriculture Technology Laboratory, Antalya, Turkey
| | - Ercan Özkaynak
- Yüksel Seed, Kurşunlu, Madenler Mahallesi, Antalya, Turkey
| | - David J. Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, EX4 4QD UK
| | - Mahmut Tör
- National Pollen and Aerobiology Research Unit (NPARU), The University of Worcester, Henwick Grove, Worcester, WR2 6 AJ UK
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Wahyuni Y, Stahl-Hermes V, Ballester AR, de Vos RCH, Voorrips RE, Maharijaya A, Molthoff J, Zamora MV, Sudarmonowati E, Arisi ACM, Bino RJ, Bovy AG. Genetic mapping of semi-polar metabolites in pepper fruits ( Capsicum sp.): towards unravelling the molecular regulation of flavonoid quantitative trait loci. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 33:503-518. [PMID: 24532977 PMCID: PMC3918126 DOI: 10.1007/s11032-013-9967-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 09/27/2013] [Indexed: 05/21/2023]
Abstract
Untargeted LCMS profiling of semi-polar metabolites followed by metabolite quantitative trait locus (mQTL) analysis was performed in ripe pepper fruits of 113 F2 plants derived from a cross between Capsicum annuum AC1979 (no. 19) and Capsicum chinense No. 4661 Selection (no. 18). The parental accessions were selected based on their variation in fruit morphological characteristics and fruit content of some target phytonutrients. Clear segregation of fruit colour and fruit metabolite profiles was observed in the F2 population. The F2 plants formed three clusters based on their metabolite profiles. Of the total of 542 metabolites, 52 could be annotated, including a range of flavonoids, such as flavone C-glycosides, flavonol O-glycosides and naringenin chalcone, as well as several phenylpropanoids, a capsaicin analogue, fatty acid derivatives and amino acid derivatives. Interval mapping revealed 279 mQTLs in total. Two mQTL hotspots were found on chromosome 9. These two chromosomal regions regulated the relative levels of 35 and 103 metabolites, respectively. Analysis also revealed an mQTL for a capsaicin analogue, located on chromosome 7. Confirmation of flavonoid mQTLs using a set of six flavonoid candidate gene markers and their corresponding expression data (expression QTLs) indicated the Ca-MYB12 transcription factor gene on chromosome 1 and the gene encoding flavone synthase (FS-2) on chromosome 6 as likely causative genes determining the variation in naringenin chalcone and flavone C-glycosides, respectively, in this population. The combination of large-scale metabolite profiling and QTL analysis provided valuable insight into the genomic regions and genes important for the production of (secondary) metabolites in pepper fruit. This will impact breeding strategies aimed at optimising the content of specific metabolites in pepper fruit.
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Affiliation(s)
- Yuni Wahyuni
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia
| | - Vanessa Stahl-Hermes
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Present Address: Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, Florianópolis, SC 88034-001 Brazil
| | - Ana-Rosa Ballester
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Present Address: Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Agustín Escardino 7, 46980 Paterna, Valencia Spain
| | - Ric C. H. de Vos
- Plant Research International, 6700 AA Wageningen, The Netherlands
- Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | | | - Awang Maharijaya
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Present Address: Bogor Agricultural University, Jl. Raya Darmaga, 16680 Bogor, Indonesia
| | - Jos Molthoff
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
| | | | - Enny Sudarmonowati
- Research Centre for Biotechnology, Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong, Bogor, 16910 Indonesia
| | - Ana Carolina Maisonnave Arisi
- Present Address: Departamento de Ciência e Tecnologia de Alimentos, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346, Florianópolis, SC 88034-001 Brazil
| | - Raoul J. Bino
- Laboratory of Plant Physiology, Wageningen University, 6700 AR Wageningen, The Netherlands
| | - Arnaud G. Bovy
- Wageningen UR Plant Breeding, 6708 PB Wageningen, The Netherlands
- Plant Research International, 6700 AA Wageningen, The Netherlands
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9
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Ahn YK, Tripathi S, Cho YI, Kim JH, Lee HE, Kim DS, Woo JG, Cho MC. De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213. BOTANICAL STUDIES 2013; 54:58. [PMID: 28510893 PMCID: PMC5430321 DOI: 10.1186/1999-3110-54-58] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/02/2013] [Indexed: 05/31/2023]
Abstract
BACKGROUND Pepper, Capsicum annuum L., Solanaceae, is a major staple economically important vegetable crop worldwide. Limited functional genomics resources and whole genome association studies could be substantially improved through the application of molecular approach for the characterization of gene content and identification of molecular markers. The massive parallel pyrosequencing of two pepper varieties, the highly pungent, Saengryeg 211, and the non-pungent, Saengryeg 213, including de novo transcriptome assembly, functional annotation, and in silico discovery of potential molecular markers is described. We performed 454 GS-FLX Titanium sequencing of polyA-selected and normalized cDNA libraries generated from a single pool of transcripts obtained from mature fruits of two pepper varieties. RESULTS A single 454 pyrosequencing run generated 361,671 and 274,269 reads totaling 164.49 and 124.60 Mb of sequence data (average read length of 454 nucleotides), which assembled into 23,821 and 17,813 isotigs and 18,147 and 15,129 singletons for both varieties, respectively. These reads were organized into 20,352 and 15,781 'isogroups' for both varieties. Assembled sequences were functionally annotated based on homology to genes in multiple public databases and assigned with Gene Ontology (GO) terms. Sequence variants analyses identified a total of 3,766 and 2,431 potential (Simple Sequence Repeat) SSR motifs for microsatellite analysis for both varieties, where trinucleotide was the most common repeat unit (84%), followed by di (9.9%), hexa (4.1%) and pentanucleotide repeats (2.1%). GAA repeat (8.6%) was the most frequent repeat motif, followed by TGG (7.2%), TTC (6.5%), and CAG (6.2%). CONCLUSIONS High-throughput transcriptome assembly, annotation and large scale of SSR marker discovery has been achieved using next generation sequencing (NGS) of two pepper varieties. These valuable informations for functional genomics resource shall help to further improve the pepper breeding efforts with respect to genetic linkage maps, QTL mapping and marker-assisted trait selection.
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Affiliation(s)
- Yul-Kyun Ahn
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Swati Tripathi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Young-Il Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Jeong-Ho Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Jong-Gyu Woo
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
| | - Myeong-Cheoul Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, 440-706 Republic of Korea
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Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery. Gene 2013; 533:494-9. [PMID: 24125952 DOI: 10.1016/j.gene.2013.09.095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 09/26/2013] [Indexed: 11/22/2022]
Abstract
Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.
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11
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Transmission ratio distortion in an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0066-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Liu S, Li W, Wu Y, Chen C, Lei J. De novo transcriptome assembly in chili pepper (Capsicum frutescens) to identify genes involved in the biosynthesis of capsaicinoids. PLoS One 2013; 8:e48156. [PMID: 23349661 PMCID: PMC3551913 DOI: 10.1371/journal.pone.0048156] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 09/21/2012] [Indexed: 12/04/2022] Open
Abstract
The capsaicinoids are a group of compounds produced by chili pepper fruits and are used widely in many fields, especially in medical purposes. The capsaicinoid biosynthetic pathway has not yet been established clearly. To understand more knowledge in biosynthesis of capsaicinoids, we applied RNA-seq for the mixture of placenta and pericarp of pungent pepper (Capsicum frutescens L.). We have assessed the effect of various assembly parameters using different assembly software, and obtained one of the best strategies for de novo assembly of transcriptome data. We obtained a total 54,045 high-quality unigenes (transcripts) using Trinity software. About 92.65% of unigenes showed similarity to the public protein sequences, genome of potato and tomato and pepper (C. annuum) ESTs databases. Our results predicted 3 new structural genes (DHAD, TD, PAT), which filled gaps of the capsaicinoid biosynthetic pathway predicted by Mazourek, and revealed new candidate genes involved in capsaicinoid biosynthesis based on KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. A significant number of SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) markers were predicted in C. frutescens and C. annuum sequences, which will be helpful in the identification of polymorphisms within chili pepper populations. These data will provide new insights to the pathway of capsaicinoid biosynthesis and subsequent research of chili peppers. In addition, our strategy of de novo transcriptome assembly is applicable to a wide range of similar studies.
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Affiliation(s)
- Shaoqun Liu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wanshun Li
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yimin Wu
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jianjun Lei
- College of Horticulture, South China Agricultural University, Guangzhou, China
- * E-mail:
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13
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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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Yoo SY, Cho NS, Park MJ, Seong KM, Hwang JH, Song SB, Han MS, Lee WT, Chung KW. A large population genetic study of 15 autosomal short tandem repeat loci for establishment of Korean DNA profile database. Mol Cells 2011; 32:15-9. [PMID: 21597912 PMCID: PMC3887661 DOI: 10.1007/s10059-011-2288-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 03/31/2011] [Accepted: 04/26/2011] [Indexed: 10/18/2022] Open
Abstract
Genotyping of highly polymorphic short tandem repeat (STR) markers is widely used for the genetic identification of individuals in forensic DNA analyses and in paternity disputes. The National DNA Profile Databank recently established by the DNA Identification Act in Korea contains the computerized STR DNA profiles of individuals convicted of crimes. For the establishment of a large autosomal STR loci population database, 1805 samples were obtained at random from Korean individuals and 15 autosomal STR markers were analyzed using the AmpFlSTR Identifiler PCR Amplification kit. For the 15 autosomal STR markers, no deviations from the Hardy-Weinberg equilibrium were observed. The most informative locus in our data set was the D2S1338 with a discrimination power of 0.9699. The combined matching probability was 1.521 × 10(-17). This large STR profile dataset including atypical alleles will be important for the establishment of the Korean DNA database and for forensic applications.
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Affiliation(s)
- Seong Yeon Yoo
- Department of Forensic Medicine, Central District Office, National Forensic Service, Daejeon 305-348, Korea
- Department of Biological Science and Department of Bioinformatics, Kongju National University, Gongju 314-701, Korea
- These authors contributed equally to this work
| | - Nam Soo Cho
- Department of Forensic Medicine, Central District Office, National Forensic Service, Daejeon 305-348, Korea
- These authors contributed equally to this work
| | - Myung Jin Park
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Ki Min Seong
- Department of Forensic Medicine, Central District Office, National Forensic Service, Daejeon 305-348, Korea
- Department of Biological Science and Department of Bioinformatics, Kongju National University, Gongju 314-701, Korea
| | - Jung Ho Hwang
- Department of Forensic Medicine, Central District Office, National Forensic Service, Daejeon 305-348, Korea
| | - Seok Bean Song
- Institute of Drug Research and Development, College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea
| | - Myun Soo Han
- DNA Analysis Center, National Forensic Service, Seoul 158-707, Korea
| | - Won Tae Lee
- Department of Forensic Medicine, Eulji University, Daejeon 301-746, Korea
| | - Ki Wha Chung
- Department of Biological Science and Department of Bioinformatics, Kongju National University, Gongju 314-701, Korea
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Lu FH, Cho MC, Park YJ. Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68. Mol Biol Rep 2011; 39:3327-35. [PMID: 21706160 DOI: 10.1007/s11033-011-1102-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Accepted: 06/15/2011] [Indexed: 12/01/2022]
Abstract
Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research.
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Affiliation(s)
- Fu-Hao Lu
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 340-802, Republic of Korea
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16
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Li X, Ramchiary N, Choi SR, Van Nguyen D, Hossain MJ, Yang HK, Lim YP. Development of a high density integrated reference genetic linkage map for the multinational Brassica rapa Genome Sequencing Project. Genome 2011; 53:939-47. [PMID: 21076509 DOI: 10.1139/g10-054] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2 lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.
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Affiliation(s)
- Xiaonan Li
- Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305 764, Republic of Korea
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17
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Kim HJ, Han JH, Kim S, Lee HR, Shin JS, Kim JH, Cho J, Kim YH, Lee HJ, Kim BD, Choi D. Trichome density of main stem is tightly linked to PepMoV resistance in chili pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:1051-1058. [PMID: 21184049 DOI: 10.1007/s00122-010-1510-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 12/04/2010] [Indexed: 05/30/2023]
Abstract
A relationship between pepper trichome and pepper mottle virus (PepMoV) resistance was examined. In an intraspecific F(2) mapping population from the cross between Capsicum annuum CM334 (trichome-bearing and PepMoV resistant) and Chilsungcho (glabrous and PepMoV susceptible), major QTLs for both traits were identified by composite interval mapping in linkage group (LG) 24 corresponding a telomere region on pepper chromosome 10. Ptel1 of putative trichome enhancing locus was a common major QTL for trichome density on the main stem and calyx. Ptel1 apart from HpmsE031 at a 1.03 cM interval was specifically associated to the trichome density on the main stem, whereas Ptel2 near m104 marker on LG2 was specific for the calyx trichome. Epistatic analysis indicated that Ptel1 engaged in controlling the trichome density by mutual interactions with the organ-specific QTLs. For PepMoV resistance, two QTLs (Pep1 and Pep2) were identified on the LG 24. Pep1 was located with Ptel1 in the R-gene cluster (RGC) for potyvirus resistance including Pvr4 with broad spectrum resistance to potyviruses. Pep1 flanking TG420 marker seemed to be the major factors determining correlation with PepMoV resistance. These results indicate that the level of trichome density on pepper main stem can be used as a morphological marker for Pvr4 in pepper breeding.
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Affiliation(s)
- Hyun Jung Kim
- Department of Plant Sciences and Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
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18
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Lee J, Hong JH, Do JW, Yoon JB. Identification of QTLs for resistance to anthracnose to two Colletotrichum species in pepper. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/s12892-010-0081-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley. Mol Genet Genomics 2010; 284:319-31. [DOI: 10.1007/s00438-010-0570-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 08/13/2010] [Indexed: 11/26/2022]
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20
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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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21
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Min WK, Kim S, Sung SK, Kim BD, Lee S. Allelic discrimination of the Restorer-of-fertility gene and its inheritance in peppers (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1289-1299. [PMID: 19727656 DOI: 10.1007/s00122-009-1134-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 08/03/2009] [Indexed: 05/28/2023]
Abstract
Cytoplasmic male sterility (CMS), one of the most important traits in crop breeding, is used for commercial F(1)-hybrid seed production in peppers (Capsicum annuum L.). A nuclear gene, Restorer-of-fertility (Rf), can induce normal pollen production in CMS plants resulting in fertility. Since the first report of fertility restoration in peppers, various inheritance modes have been suggested, including the presence of a third haplotype of the locus. The pepper Rf gene has not been cloned, and calculated genetic distances of linked markers have varied between research groups. A more precise allelic test and additional genetic mapping are needed to accurately select recombinants for use in marker-assisted backcrossing (MAB). Therefore, the reliability and application of these markers for allelic selection of the Rf gene was tested. Two different F(2) populations, Buja and Tamna, were used for the construction of a linkage map. From these linkage groups, anew closely linked flanking marker of the Rf gene were identified. Previous allelic testing revealed the existence of a third haplotype, Rfls(7701), which can function as dominant (Rf) or recessive (rf). In a previous report, Rfls(7701) was considered to be linked to unstable male sterility (MS). However, our results suggest that unstable MS was induced by a gene residing at another locus rather than by Rfls(7701) haplotype- linked allele.
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Affiliation(s)
- Woong-Ki Min
- Center for Agriculture and Life Science Research, Dongbu Advanced Research Institute, Dongbu HiTek Co., Ltd, Daejeon 305-708, Korea
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Kwon JK, Kim BD. Localization of 5S and 25S rRNA genes on somatic and meiotic chromosomes in Capsicum species of chili pepper. Mol Cells 2009; 27:205-9. [PMID: 19277503 DOI: 10.1007/s10059-009-0025-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 11/25/2008] [Accepted: 11/27/2008] [Indexed: 10/21/2022] Open
Abstract
The loci of the 5S and 45S rRNA genes were localized on chromosomes in five species of Capsicum, namely, annuum, chacoense, frutescens, baccatum, and chinense by FISH. The 5S rDNA was localized to the distal region of one chromosome in all species observed. The number of 45S rDNA loci varied among species; one in annuum, two in chacoense, frutescens, and chinense, and four in baccatum, with the exceptions that 'CM334' of annuum had three loci and 'tabasco' of frutescens had one locus. 'CM334'-derived BAC clones, 384B09 and 365P05, were screened with 5S rDNA as a probe, and BACs 278M03 and 262A23 were screened with 25S rDNA as a probe. Both ends of these BAC clones were sequenced. FISH with these BAC probes on pachytenes from 'CM334' plant showed one 5S rDNA locus and three 45S rDNA loci, consistent with the patterns on the somatic chromosomes. The 5S rDNA probe was also applied on extended DNA fibers to reveal that its coverage measured as long as 0.439 Mb in the pepper genome. FISH techniques applied on somatic and meiotic chromosomes and fibers have been established for chili to provide valuable information about the copy number variation of 45S rDNA and the actual physical size of the 5S rDNA in chili.
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MESH Headings
- Capsicum/classification
- Capsicum/genetics
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Plant/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- In Situ Hybridization, Fluorescence
- Karyotyping
- Meiosis/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
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Affiliation(s)
- Jin-Kyung Kwon
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea
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