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Capsicum chinense Türüne Ait Biber Popülasyonunun SSR Molekülerleri ile Karakterizasyonu

Year 2021, Volume: 31 Issue: 3, 722 - 732, 15.09.2021
https://doi.org/10.29133/yyutbd.928181

Abstract

Genetik kaynaklarının karakterizasyonu ve çeşitlilik düzeylerinin belirlenmesinde morfolojik tanımlayıcılar ve moleküler analiz yöntemlerinden yararlanılmaktadır. Capsicum chinense biber türü; meyve özellikleri yönünden yüksek düzeyde varyasyon göstermektedir. Bu çalışmada, Capsicum chinense türüne ait biber genetik kaynaklarının (83 genotip) SSR yöntemine göre moleküler karakterizasyonu ile tür içerisindeki mevcut popülasyondaki varyasyon düzeyi ve genetik çeşitlilik düzeylerinin saptanması amaçlanmıştır. Moleküler analizler sonucunda, incelenen 14 SSR primerinden toplam 115 bant elde edilmiştir. Yapılan değerlendirme sonucunda, bantların 66 tanesinin polimorfik (% 57.4) ve 49 tanesinin ise monomorfik (% 42.6) olduğu belirlenmiştir. Capsicum chinense türüne ait biber genotipleri, SSR markörleri ile yapılan moleküler analizler sonucunda Ağırlık atanmamış komşu birleştirme yöntemine göre üç farklı heterojen genetik gruba ayrılmıştır. Ayrıca, C. chinense türüne ait biber genotipleri arasında genetik uzaklık değerlerinin 0.15-0.75 arasında değiştiği bulunmuştur. Bu çalışma sonucunda karakterizasyonu yapılmış olan C. chinense türüne ait biber genotiplerinde halen seleksiyon ıslahı çalışmalarına devam edilmektedir.

Thanks

Bu araştırma, Kübra Taş’ın Ondokuz Mayıs Üniversitesi, Lisansüstü Eğitim Enstitüsü, Bahçe Bitkileri Ana Bilim Dalında tamamlanmış olan Yüksek Lisans tez çalışmasının bir kısmından üretilmiştir.

References

  • Acunalp, S. (2012). Ekonomik öneme sahip yerli kiraz (Prunus avium L.) genotiplerinin SSRs (Simple Sequence Repeats)’a dayalı genetik karakterizasyonu. Yüksek Lisans Tezi, Ankara Üniversitesi, Biyoteknoloji Enstitüsü, Ankara.
  • Baba, V.Y., Rocha, K. R., Gomes, G. P., de Fátima Ruas, C., Ruas, P. M., Rodrigues, R., & Gonçalves, L. S. A. (2016). Genetic diversity of Capsicum chinense accessions based on fruit morphological characterization and AFLP markers. Genetic resources and crop evolution, 63 (8), 1371-1381.
  • Balkaya, A., & Yanmaz, R. (2001). Bitki genetik kaynaklarının muhafaza imkanları ve tohum gen bankalarının çalışma sistemleri. Ekoloji Çevre Dergisi, 10(39), 25-30.
  • Barboza, G. E., Garcia, C. C., Gonzalez, S. L., Scaldaferro, M., & Reyes, X. (2019). Four new species of Capsicum (Solanaceae) from the tropical Andes and an update on the phylogeny of the genus. PloS one, 14 (1).
  • Bayraktar, K. (1970). Sebze Yetiştirme. Cilt II Kültür Sebzeleri. Ege Üniversitesi Ziraat Fakültesi Dergisi, 169- 479.
  • Baruah, J., Pandey, S. K., Sarmah, N., & Lal, M. (2019). Assessing molecular diversity among high capsaicin content lines of Capsicum chinense Jacq. using simple sequence repeat marker. Industrial Crops and Products, 141, 111769.
  • Bharath, S. M., Cilas, C., & Umaharan, P. (2013). Fruit trait variation in a caribbean germplasm collection of aromatic hot peppers (Capsicum chinense Jacq.). Hortscience, 48(5), 531-538.
  • Buso, G.S.C., Amaral, Z.P.S., Bianchetti, L.B.M., Flavia, R.B., & Ferreira, M.E. (2003). Genetic variability and phylogenetic analysis of Brazilian species of Capsicum.Capsicum and Eggplant Newsletter, 22, 13-16.
  • Conicella, C., Errico, A., & Saccardo, F. (1990). Cytogenetic and isozyme studies of wild and cultivated Capsicum annuum. Genome, 33, 279-282.
  • Erdinc, C., Turkmen, O., Demir, S., & Sensoy, S. (2017). Determination of the anthracnose (Colletotrichum lindemuthianum (Sacc. and Magn.) Lambs. Scrib.) resistance in some Turkish bean genotypes by artificial inoculation and molecular methods. JAPS, Journal of Animal and Plant Sciences, 27(1), 175-18.
  • Eshbaugh, W. H. (Vincent M. Russo) (2012). The taxonomy of the genus Capsicum. In: Peppers Botany, Production and Uses. CAB International, 14-28.
  • Fonseca, R. M., Lopes, R., Barros, W. S., Lopes, M. T. G., & Ferreira, F. M. (2008). Morphologic characterization and genetic diversity of Capsicum chinense Jacq. accesions along the upper Rio Negro-Amazonas. Embrapa Amazônia Ocidental-Artigo em periódico indexado (ALICE).
  • Geleta, N., Daba, C., & Gebeyehu, S. (2004). Determination of plant proportion and planting time in maize-climbing bean intercropping system. Proc. 10th Annual Conference of the Crop Science Society of Ethiopia, 176-182.
  • Geleta, L.F., Labuschagne, M.T., & Viljoen, C. D. (2005).Genetic variability in pepper (Capsicum annuum L.) estimated by morphological data and amplified fragment length polymorphism markers. Biodiversity and Conservation, 14, 2361-2375.
  • Greenleaf, W. H. (1986). Pepper breeding. Breeding vegetable crops. CAP International. The Cambridge University Press, United Kingdom, 76-82.
  • Hawkes, J.G. (1983). The diversity of crop plants. Harvard University Press, Cambridge, Massachusetts, 184.
  • Karaağaç, O. (2006). Bafra kırmızı biber gen kaynaklarının (Capsicum annuum var. conoides Mill.) karakterizasyonu ve değerlendirilmesi. Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü, Bahçe Bitkileri Anabilim Dalı, Yüksek Lisans Tezi, 129 s, Samsun.
  • Karaağaç, O., & Balkaya, A. (2010). Bafra kırmızı biber populasyonlarının [ Capsicum annuum L. var. conoides (Mill.) Irish] tanımlanması ve mevcut varyasyonun değerlendirilmesi. Anadolu Tarım Bilimleri Dergisi, 25(1), 10-20. Karaağaç, O., & Balkaya, A. (2017). Türkiye’de yerel sebze çeşitlerinin mevcut durumu ve ıslah programlarında değerlendirilmesi. TÜRKTOB, 23(6), 8-15.
  • Kim, S., Park, J., Yeom, S. I., Kim, Y. M., Seo, E., & Kim, K. T. (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol, 18, 210. https://doi.org/10.1186/s13059-017-1341-9
  • Lee, J. M., Nahm, S. H., Kim, Y. M., & Kim, B. D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theoretical and Applied Genetics, 108(4), 619-627.
  • Lee, S., Kim, S. Y., Chung, E., Joung, Y. H., Pai, H. S., Hur, C. G., & Choi, D. (2005). EST and microarray analyses of pathogen-responsive genes in hot pepper (Capsicum annuum L.) non-host resistance against soybean pustule pathogen (Xanthomonas axonopodis pv. glycines). Functional & integrative genomics, 4(3), 196-205.
  • Lefebvre, V., Palloix, A., & Rives, M. (1993). Nuclear RFLP between pepper cultivars (Capsicum annuum L.). Euphytica, 71, 189-199.
  • Lefebvre, V., Goffinet, B., Chauvet, J. C., Caromel, B., Signoret, P., Brand, R., & Palloix, A. (2001). Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theoretical and Applied Genetics, 102(5), 741-750.
  • Moreira, A. F. P., Ruas, P. M., Ruas, C. F., Baba, V. Y., Giordani, W., Arruda, I. M., & Gonçalves, L. S. A. (2018). Genetic diversity, population structure and genetic parameters of fruit traits in Capsicum chinense. Scientia Horticulturae, 236, 1-9.
  • Moscone, E. A., Scadalferro, M. A., & Gabriele, M. (2007).The evolution of chili peppers (Capsicum – Solanaceae): a cytogenetic perspective. Acta Horticulturae, 745, 137–169.
  • Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 70 (12), 3321-3323.
  • Okumuş, A., & Balkaya, A. (2007). Estimation of genetic diversity among Turkish kale populations (Brassica oleracea var. acephala L.) using RAPD markers. ISSN 1022-7954, Russian Journal of Genetics, 43(4), 409–413.
  • Ortiz, R., & Delgado, D. L. F. (1990). Utilization of descriptors for the characterization of lines of the genus Capsicum. Turrialba, 40(1), 112-118.
  • Park, M., Lee, J. H., Han, K., Jang, S., Han, J., Lim, J. H., ... & Kang, B. C. (2019). A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq. Theoretical and Applied Genetics, 132(2), 515-529.
  • Ramchiary, N., Kehie, M., Brahma, V., Kumaria, S., & Tandon, P. (2014). Application of genetics and genomics towards Capsicum translational research. Plant Biotechnol Reports, 8, 101-123.
  • Röder, M.S., Plaschke, P., Konig, S.U., Borner, A., Sorrells, M.E., Tanksley, S.D., & Ganal, M.W. (1995). Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics, 246, 327-333.
  • Şensoy, S., & Şahin, U. (2012). Farklı Sıhke yerel kavun genotipleri arasındaki genetik ilişkiler. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 22(3), 147-154.
  • Qin, C., Yu ,C., Shen, Y., Fang, X., Chen, L., & Min, J. (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl AcadSci USA, 111, 5135–5140. https://doi.org/10.1073/pnas.1400975111
  • Uncu, A. T. (2019). Genome-wide identification of simple sequence repeat (SSR) markers in Capsicum chinense Jacq. with high potential for use in pepper introgression breeding. Biologia, 74(2), 119-126.
  • Yi, G., Lee, J. M., Lee, S., Choi, D., & Kim, B. D. (2006). Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theoretical and Applied Genetics, 114(1), 113-130.
  • Yoon, B. J., Jang, C. D., Do, J.W., & Park, G.H. (2006). Over coming two postfertilisation genetic barriers in inter specific hybridization of anthracnose resistance. Breeding Science, 56, 31-38.
  • Zhang, X. M., Zhang, Z. H., Gu, X. Z., Mao, S. L., Li, X. X., Chadœuf, J., ... & Zhang, B. X. (2016). Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of integrative agriculture, 15(9), 1991-2001.
  • Zewdie, Y., & Zeven, A.C. (1997). Variation in Yugoslavian hot pepper (Capsicum annuum L.) Accessions. Euphytica, 97, 81-89.
  • Zhu, Z., Sun, B., Wei, J., Cai, W., Huang, Z., Chen, C., ... & Lei, J. (2019). Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Scientific reports, 9(1), 1-14.

Molecular Characterization of Capsicum chinense Populations with SSR markers

Year 2021, Volume: 31 Issue: 3, 722 - 732, 15.09.2021
https://doi.org/10.29133/yyutbd.928181

Abstract

Morphological descriptors and molecular analysis methods were used to identify plant genetic resources and determine genetic diversity levels. Capsicum chinense has a high variation in terms of fruit traits. In this study, it was aimed to identify the plant characteristics of 83 Capsicum chinense genotypes and to determine genetic diversity levels in the existing population within the species by SSR method. As a result of molecular analysis of genotypes of Capsicum chinense species, a total of 115 bands were obtained from 14 SSR markers. As a result of the evaluation, 66 of the bands were polymorphic (57.4%) and 49 were monomorphic (42.6%). As a result of analyses made with SSR markers in Capsicum chinense genotypes, it was divided into 3 heterotic main groups according to the Unweighted Neighbor-Joining method. Genetic distance values of C. chinense genotypes were found to vary between 0.15-0.75. It is planned to continue selection breeding studies in C. chinense genotypes, which have characterization with this study.

References

  • Acunalp, S. (2012). Ekonomik öneme sahip yerli kiraz (Prunus avium L.) genotiplerinin SSRs (Simple Sequence Repeats)’a dayalı genetik karakterizasyonu. Yüksek Lisans Tezi, Ankara Üniversitesi, Biyoteknoloji Enstitüsü, Ankara.
  • Baba, V.Y., Rocha, K. R., Gomes, G. P., de Fátima Ruas, C., Ruas, P. M., Rodrigues, R., & Gonçalves, L. S. A. (2016). Genetic diversity of Capsicum chinense accessions based on fruit morphological characterization and AFLP markers. Genetic resources and crop evolution, 63 (8), 1371-1381.
  • Balkaya, A., & Yanmaz, R. (2001). Bitki genetik kaynaklarının muhafaza imkanları ve tohum gen bankalarının çalışma sistemleri. Ekoloji Çevre Dergisi, 10(39), 25-30.
  • Barboza, G. E., Garcia, C. C., Gonzalez, S. L., Scaldaferro, M., & Reyes, X. (2019). Four new species of Capsicum (Solanaceae) from the tropical Andes and an update on the phylogeny of the genus. PloS one, 14 (1).
  • Bayraktar, K. (1970). Sebze Yetiştirme. Cilt II Kültür Sebzeleri. Ege Üniversitesi Ziraat Fakültesi Dergisi, 169- 479.
  • Baruah, J., Pandey, S. K., Sarmah, N., & Lal, M. (2019). Assessing molecular diversity among high capsaicin content lines of Capsicum chinense Jacq. using simple sequence repeat marker. Industrial Crops and Products, 141, 111769.
  • Bharath, S. M., Cilas, C., & Umaharan, P. (2013). Fruit trait variation in a caribbean germplasm collection of aromatic hot peppers (Capsicum chinense Jacq.). Hortscience, 48(5), 531-538.
  • Buso, G.S.C., Amaral, Z.P.S., Bianchetti, L.B.M., Flavia, R.B., & Ferreira, M.E. (2003). Genetic variability and phylogenetic analysis of Brazilian species of Capsicum.Capsicum and Eggplant Newsletter, 22, 13-16.
  • Conicella, C., Errico, A., & Saccardo, F. (1990). Cytogenetic and isozyme studies of wild and cultivated Capsicum annuum. Genome, 33, 279-282.
  • Erdinc, C., Turkmen, O., Demir, S., & Sensoy, S. (2017). Determination of the anthracnose (Colletotrichum lindemuthianum (Sacc. and Magn.) Lambs. Scrib.) resistance in some Turkish bean genotypes by artificial inoculation and molecular methods. JAPS, Journal of Animal and Plant Sciences, 27(1), 175-18.
  • Eshbaugh, W. H. (Vincent M. Russo) (2012). The taxonomy of the genus Capsicum. In: Peppers Botany, Production and Uses. CAB International, 14-28.
  • Fonseca, R. M., Lopes, R., Barros, W. S., Lopes, M. T. G., & Ferreira, F. M. (2008). Morphologic characterization and genetic diversity of Capsicum chinense Jacq. accesions along the upper Rio Negro-Amazonas. Embrapa Amazônia Ocidental-Artigo em periódico indexado (ALICE).
  • Geleta, N., Daba, C., & Gebeyehu, S. (2004). Determination of plant proportion and planting time in maize-climbing bean intercropping system. Proc. 10th Annual Conference of the Crop Science Society of Ethiopia, 176-182.
  • Geleta, L.F., Labuschagne, M.T., & Viljoen, C. D. (2005).Genetic variability in pepper (Capsicum annuum L.) estimated by morphological data and amplified fragment length polymorphism markers. Biodiversity and Conservation, 14, 2361-2375.
  • Greenleaf, W. H. (1986). Pepper breeding. Breeding vegetable crops. CAP International. The Cambridge University Press, United Kingdom, 76-82.
  • Hawkes, J.G. (1983). The diversity of crop plants. Harvard University Press, Cambridge, Massachusetts, 184.
  • Karaağaç, O. (2006). Bafra kırmızı biber gen kaynaklarının (Capsicum annuum var. conoides Mill.) karakterizasyonu ve değerlendirilmesi. Ondokuz Mayıs Üniversitesi, Fen Bilimleri Enstitüsü, Bahçe Bitkileri Anabilim Dalı, Yüksek Lisans Tezi, 129 s, Samsun.
  • Karaağaç, O., & Balkaya, A. (2010). Bafra kırmızı biber populasyonlarının [ Capsicum annuum L. var. conoides (Mill.) Irish] tanımlanması ve mevcut varyasyonun değerlendirilmesi. Anadolu Tarım Bilimleri Dergisi, 25(1), 10-20. Karaağaç, O., & Balkaya, A. (2017). Türkiye’de yerel sebze çeşitlerinin mevcut durumu ve ıslah programlarında değerlendirilmesi. TÜRKTOB, 23(6), 8-15.
  • Kim, S., Park, J., Yeom, S. I., Kim, Y. M., Seo, E., & Kim, K. T. (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol, 18, 210. https://doi.org/10.1186/s13059-017-1341-9
  • Lee, J. M., Nahm, S. H., Kim, Y. M., & Kim, B. D. (2004). Characterization and molecular genetic mapping of microsatellite loci in pepper. Theoretical and Applied Genetics, 108(4), 619-627.
  • Lee, S., Kim, S. Y., Chung, E., Joung, Y. H., Pai, H. S., Hur, C. G., & Choi, D. (2005). EST and microarray analyses of pathogen-responsive genes in hot pepper (Capsicum annuum L.) non-host resistance against soybean pustule pathogen (Xanthomonas axonopodis pv. glycines). Functional & integrative genomics, 4(3), 196-205.
  • Lefebvre, V., Palloix, A., & Rives, M. (1993). Nuclear RFLP between pepper cultivars (Capsicum annuum L.). Euphytica, 71, 189-199.
  • Lefebvre, V., Goffinet, B., Chauvet, J. C., Caromel, B., Signoret, P., Brand, R., & Palloix, A. (2001). Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data. Theoretical and Applied Genetics, 102(5), 741-750.
  • Moreira, A. F. P., Ruas, P. M., Ruas, C. F., Baba, V. Y., Giordani, W., Arruda, I. M., & Gonçalves, L. S. A. (2018). Genetic diversity, population structure and genetic parameters of fruit traits in Capsicum chinense. Scientia Horticulturae, 236, 1-9.
  • Moscone, E. A., Scadalferro, M. A., & Gabriele, M. (2007).The evolution of chili peppers (Capsicum – Solanaceae): a cytogenetic perspective. Acta Horticulturae, 745, 137–169.
  • Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences, 70 (12), 3321-3323.
  • Okumuş, A., & Balkaya, A. (2007). Estimation of genetic diversity among Turkish kale populations (Brassica oleracea var. acephala L.) using RAPD markers. ISSN 1022-7954, Russian Journal of Genetics, 43(4), 409–413.
  • Ortiz, R., & Delgado, D. L. F. (1990). Utilization of descriptors for the characterization of lines of the genus Capsicum. Turrialba, 40(1), 112-118.
  • Park, M., Lee, J. H., Han, K., Jang, S., Han, J., Lim, J. H., ... & Kang, B. C. (2019). A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq. Theoretical and Applied Genetics, 132(2), 515-529.
  • Ramchiary, N., Kehie, M., Brahma, V., Kumaria, S., & Tandon, P. (2014). Application of genetics and genomics towards Capsicum translational research. Plant Biotechnol Reports, 8, 101-123.
  • Röder, M.S., Plaschke, P., Konig, S.U., Borner, A., Sorrells, M.E., Tanksley, S.D., & Ganal, M.W. (1995). Abundance, variability and chromosomal location of microsatellites in wheat. Molecular and General Genetics, 246, 327-333.
  • Şensoy, S., & Şahin, U. (2012). Farklı Sıhke yerel kavun genotipleri arasındaki genetik ilişkiler. Yüzüncü Yıl Üniversitesi Tarım Bilimleri Dergisi, 22(3), 147-154.
  • Qin, C., Yu ,C., Shen, Y., Fang, X., Chen, L., & Min, J. (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl AcadSci USA, 111, 5135–5140. https://doi.org/10.1073/pnas.1400975111
  • Uncu, A. T. (2019). Genome-wide identification of simple sequence repeat (SSR) markers in Capsicum chinense Jacq. with high potential for use in pepper introgression breeding. Biologia, 74(2), 119-126.
  • Yi, G., Lee, J. M., Lee, S., Choi, D., & Kim, B. D. (2006). Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theoretical and Applied Genetics, 114(1), 113-130.
  • Yoon, B. J., Jang, C. D., Do, J.W., & Park, G.H. (2006). Over coming two postfertilisation genetic barriers in inter specific hybridization of anthracnose resistance. Breeding Science, 56, 31-38.
  • Zhang, X. M., Zhang, Z. H., Gu, X. Z., Mao, S. L., Li, X. X., Chadœuf, J., ... & Zhang, B. X. (2016). Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of integrative agriculture, 15(9), 1991-2001.
  • Zewdie, Y., & Zeven, A.C. (1997). Variation in Yugoslavian hot pepper (Capsicum annuum L.) Accessions. Euphytica, 97, 81-89.
  • Zhu, Z., Sun, B., Wei, J., Cai, W., Huang, Z., Chen, C., ... & Lei, J. (2019). Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Scientific reports, 9(1), 1-14.
There are 39 citations in total.

Details

Primary Language Turkish
Subjects Horticultural Production
Journal Section Articles
Authors

Kübra Taş 0000-0003-2859-1212

Ahmet Balkaya 0000-0001-9114-615X

Ali Tevfik Uncu 0000-0003-4729-5750

Publication Date September 15, 2021
Acceptance Date July 31, 2021
Published in Issue Year 2021 Volume: 31 Issue: 3

Cite

APA Taş, K., Balkaya, A., & Uncu, A. T. (2021). Capsicum chinense Türüne Ait Biber Popülasyonunun SSR Molekülerleri ile Karakterizasyonu. Yuzuncu Yıl University Journal of Agricultural Sciences, 31(3), 722-732. https://doi.org/10.29133/yyutbd.928181
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Yuzuncu Yil University Journal of Agricultural Sciences by Van Yuzuncu Yil University Faculty of Agriculture is licensed under a Creative Commons Attribution 4.0 International License.