Genetic Diversity and Phylogenetic Analyses of Turkish Cotton (Gossypium hirsutum L.) Lines using ISSR Markers and Chloroplast trnL-F Regions

References

• Aboukhalid, K., N. Machon, J. Lambourdière, J. Abdelkrim, M. Bakha, A. Douaik, … C. Al Faiz. 2017. Analysis of genetic diversity and population structure of the endangered Origanum compactum from Morocco, using SSR markers: Implication for conservation. Biological Conservation 212:172–82. doi:https://doi.org/10.1016/j.biocon.2017.05.030.
   Google Scholar
• Adhikari, S., S. Saha, A. Biswas, T. S. Rana, T. K. Bandyopadhyay, and P. Ghosh. 2017. Application of molecular markers in plant genome analysis: A review. The Nucleus 60 (3):283–97. doi:https://doi.org/10.1007/s13237-017-0214-7.
   Google Scholar
• Ahmed, M. M., H. Guo, C. Huang, X. Zhang, and Z. Lin. 2013. Selection of core SSR markers for fingerprinting upland cotton cultivars and hybrids. Australian Journal of Crop Science 7 (12):1912.
   Google Scholar
• Ali, I., N. U. Khan, S. Gul, S. U. Khan, Z. Bibi, K. Aslam, … S. Ahmed. 2019. Genetic diversity and population structure analysis in Upland cotton Germplasm. International Journal of Agriculture and Biology 22 (4):669–76.
   Web of Science ®Google Scholar
• Altenbuchner, C., S. Vogel, and M. Larcher. 2018. Social, economic and environmental impacts of organic cotton production on the livelihood of smallholder farmers in Odisha, India. Renewable Agriculture and Food Systems 33 (4):373–85. doi:https://doi.org/10.1017/S174217051700014X.
   Google Scholar
• Andérica, E. P., F. R. Montero, M. L. García, and J. G. Ligero. 2018. Genetic diversity and phylogenetic relationships of a potential cotton collection for European breeding research. Turkish Journal of Botany 42 (2):172–82. doi:https://doi.org/10.3906/bot-1706-18.
   Google Scholar
• Anderson, D. M., and K. Rajasekaran. 2016. The global importance of transgenic cotton. In: Ramawa, K., Ahuja, M. (eds). Fiber plants, 17–33. Cham: Springer.
   Google Scholar
• Basal, H., E. Karademir, H. K. Goren, V. Sezener, M. N. Dogan, I. Gencsoylu, and O. Erdogan. 2019. Cotton production in Turkey and Europe. In: Jabran, K., Chauhan, B. S. (eds). Cotton Production 297–321. Wiley Online Library.
   Google Scholar
• Bilval, B. B., K. V. Vadodariya, B. K. Rajkumar, and G. R. Lahane. 2017. Genetic diversity of parents using RAPD, ISSR and SSR molecular markers in upland cotton (Gossypium hirsutum L.). Bull Environment Pharm Life Sci 6:51–57.
   Google Scholar
• Brück, W. F. 1980. Türkische Baumwollwirtschaft. tr. C. Issawi. 242–46. Chicago: The economic history of Turkey. Türk Ziraat Tarihi 129-135.
   Google Scholar
• Chen, J., S. Glémin, and M. Lascoux. 2017. Genetic diversity and the efficacy of purifying selection across plant and animal species. Molecular Biology and Evolution 34 (6):1417–28. doi:https://doi.org/10.1093/molbev/msx088.
   PubMedGoogle Scholar
• Chohan, S., R. Perveen, M. Abid, M. N. Tahir, and M. Sajid. 2020. Cotton diseases and their management. In: Ahmad, S., Hasanuzzaman, M. (eds). Cotton production and uses, 239–70. Singapore: Springer.
   Google Scholar
• Doyle, J. J., and J. L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus 12:13–15.
   Google Scholar
• Elci, E., Y. Akiscan, and B. Akgol. 2014. Genetic diversity of Turkish commercial cotton varieties revealed by molecular markers and fiber quality traits. Turkish Journal of Botany 38 (6):1274–86. doi:https://doi.org/10.3906/bot-1405-78.
   Google Scholar
• Ellegren, H., and N. Galtier. 2016. Determinants of genetic diversity. Nature Reviews. Genetics 17 (7):422. doi:https://doi.org/10.1038/nrg.2016.58.
   PubMed Web of Science ®Google Scholar
• Fidan, M., M. E. Erez, B. İnal, S. M. Pınar, and S. Altıntaş. 2018. Antioxidant capacity and phylogenetic analysis of twenty native grape cultivars in Siirt province, Turkey. Cellular and Molecular Biology 64 (7):14–18. doi:https://doi.org/10.14715/cmb/2018.64.7.3.
   PubMedGoogle Scholar
• Filiz, E., M. E. Uras, I. I. Ozyigit, U. Sen, and H. Gungor. 2018. Genetic diversity and phylogenetic analyses of Turkish rice varieties revealed by ISSR markers and chloroplast trnl-F region. FEB-Fresenius Environmental Bulletin 27(12) 8351-8358.
   Web of Science ®Google Scholar
• Filiz, E., S. Birbilener, I. I. Ozyigit, S. Kulac, and F. C. Sakinoglu Oruc. 2015. Assessment of genetic variations of silver lime (Tilia tomentosa Moench.) by RAPD markers in urban and forest ecosystems. Biotechnology & Biotechnological Equipment 29 (4):631–36. doi:https://doi.org/10.1080/13102818.2015.1042049.
   Web of Science ®Google Scholar
• Fitmawati and A. Hartana. 2010. Phylogenetic study of Mangifera laurina and its related species using cpDNA trnL-F spacer markers. HAYATI Journal of Biosciences 17 (1):9–14. doi:https://doi.org/10.4308/hjb.17.1.9.
   Google Scholar
• Gao, W., L. Long, X. Tian, J. Jin, H. Liu, H. Zhang, … C. Song. 2016. Genome-wide identification and expression analysis of stress-associated proteins (SAPs) containing A20/AN1 zinc finger in cotton. Molecular Genetics and Genomics 291 (6):2199–213. doi:https://doi.org/10.1007/s00438-016-1252-6.
   PubMedGoogle Scholar
• Ghuge, S. B., S. S. Mehetre, V. P. Chimote, B. D. Pawar, and R. M. Naik. 2018. Molecular characterisation of cotton genotypes using SSR, ISSR and RAPD markers in relation to fiber quality traits. Journal of Cotton Research and Development 32 (1):1–12.
   Google Scholar
• Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series, Vol. 41, No. 41, 95–98. London: Information Retrieval Ltd. c1979-c2000.
   Google Scholar
• Hapsari, L., R. Azrianingsih, and E. L. Arumingtyas. 2018. Genetic variability and relationship of banana cultivars (Musa L.) from East Java, Indonesia based on the internal transcribed spacer region nrDNA sequences. Journal of Tropical Biology and Conservation 15:101–20.
   Google Scholar
• Hayat, K., A. Bardak, D. Parlak, F. Ashraf, H. M. Imran, H. A. Haq, … M. N. Akhtar. 2020. Biotechnology for cotton improvement. In: Ahmad, S., Hasanuzzaman, M. (eds). Cotton production and uses, 509–25. Singapore: Springer.
   Google Scholar
• Hinze, L. L., E. Gazave, M. A. Gore, D. D. Fang, B. E. Scheffler, J. Z. Yu, … R. G. Percy. 2016. Genetic diversity of the two commercial tetraploid cotton species in the Gossypium diversity reference set. Journal of Heredity 107 (3):274–86. doi:https://doi.org/10.1093/jhered/esw004.
   PubMedGoogle Scholar
• Hoagland, D. R., and D. I. Arnon. 1950. The water-culture method for growing plants without soil. Circular347 (2ndedit). California agricultural experiment station. pp. 32.
   Google Scholar
• Holt, S. S., L. Horová, P. Bureš, J. Janeček, and V. Černoch. 2005. The trnL-F plastid DNA characters of three Poa pratensis (Kentucky bluegrass) varieties. Plant, Soil and Environment 51 (2):94–99. doi:https://doi.org/10.17221/3561-PSE.
   Google Scholar
• Houston, R., M. Birck, B. LaRue, S. Hughes-Stamm, and D. Gangitano. 2018. Nuclear, chloroplast, and mitochondrial data of a US cannabis DNA database. International Journal of Legal Medicine 132 (3):713–25. doi:https://doi.org/10.1007/s00414-018-1798-4.
   PubMedGoogle Scholar
• Huang, B. L., S. L. Chen, and J. Mu. 2009. Evolution of the chloroplast trnL-trnF region in the gymnosperm lineages Taxaceae and Cephalotaxaceae. Biochemical Genetics 47 (5–6):351–69. doi:https://doi.org/10.1007/s10528-009-9233-7.
   PubMedGoogle Scholar
• Huang, S. 2016. New thoughts on an old riddle: What determines genetic diversity within and between species? Genomics 108 (1):3–10. doi:https://doi.org/10.1016/j.ygeno.2016.01.008.
   PubMed Web of Science ®Google Scholar
• Ijaz, B., N. Zhao, J. Kong, and J. Hua. 2019. Fiber quality improvement in Upland cotton (Gossypium hirsutum L.): Quantitative trait loci mapping and marker assisted selection application. Frontiers in Plant Science 10:1585.
   PubMed Web of Science ®Google Scholar
• Juliantari, E., N. S. Fitmawati, and N. Sofiyanti. 2018. Phylogeny of mango (Mangifera) in Eastern Sumatra using molecular markers of cpDNA rbc L. International Journal of Science and Applied Technology 3 (1):17–24.
   Google Scholar
• Kalbande, B. B., and A. S. Patil. 2016. Plant tissue culture independent Agrobacterium tumefaciens mediated In-planta transformation strategy for upland cotton (Gossypium hirsutum). Journal of Genetic Engineering and Biotechnology 14 (1):9–18. doi:https://doi.org/10.1016/j.jgeb.2016.05.003.
   PubMedGoogle Scholar
• Kamaran, S., T. M. Khan, A. Bakhsh, N. Hussain, S. Mahpara, A. Manan, … M. Iqbal. 2019. Assessment of morphological and molecular marker based genetic diversity among advanced upland cotton genotypes. Pakistan Journal of Agricultural Sciences 56 (3):645–52.
   Web of Science ®Google Scholar
• Kaya, E., R. Vatansever, and E. Filiz. 2018. Assessment of the genetic relationship of Turkish olives (Olea europaea subsp. europaea) cultivars based on cpDNA trnL-F regions. Acta Botanica Croatica 77 (1):88–92. doi:https://doi.org/10.1515/botcro-2017-0019.
   Google Scholar
• Kimura, M., and J. F. Crow. 1964. The number of alleles that can be maintained in a finite population. Genetics 49 (4):725–38.
   PubMed Web of Science ®Google Scholar
• Kovach, W. L. 2007. MVSP-A MultiVariate Statistical Package for Windows. ver. 3.1. Kovach Computing Services, Pentraeth, Wales, U.K.
   Google Scholar
• Krasovec, M., S. Sanchez-Brosseau, N. Grimsley, and G. Piganeau. 2018. Spontaneous mutation rate as a source of diversity for improving desirable traits in cultured microalgae. Algal Research 35:85–90. doi:https://doi.org/10.1016/j.algal.2018.08.003.
   Google Scholar
• Kumar, S., G. Stecher, and K. Tamura. 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33 (7):1870–74. doi:https://doi.org/10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Li, B., F. Lin, P. Huang, W. Guo, and Y. Zheng. 2017. Complete chloroplast genome sequence of Decaisnea insignis: Genome organization, genomic resources and comparative analysis. Scientific Reports 7 (1):1–10.
   PubMed Web of Science ®Google Scholar
• Librado, P., and J. Rozas. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25 (11):1451–52. doi:https://doi.org/10.1093/bioinformatics/btp187.
   PubMed Web of Science ®Google Scholar
• Mohamed, W. G., I. A. Ibrahim, and N. R. Abdelsalam. 2018. Assessment of genetic diversity in some Egyptian cotton varieties based on molecular and technological characteristics. Alexandria Science Exchange Journal 39 (January–March):112–23. doi:https://doi.org/10.21608/asejaiqjsae.2018.5797.
   Google Scholar
• Moiama, L., P. S. Vidigal Filho, M. C. Gonçalves-Vidigal, and L. P. de Carvalho. 2015. Genetic diversity and population structure of upland cotton Brazilian cultivars (Gossypium hirsutum L. race latifolium H.) using SSR markers. Australian Journal of Crop Science 9 (2):143–52.
   Google Scholar
• NCBI (National Center for Biotechnology Information). 2020. www.ncbi.nlm.nih.gov/genbank/.
   Google Scholar
• Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences 70:3321–23. doi:https://doi.org/10.1073/pnas.70.12.3321.
   PubMed Web of Science ®Google Scholar
• Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89 (3):583–90.
   PubMed Web of Science ®Google Scholar
• Nei, M. 1987. Molecular evolutionary genetics. New York: Columbia University.
   Google Scholar
• Pakyürek, M. 2019. Genetic similarity of pomegranate genotypes grown in Siirt province. Journal of Biology, Agriculture and Healthcare 9 (20):14–18.
   Google Scholar
• Parveen, S., A. Shahzad, and V. Yadav. 2016. Molecular markers and their application in plant biotechnology. In: Shahzad, A., Sharma, S., Siddiqui, S. (eds). Biotechnological strategies for the conservation of medicinal and ornamental climbers, 389–413. Cham: Springer.
   Google Scholar
• Rauf, S., M. Shehzad, J. M. Al-Khayri, H. M. Imran, and I. R. Noorka. 2019. Cotton (Gossypium hirsutum L.) breeding strategies. In: Al-Khayri, J., Jain, S., Johnson, D. (eds). Advances in plant breeding strategies: Industrial and food crops, 29–59. Cham: Springer.
   Google Scholar
• Retnoningsih, A., R. Megia, and A. Hartana. 2016. Phylogenetic relationships of Indonesian banana cultivars inferred from trnL-F intergenic spacer of chloroplast DNA. Floribunda 4 (8):202–11.
   Google Scholar
• Sahin, C. B., N. Isler, and V. Rustamova. 2020. Bazı pamuk çeşitlerinin ISSR markörleri ile karakterizasyonu. Kahramanmaras Sütçü Imam Üniversitesi Tarim Ve Doga Dergisi 23 (1):108–16.
   Google Scholar
• Salman, M., S. Majeed, I. A. Rana, R. M. Atif, and M. T. Azhar. 2019. Novel breeding and biotechnological approaches to mitigate the effects of heat stress on cotton. In: Wani, S. (ed). Recent approaches in omics for plant resilience to climate change, 251–77. Cham: Springer.
   Google Scholar
• Sen, F., A. O. Uncu, A. T. Uncu, and S. N. Erdeger. 2020. The trnL (UAA)‐trnF (GAA) intergenic spacer is a robust marker of green pea (Pisum sativum L.) adulteration in the economically valuable pistachio nuts (Pistachia vera L.). Journal of the Science of Food and Agriculture 1-6.
   Google Scholar
• Sevindik, E., and K. Okan. 2020. Genetic diversity and phylogenetic analyzes of Laurus nobilis L. (Lauraceae) populations revealed chloroplast (cpDNA) trn L Intron and trn LF region. International Journal of Fruit Science 1–12.
   Web of Science ®Google Scholar
• Sevindik, E., and K. Yalcin. 2018. Phylogenetic analysis of some Citrus L. (Rutaceae) taxa in Turkey based on chloroplast (cpDNA) trnL intron and trnL-F DNA sequences. Genetika 50 (3):1035–44. doi:https://doi.org/10.2298/GENSR1803035S.
   Google Scholar
• Sevindik, E., Z. T. Murathan, S. Filiz, and K. Yalcin. 2019. Molecular characterization based on chloroplast (trnL-F) DNA sequence of the apple genotypes in Ardahan/Turkey. Bangladesh Journal of Botany 48 (4):1099–106.
   Web of Science ®Google Scholar
• Soro, A., J. J. G. Quezada-Euan, P. Theodorou, R. F. Moritz, and R. J. Paxton. 2017. The population genetics of two orchid bees suggests high dispersal, low diploid male production and only an effect of island isolation in lowering genetic diversity. Conservation Genetics 18 (3):607–19. doi:https://doi.org/10.1007/s10592-016-0912-8.
   Web of Science ®Google Scholar
• Soysal, M. 1976. Die Siedlungs-und Landschaftsentwicklung der Çukurova, Mit besonderer Berücksichtigung der Yüregir-Ebene, 32–33. Erlangen, Germany: Fränkische Geographische Gesellschaft.
   Google Scholar
• Surgun, Y., B. Col, and B. Burun. 2012. Genetic diversity and identification of some Turkish cotton genotypes (Gossypium hirsutum L.) by RAPD-PCR analysis. Turkish Journal of Biology 36 (2):143–50.
   Web of Science ®Google Scholar
• Tsvetkov, V. E., Y. A. Semochkin, and A. A. Nikitin. 2019. A technology for production of fiberboards based on cotton stalks. Polymer Science, Series D 12 (3):328–30. doi:https://doi.org/10.1134/S1995421219030237.
   Google Scholar
• USDA (United States Department of Agriculture). 2020. United States of agriculture, foreign agricultural service, world agricultural production. Circular Series WAP3-20, March.
   Google Scholar
• Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7 (2):256–76. doi:https://doi.org/10.1016/0040-5809(75)90020-9.
   PubMed Web of Science ®Google Scholar
• Xuan, Y., Y. Wu, P. Li, R. Liu, Y. Luo, J. Yuan, … N. He. 2019. Molecular phylogeny of mulberries reconstructed from ITS and two cpDNA sequences. PeerJ 7:e8158. doi:https://doi.org/10.7717/peerj.8158.
   PubMedGoogle Scholar
• Yeh, F. C., R. C. Yang, and T. Boyle. 1999. POPGENE Version 1.32: Microsoft Windows-based freeware for population genetic analysis. Edmonton, AB, Canada: University of Alberta.
   Google Scholar