Genetic Diversity Analysis of Some Upland Cotton (Gossypium hirsutumL.) Genotypes Using SSR Markers

Yıl 2022, Cilt: 11 Sayı: 1, 80 - 89, 25.03.2022

Sadettin Çelik

https://doi.org/10.46810/tdfd.995786

Cited By: 1

Öz

Cotton plant is an important crop cultivated under biotic and abiotic stress conditions worldwide. The best way to avoid the harmful effects of chemicals used to combat these stresses is to develop tolerant or resistant varieties in plant breeding programs. In the present study, some of Upland cotton varietieswerescreened with 20 polymorphic SSR primers, and their population structure and genetic diversity analysis were examined. 17 SSR primers amplified 99 alleles with a 5.82 allele per locus. The mean PIC value of the markers was 0.312. The highest PIC value (0.491) belongs to the Nau3736 SSR marker while Bnl1611 and Bnl3449 markers had the lowest PIC value (0.105). The Genetic Distance (GD) values of the markers varied between 0.26and 1.09. The highest GD values were between Sure Grow 96 and Carmen, Sealand-542 and Siokra ¼, and between Sphinx V and Stoneville-453 cultivars. As a result, the genetically distantcultivars (Acala maxxa, Carmen, Aleppo 40, Siokra ¼, and Tex) can be recommended to use as parents in Marker-assisted selection (MAS) technology to develop new cotton varieties which are resistant or tolerant to stress factors.

Anahtar Kelimeler

Genetic diversity, MAS, PIC, SSR, Upland cotton

Teşekkür

I am grateful to Assistant of Prof. Dr. Adem BARDAK for providing cotton germplasm materials, and Dr. Halil TEKEREK and Osman YİĞİT for the assistance on laboratory analysis in Kahramanmaraş Sutçu Imam University, Agricultural Biotechnology Lab.

SSR Markörleri Kullanılarak Bazı Upland Pamuk (Gossypium hirsutum L.) Genotiplerinin Genetik Çeşitlilik Analizlerinin Yapılması

Öz

Pamuk bitkisi dünya genelinde biyotik ve abiyotik stres koşullarında yetiştirilen çok önemli bir tarla bitkisidir. Bu stres koşullarıyla mücadelede kimyasal ilaçlarının olumsuz etkilerinden kaçınmanın en etkili yolu, bitki ıslah metodlarıyla biyotik ve abiyotik stres faktörlerine dayanıklı/tolerant yeni bitki çeşitlerini geliştirmektir. Bu çalışmamızda bazı upland pamuk genotipleri 20 adet polimorfik SSR primerleriyle taranmış, populasyon yapıları ve genetik çeşitlilik analizleri yapılmıştır. 17 SSR primeri lokus başına 5.82 allel olmak üzere totalde 99 allel üretmiştir. Markörlerin ortalama PIC değerleri 0.312 olmuştur. En yüksek PIC değeri (0.491)’ni Nau3736 SSR marköründe elde edilirken, en düşük PIC değeri (0.105) Bnl1611, Bnl3449 markörlerinde elde edilmiştir. Markörlerin genetik mesafe değerleri 0.26ile 1.09arasında değişmiştir. En yüksek genetik mesafe Sure Grow 96 ve Carmen, Sealand-542 ve Siokra ¼ ile Sphinx V ve Stoneville-453 arasında ölçülmüştür. Sonuç olarak, genetik olarak birbirinden uzak olan çeşitler (Acala maxxa, Carmen, Aleppo 40, Siokra ¼, and Tex), stres faktörlerine karşı dirençli çeşit geliştirme teknolojisi olan Markör Destekli Seleksiyon (MAS) ıslah programına ebeveyn olarak kullanılabileceği güçlü bir şekilde önerilmektedir.

Anahtar Kelimeler

Genetik çeşitlilik, MAS, PIC, SSR, Upland pamuk

Kaynakça

• [1] Zhang J, Fang H, Zhou H, Sanogo S, Ma Z. Genetics, Breeding, and Marker-Assisted Selection for Verticillium Wilt Resistance in Cotton. Crop Science. 2014; 54(4):1289-1303.
• [2] Hui-Fang BS. Development of Molecular Markers and Mapping of Quantitative Trait Locf for Resistance to Verticillium Wilt Disease Using Two Inbred Line Populations in Tetraploid Cotton. [P.H.D Thesis]: New Mexico State University Las Cruces, New Mexico; 2013.
• [3] Pimentel D. Techniques for reducing pesticide use. Wiley, Hoboken; 1997.
• [4]. Cook JR. Advances in plant health management in the twentieth century. Annu Rev Phytopathol; 2000: (38):95–116.
• [5] Jia JZ. Molecular germplasm diagnostics and molecular marker assisted breeding. Scientia Agricultura Sinica. 1996; 29(4): 1-10.
• [6] Varshney R, Hoisington D, Nayak S, Graner A. Molecular Plant Breeding: Methodology and Achievements. In: Gustafson J., Langridge P., Somers D. (eds) Plant Genomics. Methods in Molecular Biology™ (Methods and Protocols). Humana Press. 2009; 513.
• [7] Young ND. A Cautiously Optimistic Vision for Marker-Assisted Breeding. Molecular Breeding. 1999; 5: 505-510.
• [8] Kohel RJ, Yu J, Park YH, Lazo GR. Molecular Mapping and Characterization of Traits Controlling Fiber Quality in Cotton. Euphytica. 2001; 121: 163-172.
• [9] Xie J, Cai Z, Liu XH, Li FH, Cao HL, Luan YC. Application of biotechnology on evaluation of genetic diversity of germplasm. CROPS (Supplement). 1998; 71-76.
• [10] Meena KK, Sorty AM, Bitla UM, Choudhary K, Gupta P, Pareek A. Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies. Front. Plant Scientist. 2017; 8:172.
• [11] Manjarrez-Sandoval P, Carter TE, Webb DM, Burton JW. Heterosis in Soybean and Its Prediction by Genetic Similarity Measures. Crop Science. 1997; 37(5):1443-1452.
• [12] Tatineni V, Cantrell RG, Davis DD. Genetic Diversity in Elite Cotton Germplasm Determined by Morphological Characteristics and RAPDs. Crop Science. 1996; 36(1):186-192.
• [13] Wendel JF, Brubaker CL, Percival AE. Genetic diversity in Gossypium hirsutum and the origin of upland cotton. American Journal of Botany. 1992; 79:1291-1310.
• [14] Schuster EW, Kumar S, Sarma SE, Willers JL, Milliken GA. Infrastructure for Data-Driven Agriculture: Identifying Management Zones for Cotton Using Statistical Modeling and Machine Learning Techniques. In Emerging Technologies for A Smarter World (Cewıt). 8th International Conference & Expo, 2013. Ieee. P.1-6.
• [15] Lacape JM, Nguyen TB, Thibivilliers S, Courtois B, Bojinov BM, Cantrell RG, et al. A combined RFLP, SSR-AFLP map of tetraploide cotton based on a G. hirsutum x G. barbadense backcross population. Genome. 2003; 46: 612-626.
• [16] Ulloa M, Saha S, Jenkins JN, Meredith WR, McCarty JC, Stelly MD. Chromosomal Assignment of RFLP Linkage Groups Harboring Important QTLs on an Intraspecific Cotton (Gossypium hirsutum L.) Joinmap. J. Hered. 2005; 96: 132-144
• [17] Smith JSC, Chin ECL, Shu HO, Smith S, Wall SJ, Senior ML, et al. An evaluation of the utility of SSR loci as molecular markers in maize (Zea Mays L.) comparisons with data from RFLPs and pedigree. Theor Appl Genet. 1997; 95:163-173.
• [18] Dudley JW, Maroof MAS, Rufener GK. Molecular Markers and Grouping of Parents in Maize Breeding Programs. Crop Science. 1991; 31: 718-723.
• [19] Senior ML, Murphy JP, Goodman MM, Stuber CW. Utility of SSRs for Determining Genetic Similarities and Relationships in Maize using an Agarose Gel System. Crop Science. 1998; 38: 1088-1098.
• [20] Smith JSC, Smith OS. Fingerprinting crop varieties. Adv. Agron. 1992; 47:85-140.
• [21] Chaters YM, Robertson A, Wilkinson MJ, Ramsay G. PCR analysis of oil seed rape cultivars (Brassica napus L. sp. oleifera) using 50-anchored simple sequence repeat (SSR) primers. Theor. Appl. Genet. . 196; 92: 442-447.
• [22] Powell W, Machray GC, Provan J. Polymorphism revealed by simple sequence repeats. Trends in Plant Sciences. 1996; 1:215-222.
• [23] Abdalla AM, Reddy OUK, El-Zik K Man, d Pepper AE. Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theoretical and Applied Genetic. 2001; 102:222-229.
• [24] Iqbal MJ, Reddy OUK, El-Zik KM, Pepper AE. A genetic bottleneck in the evolution under domestication’ of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting. Theoretical and Applied Genetics. 2001; 103:547-554.
• [25] Lu HJ, Myers GO. Genetic relationships and discrimination of ten influential upland cotton varieties using RAPD markers. Theoretical and Applied Genetic. 2002; 105:325-331.
• [26] Bertini CH, Schuster I, Sediyama T, Barros E, Moreira MA. Characterization and genetic diversity analysis of cotton cultivars using microsatellites. Genetics and Molecular Biology. 2006; 29(2): 321-329.
• [27] Liu D, Guo X, Lin Z, Nie Y, Zhang X. Genetic diversity of Asian cotton (Gossypium arboreum L.) in China evaluated by microsatellite analysis. Genetic Resources and Crop Evolution. 2006; 53(6): 1145-1152.
• 28] Nachimuthu G, Webb AA. Closing the Biotic and Abiotic Stress-Mediated Yield Gap in Cotton by Improving Soil Management and Agronomic Practices. In: Senthil-Kumar M. (eds) Plant Tolerance to Individual and Concurrent Stresses. Springer. 2017.
• [29] Liu HS, Li FM. Root respiration, photosynthesis and grain yield of two spring wheat in response to soil drying, Plant Growth Regul. 2005; 46, 233–240.
• [30] Bange M. The impact of temperature extremes on cotton performance. CSIRO Plant Industry. 2004.
• [31] Farooq M, Wahid A, Kobayashi N, Fujita D, Basra SMA. Plant drought stress: effects, mechanisms and management. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA. 2009; 29 (1): 185-212.
• [32] Islam S, Haque MS, Emon RM, Islam MM, Begum SN. Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers. Bangladesh Journal of Agricultural Research. 2012; 37(3): 389-398.
• [33] Doyle and doyle. A rapid DNA isolation procedure from small quantities of fresh leaf tissue. Phytochem Bull. 1997; 19: 11-5.
• [34] Zhang J, Stewart JM. Economical and rapid method for extracting cotton genomic DNA. J Cotton Sci. 2000; 4(3): 193-201.
• [35] Seyoum M, Du X, He SP, Jia YH, Pan Z, Sun JL. Analysis of genetic diversity and population structure in upland cotton (Gossypium hirsutum L.) germplasm using simple sequence repeats. Journal of genetics. 2018; 97(2): 513-522.
• [36] Mei M, Syed N, Gao W, Thaxton P, Smith C, Stelly D, et al. Genetic mapping and QTL analysis of fiber-related traits in cotton (Gossypium). Theoretical and applied genetics. 2004; 108(2):280-291.
• [37] Yu J, Yu S, Lu C, Wan W, Fan S, Song M, Zhang J. High‐density linkage map of cultivated allotetraploid cotton based on SSR, TRAP, SRAP and AFLP markers. Journal of Integrative Plant Biology. 2007; 49(5): 716-724.
• [38] Nguyen TB, Gigel M, Brottier P, Risterucci AM, Lacape JM. Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theoretical and applied genetics. 2004; 109(1):167-75.
• [39] Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B. A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics. 2007; 176(1):527-541.
• [40] Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theoretical and applied genetics. 2006; 112(3):430-439.
• [41] Reddy O, Pepper A, Abdurakhmonov I, Saha S, Jenkins J, Brooks T, et al. New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. Journal of cotton science. 2011; 5(2):103-113.
• [42] Qureshi SN, Saha S, Kantety RV, Jenkins JN. EST-SSR: a new class of genetic markers in cotton. 2004.
• [43] Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, et al. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic acids research. 2014; 42(D1), D1229-D1236.
• [44] Rohlf FJ. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System Version 2.1. Exeter Publishing Setauket, New York. 2000.
• [45] Nei M. Genetic distance between populations. The American Naturalist. 1972; 106(949): 283-292.
• [46] Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet.1980; 32: 314–331.
• [47] Liu J, Muse SV. Powermarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005; 21:2128-2129.
• [48] Nei M, Tajima FA, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 1983; 19: 153–170.
• [49] Pei Z, Gao JQ, Chen J, Wie Z, Li F, Luo L, et al. Genetic diversity of elite sweet sorghum genotypes assessed by SSR markers. Biologia Plantarum. 2010; 54 (4): 653-658.
• [50] Weir BS. Genetic Data Analysis II: Methods for Discrete Population Genetic Data. 2nd ed. Sunderland, MA, USA: Sinauer Associates Inc. 1996.
• [51] Pritchard JK, Wena X, Falush D. Documentation for structure software: Version 2.3. Department of Human Genetics, University of Chicago.http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.3/structure_doc.pdf; 2010.
• [52] Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 2005; 14(8):2611-2620.
• [53] Zhang Y, Wang XF, Li ZK, Zhang GY, Ma ZY. Assessing genetic diversity of cotton cultivars using genomic and newly developed expressed sequence tag-derived microsatellite markers. Genetics and Molecular research. 2011; 10(3): 1462-1470.
• [54] Lacape JM, Dessauw DM, Rajab JL, Noyer B, Hau B. Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Mol. Breed. 2007; 19:45–58.
• [55] Liu S, Cantrell RG, Mccarty JCJR, Stewart JMcD. Simple Sequence Repeat based assessment of genetic diversity in cotton race stock accessions. Crop Sci. 2000; 40:1459-1469.
• [56] Iqbal MJ, Aziz N, Saeed NA, Zafar Y, Malik KA. Genetic diversity evaluation of some elite cotton varieties by RAPD analysis. Theoretical and Applied Genetics. 1997; 94(1):139-144.
• [57] Eminur E, Hançer T. Cotton (Gossypium hirsutum L.) Germination Analysis and Molecular Characterization of Genotypes in Constrained Irrigation Conditions. Turkey Agricultural Research Journal. 2016; 3(2): 122-129.
• [58] Tyagi P, Gore MA, Bowman DT, Campbell BT, Udall JA, Kuraparthy V. Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 2014; 127(2): 283-295.
• [59] Bardak A, Bolek Y. Genetic diversity of diploid and tetraploid cottons determined by SSR and ISSR markers. Turk. J. Field Crops. 2012; 17(2): 139-144.
• [60] Gutierrez OS, Basu S, Saha JN, Jenkins DB, Shoemaker CL, Cheatham JC, et al. Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Sci. 2002; 42:1841-1847.
• [61] Zhang JF, Lu Y, Adragna H, Hughs E. Genetic improvement of New Mexico Acala cotton germplasm and their genetic diversity. Crop Sci. 2005; 45:2363-2373.
• [62] Khan AI, Fu YB, Khan IA. Genetic diversity of Pakistani cotton cultivars as revealed by simple sequence repeat markers. Communications in Biometry and Crop Sci. 2009; 4(1): 21-30.
• [63] Zhao YL, Wang HM, Chen W, Li YH, Gong HY, Sang X, H et al. Genetic diversity and population structure of elite cotton (Gossypium hirsutum L.) germplasm revealed by SSR markers. Plant Syst. Evol. 2015; 301; 327–336.
• [64] Chen G, Du XM. Genetic diversity of source germplasm of upland cotton in China as determined by SSR marker. Acta Genet. Sinica. 2006; 33: 1–10.
• [65] Abdurakhmonov IY, Kohel RJ, Yu JZ, Pepper AE, Abdullaev AA, Kushanov FN, Jenkins JN. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 2008; 92(6): 478-487.
• [66] Bardak A, Fidan Ms, Dağgeçen E, Tekerek H, Çelik S, Parlak D, Hayat K. Pamukta İlişkilendirme Haritalaması Yöntemiyle Gossypol ile İlişkili Markörlerin Belirlenmesi (Determination of Gossypol-Related Markers with the Association of Cotton Mapping Method). Journal of agricultural and nature. 2017; 20: 236.