CAPS-SSR Markırları Kullanılarak Pamuk Kromozom Subsitüsyon Hatlarının Belirlenmesi

Abstract

Pamuk (Gossypium L.) dünya genelinde tekstil endüstrisi için en önemli doğal lif kaynağı ve aynı zamanda önemli bir yağ bitkisidir. Pamuk lifleri tekstil için ana kaynak olmakla birlikte lifi, tohumu ve bitkisi ev izolasyon materyali olarak enerji tasarrufunda, proteince zengin hayvan yemi, yağı gıda olarak insan beslenmesinde, bitkisi ise altlık ve biyomateryal olarak ta değişik kullanım alanlarına sahiptir. Pamukta ıslah çalışmaları genellikle verim ve lif kaliteleri yönünden seçkin genotipler arasında yapılan melezlemeler ve daha önce geliştirilmiş çeşitlerden seleksiyon çalışmalarına dayanmaktadır. Ancak pamuk ıslah programları, kültür çeşitlerinde dar olan genetik çeşitlilikten olumsuz yönde etkilenmektedir. Bu durum araştırıcıları türler-arası melezleme ile introgresyona teşvik etmiştir. Türler-arası melezlemelerde kompleks antagonistik ilişkiler, farklı ploidi seviyelerinden dolayı sitogenetik farklılıklarla translokasyonlar ve inversiyonlar, kromozom yapısal farklılıkları, linkaj etkisi ile arzu edilmeyen tarımsal özelliklerin varlığı, rekombinasyonun azlığı, erken generasyonlarda introgresyonun kaybolması, kısırlık, Muller-Dobzhansky kompleksi nedeni ile ölümcül epistatik interaksiyonlar ve Mendel açılımının oluşmaması gibi nedenlerden dolayı sorunlar yaşanmaktadır. Kromozom substitüsyon hatlarının kullanılması ile yukarıda sözü edilen türler-arası melezlemelerdeki olumsuzluklar ortadan kaldırılabilmektedir. Bu çalışmada 17 kromozom substitüsyon hattının tanımlanması için genik CAPS-SSR markırları kullanılmıştır. Toplamda 11 CAPS-SSR markırı ve 16 restriksiyon enzimi kullanılmıştır. Bu bağlamda 11 monomorfik olan SSR markırı CAPS-SSR yöntemi ile 9 polimorfik markır olarak tespit edilmiştir. Sonuç olarak CAPS-SSR markır yöntemi kullanılarak kromozom substitüsyon hatlarının kromozom lokasyonlarının tespit edilebileceği sonucuna varılmıştır.

Keywords

• EST-SSR
• -CAPS-SSR
• CS-B
• Pamuk

Determination of Cotton (Gossypium L.) Chromosome Substitution Lines Using CAPS-SSR Markers

Abstract

Cotton (Gossypium L.) is the most important natural fiber source for the textile industry worldwide and is also an important oil plant. Although cotton fibers are the main source for textiles, its fibers, seeds and plants are used in energy saving as home insulation materials, protein-rich animal feed, oil in human nutrition as food, and its plants as litter and biomaterial. Breeding studies in cotton are generally based on cross-breeding between distinguished genotypes in terms of yield and fiber quality and selection studies from previously developed varieties. However, cotton breeding programs are negatively affected by the narrow genetic diversity in cultivars. This situation has encouraged researchers to investigate introgression through interspecies hybridization. Complex antagonistic relationships in interspecies hybridizations, translocations, and inversions with cytogenetic differences due to different ploidy levels, chromosome structural differences, the presence of undesirable agricultural traits due to the linkage effect, lack of recombination, loss of introgression in early generations, sterility, lethal epistatic interactions due to the Muller-Dobzhansky complex and problems occur due to reasons such as Mendel expansion not occurring. By using chromosome substitution lines, the negativities in interspecies hybridizations mentioned above can be eliminated. In this study, genic CAPS-SSR markers were used to identify 17 chromosome substitution lines. A total of 11 CAPS-SSR markers and 16 restriction enzymes were used. In this context, 11 monomorphic SSR markers were converted to 9 polymorphic markers by the CAPS-SSR method. As a result, it was concluded that the chromosome locations of chromosome substitution lines can be determined by using the CAPS-SSR marker method.

Keywords

• EST-SSR
• -CAPS-SSR
• CS-B
• Cotton

References

1. Arif IA, Bakir MA, Khan HA, Al Farhan AH, Al Homaidan AA, Bahkali AH, Shobrak M. 2010. A brief review of molecular techniques to assess plant diversity. Inter J Molec Sci, 11(5): 2079-2096.
2. Aydin A, Ince A. G, Uygur Gocer E, Karaca M. 2018. Single cotton seed DNA extraction without the use of enzymes and liquid nitrogen. Fresen Environ Bullet, 27(10): 6722-6726.
3. Aydin A. 2023. Determination of genetic diversity of some upland and Sea Island cotton genotypes using high-resolution capillary electrophoresis gel. Agron, 13(9): 2407.
4. Bellaloui N, Saha S, Tonos JL, Scheffler JA, Jenkins JN, McCarty JC, Stelly DM. 2020. Effects of interspecific chromosome substitution in upland cotton on cottonseed micronutrients. Plants, 9(9): 1081.
5. Gutiérrez OA, Stelly DM, Saha S, Jenkins JN, McCarty JC, Raska DA, Scheffler BE. 2009. Integrative placement and orientation of non-redundant SSR loci in cotton linkage groups by deficiency analysis. Molec Breeding 23: 693-707.
6. Ince AG, Karaca M, Onus, AN. 2009. An in silico analysis of ginger expressed sequence tags for microsatellites. AJTCAM, 6: 340–341
7. İnce AG. 2010. Doku/Organ spesifik mikrosatellit dna gen içeriklerinin capsicum cdna kütüphanelerinde ın silico ve ın vitro yaklaşımlarla belirlenmesi. Doktora Tezi Akdeniz Üniversitesi, Antalya, Türkiye, ss: 135.
8. Karaca M. 2001. Caracterization of cynodon spp. and gossypium spp. genomes using molecular and cytological techniques. PhD thesis, Dissertation University of Mississippi, Mississippi, USA, pp: 201.

9. Karaca M, Ince AG, Aydin A, Ay ST. 2013. Cross‐genera transferable e‐microsatellite markers for 12 genera of the Lamiaceae family. J Sci Food Agri, 93(8): 1869-1879.
10. Karaca M, İnce AG, Elmasulu SY, Onus AN, Turgut K. 2005. Coisolation of genomic and organelle DNAs from 15 genera and 31 species of plants. Analytical Biochem, 343(2): 353-355.
11. Karaca M, Ince AG. 2011. New non-redundant microsatellite and CAPS-microsatellite markers for cotton (Gossypium L.). Turkish J Field Crops, 16(2): 172-178.
12. Karaca M, Ince AG. 2023. A DNA extraction method for nondestructive testing and evaluation of cotton seeds (Gossypium L.). Biochem Genet, doi.org/10.1007/s10528-023-10496-5.
13. Lateef DD. 2015. DNA marker technologies in plants and applications for crop improvements. J BioSci Med, 3(5): 1-7.
14. Liu L, Saha S, Stelly D, Burr B, Cantrell R. G. 2000. Chromosomal assignment of microsatellite loci in cotton. J Heredity, 91(4): 326-332.
15. Matuszczak M, Spasibionek S, Gacek K, Bartkowiak-Broda I. 2020. Cleaved amplified polymorphic sequences (CAPS) marker for identification of two mutant alleles of the rapeseed BnaA. FAD2 gene. Molec Biol Reports, 47(10): 7607-7621.
16. Mert M. 2007. Pamuk tarımının temelleri. TMMOB Ziraat Mühendisleri Odası, Ankara, Türkiye, ss: 282.
17. Peng J, Shi C, Wang D, Li S, Zhao X, Duan A, He C. 2021. Genetic diversity and population structure of the medicinal plant Docynia delavayi (Franch.) Schneid revealed by transcriptome-based SSR markers. J Applied Res Med Arom Plant, 21: 100294.
18. Preethi P, Rahman S, Naganeeswaran S, Sabana AA, Gangaraj KP, Jerard BA, Rajesh MK. 2020. Development of EST-SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.). Molec Biol Reports, 47: 9385-9397.
19. Saha S, Tewolde H, Jenkins J. N, McCarty J. C, Stelly D. M. 2023. Chromosome substitution lines with improved essential mineral nutrients and fiber quality traits in Upland cotton. Genet Resour Crop Evolut, 2023: 1-15.
20. Shah RA, Bakshi P, Jasrotia A, Itoo H, Padder BA, Gupta R, Dolkar D. 2023. Morphological to molecular markers: Plant genetic diversity studies in Walnut (Juglans regia L.)—A Review. Erwerbs-Obstbau, 2023: 1-13.
21. Song L, Wang R, Yang X, Zhang A, Liu D. 2023. Molecular markers and their applications in marker-assisted selection (MAS) in bread wheat (Triticum aestivum L.). Agri, 13(3): 642.
22. Stelly D. M, Saha S, Raska D. A, Jenkins J. N, McCarty J. C, Gutierrez O. 2005. Registration of 17 germplasm lines of upland cotton (Gossypium hirsutum) each with a different pair of G. barbadense chromosome or chromosome arms substituted for the respective G. hirsutum chromosome or chromosome arms. Crop Sci 45 2663-2665.
23. Viot CR, Wendel JF. 2023. Evolution of the cotton genus Gossypium and its domestication in the Americas. Critical Rev Plant Sci, 42(1): 1-33.
24. Walkowiak M, Matuszczak M, Spasibionek S, Liersch A, Mikołajczyk K. 2022. Cleaved amplified polymorphic sequences (CAPS) markers for characterization of the LuFAD3A gene from various flax (Linum usitatissimum L.) cultivars. Agronomy, 12(6): 1432.
25. Wang Y, Hu X, Fu L, Wu X, Niu Z, Liu M, Ru Z. 2023. Cleaved amplified polymorphic sequence (CAP) marker development and haplotype geographic distribution of TaBOR1. 2 associated with grain number in common wheat in China. Cereal Res Commun, 51(2): 463-470.
26. Witt TW, Ulloa M, Schwartz RC, Ritchie GL. 2020. Response to deficit irrigation of morphological yield and fiber quality traits of upland (Gossypium hirsutum L.) and Pima (G. barbadense L.) cotton in the Texas High Plains. Field Crops Res, 249: 107759.
27. Younis A, Ramzan F, Ramzan Y, Zulfiqar F, Ahsan M, Lim K. B. 2020. Molecular markers improve abiotic stress tolerance in crops: a review. Plants 9(10) 1374.
28. Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Lin Z. 2020. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genom, 21(1): 1-16.