Identification of candidate genes and transcripts through in silico analysis of DNA markers

Rafieva Feruza; Barno Oripova; Abduqahhor Toshpulatov; Sevara Arslanova; Madina Kholova; Dilrabo Ernazarova; Fakhriddin Kushanov

doi:10.66432/xe71vp03

Rafieva U. Feruza * Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , Barno B. Oripova Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , Tashkent State Medical University, 2 Farobiy Street, Tashkent, 100109, Uzbekistan. , Abduqahhor Kh. Toshpulatov Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , Tashkent State Medical University, 2 Farobiy Street, Tashkent, 100109, Uzbekistan. , Sevara K. Arslanova Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , Madina D. Kholova Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , Dilrabo K. Ernazarova Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , National University of Uzbekistan, Universitet Street, Tashkent, 100174, Uzbekistan. , Fakhriddin N. Kushanov Institute of Genetics and Plant Experimental Biology, Yukori-Yuz, Qibray District, Tashkent Region, 111208, Uzbekistan. , National University of Uzbekistan, Universitet Street, Tashkent, 100174, Uzbekistan.

* Corresponding author: feruzarafiyeva25@gmail.com

DOI:

https://doi.org/10.66432/xe71vp03

Keywords:

cotton, bioinformatics, SSR markers, in silico PCR, candidate genes, fiber quality, abiotic stress.

Abstract

This article presents the results of determining candidate genes using in silico PCR using certain microsatellite DNA markers genetically linked to the genome of G. hirsutum L. and economically valuable traits. In this study, a virtual analysis of the region (100 kbp) around polymorphic microsatellite markers was performed using the NCBI database, UniPro Ugene, AUGUSTUS, and BLAST software. As a result, 29 valuable candidate genes and proteins were identified during the blast analysis of 10 SSR DNA markers related to fiber quality and salt resistance. The functions of the identified candidate genes and proteins were highlighted based on the interpretation of research results by foreign scientists. These results serve as an important basis for increasing the efficiency of marker-based selection (MAS) in cotton breeding and creating stress-resistant varieties.

References

1. Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol. 2015;33(5):524–30.

2. Liu X, Zhao B, Zheng HJ, Hu Y, Lu G, Yang CQ, et al. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Sci Rep. 2015;5:14139.

3. Meng Q, Gu J, Xu Z, Zhang J, Tang J, Wang A, et al. Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.). Ind Crops Prod. 2023;196:116471.

4. Khan Z, Khan SH, Ahmed A, Iqbal MU, Mubarik MS, Ghouri MZ, et al. Genome editing in cotton: challenges and opportunities. J Cotton Res. 2023;6(1):3.

5. Okonechnikov K, Golosova O, Fursov M, UGENE Team. Unipro UGENE: A unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166–7.

6. Stanke M, Schöffmann O, Morgenstern B, Waack S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006;7:62.

7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.

8. Gallego SF, Sprenger RR, Neess D, Pauling JK, Ejsing CS. Quantitative lipidomics reveals age-dependent perturbations of whole-body lipid metabolism in ACBP-deficient mice. Biochim Biophys Acta Mol Cell Biol Lipids. 2016;1862(2):145–55.

9. Knudsen J, Jensen MV, Hansen JK, Faergeman NJ, Neergaard TB, Gaigg B. Role of acyl-CoA binding protein in acyl-CoA transport, metabolism and cell signaling. Mol Cell Biochem. 1999;192(1-2):95–103.

10. Gorska A, Mazur AJ. Integrin-linked kinase (ILK): The known versus the unknown and perspectives. Cell Mol Life Sci. 2022;79(2):100.

11. Wenqiang Q, Ya Y, Yuying J, et al. Genome-wide analysis of CONSTANS-like genes in cotton. Int J Mol Sci. 2018;19(9):2658.

12. Sha YL, Zhang R, Wang XP, et al. Cloning and characterization of a somatic embryogenesis receptor-like kinase gene in cotton. J Integr Agric. 2012;11(6):898–909.

13. UniProt Consortium. UniProt Entry O65440: LRR receptor-like serine/threonine-protein kinase BAM3 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/O65440/entry

14. Maohua D, Na Z, Yue Z, et al. Genome-wide analysis of the SBT gene family involved in drought tolerance in cotton. Front Plant Sci. 2023;13:1097732.

15. UniProt Consortium. UniProt Entry Q7XWK5: Senescence-specific cysteine protease SAG39 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/Q7XWK5/entry

16. UniProt Consortium. UniProt Entry Q8VZG8: MDIS1-interacting receptor like kinase 2 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/Q8VZG8/entry

17. De Kock MJ, De Wit PJGM. Receptor-like proteins involved in plant disease resistance. Mol Plant Pathol. 2005;6(1):85–97.

18. Huiru S, Pengbo H, Qiang M, Meng Z, Yuan Q, Hengling W, et al. Genome-wide identification and expression analyses of the pectate lyase (PEL) gene family in cotton (Gossypium hirsutum L.). BMC Genomics. 2018;19(1):661.

19. Long GJ, Jin YL. Molecular cloning, expression profile and promoter analysis of a novel ethylene-responsive transcription factor gene GhERF4 from cotton (Gossypium hirsutum). Plant Physiol Biochem. 2008;46(1):46–53.

20. UniProt Consortium. UniProt Entry Q9LYU3: Ethylene-responsive transcription factor ERF113 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/Q9LYU3/entry

21. Wang W, Tang W, Ma T, et al. A pair of light signaling factors regulates plant immunity by modulating chlorophyll biosynthesis. J Integr Plant Biol. 2016;58(1):91–103.

22. Chenhui M, Zibo Z, Na W, et al. Genome-wide identification and comparative analysis of myosin gene family in cotton species. Genes (Basel). 2020;11(7):731.

23. Sun N, Xie YF, Wu Y, et al. Genome-wide identification of ABCC gene family and their expression in pigment deposition of cotton fiber. PLoS One. 2021;16(5):e0246649.

24. Chen L, Yan Y, Ke H, et al. SEP-like genes of Gossypium hirsutum promote flowering in a concentration-dependent manner. Front Plant Sci. 2022;13:990221.

25. Xiong LM, Schumaker KS, Zhu JK. Cell signaling during cold, drought, and salt stress. Plant Cell. 2002;14(Suppl 1):S165–83.

26. Zhu JH, Dong CH, Zhu JK. Interplay between cold-responsive gene regulation and metabolism. Curr Opin Plant Biol. 2007;10(3):290–5.

27. Sakamoto W, Miyagishima SY, Jarvis P. Chloroplast biogenesis: Control of plastid development, protein import, division and inheritance. Arabidopsis Book. 2008;6:e0110.

28. Waters MT, Langdale JA. The making of a chloroplast. EMBO J. 2009;28(19):2861–73.

29. Lurin C, Andrés C, Aubourg S, et al. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 2004;16(8):2089–103.

30. Barkan A, Small I. Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol. 2014;65:415–42.

31. Rovira AG, Smith AG. PPR proteins: Orchestrators of organelle RNA metabolism. Physiol Plant. 2019;166(2):451–59.

32. Williams-Carrier R, Brewster C, Belcher SE, et al. The Arabidopsis pentatricopeptide repeat protein LPE1 is required for chloroplast RNA translation. Plant J. 2019;99(1):56–66.

33. UniProt Consortium. UniProt Entry O82268: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/O82268/entry

34. Mulichak AM, et al. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: Implications for ligand binding and specificity. Biochemistry. 2002;41(52):15578–89.

35. UniProt Consortium. UniProt Entry O82730: Monogalactosyldiacylglycerol synthase, chloroplastic isoform X2 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/O82730/entry

36. UniProt Consortium. UniProt Entry Q9LUM0: 1-phosphatidylinositol-3-phosphate 5-kinase FAB1A isoform X1 [Internet]. UniProt KB; [cited 2026 Aug 28]. Available from: https://www.uniprot.org/uniprotkb/Q9LUM0/entry

37. Balasubramanian VK, Rai KM, Thu SW, Hii MM, Mendu V. Genome-wide identification of multifunctional laccase gene family in cotton (Gossypium spp.) and their expression during fiber development. Sci Rep. 2016;6:34309.

38. Yang L, Jiang J, Du ML, et al. A cotton MYB-like transcription factor is involved in pollen development. Plant Cell Physiol. 2013;54(6):893–906.

39. Suetsugu N, Yamada N, Kagawa T, et al. Two kinesin-like proteins mediate actin-based chloroplast movement in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010;107(19):8860–5.

40. Sun Q, Jiang HZ, Zhu XY, et al. RNA sequencing analysis of cotton response to Verticillium dahliae infection. BMC Genomics. 2013;14:852.

41. Pragya MP, Jain AJ, Takabe T, et al. Heterologous expression of serine hydroxymethyltransferase-3 from rice confers tolerance to salinity stress in E. coli and Arabidopsis. Front Plant Sci. 2019;10:217.

42. PubMed Central. PMC5381346: Identification of putative methyltransferase C9orf114 function [Internet]. NCBI PMC; [cited 2026 Aug 28]. Available from: https://pmc.ncbi.nlm.nih.gov/articles/PMC5381346