Indian Journal of Animal Research

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Indian Journal of Animal Research, volume 58 issue 9 (september 2024) : 1474-1479

Complete Chromosome Wise Identification of SSRs in the Two Published Chicken Genome Assemblies

Jayakumar Sivalingam1,*, R.P. Athe1, T.K. Bhattacharya1, R.N. Chatterjee1, U. Raj Kumar1, Satya Pal Yadav1, K.S. Raja Ravindra1, M. Balakrishnan2, M.V. Chaudhari3
1ICAR-Directorate of Poultry Research, Hyderabad-500 030, Telangana, India.
2ICAR-National Academy of Agricultural Research Management, Hyderabad-500 030, Telangana, India.
3School of Agricultural Sciences and Technology, SVKM’s Narsee Monjee Institute of Management Studies (Deemed-to-University), Shirpur-425 405, Maharashtra, India.
Cite article:- Sivalingam Jayakumar, Athe R.P., Bhattacharya T.K., Chatterjee R.N., Kumar Raj U., Yadav Pal Satya, Ravindra Raja K.S., Balakrishnan M., Chaudhari M.V. (2024). Complete Chromosome Wise Identification of SSRs in the Two Published Chicken Genome Assemblies . Indian Journal of Animal Research. 58(9): 1474-1479. doi: 10.18805/IJAR.B-5254.

ABSTRACT

Background: Microsatellites are short repeat motifs consisting 1-6 base pair (bp) and have a high degree of length polymorphism and are useful to study the genetic diversity. In Chicken, no micro satellite markers were demarcated to different chromosomes, viz., 29, 34, 35, 36, 37, 38 and 39 in the genome. In the present study, we carried out chromosome-wise identification of SSRs that will be of great use in diversity and gene mapping studies in chicken.

Methods: The perl script of MISA tool was used to screen the polymorphic microsatellites with different thresholds level.

Result: We identified a total of 397877 SSRs from the latest chicken genome assembly (GRCg7b), of which mononucleotides, dinucleotides, trinucleotides, tetranucleotides, pentanucleotides and hexanucleotides composed of 307453 (77.27%), 40991 (10.30%), 23059 (5.79%), 16723 (4.20%), 8127 (2.04%) and 1524 (0.38%), respectively.

INTRODUCTION

Microsatellites are short repeat motifs consisting 1-6 base pair (bp) and can be present both in coding and non-coding regions in prokaryotic and eukaryotic genomes (Gupta et al., 1996; Tóth et al., 2000; Katti et al., 2001). They have a high degree of length polymorphism (Sawaya et al., 2013) and are regarded as an important tool for studying genetic diversity. In chicken, recently a genome assembly of cross of broiler hen and white leghorn cock (GRCg7b) was released in January 2021 of size 1053.33 Mb.The present genome assembly has mapped the reads to all the chicken chromosomes when compared to the previous assembly of Red Jungle Fowl (GRCg6a) of size 1065.37 Mb released in March 2018.So far in Chicken, no microsatellite marker was demarcated to different chromosomes, viz., 29, 34, 35, 36, 37, 38 and 39 in the genome. But, this deficiency can be sorted out using the current genome assembly (GRCg7b) which has all the chromosomes clearly demarcated. So, we carried out chromosome-wise identification of SSRs that will be of great use in diversity and gene mapping studies in chicken.

MATERIALS AND METHODS

Chicken genome assemblies; GRCg7b (GCA_016699485.1) and GRCg6a (GCA_000002315.3) were downloaded from the NCBI and were used for identification of SSRs by MISA tool (Beier et al., 2017). The perl script of MISA tool was used to screen the polymorphic microsatellites with different thresholds level (1-10 2-6 3-5 4-5 5-5 6-5 i.e Mononucleotide repeats with minimum 10 repeats, dinucleotide repeats with minimum 6 repeats, Trinucleotide repeats with minimum 5 repeats, Tetra nucleotide repeats with minimum 5 repeats, Pentanucleotide repeats with minimum 5 repeats, Hexa nucleotide repeats with minimum 5 repeats). The minimum distance between 2 compound SSRs was set at 100 bp in length. In the present genome assembly (GRCg7b), SSRs were also identified in the chromosome 39 as per the classification of the recent genome assembly.

RESULTS AND DISCUSSION

We identified a total of 397877 SSRs from the latest chicken genome assembly (GRCg7b), of which mononucleotides, dinucleotides, trinucleotides, tetranucleotides, pentanucleotides and hexanucleotides composed of 307453 (77.27%), 40991 (10.30%), 23059 (5.79%), 16723 (4.20%), 8127 (2.04%) and 1524 (0.38%), respectively (Table 1). Similarly, in GRCg6a, a total of 384069 SSRs were identified, out of which mononucleotides, dinucleotides, trinucleotides, tetranucleotides, pentanucleotides and hexanucleotides composed of 297223 (77.38%), 40376 (10.51%), 21985 (5.72%), 16146 (4.20%), 7084 (1.84%), 1255 (0.32%) respectively (Table 2). The SSRs identified in this study can be used precisely for diversity analysis in chicken. In GRCg7b, the most frequent motifs in mono, di, tri, tetra, penta and hexa nucleotide repeats were T (129407 times; 45.85%), AT (9466 times; 25.25%), TTG (3112 times; 14.04%), AAAC (2523 times; 16.39%), AAAAC (321 times; 5.29%) and AAAAGA (42 times; 4.07%) respectively.
 

Table 1: Number and types of SSRs identified in GRCg7b genome assembly.


 

Table 2: Number and types of SSRs identified in GRCg6a genome assembly.


       
The occurrences of longer repeats are less common as in other species (Temnykh et al., 2001; Grover et al., 2007) while smaller repeats are predominant and this is because the mutation rates are higher in case of longer repeats and therefore less stable (Wierdl et al., 1997). The point mutation rates in different species determine the length distribution of microsatellites (Bell and Jurka, 1997; Kruglyak et al., 1998). The microsatellite arises due to the replication mistakes, whereas the point mutations whose rate varies within the genomes (Webster et al., 2006) breaks the repeats into two or more shorter ones and act in the opposite direction. In the perfect SSRs that contains the tandem repeats of the motifs increase in size due to replication events which then forms the compound SSRs due to mutation of the nucleotides resulting in variable length of the microsatellites over a long period of time (Messier et al., 1996; Primmer and Ellegren, 1998). The mono nucleotide repeats are more common than di, tri, penta, tetra and hexa nucleotide repeats across the genome (Table 1) which is in accordance with the previous report (Arora et al., 2013). In general, dinucleotide repeats are more common in the eukaryotic genome (Kariin and Burge, 1995; Shioiri and Takahata, 2001) and have been used in many livestock species for assessing the variability (Chatterjee et al., 2010a), genetic relatedness (Chatterjee et al., 2010b), diversity analysis and QTL mapping (Rajkumar et al., 2007; Atzmon et al., 2008). It is concluded that precise SSR microsatellites are spread over all the chromosomes based on the analysis of recently published chicken genome assembly (GRCg7b), which may be used for selection of population specific SSRs for genetic diversity and mapping studies in chicken.

CONCLUSION

From our studies, it is concluded that precise SSR microsatellites spread over all the chromosomes in the recently published chicken genome assembly (GRCg7b), which may be used for selection of population specific SSRs for genetic diversity and mapping studies in chicken.

CONFLICT OF INTEREST

All authors declare that they no conflict of interest.

REFERENCES


  1. Arora, V., Iquebal, M.A., Rai, A., Kumar, D. (2013). In silico mining of putative microsatellite markers from whole genome sequence of water buffalo (Bubalus bubalis) and development of first BuffSatDB. BMC Genomics. 14: 1-8.

  2. Atzmon, G., Blum, S., Feldman, M., Cahaner, A., Lavi, U., Hillel, J. (2008). QTLs detected in a multigenerational resource chicken population. Journal of Heredity. 99: 528-538.

  3. Beier, S., Thiel, T., Münch, T., Scholz, U., Mascher, M. (2017). MISA- web: A web server for microsatellite prediction. Bioinformatics. 33: 2583-2585.

  4. Bell, G.I. and Jurka, J. (1997). The length distribution of perfect dimer repetitive DNA is consistent with its evolution by an unbiased single-step mutation process. Journal of Molecular Evolution. 44: 414-421.

  5. Chatterjee, R., Sharma, R.P., Bhattacharya, T.K., Niranjan, M., Reddy, B.L. (2010a). Microsatellite variability and its relationship with growth, egg production and immunocompetence traits in chickens. Biochemical Genetics. 48: 71-82.

  6. Chatterjee, R.N., Bhattacharya, T.K., Dange, M., Rajkumar, U. (2010b). Assessment of genetic relatedness of crossbred chicken populations using microsatellite markers. Biochemical Genetics. 48: 727-736.

  7. Grover, A., Aishwarya, V., Sharma, P.C. (2007). Biased distribution of microsatellite motifs in the rice genome. Molecular Genetics and Genomics. 277: 469-480.

  8. Gupta, P.K., Balyan, H.S., Sharma, P.C., Ramesh, B. (1996). Microsatellites in plants: a new class of molecular markers. Current Science. 45-54.

  9. Kariin, S. and Burge, C. (1995). Dinucleotide relative abundance extremes: A genomic signature. Trends in Genetics. 11: 283-290.

  10. Katti, M.V., Ranjekar, P.K., Gupta, V.S. (2001). Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution. 18: 1161-1167.

  11. Kruglyak, S., Durrett, R.T., Schug, M.D., Aquadro, C.F. (1998). Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proceedings of the National Academy of Sciences. 95: 10774-10778.

  12. Messier, W., Li, S.H., Stewart, C.B. (1996). The birth of microsatellites. Nature. 381: 483-483.

  13. Primmer, C.R. and Ellegren, H. (1998). Patterns of molecular evolution in avian microsatellites. Molecular Biology and Evolution. 15: 997-1008.

  14. Rajkumar, U., Gupta, B.R., Ahmed, N., Venktaramaiah, A., Reddy, A.R. (2007). Genetic variation and genetic diversity in chicken populations using microsatellite assay. Indian Journal of Animal Sciences. 77: 1194-1198.

  15. Sawaya, S., Bagshaw, A., Buschiazzo, E., Kumar, P., Chowdhury, S., Black, M.A., Gemmell, N. (2013). Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PloS One. 8: e54710.

  16. Shioiri, C. and Takahata, N. (2001). Skew of mononucleotide frequencies, relative abundance of dinucleotides and DNA strand asymmetry. Journal of Molecular Evolution. 53: 364-376.

  17. Temnykh, S., DeClerck, G., Lukashova, A., Lipovich, L., Cartinhour, S., McCouch, S. (2001). Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations and genetic marker potential. Genome Research. 11: 1441-1452.

  18. Tóth, G., Gáspári, Z. And Jurka, J. (2000). Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research. 10: 967-981.

  19. Webster, M.T., Axelsson, E., Ellegren, H. (2006). Strong regional biases in nucleotide substitution in the chicken genome. Molecular Biology and Evolution. 23: 1203-1216.

  20. Wierdl, M., Dominska, M., Petes, T.D. (1997). Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics. 146: 769-779.
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