The Analysis of the Genetic Variation and the Assessment of Population Genetics and Diversity in Bovine Annexin A9, Insulin-like Growth Factor 1, and Beta-Lactoglobulin Genes in Turkish Native Cattle Breeds


Ardıçlı S. , Çobanoğlu Ö.

II. International Congress of the Turkish Journal of Agriculture - Food Science and Technology (TURJAF 2021), Gazimagusa, Cyprus (Kktc), 25 - 29 October 2021, vol.1, pp.1-2

  • Publication Type: Conference Paper / Summary Text
  • Volume: 1
  • City: Gazimagusa
  • Country: Cyprus (Kktc)
  • Page Numbers: pp.1-2

Abstract

Annexin A9 (ANXA9) is a member of the Ca2+ and phospholipid-binding protein family and it is encoded by the ANXA9 gene which was mapped to bovine chromosome 3. This region is known to be an important genomic location where QTLs for milk fat content and the other milk traits have been mapped. The beta-lactoglobulin (LGB) gene (GenBank accession number: X14710) is located on bovine chromosome 11 and plays a key role in the evaluation of milk production. Moreover, this gene has been associated with other loci that have a direct influence on growth. The insulin-like growth factor (IGF1) (GenBank accession number: AF210383) has crucial influences on growth rate and meat production traits via its functional roles in the regulation of cell proliferation. It was mapped to bovine chromosome 5. Although the above-mentioned genes have very important phenotypic effects there is limited information about them in Turkish native cattle breeds. Therefore, this study aimed to assess the genetic variation of ANXA9, LGB, and IGF1 in Turkish Grey Steppe, Anatolian Black, and East Anatolian Red cattle. The analysis was conducted on a total of 238 cattle from three native breeds including 93 Turkish Grey Steppe, 83 Anatolian Black, and 62 East Anatolian Red. Genomic DNA was purified from 4 mL blood samples using the phenol-chloroform method. Genotyping of the SNPs in the selected genes was performed by the PCR-RFLP method. In this context, A/G transition in position 951 of the ANXA9 gene (GeneBank accession number: AY785287), T/C substitution in position 5261 of the LGB gene, and the C/T alteration in position 472 of the IGF1 gene were evaluated. Amplification products were applied into the 3% agarose gel and the fragments were visualized with UV transillumination. The frequency and distribution of genotypes and alleles were calculated by the standard procedure. Population genetic parameters, including effective allele numbers (Ne), gene heterozygosity (He), polymorphism information content (PIC), fixation index (Fıs), and the level of possible variability realization (LPVR), were estimated based on the genotypic data. The Hardy–Weinberg equilibrium (HWE) was tested for all alleles by using the chi-square approximation of goodness-of-fit test statistics, with expected frequencies derived from allele frequencies. Moreover, Fisher’s exact test was used alternatively if there was a limited number of animals per genotype. On the other hand, biodiversity indices including the Shannon-Weaver index, Simpson Index, and the Gini Coefficient were evaluated through genotypic distributions. Results revealed that the number of heterozygote animals was remarkably high in all breeds regarding ANXA9 and LGB genes. There was no animal with the AA genotype in the ANXA9 in East Anatolian Red breed. Concerning Anatolian Black cattle, the CC genotype, and the BB genotype were absent in the IGF1 and LGB genes, respectively resulting in lower C and B alleles. The G and the T alleles were predominant in ANXA9 and IGF1 genes. The chi-square test showed that there were deviations from HWE in the ANXA9 (except for Anatolian Black cattle), IGF1 (except for East Anatolian Red cattle), and the LGB (except for Turkish Greys) (P<0.05). All of the markers were found to be moderately informative concerning all breeds and the total population based on the PIC evaluation (0.25<PIC<0.50). There was only one exception for this interpretation which was observed for the IGF1 marker in East Anatolian Red cattle (PIC<0.25: low informative polymorphism). The low variation levels in the IGF1 resulted in relatively low levels of Ne (<1.65). This also causes low levels of biodiversity indices including the Shannon-Weaver index, Simpson Index, and the Gini Coefficient. High numbers of heterozygous animals in the LGB caused negative values of FIS (<0) indicating lower gene homozygosity and higher LVPR values compared to other selected markers in this study. Consequently, this study focuses on the genetic variation and population and diversity parameters of the ANXA9, LGB, and IGF1 genes in Turkish native cattle breeds. To the best of our knowledge, there are limited publicly available papers about the mentioned genes in Turkish native cattle breeds. Hence, the data presented in this study may be valuable for further analysis. More detailed genetic studies conducted on native breeds should be performed to achieve an adequate characterization among breeds and to conserve animal genetic resources in Turkey.