Akademik Veri Yönetim Sistemi
II. International Congress of the Turkish Journal of Agriculture - Food Science and Technology (TURJAF 2021), Gazimagusa, Kıbrıs (Kktc), 25 - 29 Ekim 2021, cilt.1, ss.1-2
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.