Single Nucleotide Polymorphism in Exon 4 and Promoter Regions of β- Lactoglobulin Gene in Native Cattle (Bos indicus) Breeds of India

In the present study, single nucleotide polymorphism in exon II of the β-lactoglobulin gene was investigated in four Bulgarian sheep breeds: Bulgarian Dairy Synthetic Population sheep (BDSP), Copper-red Shumen sheep (CRSH), Stara Zagora sheep (STZG) and Pleven Blackhead sheep (PLBH). Two genetic variants of β-LG gene (A and B) have been identified through PCR-RFLP assay. A 103 bp fragment of the polymorphic β-LG locus were amplified and digested with endonuclease enzyme RsaI. The obtained restriction fragments revealed three genotypes: AA, AB and BB, observed in 31%, 65.5% and 3.5% of the BDSP population and in 48%, 28% and 24% of CRSH sheep population, respectively, with departure from the Hardy-Weinberg equilibrium (P<0.05) in these groups. The allele frequencies demonstrated a prevalence of the A allele (0.638 and 0.620) over the B allele (0.362 and 0.380) in both populations. On the contrary, the distribution of allele frequencies in STZG and PLBH was 0.240 and 0.100 for allele A, respectively and 0.760 and 0.900 for allele B. Therefore, the homozygous BB genotype in these sheep populations was more frequently encountered (0.520 and 0.800) than the heterozygous AB genotype (0.480 and 0.200), with HWE correspondence (P>0.1). The homozygous genotype AA was absent in STZG and PLBH sheep populations. The greatest Nei’s genetic distance calculated by UPGMA method was found between the populations BDSPand PLBH (0.5334), while the closest relationship (0.0006) was established between CRSH and BDSP. The results obtained from the present investigation confirmed the presence of the SNP polymorphism in exon II of the β-lactoglobulin gene. Therefore, the genetic variability established in this polymorphic locus could be applied in further association studies with milk production traits in sheep.

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Frecuencias alélicas para variantes SNP en el gen Nramp1 en bovinos infectados con Brucella abortus o clasificados por resistencia al patógeno

Ciencia y Tecnología Agropecuaria ◽

10.21930/rcta.vol10_num1_art:127 ◽

2009 ◽

Vol 10 (1) ◽

pp. 43

Author(s):

Fernando Cerquera M. ◽

Rodrigo Martínez S. ◽

Rubén Toro O. ◽

Jaime Tobón C. ◽

Jaime Gallego G. ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Brucella Abortus ◽

Bos Taurus ◽

Bos Indicus ◽

Natural Resistance ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Allelic Frequencies ◽

Bos Taurus Indicus

La resistencia natural a la brucelosis en bovinos ha sido asociada a factores genéticos, principalmente a algunos polimorfismos de nucleótido simple ubicados dentro del gen Nramp1. La presente investigación evalúa el efecto de variantes tipo polimorfismos de nucleótido simple presentes en regiones codificantes y en la región 3’UTR del gen Nramp1, en la clasificación de los animales como resistentes o susceptibles; además se determinan los genotipos predominantes en animales naturalmente infectados y comprobados como positivos por la presencia de anticuerpos anti Brucella abortus. Se establecieron las frecuencias genotípicas y alélicas para cinco polimorfismos de nucleótido simple identificados dentro del gen Nramp1 en animales de las razas blanco orejinegro (Bos taurus taurus) y cebú (Bos taurus indicus) y en muestras serológicamente positivas provenientes de animales cruzados (Bos taurus x Bos indicus). La determinación de genotipos se realizó mediante la metodología polimorfismo conformacional de cadena sencilla. Se realizó un ensayo de desafío infeccioso in vitro, para estimar la capacidad de los macrófagos bovinos para controlar la sobrevivencia bacterial, lo que permitió definir los individuos como resistentes o susceptibles. Los resultados sugieren una asociación significativa del SNP4 (p = 0,0506) con la variación para el fenotipo de susceptibilidad, pues se encontró el genotipo homocigoto (BB) en alta frecuencia en animales catalogados como resistentes y el genotipo heterocigoto (AB) en alta frecuencia en animales catalogados como susceptibles y en animales con títulos de anticuerpos anti Brucella abortus. Allelic frequencies for SNP variants in the gene Nramp1 in bovine infected with Brucella abortus or classified by resistance to the pathogen The natural resistance to brucellosis in cattle has been associated to genetic factors mainly to some single nucleotide polymorphism (SNP), located within Nramp1 gen. The current research has studied the effect of nucleotide variants to be found in coding regions and other one located in 3 non translated region of Nramp1 gene, on the animal classification as resistant or susceptible, moreover was identified the main genotypes to be found on the infected animals, confirmed as positives by antibody antibrucella titles. Was established the genotypic and allelic frequencies for five single nucleotide polymorphism in animals from blanco orejinegro (Bos taurus taurus) and zebu breeds (Bos taurus indicus) and serum samples belonging to positive crossbred animals (Bos taurus x Bos indicus). The genotype was defined by the methodology known as “single strand conformational polymorphism”. To estimate the macrophage capacity to control the bacterial survival, an in vitro assay was performed, which allowed define the phenotype as resistant or susceptible. The results suggest a significant association for SNP4 (p = 0.0506) with the phenotypic variation for resistant or susceptibility, because was found the genotype (BB) at higher frequency in susceptible animals and naturally infected animals, than those resistant animals.

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Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

PLoS ONE ◽

10.1371/journal.pone.0242200 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242200

Author(s):

Natalia Anatolievna Zinovieva ◽

Arsen Vladimirovich Dotsev ◽

Alexander Alexandrovich Sermyagin ◽

Tatiana Evgenievna Deniskova ◽

Alexandra Sergeevna Abdelmanova ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Candidate Genes ◽

High Density ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Selection Signatures ◽

Single Nucleotide ◽

Cattle Breeds ◽

Native Cattle ◽

Genomic Regions

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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