scholarly journals Polymorphisms in JAK2 Gene are Associated with Production Traits and Mastitis Resistance in Dairy Cattle

2020 ◽  
Vol 20 (2) ◽  
pp. 409-423 ◽  
Author(s):  
Nawab Ali ◽  
Sadaf Niaz ◽  
Naimat Ullah Khan ◽  
Ali Gohar ◽  
Irfan Khattak ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Upstream Region ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Holstein Friesian ◽  
Hardy Weinberg Equilibrium ◽  
Exon 20 ◽  
Dna Pool ◽  
Lactating Dairy Cattle

AbstractThe present study was designed to investigate the effects of single nucleotide polymorphisms (SNPs) in the JAK2 gene on the production and mastitis related traits in dairy cattle. Blood and milk samples were collected from 201 lactating dairy cattle of three breeds, i.e. Holstein Friesian (HF), Jersey (J) and Achai (A) and their crosses maintained at well-established dairy farms in Khyber Pakhtunkhwa, Pakistan. Generalized linear model was used to evaluate the association between genotypes and the studied traits. A DNA pool was made from randomly selected 30 samples which revealed three SNPs, i.e. SNP 1 in 5’ upstream region (G>A, rs379754157), SNP 2 in intron 15 (A>G, rs134192265), and SNP 3 in exon 20 (A>G, rs110298451) that were further validated in the population under study using SNaPshot technique. Of the three SNPs, SNP 1 did not obey Hardy-Weinberg equilibrium (P<0.05). SNP 2 and SNP 3 were found to be in strong linkage disequilibrium and allele G was highly prevalent compared to allele A in these SNPs. in SNP 1, the GG genotype was associated with significantly (P<0.01) higher SCC, whereas SNP 2 and SNP 3 were significantly (P<0.01) associated with higher lactose percentage compared to the other geno-types. The haplogroups association analysis revealed that H1H2 (GG GG AG) has significantly lower SCC than H2H2 (GG GG GG). The results infer that JAK2 could be an important candidate gene and the studied SNPs might be useful genetic markers for production and mastitis related traits.

scholarly journals Association of genetic variants in STAT5B gene with milk performance and mastitis related traits in dairy cattle

2021 ◽  
Vol 91 (5) ◽  
pp. 459-471
Author(s):  
Nawab Ali ◽  
◽  
Sadaf Niaz ◽  
Irfan Khattak ◽  
Naimat U. Khan ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Association Analysis ◽  
Milk Composition ◽  
Clinical Mastitis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Holstein Friesian ◽  
Hardy Weinberg Equilibrium ◽  
Milk Performance

Udder performance and health are important traits in dairy cattle worldwide. The present study aimed to explore the association of single nucleotide polymorphisms (SNPs) in the STAT5B gene in dairy cattle with milk performance and mastitis related traits. The study included 201 cows of three pure breeds (i.e. Holstein Friesian, Jersey and Achai) and two crossbred cattle at four established dairy farms in Khyber Pakhtunkhwa, Pakistan. The milk samples were analysed for somatic cell count (SCC) and milk composition (i.e. fat , protein and lactose percentages). The generalized linear model was deployed for association analysis using SAS. The pool DNA sequencing showed four (three synonymous and a 3/ UTR) SNPs in STAT5B. These SNPs were further validated in all DNA samples using SNaPshot assay. The breed-wise analysis showed that most of the SNPs were consistent with Hardy-Weinberg equilibrium (P>0.05). The association analysis revealed a significantly higher protein percentage in TT genotype and lower SCC in CC genotypes of SNP 1 (exon 2, C>T), whereas in SNP 2 (exon 16, T>C) the TT genotypes revealed significantly lower SCC and SCS compared with other genotypes (P<0.05). SNP 4 (3/ UTR, C>T) showed significantly lower SCC and frequency of clinical mastitis in the heterozygous (CT) genotype compared to the homozygous genotypes. The in silico predictions revealed changes in the RNA secondary structure for SNP 2 and SNP 3. The study suggests that STAT5B should be considered as a candidate gene, and the variants identified as useful genetic markers for improved milk composition and udder health.

scholarly journals Confirmed effects of candidate variants for milk production, udder health, and udder morphology in dairy cattle

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Thierry Tribout ◽  
Pascal Croiseau ◽  
Rachel Lefebvre ◽  
Anne Barbat ◽  
Mekki Boussaha ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Milk Production ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Udder Health ◽  
Gwas Approach

Abstract Background Over the last years, genome-wide association studies (GWAS) based on imputed whole-genome sequences (WGS) have been used to detect quantitative trait loci (QTL) and highlight candidate genes for important traits. However, in general this approach does not allow to validate the effects of candidate mutations or determine if they are truly causative for the trait(s) in question. To address these questions, we applied a two-step, within-breed GWAS approach on 15 traits (5 linked with milk production, 2 with udder health, and 8 with udder morphology) in Montbéliarde (MON), Normande (NOR), and Holstein (HOL) cattle. We detected the most-promising candidate variants (CV) using imputed WGS of 2515 MON, 2203 NOR, and 6321 HOL bulls, and validated their effects in three younger populations of 23,926 MON, 9400 NOR, and 51,977 HOL cows. Results Bull sequence-based GWAS detected 84 QTL: 13, 10, and 30 for milk production traits; 3, 0, and 2 for somatic cell score (SCS); and 8, 2 and 16 for udder morphology traits, in MON, NOR, and HOL respectively. Five genomic regions with effects on milk production traits were shared among the three breeds whereas six (2 for production and 4 for udder morphology and health traits) had effects in two breeds. In 80 of these QTL, 855 CV were highlighted based on the significance of their effects and functional annotation. The subsequent GWAS on MON, NOR, and HOL cows validated 8, 9, and 23 QTL for production traits; 0, 0, and 1 for SCS; and 4, 1, and 8 for udder morphology traits, respectively. In 47 of the 54 confirmed QTL, the CV identified in bulls had more significant effects than single nucleotide polymorphisms (SNPs) from the standard 50K chip. The best CV for each validated QTL was located in a gene that was functionally related to production (36 QTL) or udder (9 QTL) traits. Conclusions Using this two-step GWAS approach, we identified and validated 54 QTL that included CV mostly located within functional candidate genes and explained up to 6.3% (udder traits) and 37% (production traits) of the genetic variance of economically important dairy traits. These CV are now included in the chip used to evaluate French dairy cattle and can be integrated into routine genomic evaluation.

scholarly journals Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle

2010 ◽  
Vol 78 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Erik W Berkowicz ◽  
David A Magee ◽  
Klaudia M Sikora ◽  
Donagh P Berry ◽  
Dawn J Howard ◽  
...  
Keyword(s):  
Body Size ◽  
Growth Factor ◽  
Single Nucleotide Polymorphisms ◽  
Dairy Cattle ◽  
Milk Production ◽  
Milk Fat ◽  
Milk Protein ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Holstein Friesian

The imprinted insulin-like growth factor 2 gene (IGF2) encodes a fetal mitogenic hormone protein (IGF-II) and has previously been shown to be associated with performance in dairy cattle. In this study we assessed genotype-phenotype associations between four single nucleotide polymorphisms (SNPs) located within the bovine IGF2 locus on chromosome 29 and a range of performance traits related to milk production, animal growth and body size, fertility and progeny survival in 848 progeny-tested Irish Holstein-Friesian sires. Two of the four SNPs (rs42196909 and IGF2.g-3815A>G), which were in strong linkage disequilibrium (r2=0·995), were associated with milk yield (P⩽0·01) and milk protein yield (P⩽0·05); the rs42196901 SNP was also associated (P⩽0·05) with milk fat yield. Associations (P⩽0·05) with milk fat percentage and milk protein percentage were observed at the rs42196901 and IGF2.g-3815A>G SNPs, respectively. The rs42196909 and IGF2.g-3815A>G SNPs were also associated with progeny carcass conformation (P⩽0·05), while an association (P⩽0·01) with progeny carcass weight was observed at the rs42194733 SNP locus. None of the four SNPs were associated with body size, fertility and progeny survival. These findings support previous work which suggests that the IGF2 locus is an important biological regulator of milk production in dairy cattle and add to an accumulating body of research showing that imprinted genes influence many complex performance traits in cattle.

Association of bovineCD4andSTAT5bsingle nucleotide polymorphisms with somatic cell scores and milk production traits in Chinese Holsteins

2011 ◽  
Vol 78 (2) ◽  
pp. 242-249 ◽  
Author(s):  
Yanghua He ◽  
Qin Chu ◽  
Peipei Ma ◽  
Yachun Wang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Somatic Cell ◽  
Milk Production ◽  
Milk Yield ◽  
Milk Fat ◽  
Protein Yield ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Chinese Holstein

CD4+T cells play a key role in the immune response of pathogen-induced mastitis in dairy cattle. Mammary gland factor STAT5b is involved in the regulation of CD4+T cell differentiation during inflammatory response and milk production. Little is known about the genetic variation effects of bovineCD4andSTAT5bgenes on somatic cell score (SCS) and milk production traits in dairy cattle. The aim of the study was to investigate the single nucleotide polymorphisms (SNPs) of bovineCD4andSTAT5bin Chinese Holsteins and to analyse their association with estimated breeding values (EBVs) for SCS and milk production traits. In the present study, SNPs ofCD4(NC_007303 g.13598C>T) andSTAT5b(NC_007317 g.31562 T>C) were identified and genotyped in Chinese Holstein population. The results showed that both SNPs were significantly associated with the EBVs for milk yield and protein yield in Chinese Holstein cows, and the SNP inCD4was associated with the EBV for SCS (P<0·01). The additive effect ofCD4SNP on protein yield was significant (P<0·05), and the dominant effect ofSTAT5bSNP was significant on milk yield and protein yield (P<0·01). Cows with combination genotype C7 (CCTT:CD4g.13598C>T andSTAT5bg.31562 T>C) had the highest SCS EBV but lower milk yield, while cows with C2 (TTTC) produced more milk, fat and protein than the other eight combination genotypes. These results suggested that the SNPs inCD4andSTAT5bmay be potential genetic markers for SCS and milk/protein yields selecting and warrant further functional research.

scholarly journals POLYMORPHISMS IN CANDIDATE GENES FOR BEEF QUALITY IN PINZGAU CATTLE

AGROFOR ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Anna TRAKOVICKÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Rudolf NÁDASKÝ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Markers ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Beef Quality ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Average Value ◽  
Hardy Weinberg Equilibrium ◽  
Stearoyl Coa Desaturase ◽  
Slight Deficiency

The aim of present study was to identify the polymorphisms in genes encodingcalpastatin (CASTUoG), calpain (CAPN1, CAPN2), diacylglycerol Oacyltransferase(DGAT1), thyroglobulin (TG5), and Stearoyl-CoA Desaturase(SCD) in order to analyse genetic structure of Pinzgau cattle. The genomic DNAfor genotyping was obtained from in total 56 blood samples of Pinzgau bulls. Afterextraction, the concentration of DNA was controlled by the spectrophotometrymeasurement. The genotyping of each individual was carried out by using PCRRFLPmethods. The average value of observed (0.37±0.05) and expectedheterozygosity (0.39±0.06) clearly indicated the prevalence of homozygousindividuals. Observed Wright's fixation indexes showed positive values across allloci (0.03±0.06), which confirmed slight deficiency of heterozygote animalscompared to the Hardy-Weinberg equilibrium expectations. The Hardy-Weinbergequilibrium was found in population, which signalizes only slight impact of factorssuch as selection, migration or inbreeding. The effectiveness of loci allele impact inpopulations has been described also by effective allele numbers (1.68±0.13) thatexpressed the decrease of allele activity in population. The loss of heterozygosityin analysed population was found across all of genetic markers. Each of theevaluated indicators clearly points to the need of genetic diversity monitoring.Moreover, the analyses of single nucleotide polymorphisms in genes significantlyinvolved in control of economically important production traits are still very usablemethods for identification of genetic markers that can be used in marker assistedselection of cattle.

scholarly journals Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations

2021 ◽  
Author(s):  
Johannes Geibel ◽  
Nora Paulina Praefke ◽  
Steffen Weigend ◽  
Henner Simianer ◽  
Christian Reimer
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Phenotypic Traits ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide ◽  
Tag Snps ◽  
Commercial Chicken ◽  
Translocation Breakpoints

Abstract BackgroundStructural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SV and surrounding SNPs.ResultsThe final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40 %, INV: 27 %, BND: 19 % of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50 % of the difference between SNP – SNP and DUP – SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays.ConclusionsThe results imply that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.

Association of polymorphisms in exons 2 and 10 of the insulin-like growth factor 2 (IGF2) gene with milk production traits in Polish Holstein-Friesian cattle

2009 ◽  
Vol 77 (1) ◽  
pp. 37-42 ◽  
Author(s):  
Emilia Bagnicka ◽  
Eulalia Siadkowska ◽  
Nina Strzałkowska ◽  
Beata Żelazowska ◽  
Krzysztof Flisikowski ◽  
...  
Keyword(s):  
Growth Factor ◽  
Milk Production ◽  
Insulin Like Growth Factor ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Milk Production Traits ◽  
Milk Traits ◽  
Exon 2 ◽  
Holstein Friesian ◽  
Exon 10

Insulin-like growth factor 2 (IGF2) is considered to be a regulator of post-natal growth and differentiation of the mammary gland. In the present work, associations of two single nucleotide polymorphisms in the bovine IGF2 gene with milk production traits were studied in dairy Holstein-Friesian cows: the already described g.8656C>T transition in exon 2 (RFLP-BsrI) and the newly found g.24507G>T transversion in exon 10 (RFLP-HaeIII), found by sequencing 273-bp exon 10 of the IGF2 gene in six individuals. Associations were analysed individually and in combination with the multi-trait repeatability test-day animal model. The CT/GT haplotype appeared to be associated with most of the milk traits studied (differences were significant at P⩽0·001). The most frequent CT/GG haplotype seemed inferior to others in fat and protein content and daily yield of fat and protein but superior (together with the TT/GG genotype) when the daily milk yield is considered.

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