The relationships between leptin gene polymorphism and some performance traits in Simmental and Brown Swiss cattle

This study was carried out to determine the genotype and allele frequencies and association between the Leptin gene Sau3AI polymorphism and some performance characteristics in Simmental (n=60) and Brown Swiss (n=62) breed cattle raised in the province of Erzurum, Turkey. In the study, leptin/Sau3AI gene polymorphisms in DNA isolated from blood samples obtained from Simmental and Brown Swiss cattle were determined using PCR-RFLP method. As genotype frequencies of leptin/Sau3AI gene in the population, in Brown Swiss cattle, 88,7% with genotype AA, 9,7% with AB and 1,6% with BB genotypes were determined, Simmental breed cattle, 78,3% with genotype AA, 16,7% with AB and with 5,0% BB genotypes were determined. AA genotype frequencies were the highest in the population, and those with BB genotypes had the lowest frequency in both breeds. When the population was examined in terms of allele frequencies, the A allele was 0,87 and B allele was 0,13 in the Simmental cattle, and the A allele was 0,94 and B allele was 0,06 in the Brown Swiss breed. According to Hardy-Weinberg genetic balance test, the distribution of genotype frequencies was balanced (P>0.05) in the Brown Swiss breed but not in the Simmental breed in the population studied. As a result of the analysis performed in the Simmental breed, the general averages were found to be 5422,4 ± 1901,74 kg for actual milk yield, 5626,6 ± 1475,85 kg for 305-day milk yield, 298,7 ± 84,80 days for lactation duration and 18,5 ± 4,84 kg for daily milk yield. According to the statistical analysis results, the effect of genotype on the actual milk yield during lactation, lactation duration and daily milk yield was significant. As a result of the analysis made in the Brown Swiss breed, the general averages were 3917,8 ± 1584,38 kg for actual milk yield, 4614,3 ± 982,62 kg for 305 days milk yield, 254.9 ± 99.88 days for lactation duration and 16,0 ± 3,82 kg for daily milk yield. According to the statistical analysis results, the effect of genotype on performance characteristics was insignificant in Simmental and Brown Swiss cattle.

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Background Reference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1). Results Read mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA_Angus_1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA_Angus_1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA_Angus_1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA_Angus_1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes using a two-step imputation approach. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies. Conclusions The ARS-UCD1.2 and UOA_Angus_1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection that already reached fixation using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.

The study of genetic distinctions of brown Swiss cattle breed with using STR-markers

The study of allele pool condition and genetic diversity of Brown Swiss cattle breed was conducted with using STR-markers. Sample collection included samples (n=347) of five breeds: Russian selection Brown Swiss (BSH1), German selection Brown Swiss (BSH2), Jersey (DJ), Simmental (SIM), Kostromskaya(KOS) and Holstein (HOLSH). Polymorphism of 11 microsatellite loci was studied on 16-channell genetic analyzer ABI3130xl. A total of 393 allales with minimal number in DJ group (54) and maximal in SIM group (84) were founded. The number of alleles per locus ranged from 25 (BM1824) to 50 (TGLA122) and average number of alleles per locus ranged from 4.33 (TGLA126) to 8.33 (TGLA122) with a mean of 5.95. Effective number of alleles per locus varied from 2.88 (DJ) to 3.76 (BSH2). Maximal (4.64) and minimal (3.73) numbers of informative alleles were found in BSH2 and BSH1 groups, respectively. Observed heterozygosity range exceeded 0.70 in all groups, except DJ. A total of 23 private alleles were detected ranged from 0,005 (SIM) to 0,385 (DJ). AMOVA analysis showed that 80.068% of variation was observed within populations while 5.186% of variability was intergroup differences. The population structure analysis showed a high level of belonging of all groups to their own cluster. The FCA method revealed an overlapping of multilocus genotypes of BSH1, BSH2 иKOS groups. The results we obtained reveal a high level of genetic diversity in Russian population of Brown Swiss cattle breed.

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

BackgroundReference-guided read alignment and variant genotyping are prone to reference allele bias, particularly for samples that are greatly divergent from the reference genome. A Hereford-based assembly is the widely accepted bovine reference genome. Haplotype-resolved genomes that exceed the current bovine reference genome in quality and continuity have been assembled for different breeds of cattle. Using whole genome sequencing data of 161 Brown Swiss cattle, we compared the accuracy of read mapping and sequence variant genotyping as well as downstream genomic analyses between the bovine reference genome (ARS-UCD1.2) and a highly continuous Angus-based assembly (UOA_Angus_1).ResultsRead mapping accuracy did not differ notably between the ARS-UCD1.2 and UOA_Angus_1 assemblies. We discovered 22,744,517 and 22,559,675 high-quality variants from ARS-UCD1.2 and UOA_Angus_1, respectively. The concordance between sequence- and array-called genotypes was high and the number of variants deviating from Hardy-Weinberg proportions was low at segregating sites for both assemblies. More artefactual INDELs were genotyped from UOA_Angus_1 than ARS-UCD1.2 alignments. Using the composite likelihood ratio test, we detected 40 and 33 signatures of selection from ARS-UCD1.2 and UOA_Angus_1, respectively, but the overlap between both assemblies was low. Using the 161 sequenced Brown Swiss cattle as a reference panel, we imputed sequence variant genotypes into a mapping cohort of 30,499 cattle that had microarray-derived genotypes. The accuracy of imputation (Beagle R2) was very high (0.87) for both assemblies. Genome-wide association studies between imputed sequence variant genotypes and six dairy traits as well as stature produced almost identical results from both assemblies.ConclusionsThe ARS-UCD1.2 and UOA_Angus_1 assemblies are suitable for reference-guided genome analyses in Brown Swiss cattle. Although differences in read mapping and genotyping accuracy between both assemblies are negligible, the choice of the reference genome has a large impact on detecting signatures of selection using the composite likelihood ratio test. We developed a workflow that can be adapted and reused to compare the impact of reference genomes on genome analyses in various breeds, populations and species.

Changes in the genealogical structure of the brown swiss cattle during breeding

The population of the Brown Swiss cattle is differentiated into 12 lines and related groups, 65.2% of which are animals of the genealogical groups Meridian 90827, Master 106902, Concentrate 106157 and Hill 76059. Animals belonging to the line Nevod 3313 have disappeared. Total number of Brown Swiss animals in the lines of Amur 3033, Baro 18, Sector 4272-about 1.5%, in the line of R’yany 1318-0.03%. There is an accumulation of genetic material of the Brown Swiss breed of American selection and the displacement of genes that were possessed by animals of the local Brown Swiss cattle of domestic selection. For this reason, alleles B1G2QT1A`1P`, B1I`Q', I1E`3G`G``1 are eliminated from the breed, their frequency of occurrence in the herd is 0.005 or less. Marker EAB alleles B1G2QT1A`1P` and B1I`Q' in the Baro 18 line were detected in 5.1% and 6.4% of animals, respectively, in the Amur 3033 line I1E`3G`G``1 is found in 15% of offspring. In 2018, 61 EAB locus alleles were identified in the lines, their number varies from 15 (line Laddi 125640) to 56 (line Meridian 90827). Studies have shown that the largest distribution (more than 60%) is characterized by EAB alleles of American selection, especially B1P2Y2G`Y`, B2G2KY2E`1F`2O`G``1, B2O3Y2A`2E`2G`P`Q`Y`, G3O1T1Y2E`3F`2G``2, I1Y2E`2G`I`G``1 (?q=0.479). The G2E`3F`2O` allele is extremely rare. EAB-alleles characteristic of domestic breeding were detected in 35% of animals. Among them, G1O` (0.067) and the recessive EAB b allele (0.106) are widely distributed. Alleles B1I1T1A`1P`, B1I`P`, B2P2T2P`B``, I`Q`, P2(E`3)I` are eliminated from the breed (?q < 1%). Alleles of the Jersey cattle were found with a frequency of 0.046.The alleles G2O2E`2I` (line Hill 76059 – 20.5%) and O2E`2G``1 (line Meridian 90827 – 4.3%) were widely distributed.