The effect of selection on casein genetic polymorphisms and haplotypes in Italian Holstein cattle

Exploring genome-wide differentiation and signatures of selection in Italian and North American Holstein populations

Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application.

Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level

In this study, we explored mating allocation in Holstein using genomic information for 24,333 Holstein females born in Denmark, Finland, and Sweden. We used 2 data sets of bulls: the top 50 genotyped bulls and the top 25 polled genotyped bulls on the Nordic total merit scale. We used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and β-casein. We found that it was possible to reduce genetic relationships and eliminate expression of genetic defects with minimal effect on the genetic level in total merit index. Compared with maximizing only Nordic total merit index, the relative frequency of polled offspring increased from 13.5 to 22.5%, and that of offspring homozygous for β-casein (A2A2) from 66.7 to 75.0% in one generation, without any substantial negative impact on other comparison criteria. Using only semen from polled bulls, which might become necessary if dehorning is banned, considerably reduced the genetic level. We also found that animals carrying the polled allele were less likely to be homozygous for β-casein (A2A2) and more likely to be carriers of the genetic defect HH1. Hence, adding economic value to a monogenic trait in the economic score used for mating allocation sometimes negatively affected another monogenetic trait. We recommend that the comparison criteria used in this study be monitored in a modern genomic mating program.

Development of a duplex qPCR assay with locked nucleic acid probes for A, B and E kappa-casein variants detection

Milk proteins determine important milk technological characteristics. Among caseins, Ƙ-casein has been correlated with fat and protein content and cheese yield. Fourteen Ƙ-caseins variants have been described but the alleles A, B and E are the most important ones due to their frequency and/or influence on the technological aptitudes of milk. Therefore, in the present study two different duplex qPCR assays with locked nucleic acid probes (for positions 13104 and 13124 of the Ƙ-casein gene) were developed for the detection of A, B and E variants. Firstly, DNA isolation method from milk somatic cells and hair was optimised. The developed 13124-qPCR assay showed an increased sensitivity reaching up to 6.7 copies DNA copies/reaction at a 95% confidence level with A, B and E alleles reference samples. The 13104-qPCR assay reached up to 6.7 DNA copies/reaction for A allele reference sample and 67 DNA copies/reaction for B and E samples. Intra-assay variation results were below 6%. Applicability was determined using DNA samples from animals with known genotype for Ƙ-casein (AA, AB, BB, BE, AE, EE) and both assays were able to discriminate among the six genotypes with 100% accuracy. Thus, this qPCR method represents a sensitive and rapid option for the detection of Ƙ-casein alleles in both hair and milk samples.

Guzerat indicine cattle and A2 milk production

Cow milk might be associated to gastrointestinal disorders and abdominal pain in some people, which are, in part, due to the digestion of A1 beta-casein. Within this context, A2 milk has emerged as an alternative since it only contains A2 beta-casein that does not cause these complications. This milk is produced by cows with the A2A2 genotype. The aim of this study was to investigate the allele and genotype frequencies for the beta-casein gene in Guzerat cattle and to evaluate the feasibility of selection and production of A2 milk. The genotypes of 283 Guzerat cows from 10 herds were analyzed. The frequency of the A2A2 genotype was 0.80 and the frequency of the A2 allele was 0.90. These frequencies are slightly lower than those reported in previous studies involving populations of the same breed, but the number of animals, herein, genotyped was higher. Thus, the estimates are believed to be better and are also equally high. The Guzerat cattle has the potential for A2 milk production since most animals of the herd carry the favorable genotype for A2 milk production. Furthermore, the frequency of the A2A2 genotype can be rapidly increased by marker-assisted selection without compromising genetic variability.

The Polymorphism in Various Milk Protein Genes in Polish Holstein-Friesian Dairy Cattle

Simple Summary

The aim of the present study was to evaluate the genetic variability within casein alpha S1 (CSN1S1), casein alpha S2 (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3), and progestagen-associated endometrial protein (PAEP) genes. The study was conducted on 1900 Polish Black and White Holstein-Friesian dairy cows that were genotyped using customized EuroGenomics microarrays. Out of investigated 24 genetic variants within four genes coding milk protein, 16 expressed genetic diversity. The fact that many of the investigated Single Nucleotide Polymorphisms (SNPs) were monomorphic may suggest that in the past the reproduction program favored one of these genotypes. Populations of high-yielding cows become more and more even and similar in terms of genotype, which may have an adverse effect in future breeding, therefore, the variability in genetic variants of genes coding milk protein should be monitored.

Abstract

The aim of the present study was to evaluate the genotype and allele frequencies of 24 polymorphisms in casein alpha S1 (CSN1S1), casein alpha S2 (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3), and progestagen-associated endometrial protein (PAEP) genes. The study included 1900 Polish Black and White Holstein-Friesian dairy cows that were subjected to genotyping via microarrays. A total of 24 SNPs (Single Nucleotide Polymorphisms) within tested genes were investigated. Two CSN1S1 SNPs were monomorphic, while allele CSN1S1_3*G in CSN1S1_3 SNP dominated with a frequency of 99.39%. Out of seven CSN2 SNPs, four were polymorphic; however, only for CSN2_3 all three genotypes were detected. Only three out of nine SNPs within CSN3 were monomorphic. Three PAEP SNPs were also found to be polymorphic with heterozygotes being most frequent. Hardy–Weinberg equilibrium (HWE) was observed for eight variants. It was shown that only CSN3_6 was not in HWE. The fact that many of investigated SNPs were monomorphic may suggest that in the past the reproduction program favored one of these genotypes. SNPs that are included in commercially available microarrays should be monitored in relation to changes in their frequencies. If a SNP has turned monomorphic, maybe it should be considered for removal from the microarray.