Single-step genome-wide association analyses for selected infrared-predicted cheese-making traits in Walloon Holstein cows.

This study aimed to perform genome-wide association study to identify genomic regions associated with milk production and cheese-making properties (CMP) in Walloon Holstein cows. The studied traits were milk yield, fat percentage, protein percentage, casein percentage (CNP), calcium content, somatic cell score (SCS), coagulation time, curd firmness after 30 min from rennet addition, and titratable acidity. The used data have been collected from 2014 to 2020 on 78,073 first-parity (485,218 test-day records), 48,766 second-parity (284,942 test-day records), and 21,948 third-parity (105,112 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA) of 6,617 animals (1,712 males), were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of ∼216 KB) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for positional candidate genes. Heritability estimates for the studied traits ranged from 0.10 (SCS) to 0.53 (CNP), 0.10 (SCS) to 0.50 (CNP), and 0.12 (SCS) to 0.49 (CNP) in the first, second, and third parity, respectively. Genome-wide association analyses identified 6 genomic regions (BTA1, BTA14 [4 regions], and BTA20) associated with the considered traits. Genes including the SLC37A1 (BTA1), SHARPIN, MROH1, DGAT1, FAM83H, TIGD5, MROH6, NAPRT, ADGRB1, GML, LYPD2, JRK (BTA14), and TRIO (BTA20) were identified as positional candidate genes for the studied CMP. The findings of this study help to unravel the genomic background of a cow's ability for cheese production and can be used for the future implementation and use of genomic evaluation to improve the cheese-making traits in Walloon Holstein cows.

Single-step genome-wide association for selected milk fatty acids in Dual-Purpose Belgian Blue cows.

The aim of this study was to estimate genetic parameters and identify genomic regions associated with selected individual and groups of milk fatty acids (FA) predicted by milk mid-infrared spectrometry in Dual-Purpose Belgian Blue cows. The used data were 69,349 test-day records of milk yield, fat percentage, and protein percentage along with selected individual and groups FA of milk (g/dL milk) collected from 2007 to 2020 on 7,392 first-parity (40,903 test-day records), and 5,185 second-parity (28,446 test-day records) cows distributed in 104 herds in the Walloon Region of Belgium. Data of 28,466 SNPs, located on 29 Bos taurus autosomes (BTA), of 1,699 animals (639 males and 1,060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 25-SNP sliding window (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Average daily heritability estimated for the included milk FA traits ranged from 0.01 (C4:0) to 0.48 (C12:0) and 0.01 (C4:0) to 0.42 (C12:0) in the first and second parities, respectively. Genetic correlations found between milk yield and the studied individual milk FA, except for C18:0, C18:1 trans, C18:1 cis-9, were positive. The results showed that fat percentage and protein percentage were positively genetically correlated with all studied individual milk FA. Genome-wide association analyses identified 11 genomic regions distributed over 8 chromosomes [BTA1, BTA4, BTA10, BTA14 (4 regions), BTA19, BTA22, BTA24, and BTA26] associated with the studied FA traits, though those found on BTA14 partly overlapped. The genomic regions identified differed between parities and lactation stages. Although these differences in genomic regions detected may be due to the power of quantitative trait locus detection, it also suggests that candidate genes underlie the phenotypic expression of the studied traits may vary between parities and lactation stages. These findings increase our understanding about the genetic background of milk FA and can be used for the future implementation of genomic evaluation to improve milk FA profile in Dual-Purpose Belgian Blue cows.

Estimation of inbreeding, between-breed genomic relatedness and definition of sub-populations in red-pied cattle breeds.

Currently, enhancing the collaboration between related breeds is of main importance to increase the competitivity and the sustainability of local breeds. One type of collaboration is the development of an across-breed reference population that will allow a better management of local breeds. For this purpose, the genomic relatedness between the local target breed and possible breeds to be included in the reference population should be estimated. In Europe, there are several local red-pied cattle breeds that would benefit from this kind of collaboration. However, how different red-pied cattle breeds from the Benelux are related to each other and can collaborate is still unclear. The objectives of this study were therefore: (1) to estimate the level of inbreeding of the East Belgian Red and White (EBRW), the Red-Pied of the Ösling (RPO) and Dutch red-pied cattle breeds; (2) to determine the genomic relatedness of several red-pied cattle breeds, with a special focus on two endangered breeds: the EBRW and the RPO, and (3) based on the second objective, to detect animals from other breeds that were genomically close enough to be considered as advantageous in the creation of an across-breed reference population of EBRW or RPO. The estimated inbreeding levels based on runs of homozygosity were relatively low for almost all the studied breeds and especially for the EBRW and RPO. This would imply that inbreeding is currently not an issue in these two endangered breeds and that their sustainability is not threatened by their level of inbreeding. The results from the principal component analysis, the phylogenetic tree and the clustering all highlighted that the EBRW and RPO breeds were included in the genomic continuum of the studied red-pied cattle breeds and can be therefore considered as genomically close to Dutch red-pied cattle breeds, highlighting the possibility of a collaboration between these breeds. Especially, EBRW animals were closely related to Deep Red and Improved Red animals while, to a lesser extent, the RPO animals were closely related to the Meuse-Rhine-Yssel breed. Based on these results, we could use distance measures, based either on the principal component analysis or clustering, to detect animals from Dutch breeds that were genomically closest to the EBRW or RPO breeds. This will finally allow the building of an across-breed reference population for EBRW or RPO for further genomic evaluations, considering these genomically closest animals from other breeds.

Genome-wide association study for selected cheese-making properties in Dual-Purpose Belgian Blue cows.

This study aimed to estimate genetic parameters and identify genomic region(s) associated with selected cheese-making properties (CMP) in Dual-Purpose Belgian Blue (DPBB) cows. Edited data were 46,301 test-day records of milk yield, fat percentage, protein percentage, casein percentage, milk calcium content (CC), coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and milk titratable acidity (MTA) collected from 2014 to 2020 on 4,077 first-parity (26,027 test-day records), and 3,258 second-parity DPBB cows (20,274 test-day records) distributed in 124 herds in the Walloon Region of Belgium. Data of 28,266 SNP, located on 29 Bos taurus autosomes (BTA) of 1,699 animals were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 25 consecutive SNPs (with an average size of ∼2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Heritability estimates for the included CMP ranged from 0.19 (CC) to 0.50 (MTA), and 0.24 (CC) to 0.41 (MTA) in the first and second parity, respectively. The genetic correlation estimated between CT and a30 varied from -0.61 to -0.41 and from -0.55 to -0.38 in the first and second lactations, respectively. Negative genetic correlations were found between CT and milk yield and composition, while those estimated between curd firmness and milk composition were positive. Genome-wide association analyses results identified 4 genomic regions (BTA1, BTA3, BTA7, and BTA11) associated with the considered CMP. The identified genomic regions showed contrasting results between parities and among the different stages of each parity. It suggests that different sets of candidate genes underlie the phenotypic expression of the considered CMP between parities and lactation stages of each parity. The findings of this study can be used for future implementation and use of genomic evaluation to improve the cheese-making traits in DPBB cows.

Recombinant factor IX: discrepancies between one-stage clotting and chromogenic assays.

New and modified recombinant factor IX (rFIX) products are in development and accurate potency estimation is important to ensure the consistency of production and efficacy of these therapeutics. Collaborative study data obtained during the replacement of the 3rd International Standard (IS) for FIX concentrate suggested that there was a discrepancy between potency estimates for rFIX using clotting and chromogenic methods, when the rFIX candidate was measured against the plasma-derived FIX (pdFIX) IS. This study explores potential chromogenic and one-stage clotting method discrepancies in more detail. Five batches each of rFIX and pdFIX were assayed against the 4th IS FIX concentrate (a pdFIX) by activated partial thromboplastin time (APTT) one-stage clotting assay and specific functional chromogenic assay. The potency of rFIX by chromogenic assay was consistently around 70% of the one-stage clotting potency (average 78 and 108 IU mL(-1) respectively). These differences were not observed with pdFIX, which had similar potencies (average 96 IU mL(-1) ) by each assay method. In addition, different APTT reagents yielded different potency estimates for rFIX when assayed against the pdFIX IS, with a variation of up to 23%. In all cases, the differences were largely resolved when a rFIX reference was used as the standard. This study highlights some of the challenges associated with assay of rFIX products in the laboratory and that careful consideration needs to be given to the choice of reference material used. This is especially important with the imminent arrival of new and modified rFIX products.

Partial purification of somatomedin from human plasma.

Fractional precipitation of human plasma using ethanol, followed by chromatography on S.P. Sephadex, yielded a somatomedin-enriched fraction freed from substantial amounts of inhibitory substances. Heat coagulation of the proteins present in this fraction allowed the recovery of appreciable amounts of active components which were then chromatographed on Sephadex G-75 and S.P. Sephadex. A major part of the activity was associated with components less than 4,000 daltons, suggesting that somatomedin, or an active fragment thereof, had been dissociated from a carrier protein by the heat treatment. The range of pH employed throughout was 5.3-9.8. Recoveries of about 30% of biological activity with fold-purification up to 38, as measured by radioactive sulphate uptake in the chick pelvic cartilage assay, were higher than those obtained using acid-ethanol extraction.