Improvement of Genomic Predictions in Small Breeds by Construction of Genomic Relationship Matrix Through Variable Selection.

Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value-which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models-especially those using XGBoost-in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds.

Crossbred young bulls and heifers sired by double-muscled Piemontese or Belgian Blue bulls exhibit different effects of sexual dimorphism on fattening performance and muscularity but not on meat quality traits.

As double-muscled Belgian Blue (BB) and Piemontese (PIEM) breeds are heavily selected for different objectives (the former mainly for muscularity, the latter for ease of calving), the aim of this study was to compare sexual dimorphism in 56 crossbred young bulls and heifers obtained from dairy cows mated to bulls of the two beef breeds. Young PIEM- and BB-sired bulls had similar fattening performances and beef traits, although the BB crossbreds were slightly more muscular. Otherwise, the BB-sired heifers exceeded the PIEM-sired heifers in growth rate (1.12 vs. 0.98kg/d), feed efficiency (0.129 vs. 0.121kg/kg DM), increases in muscle scores (1.45 vs. 0.98 SEUROP scores) and carcass yield (0.612 vs. 0.605), but not in fatness, retail cut proportions and meat quality traits. Sexual dimorphism is, therefore, less distinct in BB than in PIEM crossbreds. In conclusion, BB sires are to be preferred for "product quality", and PIEM sires for "process quality", on account of welfare and ethical issues.

Characterization of muscle fiber type in the pectoralis major muscle of slow-growing local and commercial chicken strains.

The study aimed to characterize muscle fiber type of the pectoralis major muscle of slow-growing chickens belonging to the Padovana local breed, the commercial strain Berlanda gaina, and their cross. Forty-five chickens (both males and females) from the different genotypes were grown up to 180 d. Histochemical and morphometrical analyses were performed to characterize muscle fiber types, myofiber density, and myofiber size of the different genotypes. The effects of genotype, sex, and their interaction were estimated. Muscle samples appeared almost entirely made up of IIB fiber type, whereas a low percentage of area (5 to 6%) was composed of hypercontracted fiber. Myofiber density was significantly higher (P < 0.05) in Padovana strains and cross-sectional area was significantly lower (P < 0.01) than in Berlanda strain. Muscle fiber characteristics appeared not to be affected by the interaction of genotype × sex.

Glycoconjugate histochemistry of bovine Brunner glands.

The principal aims of this study have been to elucidate the nature of glycoconjugates produced by the two distinct parts of bovine Brunner glands, peripheral and central areas of lobules, and to investigate the presence of sialyl acid residues. Bovine duodenal tissues, embedded in paraffin wax, were investigated by means of both conventional histochemical methods (PAS, AB, HID) and biotinylated lectins (Con A, DBA, SBA, GS-I-B4, PNA, sWGA, GS-II, UEA-I, LPA, LFA). Conventional histochemical methods allowed us to accurately define two different areas: a central and a peripheral area. The central area, composed of secretory tubular tracts and the excretory duct, contained neutral glycoconjugates. The peripheral area was formed by both terminal alveolar and tubular secretory tracts and contained both neutral and acidic glycoconjugates, the latter partly carboxylated and partly sulfated. Lectin histochemistry confirmed differences highlighted by conventional histochemical methods and allowed us to characterise glycoprotein profiles of the preterminal and terminal tracts. The preterminal tracts and the excretory duct contained glycoconjugates with terminal D-Gal beta(1-3)GalNAc, alpha-D-Gal, alpha/beta-D-GalNAc, alpha/beta-D-GlcNAc, and internal beta(1-4) D-GlcNAc and alpha-Man residues. The terminal tracts were characterised by terminal alpha-L fucose, beta-D-GalNac, alpha/betaD-GlcNAc, alpha-D-Gal, alpha-D-GalNAc, and sialic acid residues. Internal beta(1-4) D-GlcNAc and alpha-Man residues were also identified. Finally, secretion of bovine Brunner glands is characterised by both O-linked and N-linked glycoproteins: cells located in the preterminal tracts and in the excretory duct produce mainly O-linked glycoproteins while cells located in the terminal tracts produce N-linked glycoproteins.