Genomic selection of milk fatty acid composition in Sarda dairy sheep: Effect of different phenotypes and relationship matrices on heritability and breeding value accuracy

Abstract

Fatty acid (FA) composition is one of the most important aspects of milk nutritional quality. However, the inclusion of this trait as a breeding goal for dairy species is hampered by the logistics and high costs of phenotype recording. Fourier-transform infrared spectroscopy (FTIR) is a valid and cheap alternative to laboratory gas chromatography (GC) for predicting milk FA composition. Moreover, as for other novel phenotypes, the efficiency of selection for these traits can be enhanced by using genomic data. The objective of this research was to compare traditional versus genomic selection approaches for estimating genetic parameters and breeding values of milk fatty acid composition in dairy sheep using either GC-measured or FTIR-predicted FA as phenotypes. Milk FA profiles were available for a total of 923 Sarda breed ewes. The youngest 100 had their own phenotype masked to mimic selection candidates. Pedigree relationship information and genotypes were available for 923 and 769 ewes, respectively. Three statistical approaches were used: the classical-pedigree-based BLUP, the genomic BLUP that considers the genomic relationship matrix G, and the single-step genomic BLUP (ssGBLUP) where pedigree and genomic relationship matrices are blended into a single H matrix. Heritability estimates using pedigree were lower than ssGBLUP, and very similar between GC and FTIR regarding the statistical approach used. For some FA, mostly associated with animal diet (i.e., C18: 2n -6, C18: 3n -3), random effect of combination of flock and test date explained a relevant quota of total variance, reducing the heritability estimates accordingly. Genomic approaches (genomic BLUP and ssGBLUP) outperformed the traditional pedigree method both for GC and FTIR FA. Prediction accuracies in the older cohort were larger than the young cohort. Genomic prediction accuracies (obtained using either G or H relationship matrix) in the young cohort of animals, where their own phenotypes were masked, were similar for GC and FTIR. Multiple-trait analysis slightly affected genomic breeding value accuracies. These results suggest that FTIR-predicted milk FA composition could represent a valid option for inclusion in breeding programs.of Georgia, Athens) for her useful suggestions on implementing genomic models.

Multi-breed genome-wide association studies across countries for electronically recorded behavior traits in local dual-purpose cows

“…Apart from BACT, genetic parameter estimates from the pedigree-based approach ( A matrix) were very similar or slightly smaller compared to the H matrix approach (i.e., additionally considering genomic marker data). This result is in agreement with other studies focusing on genetic parameter estimations based on different genetic relationship matrices [26,27]. Basic dairy cattle habits (e.g., HACT, NACT and FEED) underlie moderate genetic control.…”

Functional Odd- and Branched-Chain Fatty Acid in Sheep and Goat Milk and Cheeses

“…Indeed, specific FA of dairy products can affect human health and can have an important role in the prevention of metabolic diseases. This increasing attention is also demonstrated by recent studies that investigated the feasibility of improving milk FA profile in sheep and goats though breeding schemes [1][2][3]. A significant amount of attention has been focused in the last decade on polyunsaturated fatty acid of the omega3 family (PUFA n-3) and conjugated linoleic acid (CLA) concentrations of dairy products.…”

“…SEM = standard error of means; 2 MvsC = Milk vs. Cheese;3 Fatty acids: expressed as mg/100 mg of FAME; ** p ≤ 0.01, * p < 0.05, ns not significant p ≥ 0.05.…”

Genetic Parameters of Bovine Milk Fatty Acid Profile, Yield, Composition, Total and Differential Somatic Cell Count

“…For this reason, several studies have explored the phenotypic and genetic relationships of milk FA with yield and composition [6,8,9]. In addition, the genetic aspects of FA and their possible use in genomic selection have been investigated also in sheep [10,11] and goat [12,13] milk. Recently, the laboratory of the Breeders Association of Veneto Region (Padova, Italy) has expanded the range of information provided in the frame of the monthly milk recording procedures, including the FA profile in addition to more traditional milk composition traits such as fat, protein, casein, lactose and urea content.…”