Abstract
Most of the milk produced by sheep is used for the production of high-quality cheese. Consequently, traits related to milk coagulation properties and cheese yield are economically important to the Spanish dairy industry. The present study aims to identify candidate genes and their regulators related to 14 milk and cheese-making traits and to develop a low-density panel of markers that could be used to predict an individual’s genetic potential for cheese-making efficiency. In this study, we performed a combination of the classical genome-wide association study (GWAS) with a stepwise regression method and a pleiotropy analysis to determine the best combination of the variants located within the confidence intervals of the potential candidate genes that may explain the greatest genetic variance for milk and cheese-making traits. Two gene networks related to milk and cheese-making traits were created using the genomic relationship matrices built through a stepwise multiple regression approach. Several co-associated genes in these networks are involved in biological processes previously found to be associated with milk synthesis and cheese-making efficiency. The methodology applied in this study enabled the selection of a co-association network comprised of 374 variants located in the surrounding of genes showing a potential influence on milk synthesis and cheese-making efficiency.
Highlights
Sheep milk production is highly important in Mediterranean and Middle Eastern countries.Spain holds one of the highest dairy sheep livestock counts in Europe [1], and almost all the sheep milk produced is used for the production of high-quality cheese [2]
The milk traits included five traits related to milk production, that is, milk yield (MY, kilograms), fat percentage (FP, %), lactose percentage (LP, %), protein percentage (PP, %), and dry milk extract
Our main aim was to identify SNPs located within a confidence interval of genes that are relevant to the traits considered, which could be used in genomic selection programmes applied in dairy sheep
Summary
Spain holds one of the highest dairy sheep livestock counts in Europe [1], and almost all the sheep milk produced is used for the production of high-quality cheese [2]. Milk composition has a strong influence on the technological and organoleptic characteristics of dairy products [3]. Sheep milk properties enable sheep cheeses to have better sensory characteristics than cheeses from goat and cow milk [4]. Genetic parameters for these traits have been widely studied [5,6,7]. Few genetic studies have investigated the genetic component involved in the cheese-making process through the analysis of milk traits (milk yield and composition) and cheese-making traits (milk coagulation properties (MCP) and cheese yield-related traits) [8,9,10].
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