THE PRODUCTION OF SHEEP’S MILK IN SPAIN CONSTITUTES 21 % OF THE TOTAL EU, WITH CASTILE AND LEON BEING THE MOST PRODUCING REGION AND WITH THE HIGHEST CENSUS OF OUR COUNTRY. THIS PRODUCTION IS DESTINED ALMOST ENTIRELY TO THE MANUFACTURE OF HIGH QUALITY CHEESE, SO THE INCREASE IN THE CHEESE YIELD, HIGHLY DEPENDENT ON THE PROTEIN AND FAT CONTENT OF THE MILK, AS WELL AS ITS COAGULATION PROPERTIES (MCP), ARE OF GREAT INTEREST FOR THIS SECTOR. THIS PROJECT, PROTMILKOMA, AIMS TO USE THE PARALLEL MASS SEQUENCE TECHNIQUE OF THE TRANSCRIPTOME, OR RNASEQ, FOR THE DETECTION OF GENETIC VARIANTS WITH EFFECTS ON DAIRY PRODUCTION CHARACTERS, MAINLY THE PERCENTAGE OF PROTEIN (PP) AND MCP. IN ADDITION, THE PROJECT PROPOSES TO CHARACTERISE THE MICROBIOTA OF THE HEALTHY BREAST GLAND OF THE SHEEP, WHOSE COMPOSITION AND BALANCE CAN AFFECT THE WELFARE AND PRODUCTIVITY OF THE ANIMAL, AS WELL AS THE QUALITY AND TECHNOLOGICAL PROPERTIES OF THE MILK PRODUCED. TO THIS END, THREE SPECIFIC OBJECTIVES ARE SET. IN THE FIRST ONE THE MAMMARY TRANSCRIPTOME OF SHEEP WITH DIVERGENT PHENOTYPE FOR PP WAS ANALYSED, PERFORMING AN EXPERIMENT OF RNASEQ IN TWO SHEEP BREEDS, CHURRA AND ASSAF (4 ANIMALS HIGH PP VS 4 AN. UNDER PP, IN EACH BREED). FROM ALL VARIANTS IDENTIFIED WITH EXTREME FREQUENCIES BETWEEN THE TWO GROUPS, ESPECIALLY THOSE LOCATED IN THE GENES OF THE CASEINS AND WHEY PROTEINS AND THOSE OF THE GENES IDENTIFIED AS DIFFERENTIALLY EXPRESSED (DEGS), A GROUP OF SNPS WILL BE SELECTED FOR INCLUSION IN A LOW-DENSITY CHIP, THE MILKPROTEIN-CHIP (3.2K), WHOSE GENOTYPING IN COMMERCIAL POPULATIONS (600 CHURRAS AND 600 ASSAF) WILL SERVE TO CONFIRM POSSIBLE ASSOCIATIONS WITH DAIRY CHARACTERS. IN THE SECOND OBJECTIVE, IN PARALLEL, A RNASEQ EXPERIMENT WAS PERFORMED TO COMPARE THE MAMMARY TRANSCRIPTOME OF ASSAF SHEEP WITH DIVERGING EXTREME PHENOTYPE FOR MILK COAGULABILITY AND CHEESE YIELD CHARACTERS (4 AN. OF OPTIMAL MCP VS 4 AN. OF POOR PCM). TO DO THIS, A DETERMINATION OF SEVERAL PARAMETERS RELATED TO MCPS (RCT, K20, A30, A45, AND A90, CHEESE YIELD, MILK CITRATE CONTENT AND PH) WILL BE PERFORMED. AGAIN, THE DIVERGING VARIABILITY IDENTIFIED IN THIS EXPERIMENT WILL SELECT SNPS (LOCATED IN THE GENES OF MILK PROTEINS, IN THE SDRS AND THE GENES OF THE CITRATE SYNTHESIS ROUTE) TO BE INCLUDED IN THE MILKPROTEIN-CHIP. THE GENOTYPES OF THIS CHIP GENERATED IN 400 ASSAF SHEEP WITH MEASURES AVAILABLE FOR THE TECHNOLOGICAL CHARACTERS UNDER STUDY WILL ALLOW TO IDENTIFY VARIANTS ASSOCIATED WITH THESE PHENOTYPES. FINALLY, THE THIRD OBJECTIVE WILL CHARACTERISE THE MAMMARY MICROBIOTA OF THE ASSAF SHEEP SAMPLED IN OBJECTIVE 2 BY ANALYSING THE VARIABILITY OF THE 16S RRNA GENE BY SEQUENCING, TO BE USED FOR TAXONOMIC ALLOCATION AND QUANTIFICATION OF THE MAMMARY MICROBIOTA. THE AIM IS TO IDENTIFY MICROBIAL PROFILES THAT COULD HAVE A POSITIVE EFFECT ON MILK’S CHEESE YIELD. IN ADDITION, SAMPLES WITH GREATER MICROBIAL VARIABILITY WILL BE SUBJECTED TO COMPLETE SEQUENCING OF BACTERIAL DNA USING A METAGENOMIC APPROACH. TOGETHER, PROTMILKOMA AIMS, THROUGH THE MOST MODERN TOOLS AND GENOMIC TECHNOLOGIES, TO PROVIDE PRACTICAL SOLUTIONS TO THE DAIRY SHEEP SECTOR.