Abstract :
[en] The current study aimed to identify single nucleotide polymorphism (SNP) markers and candidate genes associated with titratable acidity (TA), total caseins (TC) and dry cheese yield (DC) predicted from MIR spectra as indirect predictors of milk cheese-making properties in early lactation cows. These predicted MIR novel phenotypes were obtained by using equations developed through GplusE and former EU projects. Only autosomes SNPs (n=29) with call rates >0.95, minor allele frequencies (MAF) >0.05 and significant deviations from Hardy-Weinberg equilibrium (P>10-7) were used for the genome-wide association study. After quality control edits, 32,687 SNPs remained for further analysis. The detection of SNPs affecting TA, TC and DC were obtained based on the proportion of variation explained by each SNP. The SNPs were considered as outliers if the proportion of variance explained was higher than 5×IQR+Q3, where IQR is the interquartile range and Q3 is the third quartile of the distribution. The putative genes located within or close to an outlier SNP were further identified. A total of 1,109 SNPs were considered as outliers with 8, 13, and 4% in common to all, between TC and DC, and between TC and TA traits, respectively. The remaining 833 were trait specific SNPs, with 18, 28, and 29% affecting TC, TA and DC, respectively. The 84 common SNPs to all traits were identified on BTA14 (75%), 1 (19%), 19 (5%) and 6 (1%). The trait specific markers were located on 26 out of 29 chromosomes. For TA, 86% of SNPs were located on chromosomes 1, 20, 7, and 14. On the other hand, TC showed the majority of SNPs on BTA6, BTA20 and BTA10 whereas for DC, SNPs were mainly on BTA5, BTA14 and BTA27. The top 5% outlier SNPs were located on BTA14, BTA1 and BTA20 with 20 (RPL8; FOXH1; CYHR1; OPLAH; HSF1; CPSF1; DGAT1; CYC1; GRINA; PARP10; NRBP2; PUF60; RNF19A; RRM2B; C8orf33; FBXO43; LY6H; ANKRD46; NAPRT; LY6E), 11 (FAM3B; MX1; HSF2BP; RRP1B; CSTB; C21orf2; LRRC3; DSCAM; ADARB1; ITGB2; MX2) and 3 (ANKH; TRIO; OTULIN) potential candidate genes affecting MIR indirect predictors (TA, TC and DC) of cheese-making properties in early lactation, respectively.
