Polymorphisms in epigenetic and meat quality related genes in fourteen cattle breeds and association with beef quality and carcass traits.

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

Direct sequencing of DNA pooling for screening highly informative SNPs in dairy cattle.

In this study, 139 bovine single nuclear polymorphisms (SNPs) were firstly selected and then directly sequenced using DNA pooling. Based on the ratio of two signal peak values, 92 SNPs with the ratio over 1/2 were considered as potential highly informative markers. To further verify the reliability of screening system, 59 SNP markers were genotyped in 122 Holstein cattle using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) method. The results showed that 56 SNPs had a call rate higher than 85%. The minor allele frequency (MAF) of these 56 markers ranged from 0.27 to 0.5, with an average of 0.41; and in which 54 markers had a MAF over 0.3, covering 96.4% of this group of markers (54/56). Our findings indicate that direct sequencing of DNA pooling is a useful and efficient tool for identifying highly informative SNPs.

[Study on relationships between seven microsatellite loci and somatic cell score in Beijing Holstein cows].

Genetic variation of seven microsatellite loci BM1818, BM1258, BM1443, BM1905, BM302, BM4505 and CYP21 which were closely linked to somatic cell score (SCS) was analyzed in 240 Beijing Holstein cows with nondenaturing polyacrylamide gel electrophoresis. Allele frequencies, heterozygosity, polymorphic information content, the effective number of alleles of seven microsatellite loci were calculated. Relationships between seven microsatellite loci and somatic cell score in Beijing Holstein cows were primarily analyzed by least squares linear model. Least squares means of SCS for BM1818 (284 bp/284 bp), BM1258 (106 bp/92 bp), BM1443 (166 bp/160 bp), BM1905 (187 bp/187 bp), BM302 (142 bp/140 bp), BM4505 (240 bp/236 bp) and CYP21 (215 bp/198 bp) were relatively lower,and their genotypes were the most favorable genotypes in respective locus for mastitis resistance. Least squares means of SCS for BM1818 (286 bp/286 bp), BM1258 (102 bp/102 bp), BM1443 (170 bp/160 bp), BM1905 (197 bp/195 bp), BM302 (154 bp/145 bp), BM4505 (240 bp/238 bp) and CYP21 (204 bp/192 bp) were relatively higher,and their genotypes were the most unfavorable genotypes in respective locus for mastitis resistance. The information found in the present study would be very important for improving mastitis resistance in dairy cattle by marker assisted selection.