Correction: Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis.

[This corrects the article DOI: 10.1371/journal.pone.0159719.].

Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis.

Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine-cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5' splicing and alternative 3' splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis.

Two novel SNPs in HSF1 gene are associated with thermal tolerance traits in Chinese Holstein cattle.

Heat-shock transcription factors (HSFs) play an important role in regulating heat stress response. The activation of heat-shock protein (HSP) genes is mediated by HSFs, which bind to promoters of HSP genes. In this research, two novel single nucleotide polymorphisms, T909C and G4693T, and their association with thermal tolerance were investigated in 951 Chinese Holstein cattle. Linkage disequilibrium and haplotype construction were analyzed using SHEsis software. Four haplotypes were constructed, and nine haplotype combinations were found. Potassium content in erythrocytes (PCE), decreased rate of milk production (R), rectal temperature (RT), and heat-tolerance coefficient (HTC) were selected for the thermotolerance index. Association analysis showed that thermal tolerance in Chinese Holstein cattle was significantly affected by T909C and G4693T. The PCE of cows with CC or TC genotype was lower than that of TT at the 909 position (p < 0.05). Cows with TT genotype had lower PCE (p < 0.01) and higher HTC (p < 0.05) at the 4693 position. Cows with H2H4 haplotype combination had lower PCE (p < 0.01), R (p < 0.05) and RT (p < 0.05) and higher HTC (p < 0.05) than those with H1H3 haplotype combination. Bioinformatic analysis predicted that the 4693 position was located in the microRNA-binding (bta-miR-484) region. Quantitative reverse transcription-polymerase chain reaction demonstrated that 4693-T mutation caused the disruption of microRNA target binding, resulting in the relief of the transcriptional repression, which, in turn, resulted in increased expression. Thus, the HSF1 gene is useful in dairy cattle thermal tolerant breeding.

[Genetic polymorphism of k-casein gene exon 4 and its cor-relation with milk production traits in Chinese Holsteincows.].

K-casein gene was regarded as a candidate gene for milk production traits of cows. In this study, a 779 bp fragment of k-casein gene of Chinese Holstein was amplified by polymerase chain reaction (PCR), the polymorphisms of three loci of k-casein gene were detected by PCR-RFLP with restriction endonuclease Taq, Hind, Pst. After sequencing, T/C single nucleotide polymorphism (SNP) was identified at nucleotide 10 891C/A SNP was identified at nucleotide 10 927 and G/A SNP was identified at nucleotide 10 988 in exon4 of k-casein gene. Both alleles (A and B) of three loci were found in the population that showed low polymorphism. The gene frequencies of A and B were 86.03% and 13.97%, respectively. The genotype frequencies of AA, AB, and BB were 73.71%, 24.63%, and 1.66%, respectively. Statistical results of c2 test indicated that three polymorphism sites in the population fitted with Hardy-Weinberg equilibrium (P > 0.05). Meanwhile, the effect of polymorphism of k-casein gene on milk production traits was analyzed. The results indicated that in the three loci, the different genotype of k-casein gene had no significant influence on milk yield and milk protein percent (P > 0.05). The cows with genotypes BB and AB showed higher milk fat percent than those with genotype AA ( P < 0.05 ) ; with genotype AB showed higher fat protein ratio than those with genotype AA ( P < 0.05 ). The polymorphism of the three loci in the experimental population is closely linked. The conclusion is that k-casein B allele can be used as the molecular genetic markers of modifying milk fat percent in Chinese Holstein cows.