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.

[Analysis of the genetic structure of 12 Chinese and foreign cattle breeds using DNA microsatellite markers].

The genetic diversity of 9 Chinese native cattle breeds and 3 introduced breeds were analyzed using 12 microsatellite DNA markers recommended by the Food and Agriculture Organization of the United Nations (FAO) and the International Society of Animal Genetics (ISAG) through fluorescence-multiple PCR. According to the allele frequencies of 12 microsatellite locus, mean heterozygosity (H), polymorphism information content (PIC) , DA and DS genetic distances were calculated for each breed. Cluster analysis based on UPGMA method indicated that 12 breeds were clustered into four groups. Group I belonged to the southern-China cattle including Enshi, Liping, Zhaotong and Chuannan Mountainous; Group II belonged to the central-China cattle including Jiaxian Red and Zaosheng, Pinglu Mountainous; Group III belonged to the northern-China cattle including Yanbian and Changbai; Group IV consisted of foreign breeds including Germany Yellow, Simmental and Charolais. The results may provide an academic basis for preservation and utilization of Chinese native cattle breeds.

[Analysis on the genetic structure of 8 Asia buffalo populations].

One hundred and forty seven alleles were detected when thirteen microsatellite loci were analyzed applying fluorescence-multiplex PCR technology in eight buffalo populations were analyzed, including six indigenous Chinese native breeds (DechangXinglongFuzhongWenzhouDongliuFu'an), and two introduced breeds (MurrahNili-Ravi). Seven populations have their own unique alleles, total number is twenty-three. As to all the eight populations, effective number of alleles (Ne) was between 2.2908 and 4.2308, heterozygosity (H) between 0.4951 and 0.7194, and polymorphism information content (PIC) between 0.4495 and 0.6776. Eleven of the thirteen microsatellite loci were of high polymorphism and were then the appropriate, polymorphism marker could be used to analyze properly genetic diversity of the involved buffalo populations. Cluster analysis indicated that Fuzhong and Dongliu were clustered together, then with an independent cluster of Xinglong. Wenzhou and Fu'an were clustered together, Dechang was an independent cluster. Murrah and Nili-Ravi were clustered together.