Additional file 1: Figure S1. of A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

MDS plot of the 20 breeds. Each color in the plot corresponds to the color in the legend. Figure S2. Provesti’s genetic distances based Neighbor-Joining tree of 20 cattle breeds. Tree is clearly divided into three groups - one group consists of the Zebu and composite cattle, one consists of European taurine and one group is formed entirely of Asian breeds, mostly Korean. Figure S3. DAPC plot of four Korean breeds. This includes Chosun cattle (CS) breed which was later removed from the study. Figure S4. Optimum value of k for the admixture analysis. (DOCX 233 kb

Additional file 2: Table S1. of A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds

Pairwise Fst values between 20 populations used in the study. Table S2. Absolute genetics distance or Provesti’s distance between the 20 cattle populations used in the study. (DOCX 26 kb

Additional file 1: of Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

Table S1. Summary of sequencing data (DOCX 28 kb

Additional file 4: of Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

Protein sequences which have locations with depth > 10×. (XLSX 101 kb

Additional file 3: of Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes

FASTA sequences for scaffolds which have locations with depth > 10×. (XLSX 9907 kb

Artificial selection increased body weight but induced increase of runs of homozygosity in Hanwoo cattle

<div><p>Artificial selection has been demonstrated to have a rapid and significant effect on the phenotype and genome of an organism. However, most previous studies on artificial selection have focused solely on genomic sequences modified by artificial selection or genomic sequences associated with a specific trait. In this study, we generated whole genome sequencing data of 126 cattle under artificial selection, and 24,973,862 single nucleotide variants to investigate the relationship among artificial selection, genomic sequences and trait. Using runs of homozygosity detected by the variants, we showed increase of inbreeding for decades, and at the same time demonstrated a little influence of recent inbreeding on body weight. Also, we could identify ~0.2 Mb runs of homozygosity segment which may be created by recent artificial selection. This approach may aid in development of genetic markers directly influenced by artificial selection, and provide insight into the process of artificial selection.</p></div

Blood transcriptome comparison between sexes and their function in 4-week Rhode Island red chickens

Sex is a major biological factor in the development and physiology of a sexual reproductive organism, and its role in the growing process is needed to be investigated in various species. We compare blood transcriptome between 5 males and 5 females in 4-week-old Rhode Island Red chickens and perform functional annotation of differentially expressed genes (DEGs). The results are as follows. 141 and 109 DEGs were located in autosomes and sex chromosomes, respectively. The gene ontology (GO) terms are significantly (p p SMAD2W and the BMP5 were involved in the TGF-beta signaling pathway, and both play an important role in maintaining tissue development. The major DEGs related to the development of neurons and synapses include the up-regulated NRN1, GDF10, SLC1A1, BMP5, NBEA, and NRXN1. Also, 7 DEGs were validated using RT-qPCR with high correlation (r2 = 0.74). In conclusion, the differential expression of blood tissue in the early growing chicken was enriched in TGF-beta signaling and related to the development of neurons and synapses including SMAD2W and BMP5. These results suggest that blood in the early growing stage is differentially affected in tissue development, nervous system, and pigmentation by sex. For future research, experimental characterization of DEGs and a holistic investigation of various tissues and growth stages will be required.</p

Candidate regions associated with years.

<p>Statistical test using Analysis 1 was performed. Only the regions with Pvalue less than 0.01 are shown.</p

Candidate regions associated with cattle body weight.

<p>Statistical test using Analysis 2 was performed. Only the regions with Pvalue less than 0.01 are shown.</p

Scatterplots for KPN, F_roh, Body weight.

<p>Correlation between each elements was tested by spearman’s method. KPN vs F_roh: ρ = 0.46697, p-value = 5.203e-08; F_roh vs Body weight: ρ = -0.03930, p-value = 0.69900; KPN vs Body weight: ρ = 0.33921, p-value = 0.00059.</p