List of genes and the number of variants in the highly variable regions of SNVs and InDels.

<p>The number of variants was based on the result of multi-sample calling from GATK.</p><p>List of genes and the number of variants in the highly variable regions of SNVs and InDels.</p

Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.

<p>The red line denotes the top 1% of empirical distribution.</p

Summary of sequencing information and rawdata QC result using trimmomatic.

<p>Coverage was calculated based on the size of reference genome Galgal4(1046.93MB).</p><p>Summary of sequencing information and rawdata QC result using trimmomatic.</p

List of commonly predicted genes from assembled sequences of each sample.

<p>List of commonly predicted genes from assembled sequences of each sample.</p

Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.

<p>Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.</p

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (<i>Coturnix coturnix</i> japonica)

<div><p>Japanese quail (<i>Coturnix coturnix</i> japonica) reach sexual maturity earlier, breed rapidly and successfully, and cost less and require less space than other birds raised commercially. Given the value of this species for food production and experimental use, more studies are necessary to determine chromosomal regions and genes associated with gender and breed-differentiation. This study employed <i>Trinity</i> and <i>edgeR</i> for transcriptome analysis of next-generation RNA-seq data, which included 4 tissues obtained from 3 different breeding lines of Japanese quail (random bred control, heavy weight, low weight). Differentially expressed genes shared between female and male tissue contrast groups were analyzed to identify genes related to sexual dimorphism as well as potential novel candidate genes for molecular sexing. Several of the genes identified in the present study as significant sex-related genes have been previously found in avian gene expression analyses (<i>NIPBL</i>, <i>UBAP2</i>), and other genes found differentially expressed in this study and not previously associated with sex-related differences may be considered potential candidates for molecular sexing (<i>TERA</i>, <i>MYP0</i>, <i>PPR17</i>, <i>CASQ2</i>). Additionally, other genes likely associated with neuronal and brain development (<i>CHKA</i>, <i>NYAP</i>), as well as body development and size differentiation (<i>ANKRD26</i>, <i>GRP87</i>) in quail were identified. Expression of homeobox protein regulating genes (<i>HXC4</i>, <i>ISL1</i>) shared between our two sex-related contrast groups (Female Brain vs. Male Brain and Ovary vs. Testis) indicates that these genes may regulate sex-specific anatomical development. Results reveal genetic features of the quail breed and could allow for more effective molecular sexing as well as selective breeding for traits important in commercial production.</p></div

Summary of RNA-seq samples and their mapping rate

<p>Summary of RNA-seq samples and their mapping rate</p

Top 10 most significant DEGs between HW and LW Quail.

<p>*The log2 fold change (log FC), log2 counts-per-million (logCPM), and P-values were calculated using edgeR.</p><p>^Expanded gene names, listed in alphabetical order: ANR26 = ANR26 protein-coding gene; CHKA = choline kinase alpha; GPR87 = G protein-coupled receptor 87; IFI6 = Interferon, Alpha-Inducible Protein 6; MSLNL = Mesothelin-Like; MTA70 = Methyltransferase Like 3; NYAP1 = Neuronal Tyrosine-Phosphorylated Phosphoinositide-3-Kinase Adaptor 1; OASL2 = 2'-5'-oligoadenylate synthase-like protein 2; RBBP7 = Retinoblastoma Binding Protein 7; T22D1 = Inosine-5'-monophosphate dehydrogenase</p><p>Top 10 most significant DEGs between HW and LW Quail.</p

Whole-Genome Analyses of Korean Native and Holstein Cattle Breeds by Massively Parallel Sequencing

<div><p>A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.</p></div