Non-synonymous SNPs and protein coding SNPs within the promoter region of genes (regulatory SNPs) might have a significant effect on carcass traits. Imputed sequence level data of 10,215 Hanwoo bulls, annotated and filtered to include only regulatory SNPs (450,062 SNPs), were used in a genome-wide association study (GWAS) to identify loci associated with backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). A total of 15, 176, and 1 SNPs were found to be significantly associated (p < 1.11 × 10⁻⁷) with BFT, CWT, and EMA, respectively. The significant loci were BTA4 (CWT), BTA6 (CWT), BTA14 (CWT and EMA), and BTA19 (BFT). BayesR estimated that 1.1%~1.9% of the SNPs contributed to more than 0.01% of the phenotypic variance. So, the GWAS was complemented by a gene-set enrichment (GSEA) and protein–protein interaction network (PPIN) analysis in identifying the pathways affecting carcass traits. At p < 0.005 (~2,261 SNPs), 25 GO and 18 KEGG categories, including calcium signaling, cell proliferation, and folate biosynthesis, were found to be enriched through GSEA. The PPIN analysis showed enrichment for 81 candidate genes involved in various pathways, including the PI3K-AKT, calcium, and FoxO signaling pathways. Our finding provides insight into the effects of regulatory SNPs on carcass traits.

Hanwoo was originally raised for draft purposes, but the increase in local demand for red meat turned that purpose into full-scale meat-type cattle rearing; it is now considered one of the most economically important species and a vital food source for Koreans. The application of genomic selection in Hanwoo breeding programs in recent years was expected to lead to higher genetic progress. However, better statistical methods that can improve the genomic prediction accuracy are required. Hence, this study aimed to compare the predictive performance of three machine learning methods, namely, random forest (RF), extreme gradient boosting method (XGB), and support vector machine (SVM), when predicting the carcass weight (CWT), marbling score (MS), backfat thickness (BFT) and eye muscle area (EMA). Phenotypic and genotypic data (53,866 SNPs) from 7324 commercial Hanwoo cattle that were slaughtered at the age of around 30 months were used. The results showed that the boosting method XGB showed the highest predictive correlation for CWT and MS, followed by GBLUP, SVM, and RF. Meanwhile, the best predictive correlation for BFT and EMA was delivered by GBLUP, followed by SVM, RF, and XGB. Although XGB presented the highest predictive correlations for some traits, we did not find an advantage of XGB or any machine learning methods over GBLUP according to the mean squared error of prediction. Thus, we still recommend the use of GBLUP in the prediction of genomic breeding values for carcass traits in Hanwoo cattle.

Yeonsan Ogye (YO), an indigenous Korean chicken breed (Gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short reads (376.6X) and low-depth Pacific Biosciences (PacBio) long reads (9.7X). The contig and scaffold NG50s of the hybrid de novo assembly were 362.3 Kbp and 16.8 Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single-copy orthologous genes using Benchmarking Universal Single-Copy Orthologs and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long reads (50X) and scaffolded with short reads) and superior to other avian genomes (92%–93%; assembled with short read-only or hybrid methods). Compared to galGal4 and galGal5, the draft genome included 551 structural variations including the fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing and reduced representation bisulfite sequencing data were analyzed from 20 tissues, including 4 black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long noncoding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions. We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.

The native cattle breeds are an important genetic resource for meat and milk production throughout Asia. In Asia cattle were domesticated around 10,000 years ago and in Korea cattle are being raised since 2000 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo, Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is a part of a Food and Agricultural Organization and national genetic evaluation plans, others get little attention. This study is an effort to understand and provide a detailed insight into the population structure and genetic variability of the Korean cattle breeds along with other Asian breeds using various methods. In this study we report the genetic variation and structure of the Korean cattle breeds and their comparison with five other Asian cattle breeds along with a panel of animals from European taurine, African taurine and indicine cattle breeds. Asian cattle were found to be least differentiated which reflects their recent history. Amongst the Asian breeds Hainan, which is an indicine breed, had the lowest gene diversity while Yanbian had the highest followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju Black. The genetic diversity in Asian cattle breeds was found to be comparable to the European taurines and more than the African taurines and Zebu cattle. Korean cattle breed, Brown Hanwoo was consistently found to be closer to Yanbian, a Chinese cattle breed. We found low divergence and moderate levels of genetic diversity among the native Korean breeds. Indicine introgression from Hainan was seen in other Asian breeds. From Europe, Limousin, Holstein and Hereford introgression was found in Asian breeds. In this study we provide a genome-wide insight into the genetic history of the native cattle breeds of Korea. The outcomes of this study will help in prioritization and designing of the conservation plans.

Copy number variation (CNV) has great significance both functionally and evolutionally. Various CNV studies are in progress to find the cause of human disease and to understand the population structure of livestock. Recent advances in next-generation sequencing (NGS) technology have made CNV detection more reliable and accurate at whole-genome level. However, there is a lack of CNV studies on chickens using NGS. Therefore, we obtained whole-genome sequencing data of 65 chickens including Red Jungle Fowl, Cornish (broiler), Rhode Island Red (hybrid), and White Leghorn (layer) from the public databases for CNV region (CNVR) detection. Using CNVnator, a read-depth based software, a total of 663 domesticated-specific CNVRs were identified across autosomes. Gene ontology analysis of genes annotated in CNVRs showed that mainly enriched terms involved in organ development, metabolism, and immune regulation. Population analysis revealed that CN and RIR are closer to each other than WL, and many genes (LOC772271, OR52R1, RD3, ADH6, TLR2B, PRSS2, TPK1, POPDC3, etc.) with different copy numbers between breeds found. In conclusion, this study has helped to understand the genetic characteristics of domestic chickens at CNV level, which may provide useful information for the development of breeding systems in chickens.

Hanwoo is one of the most economically important animal species in Korea due to its significant contribution to nutrition. However, the current selection index only focuses to improve carcass traits of Hanwoo. Thus, this study aimed to estimate the genetic parameters of birth weight (BW) and weaning weight (WW) and their genetic and phenotypic relationship to the age at first calving (AFC) and gestation length (GL) of Hanwoo. The genetic parameters for birth weight (BW) and weaning weight (WW) were estimated using the data obtained from 52,173 and 35,800 Hanwoo calves born from February 1998 to March 2017, respectively. Further, these data were used to determine their genetic and phenotypic correlation to age at first calving (AFC) and gestation length (GL). The heritability estimates of BW and WW and correlation coefficients were obtained using the average information restricted maximum likelihood (AIREML) procedure, fit in single and two-trait linear animal models. The estimated direct heritability for BW and WW was moderate (0.22 ± 0.02) and high (0.51 ± 0.03), respectively, while the maternal heritability for both traits was 0.12 ± 0.01 and 0.17 ± 0.01, respectively. The genetic correlation of BW and reproductive traits (AFC and GL) showed a moderate and high positive correlation coefficient of 0.33 ± 0.06 and 0.53 ± 0.02, respectively, while close to zero and low positive phenotypic correlations of 0.06 ± 0.01 and 0.21 ± 0.06 were also observed between the correlated traits, respectively. For the correlation analysis between WW and AFC, both the genetic and phenotypic correlation showed close to zero values of 0.04 ± 0.06 and −0.01 ± 0.01, respectively. Meanwhile, the genetic and phenotypic correlation between WW and GL showed low and negative correlations of −0.09 ± 0.06 and −0.09 ± 0.01, respectively. These obtained estimated variances for BW and WW and their corresponding genetic and phenotypic correlation to AFC and GL can be used as information for genetic improvement and subsequent economic improvement of Hanwoo farming.