Deciphering signature of selection affecting beef quality traits in Angus cattle

김희발,윤준,Tadelle Dessie,조서애,오성종,이학교,김희발 한국유전학회 2018 Genes & Genomics Vol.40 No.1

Artificial selection towards a desired phenotype/ trait has modified the genomes of livestock dramatically that generated breeds that greatly differ in morphology, production and environmental adaptation traits. Angus cattle are among the famous cattle breeds developed for superior beef quality. This paper aimed at exploring genomic regions under selection in Angus cattle that are associated with meat quality traits and other associated phenotypes. The whole genome of 10 Angus cattle was compared with 11 Hanwoo (A-H) and 9 Jersey (A-J) cattle breeds using a crosspopulation composite likelihood ratio (XP-CLR) statistical method. The top 1% of the empirical distribution was taken as significant and annotated using UMD3.1. As a result, 255 and 210 genes were revealed under selection from A–H and A–J comparisons, respectively. The WebGestalt gene ontology analysis resulted in sixteen (A–H) and five (A–J) significantly enriched KEGG pathways. Several pathways associated with meat quality traits (insulin signaling, type II diabetes mellitus pathway, focal adhesion pathway, and ECM-receptor interaction), and feeding efficiency (olfactory transduction, tight junction, and metabolic pathways) were enriched. Genes affecting beef quality traits (e.g., FABP3, FTO, DGAT2, ACS, ACAA2, CPE, TNNI1), stature and body size (e.g., PLAG1, LYN, CHCHD7, RPS20), fertility and dystocia (e.g., ESR1, RPS20, PPP2R1A, GHRL, PLAG1), feeding efficiency (e.g., PIK3CD, DNAJC28, DNAJC3, GHRL, PLAG1), coat color (e.g., MC1-R) and genetic disorders (e.g., ITGB6, PLAG1) were found to be under positive selection in Angus cattle. The study identified genes and pathways that are related to meat quality traits and other phenotypes of Angus cattle. The findings in this study, after validation using additional or independent dataset, will provide useful information for the study of Angus cattle in particular and beef cattle in general.

학술발표초록 ; 육종 ( 포스터발표 ) ; 한우 genomic DNA library 구축과 fatty acid synthase ( FAS ) 유전자 동정

김희발,박응우,김형선,윤두학,김태헌,정일정,한재용 한국동물자원과학회 ( 구 한국축산학회 ) 1996 한국축산학회 심포지움자료집 Vol.- No.-

The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

이영섭,김희발,김현정,조서애 한국유전체학회 2014 Genomics & informatics Vol.12 No.4

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimatethe genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-basedprediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariancematrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package “rrBLUP” for the BLUP analysis. The SNP-SNP relationshipmatrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar toG-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other twoBLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

Reanalysis of Ohno’s hypothesis on conservation of the size of the X chromosome in mammals

김형민,김희발,이태헌,성삼선,이창규 한국통합생물학회 2012 Animal cells and systems Vol.16 No.6

In 1964, Susumu Ohno, an evolutionary biologist, hypothesized that the size of X chromosome was conserved in mammalian evolution, and that this was based on chromosomal length. Today, unlike Ohno’s method which was based on estimated lengths, we know the exact lengths of some mammalian sequences. The aim of this study was to reanalyze Ohno’s hypothesis. In mammalian species, variation in the length of the X chromosome is greater than in the autosomes; however, this variation is not statistically significant. This means that differences in chromosomal length occur equally in the X chromosome and in the autosomes. Interspersed nuclear elements and genetic rearrangements were analyzed to maintain the same variance between the length of the X chromosome and the autosomes. The X chromosome contained fewer short interspersed elements (SINEs) (0.90 on average); however, it did contain more long interspersed elements (LINEs) than did autosomes (1.56 on average). An overall correlation of LINEs and SINEs with genetic rearrangements was observed; however, synteny breaks were more closely associated with LINEs in the autosomes, and with SINEs in the X chromosome. These results suggest that the chromosomespecific activities of LINEs and SINEs result in the same variance between the lengths of the X chromosome and the autosomes. This is based on the function of interspersed nuclear elements, such as LINEs, which can inactivate the X chromosome and the reliance of non-autonomous SINEs on LINEs for transposition.

Multi-tissue observation of the long non-coding RNA effects on sexually biased gene expression in cattle

윤준,김희발 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.7

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

Identification of Stage-specific Genes Related to Porcine Folliculogenesis

이재희,이승태,김희발,임정묵 사단법인 한국동물생명공학회 2013 Reproductive & developmental biology Vol.37 No.1

Although assisted reproductive technology is very useful to develop novel and therapeutic biomaterials for reproduction, research on molecular mechanism of folliculogenesis in pig is not clear. Therefore, the alteration of gene expression during follicular development in pigs was examined in this study. The expression of folliculogenesis-related genes was quantified in preantral (250~300 μm) and antral (>300 μm in diameter) follicles, and overall gene expression was evaluated by a genome-wide microarray. The microarray results showed that 219 genes were differentially expressed, and of those, 10 and 22 known genes showed higher and less expression at the preantral stage than at antral stages, respectively. Among them, the expression of NR0B1, PPARG, GATA4, and ANXA2 genes related to folliculogenesis was validated by quantitative real-time PCR analysis. The expression of PPARG and GATA4 genes were increased at antral stages, but a significantly stage-specific increase (p<0.05) was only detected in annexin A2 (ANXA2) in antral-stage follicles. The expression of NR0B1 genes was increased at preantral stage and these patterns of gene expression were comparable to the results obtained by microarray analysis. We propose that the systematical regulation of genes supporting specific follicle stage should be employed for improved in-vitro folliculognesis.

능력검정 자료를 이용한 국내 산란계의 생산성 변화 추이와 개량 진도 추정

오봉국,최연호,김희발 한국가금학회 2009 한국가금학회 정기총회 및 학술발표회 Vol.26 No.-

The results of the official Korean chicken random sample tests for laying hens over a period of 40 years(1967 to 2007) were analysed with the statistical model and presented graphically. During the 40-year period, significant improvements of major economic traits, excluding mean body weight at 300 days of age(BW300) were documented. Age at the first egg(AGE50) decreased by 0.8 day per year, hen-day(HD500) egg production increased 0.64 % and hen-housed(HH500) egg production increased 3.2 eggs per year. Feed conversion ratio(FR500) decreased 0.027 per year. These results showed that over the past 40 years egg production has increased by 126 eggs and mean egg weight has increased by 5.5 gram. Feed conversion ratio dropped from 3.0 to 2.0. Regression coefficients for traits HD500, HH500, EW500 (mean egg weight to 500 days of age) were higher in the first 1.0-year period than during the following three 10-year periods.

발현 네트워크 분석에 기반한 난생동물과 포유동물의 각인유전자 기능 예측

김효영,문선진,김희발 한국가금학회 2007 한국가금학회 정기총회 및 학술발표회 Vol.24 No.-

Early studies have been reported that there is little evidence of imprinted genes in birds. If imprinted genes are intimately connected with acquiring resources from parents, we would not expect any in the chicken that leave their offspring to their own devices after conception. We identified the imprinted genes of human and mouse as well as orthologues in human, mouse and chicken to show how considerable conservation can be existed in distant species, chicken. This result was significant using statistical test, providing an evidence that the oviparous genome is predicted to have imprinted genes.

Genome Wide Association Studies Using Multiple-lactation Breeding Value in Holsteins

고광현,오재돈,김희발,박경도,이준호 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.3

A genome wide association study was conducted using estimated breeding value (EBV) for milk production traits from 1st to 4th lactation. Significant single nucleotide polymorphism (SNP) markers were selected for each trait and the differences were compared by lactation. DNA samples were taken from 456 animals with EBV which are Holstein proven bulls whose semen is being sold or the daughters of old proven bulls whose semen is no longer being sold in Korea. High density genome wide SNP genotype was investigated and the significance of markers associated with traits was tested using the breeding value estimated by a multiple lactation model as a dependent variant. As the result of significance comparisons by lactations, several differences were found between the first lactation and subsequent lactations (from second to 4th lactation). A similar trend was noted in mean deviation and correlation of the estimated effects by lactation. Since there was a difference in the genes associated with EBV for each trait between first and subsequent lactations, a multi-lactation model in which lactation is considered as a different trait is genetically useful. Also, significant markers in all lactations and common markers for different traits were detected, which can be used as markers for quantitative trait loci exploration and marker assisted selection in milk production traits.

학술발표초록 ; 육종 ( 포스터발표 ) ; Myo - D 유전자 동정과 다형성 분석

김형선,박응우,윤두학,김희발,김태헌,정일정 한국동물자원과학회 ( 구 한국축산학회 ) 1996 한국축산학회 심포지움자료집 Vol.- No.-