Genome wide QTL mapping to identify candidate genes for carcass traits in Hanwoo (Korean Cattle)

이승환,Julius van der Werf,이상홍,임다정,박응우,Cedric Gondro,윤두학,오성종,김언현,John Gibson,John Thompson 한국유전학회 2012 Genes & Genomics Vol.34 No.1

Meat quality traits are the most economically important traits affecting the beef industry in Korea. We performed a whole genome quantitative trait locus (QTL) mapping study of carcass data in Hanwoo Korean cattle. Two hundred sixty-six Hanwoo steers from 65 sires were genotyped using a 10K Affymetrix SNP chip. The average SNP interval across the bovine genome was 1.5Mb. Associations between each individual SNP and four carcass traits [carcass weight (CWT),eye muscle area (EMA), back fat thickness (BFT), and marbling (MAR)] were assessed using a linear mixed model of each trait. Combined linkage and linkage disequilibrium analysis (LDLA) detected six potential QTL on BTA04, 06, 13,16, 17, and 23 at the chromosome-wise level (P<0.05). Two MAR QTL were detected at 52.2 cM of BTA06 and 46.04cM of BTA17. We identified three genes (ARAP2,LOC539460, and LOC511424) in the QTL region of BTA06and seven genes (RPS14, SCARB1, LOC782103, BRI3BP,AACS, DHX37, and UBC) in the QTL region of BTA17. One significant QTL for CWT was detected at 100 cM on BTA04and the corresponding QTL region spanned 1.7 cM from 99.7to 101.4 cM. For EMA QTL, one significant QTL was detected at 3.9 cM of BTA23 and the most likely QTL interval was 1.4 cM, placing 15 candidate genes in the marker bracket. Finally, two QTL for BFT were identified at 68 cM on BTA13and 24 cM on BTA16. The LPIN3 gene, which is functionally associated with lipodystrophy in humans, is located in the BFT QTL on BTA13. Thus, two potential candidate genes, acetoacetyl-CoA synthetase (AACS) and lipin (LPIN), were detected in QTL regions on BTA17 for MAR and BTA13 for BFT,respectively. In conclusion, LDLA analysis can be used to detect chromosome regions harboring QTL and candidate genes with a low density SNP panel, yielding relatively narrow confidence intervals regarding location.

Parameter estimation and assessment of bias in genetic evaluation of carcass traits in Hanwoo cattle using real and simulated data

Mohammed Bedhane,Julius van der Werf,Sara de las Heras-Saldana,Leland Ackerson IV,Dajeong Lim,박병호,박미나,Seung-Hee Roh,Samuel Clark 한국축산학회 2023 한국축산학회지 Vol.65 No.6

Most carcass and meat quality traits are moderate to highly heritable, indicating that they can be improved through selection. Genetic evaluation for these types of traits is performed using performance data obtained from commercial and progeny testing evaluation. The performance data from commercial farms are available in large volume, however, some drawbacks have been observed. The drawback of the commercial data is mainly due to sorting of animals based on live weight prior to slaughter, and this could lead to bias in the genetic evaluation of later measured traits such as carcass traits. The current study has two components to address the drawback of the commercial data. The first component of the study aimed to estimate genetic parameters for carcass and meat quality traits in Korean Hanwoo cattle using a large sample size of industry-based carcass performance records (n = 469,002). The second component of the study aimed to describe the impact of sorting animals into different contemporary groups based on an early measured trait and then examine the effect on the genetic evaluation of subsequently measured traits. To demonstrate our objectives, we used real performance data to estimate genetic parameters and simulated data was used to assess the bias in genetic evaluation. The results of our first study showed that commercial data obtained from slaughterhouses is a potential source of carcass performance data and useful for genetic evaluation of carcass traits to improve beef cattle performance. However, we observed some harvesting effect which leads to bias in genetic evaluation of carcass traits. This is mainly due to the selection of animal based on their body weight before arrival to slaughterhouse. Overall, the non-random allocation of animals into a contemporary group leads to a biased estimated breeding value in genetic evaluation, the severity of which increases when the evaluation traits are highly correlated.

Genetic polymorphisms of the bovine <i>Fatty acid binding protein 4</i> gene are significantly associated with marbling and carcass weight in Hanwoo (<i>Korean Cattle</i>)

Lee, S. H.,van der Werf, J. H. J.,Lee, S. H.,Park, E. W.,Oh, S. J.,Gibson, J. P.,Thompson, J. M. Blackwell Publishing Ltd 2010 Animal genetics Vol.41 No.4

<P>Summary</P><P>The objective of this study was to investigate an association between polymorphisms in the <I>FABP4</I> gene and phenotypic variation for marbling and carcass weight (CWT) in a population of Hanwoo steers. We re-sequenced 4.3 kb of the <I>FABP4</I> gene region in 24 Hanwoo bulls and identified 16 SNPs and 1 microsatellite polymorphism. Of these 16 SNPs, three SNPs [g.2774G>C (intron I), g.3473A>T (intron II) and g.3631G>A (exon III, creating a p.Met >Val amino acid substitution)] were genotyped in 583 steers to assess their association with carcass traits. The g.3473A allele showed a significant increasing effect on CWT (<I>P = </I>0.01) and the g.3631G allele was associated with higher marbling score (<I>P = </I>0.006). One haplotype of these three SNPs (CAG) was significantly associated with CWT (<I>P = </I>0.02) and marbling score (<I>P = </I>0.05) and could potentially be of value for marker assisted selection in Hanwoo cattle. The CAG haplotype effect for CWT was larger (11.14 ± 5.03 kg) than the largest single locus effect of g.3473A>T (5.01 ± 2.2 kg).</P>

<i>hsphase</i> : an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups

Ferdosi, Mohammad H,Kinghorn, Brian P,van der Werf, Julius HJ,Lee, Seung Hwan,Gondro, Cedric BioMed Central 2014 BMC bioinformatics Vol.15 No.-

<P><B>Background</B></P><P>Identification of recombination events and which chromosomal segments contributed to an individual is useful for a number of applications in genomic analyses including haplotyping, imputation, signatures of selection, and improved estimates of relationship and probability of identity by descent. Genotypic data on half-sib family groups are widely available in livestock genomics. This structure makes it possible to identify recombination events accurately even with only a few individuals and it lends itself well to a range of applications such as parentage assignment and pedigree verification.</P><P><B>Results</B></P><P>Here we present <I>hsphase</I>, an R package that exploits the genetic structure found in half-sib livestock data to identify and count recombination events, impute and phase un-genotyped sires and phase its offspring. The package also allows reconstruction of family groups (pedigree inference), identification of pedigree errors and parentage assignment. Additional functions in the package allow identification of genomic mapping errors, imputation of paternal high density genotypes from low density genotypes, evaluation of phasing results either from <I>hsphase</I> or from other phasing programs. Various diagnostic plotting functions permit rapid visual inspection of results and evaluation of datasets.</P><P><B>Conclusion</B></P><P>The <I>hsphase</I> package provides a suite of functions for analysis and visualization of genomic structures in half-sib family groups implemented in the widely used R programming environment. Low level functions were implemented in C++ and parallelized to improve performance. <I>hsphase</I> was primarily designed for use with high density SNP array data but it is fast enough to run directly on sequence data once they become more widely available. The package is available (GPL 3) from the Comprehensive R Archive Network (CRAN) or from http://www-personal.une.edu.au/~cgondro2/hsphase.htm.</P>

Detection of recombination events, haplotype reconstruction and imputation of sires using half-sib SNP genotypes

Ferdosi, Mohammad H,Kinghorn, Brian P,van der Werf, Julius H J,Gondro, Cedric BioMed Central 2014 Genetics, selection, evolution Vol.46 No.1

<P><B>Background</B></P><P>Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring’s sequence based on sequence data of the sire.</P><P><B>Methods</B></P><P>The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire’s genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R<SUP>2</SUP>) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs – AlphaPhase, BEAGLE and PedPhase 3.</P><P><B>Results</B></P><P>Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE.</P><P><B>Conclusions</B></P><P>In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).</P>

Effectiveness of herbal medicines to prevent and control symptoms of urinary tract infections and to reduce antibiotic use: A literature review

Hermanvan Wietmarschen,Noortjevan Steenbergen,Esther van der Werf,Erik Baars 한국한의학연구원 2022 Integrative Medicine Research Vol.11 No.4

Background Antimicrobial resistance is a rapidly growing global issue affecting the effective treatment of infectious diseases. This provides a window of opportunity for the use and implementation of well researched effective complementary therapies such as herbal medicines. In this literature review, an overview is provided of the effectiveness of herbal medicine to control symptoms of urinary tract infections and reduce antibiotic use. Methods PubMed, CAM-Quest, CORE-Hom, ScienceDirect, CAMBase, Anthromedics.org and AnthroMedLibrary databases were searched for peer-reviewed meta-analyses, systematic reviews and randomized controlled trials from 2005 till 8 October 2020. Included were clinical studies on the use of herbal medicine for clinically diagnosed urinary tract infection with any control group except another herbal medicine. Study quality was assessed using the Joanna Briggs Institute critical appraisal tools. Results Of the 408 citations identified, 23 met the inclusion criteria: 5 meta-analyses, 3 systematic reviews and 15 randomized controlled trials. Of these studies 13 involved the use of cranberry products, 4 studies concerned traditional Chinese herbal medicines, and 6 studies dealt with other herbal medicines. Conclusions The latest published meta-analysis including 28 trials reports a clear benefit of Cranberry products for the prevention of recurrent UTIs in women. Five TCM formulas were found to be equally or more effective than antibiotics in the treatment of UTIs. Furthermore, Rosa canina seems to have the potential to prevent UTI in women undergoing a caesarean section. ‘Acidif Plus Tablets’ as well as ‘Canephron’ seem to be promising candidates for treating women with uncomplicated recurrent UTI.

Genetic Relationships among Australian and Mongolian Fleece-bearing Goats

Bolormaa, S.,Ruvinsky, A.,Walkden-Brown, S.,van der Werf, J. Asian Australasian Association of Animal Productio 2008 Animal Bioscience Vol.21 No.11

Microsatellites (MS) are useful for quantifying genetic variation within and between populations and for describing the evolutionary relationships of closely related populations. The main objectives of this work were to estimate genetic parameters, measure genetic distances and reconstruct phylogenetic relationships between Australian Angora/Angora_Aus/ and Cashmere/Cashmere_Aus/ populations and three Mongolian Cashmere goat (Bayandelger/BD/, Zavkhan Buural/ZB/, and Gobi Gurvan Saikhan/GGS/) populations based on variation at fourteen MS loci. The level and pattern of observed and expected heterozygosity and polymorphic information content of the fourteen loci studied across the populations were quite similar and high. Except for SRCRSP07, all studied microsatellites were in Hardy-Weinberg Equilibrium (p<0.001). Moderate genetic variation (7.5%) was found between the five goat populations with 92.5% of total genetic variation attributable to diversity existing between the individuals within each population. The greatest Nei's genetic distances were found between the Angora and four Cashmere populations (0.201-0.276) and the lowest distances were between the Mongolian Cashmere goat populations (0.026-0.031). Compared with other Cashmere goat populations, the GGS (crossbred with Russian Don Goats) population had the smallest pairwise genetic distance from the Australian Angora population (0.192). According to a three-factorial correspondence analysis (CA), the three different Mongolian Cashmere populations could hardly be distinguished from each other.

Genetic parameters and inbreeding effects for production traits of Thai native chickens

Siriporn Tongsiri,Gilbert M. Jeyaruban,Susanne Hermesch,Julius H.J. van der Werf,Li Li,Theerachai Chormai 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.7

Objective: Estimate genetic parameters, the rate of inbreeding, and the effect of inbreeding on growth and egg production traits of a Thai native chicken breed Lueng Hang Kao Kabinburi housed under intensive management under a tropical climate. Methods: Genetic parameters were estimated for weight measured at four weekly intervals from body weight at day 1 (BW1D) to body weight at 24 weeks (BW24) of age, as well as weight at first egg, age at first egg (AFE), egg weight at first egg, and total number of eggs (EN) produced during the first 17 weeks of lay using restricted maximum likelihood. Inbreeding depression was estimated using a linear regression of individual phenotype on inbreeding coefficient. Results: Direct additive genetic effect was significant for all traits. Maternal genetic effect and permanent environmental hen effects were significant for all early growth traits, expect for BW24. For BW24, maternal genetic effect was also significant. Permanent environmental hen effect was significant for AFE. Direct heritabilities ranged from 0.10 to 0.47 for growth traits and ranged from 0.15 to 0.16 for egg production traits. Early growth traits had high genetic correlations between them. The EN was lowly negatively correlated with other traits. The average rate of inbreeding for the population was 0.09% per year. Overall, the inbreeding had no effect on body weight traits, except for BW1D. An increase in inbreeding coefficient by 1% reduced BWID by 0.09 g (0.29% of the mean). Conclusion: Improvement in body weight gain can be achieved by selecting for early growth traits. Selection for higher body weight traits is expected to increase the weight of first egg. Due to low but unfavorable correlations with body weight traits, selection on EN needs to be combined with other traits via multi-trait index selection to improve body weight and EN simultaneously.

Genetic parameters for milk yield in imported Jersey and JerseyFriesian cows using daily milk records in Sri Lanka

Samaraweera Amali Malshani,Boerner Vinzent,Cyril Hewa Waduge,van der Werf Julius,Hermesch Susanne 아세아·태평양축산학회 2020 Animal Bioscience Vol.33 No.11

Objective: This study was conducted to estimate genetic parameters for milk yield traits using daily milk yield records from parlour data generated in an intensively managed commercial dairy farm with Jersey and Jersey-Friesian cows in Sri Lanka. Methods: Genetic parameters were estimated for first and second lactation predicted and realized 305-day milk yield using univariate animal models. Genetic parameters were also estimated for total milk yield for each 30-day intervals of the first lactation using univariate animal models and for daily milk yield using random regression models fitting second-order Legendre polynomials and assuming heterogeneous residual variances. Breeding values for predicted 305-day milk yield were estimated using an animal model. Results: For the first lactation, the heritability of predicted 305-day milk yield in Jersey cows (0.08±0.03) was higher than that of Jersey-Friesian cows (0.02±0.01). The second lactation heritability estimates were similar to that of first lactation. The repeatability of the daily milk records was 0.28±0.01 and the heritability ranged from 0.002±0.05 to 0.19±0.02 depending on day of milk. Pearson product-moment correlations between the bull estimated breeding values (EBVs) in Australia and bull EBVs in Sri Lanka for 305-day milk yield were 0.39 in Jersey cows and –0.35 in Jersey-Friesian cows. Conclusion: The heritabilities estimated for milk yield in Jersey and Jersey-Friesian cows in Sri Lanka were low, and were associated with low additive genetic variances for the traits. Sire differences in Australia were not expressed in the tropical low-country of Sri Lanka. Therefore, genetic progress achieved by importing genetic material from Australia can be expected to be slow. This emphasizes the need for a within-country evaluation of bulls to produce locally adapted dairy cows.