Accounting for Population Structure and Phenotypes From Relatives in Association Mapping for Farm Animals: A Simulation Study

Several methods are available for genome-wide association analysis, including the classical GWAA (cGWAA) based on fixed, single-SNP regression; efficient mixed-model association expedited (EMMAX) that fits single-SNP regressions together with a relationship matrix to account for population structure; and single-step GWAA (ssGWAA) where all data, including non-genotyped animals, are used. The objectives of this study were to: 1) investigate the ability of ssGWAA to account for population structure and correctly identify quantitative trait nucleotides (QTN); and 2) compare ssGWAA with cGWAA and EMMAX. Three simulated datasets were used, which mimic fish, beef cattle, and dairy cattle populations. The fish population was composed of 2,040 fish, out of which 1,040 were genotyped and had phenotypes for a trait with heritability of 0.25. The beef cattle population had 6,010 animals in the pedigree, but only 1,500 with phenotypes (h2 = 0.35) and genotypes. Lastly, the dairy cattle population had 40,800 pedigreed animals, of which 20,000 females had phenotypes (h2 = 0.32) and 2,400 males were genotyped. All phenotypes, pedigree, and genotypes were used in ssGWAA, whereas only genotypes and phenotypes were used in cGWAA and EMMAX for the fish and beef cattle analyses. For the dairy cattle analysis using the last two methods, deregressed proofs had to be used instead of phenotypes. The ability to correctly identify QTN and the number of statistically significant SNP (P < 0.05/number of SNP) was assessed among methods. In all populations, cGWAA was able to identify some of the strongest QTN but showed a large number of false positives. EMMAX and ssGWAA did not show false associations and correctly identified the top QTN, with more signals observed in ssGWAA. The ssGWAA accounts for population structure and is a proper association method, especially for livestock populations where sparse genotyping is a reality and phenotypes may not be recorded in genotyped animals.

Temperament (docility) is a key breeding goal in the cattle industry due to its direct relationship with animal welfare, cattle handler's safety and animal productivity. Over the past six decades, numerous studies have reported heritability estimates for temperament-related traits in cattle populations ranging from low to high values. Therefore, the primary objective of this study was to perform a comprehensive systematic review with meta-analysis to obtain weighted estimates of heritability for temperament-related traits in worldwide cattle populations. After data editing and quality control, 106 studies were included in the systematic review, of which 29.2% and 70.8% reported estimates of heritability for temperament-related traits in dairy and beef cattle populations, respectively. Meta-analyses were performed for 95 heritability estimates using a random model approach. The weighted heritability estimates were as follow: (a) flight score at weaning = 0.23 (95% CI: 0.15-0.32); (b) flight speed at weaning = 0.30 (95% CI: 0.26-0.33); (c) joint analysis of flight speed and flight score at weaning = 0.27 (95% CI: 0.22-0.31); (d) flight speed at yearling = 0.26 (95% CI: 0.21-0.30); (e) joint analysis of flight speed at weaning and yearling = 0.27 (95% CI: 0.24-0.30); (f) movement score = 0.12 (95% CI: 0.08-0.15); (g) crush score at weaning = 0.21 (95% CI: 0.17-0.25); (h) pen score at weaning = 0.27 (95% CI: 0.19-0.34); (i) pen score at yearling = 0.20 (95% CI: 0.17-0.23); (j) joint analysis of pen score at weaning and yearling = 0.22 (95% CI: 0.18-0.26); (k) cow's aggressiveness at calving = 0.10 (95% CI: 0.01-0.19); (l) general temperament = 0.13 (95% CI: 0.06-0.19); (m) milking temperament = 0.16 (95% CI: 0.11-0.21); and (n) joint analysis of general and milking temperament = 0.14 (95% CI: 0.11-0.18). The heterogeneity index ranged from 0% to 77%, and the Q-test was significant (p < 0.05) for four single-trait meta-analyses. In conclusion, temperament is moderately heritable in beef cattle populations, and flight speed at weaning had the highest weighted heritability estimate. Moreover, between-study heterogeneity was low or moderate in beef cattle traits, suggesting reasonable standardization across studies. On the other hand, low-weighted heritability and high between-study heterogeneity were estimated for temperament-related traits in dairy cattle, suggesting that more studies are needed to better understand the genetic inheritance of temperament in dairy cattle populations.

Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12428767 genotypes in total post-editing) and 80 sheep (1557360 SNPs genotypes in total post-editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of <0.300, 0.300-0.549, and ≥0.550 in the cattle (sheep in parenthesis) was 0.9467 (0.9864), 0.9707 (0.9953), and 0.9994 (0.99997) respectively; the respective allele concordance rate was 0.9730 (0.9930), 0.9849 (0.9976), and 0.9997 (0.99998). Hence, concordance eroded as the GC score of the called genotype reduced, albeit the impact was not dramatic and was not very noticeable until a GC score of <0.55. Moreover, the impact was greater and more consistent in the cattle population than in the sheep population. Furthermore, an impact of GC score on genotype concordance rate existed even for the same SNP GenTrain value; the GenTrain value is a statistical score that depicts the shape of the genotype clusters and the relative distance between the called genotype clusters.

One important factor in determining beef cattle development policies is knowing the trend model for beef cattle production and population based on a large of data. This research aims to analyze the trend model of beef cattle production and population and predict them. The data collected from 2011 to 2020 consists of the production and population of beef cattle. Data was taken from the West Papua Province Livestock and Animal Health Service. The trend models and prediction data were analyzed using Minitab version 17. The research showed that the contribution of beef cattle production and population in Manokwari to West Papua is 0.251 and 0.354, respectively. The results of the trend model for the production and population of beef cattle are Yt = 1475291- 440243t + 47760t^2 and Yt = 21626-3t-14t^2, respectively. It can be concluded that the growth rate of the beef cattle population and production in Manokwari is -0.364% and 13%, respectively. Based on the model, in 2026 the number of beef cattle in Manokwari started to decline, and vice versa, production increased in 2025.

Copy number variants (CNVs) are a form of genomic variation that changes the structure of the genome through deletion or duplication of stretches of DNA. The objective of the present study was to characterize CNVs in a large multibreed population of beef and dairy bulls. The CNVs were called on the autosomes of 5,551 cattle from 22 different beef and dairy breeds, using 2 freely available software suites, QuantiSNP and PennCNV. All CNVs were classified into either deletions or duplications. The median concordance between PennCNV and QuantiSNP, per animal, was 18.5% for deletions and 0% for duplications. The low concordance rate between PennCNV and QuantiSNP indicated that neither algorithm, by itself, could identify all CNVs in the population. In total, PennCNV and QuantiSNP collectively identified 747,129 deletions and 432,523 duplications; 80.2% of all duplications and 69.1% of all deletions were present only once in the population. Only 0.154% of all CNVs identified were present in more than 50 animals in the population. The distribution of the percentage of the autosomes that were composed of deletions, per animal, was positively skewed, as was the distribution for the percentage of the autosomes that were composed of duplications, per animal. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of deletions were 0.019%, 0.037%, and 0.201%, respectively. The first quartile, median, and third quartile of the distribution of the percentage of the autosomes that were composed of duplications were 0.013%, 0.028%, and 0.076%, respectively. The distributions of the number of deletions and duplications per animal were both positively skewed. The interquartile range for the number of deletions per animal in the population was between 16 and 117, whereas for duplications it was between 8 and 23. Per animal, there tended to be twice as many deletions as duplications. The distribution of the length of deletions was positively skewed, as was the distribution of the length of duplications. The interquartile range for the length of deletions in the population was between 25 and 101 kb, and for duplications the interquartile range was between 46 and 235 kb. Per animal, duplications tended to be twice as long as deletions. This study provides a description of the characteristics and distribution of CNVs in a large multibreed population of beef and dairy cattle.

Greenhouse gas emissions from the enteric fermentation and manure storage of dairy and beef cattle in China during 1961–2010

The purpose of this study was to determine the capacity of agricultural crop waste for large ruminants Feed-in Bireun District. This research uses primary and secondary data sources. The observed variables consisted of beef cattle and buffalo population, production of feed crop waste, the requirement for digested dry matter (DDM), and the capacity of the DDM from food crop waste as large ruminant feed. The data is presented descriptively in the form of data processing results from secondary data with previous studies’ results. The beef cattle population in Bireun Regency is 38,151.44 livestock units (LU) and buffalo 1. 552 LU. The requirement of forage is 45,261.92 tons of DDM per year. DDM production per year from agricultural crop waste from rice, corn, and soybeans is 63,315.28 tons of DDM per year. The highest production of DDM is derived from rice crop waste amounting to 36,653.68 tons per year, while DDM originated from corn crop waste 3,637.5 tons per year and soybeans 23,024.1 tons per year. The potential of forage feed from food crop waste is 54,901.73 tons of DDM per year and can still be used for 48,159.41 LU. It was concluded that Bireun Regency could increase the population of ruminant animals by increasing the benefits of forage originating from food crop waste.

Penelitian bertujuan untuk mengetahui nilai pertumbuhan alami (natural increase) sapi potong dan faktor-faktor yang mempengaruhinya di Kecamatan Pangkalan Lada Kabupaten Kotawaringin Barat. Penelitian ini bersifat deskriptif analitik dengan penentuan responden berdasarkan purposive sampling. Jumlah sampel yang digunakan dalam penelitian adalah 178 responden dari 10 desa dengan total populasi sapi potong 713 ekor terdiri atas 3 (tiga) bangsa sapi yaitu sapi Bali (457 ekor), sapi Limosin (151 ekor) dan sapi Simental (105 ekor). Peubah yang diamati meliputi karakteristik peternak dan usaha peternakan, struktur populasi sapi potong, dinamika populasi sapi potong dan natural increase. Hasil penelitian menunjukkan struktur populasi sapi potong berdasarkan umur di Kecamatan Pangkalan Lada sebagai berikut: pedet jantan (6,45%), pedet betina (13,88%), jantan muda (4,07%), betina muda (10,80%), jantan dewasa (22,30%) dan betina dewasa (42,50%). Calf crop sapi potong (65,91%) sedangkan rasio sex sapi potong jantan banding betina adalah (31,72% : 68,28%). Persentase kelahiran sapi potong terhadap induk (65,91%); Persentase kelahiran sapi potong terhadap sampel (21,64%). Persentase kematian sapi potong (1,34%). Persentase natural increase sapi sapi potong di Kecamatan Pangkalan Lada (20,30%). Kesimpulannya struktur populasi sapi potong di Kecamatan Pangkalan Lada didominasi oleh jantan dan betina dewasa. Natural increase sapi potong di Kecamatan Pangkalan Lada tergolong rendah, sedangkan faktor-faktor yang berpengaruh terhadap natural increase adalah tingkat kelahiran rendah, tingkat kematian tinggi dan populasi betina dewasa produktif rendah. ABSTRACT The research aims to determine the value of natural increase and factors that influence the value of natural increase of beef cattle in Pangkalan Lada District, West Kotawaringin Regency. This research is descriptive analytical. by determining respondents based on purposive sampling. The number of samples used in the research was 178 respondents from 10 villages with a total beef cattle population of 713 heads consisting of 3 (three) breeds of cattle, namely Bali cattle (457 heads), Limosin cattle (151 heads) and Simental cattle (105 heads). The parameters observed include the characteristics of breeders and livestock businesses, beef cattle population structure, beef cattle population dynamics and Natural Increase. The results of the research show that the population structure of beef cattle based on age in Pangkalan Lada District is as follows: male calf (6.45%), female calf (13.88%), young bull (4.07%), heifer (10.80% ), bull (22.30%) and cow (42.50%). Calf crop beef cattle (65.91%) while the sex ratio of male to female beef cattle is (31.72% : 68.28%) The percentage of beef cattle births to mothers is (65.91%); The percentage of beef cattle births in the sample was (21.64%). The percentage of beef cattle deaths is (1.34%). The percentage of natural increase in beef cattle in Pangkalan Lada District is (20.30%). Conclusion: The population structure of beef cattle in Pangkalan Lada District is dominated by bull and cow. The natural increase in beef cattle in Pangkalan Lada District is relatively low, while the factors that influence the natural increase are low birth rates, high death rates and low productive cow population.

To investigate relationships between serological titres to 2 serovars, pomona (L. pomona) and hardjo (L. hardjo), of Leptospira interrogans and abortions, log linear and logit models were fitted to herd and individual cow data from cattle serologically negative for brucellosis. Serological titres to both serovars were significantly related to abortions in individual cows, with L. pomona having a stronger relationship than L. hardjo. L. hardjo was not significant when herd data were analysed. Differences between dairy and beef cattle in the serological titres found to both L. pomona and L. hardjo were detected when data sets of all cattle or cattle with no history of abortion were analysed. The beef/dairy differences may be due to different management practices and/or to different geographical distributions of both serovars and populations of beef and dairy cattle. If there are no cattle in a herd with a reciprocal titre of 3000 or greater for L. pomona, it is unlikely that L. pomona is associated with the abortion problem. There was no specific L. hardjo titre which separated high and low probabilities that the serum came from a cow or herd with an abortion history.

Received: 2016-02-23  |  Accepted: 2016-04-21  |  Available online: 2016-05-30 dx.doi.org/10.15414/afz.2016.19.02.59-63 The aim of the paper was to evaluate trends in inbreeding and loss of genetic diversity in four beef cattle breeds (Blonde d´Aquitaine-BA, Charolais-CH, Limousine-LI, Simmental-SM). The highest ratio of inbred animals was found in the SM breed (63.6 %) and the lowest in the LI (14.1 %). The highest average inbreeding intensity we found in the SM, the lowest in the BA. The amount of genetic diversity in the reference population accounting for diversity loss due to genetic drift and unequal founder contributions was the highest in the SM (6.2 %), following the BA (3.5 %), LI (1.1 %) and CH (0.9 %). The proportion of genetic diversity lost due to genetic drift was higher in BA, CH, LI than the loss of genetic diversity due to unequal founder contribution. Keywords: beef cattle, pedigree analysis, inbreeding, genetic diversity References Boichard, D., Maignel,L. and Verrier. E. (1997) The value of using probabilities of gene origin to measure genetic variability in a population. Genet. Sel. Evol ., vol.29, no. 5, pp.5-23. doi: http://dx.doi.org/10.1186/1297-9686-29-1-5 Cabalero, A. and Toro, M.A. (2000) Interrelations between effective population size and other tools for management of conserved populations. Genet. Res ., vol. 75, no. 3, pp.331-343. doi: http://dx.doi.org/10.1017/S0016672399004449 Gutiérrez, J.P. and Goyache, F. ( 2005) Note on ENDOG: a computer program for analysis pedigree information. J. Anim.Breed. Genet ., vol.122. pp.172-176. Gutiérrez, J.P., Goyache, F. and Cervantes, F. ( 2009) Endog v 4.6. A computer program for monitoring genetic variability of populations using pedigree information. User guide . Madrid: Universidad Complutense de Madrid. 45 p.. Kadlečík, O. and Pavlík,I. (2012) Genealogical analysis in small populations: The case of four Slovak beef cattle breeds. Slovak J. Anim. Sci., vol. 45, no. 4. pp. 111-117. Kasarda. R. and Kadlečík. O. (2007) An economic impact of inbreeding in the purebred population of Pinzgau cattle in Slovakia on milk production traits. Czech J. Anim. Sci., vol. 52, no. 1, pp. 7-11. Krupa, E., Žáková, E. and Krupová, Z. (2015) Evaluation of inbreeding and genetic variability of five pig breeds in Czech Republic. Asian Australas. J.Anim. Sci.. vol. 28, no. 1, pp. 25-36. doi: http://dx.doi.org/10.5713/ajas.14.0251 Lacy, R.C. (1989) Analysis of founder representation in pedigree: Founder equivalents and founder genome equivalents. Zool.Biol ., vol. 8, no. 2, pp. 111-123. doi: http://dx.doi.org/10.1002/zoo.1430080203 Lacy, R.C. (1995) Classification of genetic terms and their use in the management of captive populations. Zoo. Biol ., vol. 14, no. 6, pp. 565-577. doi: http://dx.doi.org/10.1002/zoo.1430140609 Melka, M.G. et al. (2013) Analyses of genetic diversity in five Canadian dairy breeds using pedigree data. J. Anim. Breed. Genet ., vol. 130, pp. 476–486. doi:http://dx.doi.org/10.1111/jbg.12050 McParland, S. et al. (2007) Inbreeding trends and pedigree analysis of Irish dairy and beef cattle populations. Journal of Animal Science , vol. 85, no. 2, pp.322-331. doi: http://dx.doi.org/10.2527/jas.2006-367 Maignel, L., Boichard, D. and Verrier.E. (1996) Genetic variability of French dairy breeds estimated from pedigree information. Interbul Bulletin , vol. 14, pp.49-54. Meuwissen, T.H.E. and Luo,Z. (1992) Computing in breeding coefficients in large populations. Genet. Sel. Evol., vol. 24. pp. 305-313. doi:http://dx.doi.org/10.1186/1297-9686-24-4-305 Pavlík.I, et al. (2014) Pedigree analysis of Thoroughbred horses in Slovakia. Acta fytotechnica et zootechnica, vol. 17, no. 4, pp. 122-126. doi: http://dx.doi.org/10.15414/afz.2014.17.04.122-126 Stachowic, K. et al. (2011) Schenkel Rates of inbreeding and genetic diversity in Canadian Holstein and Jersey cattle. J. Dairy Sci ., vol. 94, no.  10, pp. 5160–5175. doi: http://dx.doi.org/10.3168/jds.2010-3308 ŠIDLOVÁ, V. et al. (2015) Genomic variability among cattle populations based on runs of homozygosity. Poljoprivreda , vol. 21. no. 1 (Supplement), pp. 44-47. Tang, G. Q. et al. (2013) Inbreeding and genetic Ddversity in three imported swine breeds in China using pedigree data Asian Australas. J. Anim .Sci ., vol.26, no. 6, pp.755-765.  doi: http://dx.doi.org/10.5713/ajas.2012.12645 Trakovická, A. et al.(2015) Impact of SNPs in candidate genes on economically important traits in Pinzgau cattle. Poljoprivreda . vol. 21, no. 1(Supplement), pp. 150-154. doi: http://dx.doi.org/10.18047/poljo.21.1.sup.35

ObjectivesDark-cutting beef carcasses are graded Canada B4 in the Canadian Beef Grading System, resulting in economic loss for beef producers. Dark-cutting beef is caused by depletion of muscle glycogen before slaughtering, which may also be affected by animal genetics. This study aimed to identify possible single nucleotide polymorphisms (SNPs) associated with dark-cutting through a case-control genome-wide association study (GWAS) and explore the biological relevance of these SNPs to the formation of dark cutting beef. Materials and MethodsTwo cattle populations were used in this study, population I had 64 beef cattle, of which 40 were graded Canada B4 (dark-cutters, treated as cases), and population II had 837 beef cattle, of which 30 were graded Canada B4. The 2 populations were genotyped using GeneSeek Genomic Profiler for Beef Cattle-HD (GGP-HD) of 76,783 SNPs and Illumina BovineSNP50v2 BeadChip of 54,609 SNPs, respectively. All SNPs with a call rate lower than 90% or a minor allele frequency (MAF) lower than 5% were removed in quality control. Association analyses were conducted using Plink 1.9 and dark-cutting beef was analyzed as a binary trait (cases versus controls) through a logistic regression model under an additive model. UCSC Genome Browser RefSeq genes harboring (1 Mb window) the top 50 SNPs with lowest raw P values in each population were used for GO (Gene Ontology) analysis through DAVID (Database for Annotation, Visualization and Integrated Discovery). ResultsIn total, 418 SNPs were detected in population I, 383 SNPs in population II and 267 SNPs in the combined data with a less stringent significance level (P < 0.01); 12 SNPs in population I, 30 SNPs in population II and 22 SNPs in the combined data with a significance level (P < 0.001); 2 SNPs in population II and 2 SNPs in the combined data with a relatively stringent significance level (P < 0.0001). These detected SNPs showed suggestive association with dark-cutting beef. GO analysis revealed that genes (717 in total) harboring top-scoring variants (150 SNPs in total) were involved in molecular functions like poly (A) RNA binding, and calcium ion and GTP binding which are related to energy metabolism. ConclusionBased on our association study with a relatively small sample size, no evidence was found for a large genetic effect for beef dark-cutting, the trait may therefore be polygenic. Significant SNPs showed suggestive association with dark-cutting beef. Although the detected SNP associations require validation in a larger dataset, the results suggested the possibility in the future for marker-assisted selection or genomic selection in beef cattle to reduce dark cutting.

Livestock animal product is one of important materials to increase of human body endurance. There is some protein in livestock product to support healthy human. The government is also keep growth of livestock productivity, because the population growth of human can influence consume of some products which comes from animal. The objective of this paper was to know the correlation between population and production of livestock animal. In this research was using secondary data from Indonesia Central Bureau of Statistics 2018. Data are population of beef cattle, laying hens, goat, broiler and production of beef, eggs, lamb, chicken meat in 2009-2018. The method was using descriptive statistics and pearson’s correlation analysis. The results of this research, there are correlation between population and production of goat, laying hens, and broiler (sig. &lt; 0.05), but there is no correlation between population and production of beef cattle (sig. &gt; 0.05). Many factors can influence about productivity of livestock animal. The important factors are feed maintenance management and prevent of diseases management.Keywords : Population of Livestock Animal, Production of Livestock Product, Statistics Descriptive, Correlation Analysis

A study has been conducted with the aim to determine the actual behavior of beef cattle farmers' income and formulate micro-policies for beef cattle farmers' income in Kupang district. Sampling in this study was conducted in stages. The first stage was purposive sampling of four sub-districts, the second stage was snow ball sampling of 40 farmers and traders and six government officials using an interview approach. The number of key informants depends on the saturation of information obtained. The software used in this research is Ventana Simulation (Vensim) PLE. The results showed that the actual behavior of calf production and income from beef cattle farmers tended to decrease, each by 20.61% and 3.73% per year, respectively. Therefore, policy interventions are needed: 1) increasing calving rate can increase the population of young beef cattle by 3.35% per year and profits by 3.49% per head per year; 2) adding feed supplementation can increase the population of young beef cattle by an average of 4% per year, fattening males by 2.81% per year, and profits by 4.03% per head per year; 3) increasing stakeholder service intensity can increase the population of young beef cattle by 3.12% per year, fattening male production by 5.04% per year, and average profits by 3.37%.

Post-partum anoestrus in tropical beef cattle: A systems approach combining gene expression and genome-wide association results

Methane emission inventories for enteric fermentation and manure management of yak, buffalo and dairy and beef cattle in China from 1988 to 2009