bluuebunny/crossref_metadata_2025_split huggingface dataset:
1 Physiological and performance recovery after fourteen hours of feed restriction or transportation in Holstein bulls fed high concentrate diets
Authors: Marti Sonia , Garcia Elena , Gerard Christine , Grau Joan , Cirier Nicolas , Gómez Maria Soledad , Pisoni Lucía , Devant Maria 
Published: November 2020

Abstract
One hundred and eight Holstein calves (225 ± 1.1 kg and 187 ± 5.2 d) were used to evaluate the physiological and performance recovery after 14 h transportation or feed restriction. Calves were distributed into 6 pens (2 pens/treatment) according to control (CTR, n = 36) calves with ad libitum access to concentrate, straw and water; restricted (RES, n = 36) calves with concentrate restriction but with access to water and straw for 14 h; and transported (TRA, n = 36) calves that were loaded into a trailer and transported without feed or water for 14 h. On days 0, 7, 21, and 35 BW was recorded. Concentrate intake were recorded daily. Blood samples for non-esterified fatty acids (NEFA), beta-hydroxybutyrate (BHBA), and serum amyloid-A (SAA) were collected at -24, -14, 0 h, and 6, 24, and 168 h post-treatment. Data were analyzed using mixed models with repeated measures. At 24 h, RES and TRA had greater (P &lt; 0.05) concentrate intake compared with CTR. However, from d 7 to 35 after treatments, only TRA had similar concentrate intake than CTR, while RES had lesser (P &lt; 0.05) concentrate intake than CTR and TRA. RES at 6 h had greater (P &lt; 0.05) NEFA concentrations than TRA, and NEFA concentrations were still higher for the RES and TRA groups than those for the CTR after 24 h. After 24 h concentrations of serum BHBA for TRA and RES were significantly greater (P &lt; 0.05) when compared with those for the CTR. Serum concentration of SAA for TRA and RES was greater (P &lt; 0.05) than CTR until 168 h. Results showed similar effects of 14 h of feed restriction and transportation of calves on serum anorexia and inflammation parameters; however, feed intake was recovered after d 35 in transported calves but not in feed restricted calves without transportation.
13 Genetic selection using pooled semen
Authors: de Sousa Ithalo Coelho , Fernando Rohan , Dekkers Jack C , Nascimento Moysés , Leach Richard J , Serão Nick V 
Published: November 2020

Abstract
The use of pooled semen (PS), standard procedure at the commercial level of the swine industry, limits genetic progress, since the offspring parentage is unknown. Literature suggests that some boars have a greater number of progeny than others in the same litter when PS is used. The objective of this study was to evaluate different pedigree-relationship matrices for selection purposes when PS is used. Data on a trait with heritability of 0.4 were simulated 1,000 times for 12 scenarios: combination of sires per pool (2 or 3), number of phenotyped progeny (1 or 12), and three boar dominance levels: no dominance (equal probability of parentage), medium dominance, and complete dominance (all progeny from one boar). Ten pools were created for each scenario based on 5 sires and used for 5 dams each. Breeding values (BV) of the progeny were estimated (EBV) using three relationship matrices: known parents (A), using equal probabilities of parentage (E), and probabilities based on known boar dominance (D). Results for each relationship matrix were compared using the average of the true BV (TBV) of the 10% best animals selected based on EBV. Results are presented as percentage TBV of the selected animals compared to using A (Table). In general, D resulted in better results than E as boar dominance increased. Similar results between E and D were obtained when 12 progenies were phenotyped. When one was phenotyped, D was superior than E in the presence of boar dominance. Knowing the probability of each sire contributing to the progeny increases response to selection when pooled semen is used.
39 Impact of inclusion rates of crossbred phenotypes and genotypes in nucleus selection programs
Authors: See Garrett , Mote Benny E , Spangler Matthew L 
Published: November 2020

Abstract
The aim of this study was to investigate different inclusion rates of purebred (PB) and CB phenotypes and genotypes in genetic evaluations. Assuming PB and CB traits with moderate heritabilities (h2 = 0.4), a three-way swine crossbreeding scheme was simulated, and selection was practiced for 6 generations. The goal was to increase the CB phenotype. Phenotypes, genotypes and pedigrees for three purebred breeds (each consisting of 25 males and 175 females), F1 crosses (400 females) and terminal cross progeny (2500) were simulated using AlphaSimR. The genome consisted of 18 chromosomes with 1,800 QTL and 59.4k SNP markers. Selection was performed using EBV produced by the BLUPf90 suite of programs for each phenotyping/genotyping strategy. Strategies investigated were 1) increasing the proportion of CB with genotypes, phenotypes and sire pedigree information, 2) decreasing the proportion of PB phenotypes and genotypes, and 3) altering the genetic correlation between PB and CB traits (rpc). Each strategy was replicated 15 times. Results showed that including CB performance improved the CB phenotype regardless of rpc or phenotyping/genotyping strategy. Compared to using only PB information, including 10% of possible CB animals per generation with sire pedigrees and phenotypes increased the response in CB phenotype when rpc was 0.1, 0.3, 0.5, 0.7, and 0.9 by 192, 64, 41, 25 and 21%, respectively. Including CB genotypes dramatically improved the previously mentioned increases in response. Minimal change was observed in the CB phenotype when PB phenotypes were included or removed, if CB phenotypes, genotypes and sire pedigrees were included. PB genotypes were more informative than phenotypes in enabling prediction for CB traits. In practice, the inclusion rates of CB and PB data depends upon the degree of connectedness between CB animals and PB selection candidates and the cost-benefit ratio of increased CB performance and genotyping/phenotyping costs.
14 Genome-wide association study of frozen sperm quality in cocks
Authors: Dementieva Natalia , Kudinov Andrey , Pozovnikova Marina , Nikitkina Elena , Pleshanov Nikolay , Silyukova Julia , Krutikova Anna , Plemyashov Kirill 
Published: November 2020

Abstract
Preservation of the genetic material of unique breeds of hens involves the use of semen cryobanks. The aim of the study was to search for genomic associations with rooster sperm quality after freezing. We took into account the decrease in sperm motility after thawing. Genotyping of 96 individuals (roosters) using the Affymetrix Axiom®600k Array chip was performed. Genomic data were obtained using the Plink 1.9 software. DNA samples were taken with genotyping quality at SNP loci more than 95%, SNP with MAF &gt; 0.01. GWAS was performed using EMMAX. SNP information in the corresponding genes was determined using the genomic browsers NCBI and Ensembl. Assessment of rooster sperm quality showed high individual variability in total motility before freezing (20–95%), and after freezing (5–70%). Significant SNPs were detected on the chromosomes GGA1 (rs315598192, rs316943858), GGA2 (rs312981435), GGA3 (rs13694743), GGA11 (rs314024471), GGA19 (rs316346648), GGA22 (rs31797024248, rga31780824824, gga22 (rs3178082424). Candidate genes ZC3HC1, CACNA2D1, BCKDHB, AMFR, and GOSR1 were identified. The annotated genes were associated with cell cycle regulation, the formation of calcium cytoskeleton, and the formation of a multienzyme complex associated with the inner membrane of mitochondria, glycosylated transmembrane receptor. The experimental data and results can be used to study the localization of regions and genes associated with phenotypic traits of frozen sperm quality. Authors acknowledge financial support from Russian Science Foundation № 18-16-00071.
30 Inbreeding in American Angus cattle before and after the implementation of genomic selection
Authors: Lozada-Soto Emmanuel A , Tiezzi Francesco , Lu Duc , Miller Stephen P , Cole John B , Maltecca Christian 
Published: November 2020

Abstract
The aim of this study was to characterize the American Angus cattle population in terms of changes to the inbreeding rate (ΔF) and effective population size (Ne) before and after the implementation of genomic selection (GS). Genomic information (89,206 SNPs) was obtained for 25,960 bulls and 134,962 cows born between the years 2000 and 2017. Bulls and cows were independently grouped into two groups based on year of birth, pre-GS (2000–2009), and post-GS (2010–2017). Genomic inbreeding (FGRM) was calculated assuming fixed allele frequencies (0.5). Inbreeding based on runs of homozygosity (FROH) was calculated using software SNP1101 (Sargolzaei, 2014). The yearly ΔF for each group was estimated by regressing the inbreeding coefficients on year of birth. The generation intervals (L) were calculated for each of the four pathways of selection at both time periods (pre-GS and post-GS), where the mean of the sires of sires and dams of sires pathways was taken to be the generation interval for the bulls and the mean of the sires of dams and dams of dams pathways was taken to be the generation interval for the cows. The L and ΔF of the three inbreeding coefficients were used to estimate the Ne. Estimates of ΔF and Ne for both sexes at the two time periods can be found in table 1. In both sexes, ΔFROH decreased and NeROH increased from pre-GS to post-GS. For bulls, ΔFGRM and NeGRM did not change, and for cows, ΔFGRM decreased and NeGRM increased from pre-GS to post-GS. These results suggest that the implementation of genomic selection in Angus cattle has not caused the increased inbreeding rates and reduced effective population sizes seen in other species, but instead has been beneficial for the preservation of genetic diversity.
17 Investigating pig survival in different productive stages using genomic models
Authors: Leite Natalia , Lourenco Daniela , Knol Egbert , Lopes Marcos , Silva Fabyano 
Published: November 2020

Abstract
Pig survival is an economically important trait with animal welfare implications. Although survival is highly affected by the environment, previous studies reported genetic variability of this trait, indicating the opportunity for improvement through selection. Genomic information is currently included in the major commercial pig breeding programs, which can be incorporated by single-step genomic BLUP (ssGBLUP). The objectives of this study were to: 1) estimate (co)variance components for farrowing, lactation, nursery, and finishing survival; and 2) compare the individual breeding value accuracies obtained using traditional pedigree-based BLUP (BLUP) and ssGBLUP methods. Individual survival records were collected for a crossbred pig population, and two-trait threshold models, which included maternal effects, were used for (co)variance components estimation. Direct and maternal breeding values were estimated using BLUP and ssGBLUP methods, and individual accuracies were obtained based on posterior standard deviation. Heritabilities for the four survival phases were low, ranging from 0.04 to 0.12. Pre-weaning survival was controlled by dam and piglet additive gene effects. The additive direct and maternal components were equally important at farrowing, whereas the piglet’s own genetic merit was the most expressive during lactation. Common environment estimates were higher than maternal genetic effects, indicating early life experiences related to the sow, but independent of the maternal genetic component. Nursery and finishing survival showed the same or higher heritabilities compared to pre-weaning stages. The genetic correlation between the pre-weaning phases was high (0.68), whereas the correlation between the post-weaning measurements was moderate (0.42). The incorporation of genomic information through ssGBLUP increased the individual accuracy, on average, from 0.36 to 0.41 for direct and from 0.29 to 0.37 for maternal effects compared to BLUP. Although the heritabilities for survival in different productive stages are low, genetic gains can be obtained, given that breeding values benefit from the inclusion of genomic information.
42 Genetic differentiation of Russian goats and wild relatives based on microsatellite loci
Authors: Selionova Marina I , Aibazov Magomet M , Mamontova Tatyana V , Petrov Sergey N , Kharzinova Veronica R , Arsen Dotsev V , Zinovieva Natalia A 
Published: November 2020

Abstract
Goat breeding is a traditional livestock industry for many regions of Russia. Due to unpretentiousness and high adaptive qualities, the Karachai, Dagestan wool and Dagestan down breeds are widespread in the North Caucasus. Moreover, their uniqueness is determined by sharing a common habitat with their wild relatives, West Caucasian and Dagestani turs, thus forming hybrid zones. The aim of the research was to study allele pool and interbreed differentiation of domestic goat breeds and wild relatives by microsatellites. Research was performed based on 16 loci on the ABI 3130xl analyzer. Population genetic characteristics were calculated in GenAlEx 6.5, and the phylogenetic tree was constructed in Populations 1.2.30 and SplitsTree 4.14.5. The sample collection included goat breeds (n = 226): Karachai (KRCH), Dagestan down (DAGD), Dagestan wool (DAGW) (North Caucasus), Soviet wool (SOVW) (Siberia), Orenburg (OREN) (South Ural), and wild goats (n = 72). Wild goats comprised mountain goats: Siberian goats (Capra sibirica) from the Altai, Tajikistan, Kyrgyzstan and the Himalayas; bezoar goats (Capra aegagrus) from Turkey and Pakistan; and tur (Capra caucasica) from the West Caucasus (Kuban), Central Caucasus, and East Caucasus (Dagestan). The Karachai breed was characterized by the highest level of genetic diversity: the average number of alleles per locus (NA) and allelic richness (AR) were 9,154 and 7,713, respectively, while these indices varied from 6,538 to 7,538 and from 6,425 to 7,538 (Table 1) in other breeds, respectively. The values of genetic distances showed differentiation of Karachai, Dagestan down and Dagestan wool breeds from Orenburg and Soviet wool breeds (Table 2). The formation of three clusters was established. The first one included subspecies of the Caucasian tur, the second one comprised Siberian goats, and the third contained domestic goats. Bezoar goats were in the root of the third cluster that confirmed their participation as an ancestral form of domestic goats.
302 Phenomics and its potential impact on livestock development in low income countries: Innovative applications of emerging related digital technology
Authors: Ekine Chinyere , Mrode Raphael , Marshall Karen , Chagunda Mizeck , Muasa Bridgit , Ojango Julie , Mwai Okeyo 
Published: November 2020

Abstract
Infrastructure and institutional frameworks supporting sustainable phenotyping systems are lacking in most developing countries, which are characterized by subsistence agricultural systems with small, highly dispersed farms having few animals, which makes performance recording inefficient, unattractive and expensive. Nevertheless, capturing performance data in near real time using digital devices for livestock improvement is fast gaining ground in many emerging economies around the world because of technological advancements made in the use of information and communications technologies (ICT), mobile devices and a myriad of digital innovations. Several initiatives in developing countries have demonstrated that ICT models for livestock performance recording in small-holder farming systems coupled with appropriate feedback to farmers for improved management and decision making is sustainable. More work needs to be done in developing and designing simple, efficient, inexpensive, non-evasive and sturdy phenotyping devices to support the collection of a range of existing or new quantitative data relating to animal welfare, production, reproduction, product quality, feed efficiency, etc. on farms. Most suitable technologies will be those that will support routine data collection to be transmitted in real time/near real time, but can also function without the internet, and can be easily incorporated into genetic/genomic improvement programs with a community-based breeding program approach. Animal scientists will need to collaborate with an interdisciplinary team of scientists (software developers, engineers, programmers, etc.) to design these next generation of innovative technologies needed for phenotypic data collection. Efficient methods for data collection will generate a lot of data and will need trained scientists to transform this data into information needed for improving animal production systems. Application of these technologies will be critical in attracting youth into agriculture and thus ensure sustainable systems for phenomics in developing countries.
293 ASAS-EAAP Talk: #Phenotypeisking
Authors: Coffey Mike 
Published: November 2020

Abstract
The objective of this text is to describe the changing face of phenotypes collection for use in national genetic and genomic evaluations of dairy cattle and to offer possible new scenarios that may exist. Dairy cattle have been chosen as an exemplar, but some of the principles could be applied to other livestock species. National evaluations in many established countries have evolved over many decades into sophisticated layers of management, ownership and funding streams, but all have created large gains for farmers, dairy cows and consumers. Usually, milk recording data has been gathered for management purposes and passed the national evaluation centers freely in return for genetic evaluations that added value to the recording service. Conformation and functional phenotypes were often recorded by breed societies and sometimes evaluated by them. These long standing and established processes are becoming disrupted by the advent of genomic evaluation whereby limited and high-quality phenotypes can be used to train a SNP key that can subsequently be used to make genomic predictions for the rest of the industry. Larry Schaefer suggested that breeding company costs would greatly reduce, but did not suggest that the cost and effort of gathering phenotypes would increase. In the age of the low-cost genotype, where will the increasingly sophisticated and high-cost phenotypes come from? This is causing disruption in the industry, challenging existing structures, creating opportunities for new entrants with new technology, making phenotypes very valuable, altering the balance of power between industry players and farmers and offering genomic evaluations for traits previously thought too difficult or expensive to records. The problems with such disruption is that it can result in “cherry picking” by new entrants, thereby reducing the sustainability of the remaining services valued by farmers. The future is not what it used to be.
301 Methods of genome-wide association studies and their applications in dairy cattle
Authors: Ma Li 
Published: November 2020

Abstract
Genome-wide association studies (GWAS) has been widely used to map quantitative trait loci (QTL) of complex traits and diseases since 2007. To date, the human GWAS catalog has accumulated 4,410 publications and 172,351 associations, and the animal QTLdb has curated 983 publications and 130,407 QTLs for cattle, largest in livestock species. During the past 13 years of development, GWAS methods has evolved from simple linear regression, using principal components to address sample relatedness, mixed models, to Bayesian full model approaches. These methods have their advantages and limitations, so it is important to choose an appropriate method, especially for studies in livestock where sample size is often limited. Note that the most popular GWAS approach, the mixed model method, originated from animal breeding and genetics research. Leveraging the national cattle genomic database at the Council on Dairy Cattle Breeding (CDCB), we have conducted GWAS analyses of various dairy traits to identify QTLs and SNP markers of importance. Combining with sequence and functional annotation data, we seek to understand the genetic basis of complex traits and to reveal useful knowledge that can be incorporated into more accurate genomic predictions in the future.
59 Neutrophils and respiratory health of feedlot cattle supplemented with autolized yeast
Authors: Garbosa Gabriela , Bertagnon Heloísa , Bonato Melina A , Borges Liliana L 
Published: November 2020

Abstract
The objective of this study was to evaluate whether autolyzed yeast (AY) in the diet interferes with the innate immunity and healthy of feedlot finished steer. At 0, 14, 42, 70, and 105 days of feedlot, the following were measured: neutrophil-lymphocyte ratio (N/L), neutrophilic oxidative metabolism, and respiratory disease indicators (frequency of animal with mucopurulent nasal secretion and orbital temperature) and frequency of pneumonia (histopathological analyses at slaughter day). For this, 36 ½ Angus steers (average BW 330kg and 11 months of age), were distributed in three treatments, with 12 animals each: Control; YA 4g (4g/animal/day, RumenYeast®); and AY 7g (7g/animal/day, RumenYeast®) for 105d. For all results, significant data were considered that show significance level P ≤ 0.05 and statistical trend, 0.05 &gt; P &lt; 0.1. On days 42 and 70, the AY 4g increased neutrophil oxidative metabolism (P = 0.06 and 0.01) and reduced N:L ratio (P = 0.08 and 0.01) comparing to the control group. This neutrophil oxidative metabolism increase was punctual for AY 7g, at 70d (P = 0.01), but the reduction of the N:L ratio occurs at 42 and 70d (P = 0.08 and 0.01). These immune increments promoted fewer respiratory diseases indicators, especially in the AY 4g, observed by a higher frequency of animals without nasal secretion at 42, 70 e 105d comparing to the control group (P = 0.03, 0.001 and 0.001), a lower orbital temperature at 105d (P = 0.02), and a lower frequency of pneumonia (P = 0.06). The AY 7 showed a higher frequency of animals with nasal secretion 14d (P = 0.04) and a lower frequency of animals without mucopurulent nasal secretion at 42 and 70d (P = 0.03 and 0.001), without significant difference for orbital temperature or pneumonia comparing to the other groups. We conclude the autolyzed yeast included in the diet improved the neutrophils functions of the animal and the health of the respiratory tract of feedlot cattle, especially when used at 4g/animal/day.