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A copy number variation (CNV) is information of DNA segment containing deletion, duplication or insertion exist within diverse populations. This study detected 53 CNVs regions that overlapped with immune response, body size and parasitic resistance traits in Pakistani cattle breeds. This study characterized genetic diversity and provides lineage differentiated CNVs in these indigenous cattle breeds.

Background The simplicity of the CRISPR/Cas9 system has enabled its widespread applications in generating animal models, functional genomic screening and in treating genetic and infectious diseases. However, unintended mutations produced by off-target CRISPR/Cas9 nuclease activity may lead to negative consequences. Especially, a very recent study found that gene editing can introduce hundreds of unintended mutations into the genome, and have attracted wide attention. Results To address the off-target concerns, urgent characterization of the CRISPR/Cas9-mediated off-target mutagenesis is highly anticipated. Here we took advantage of our previously generated gene-edited sheep and performed family trio-based whole genome sequencing which is capable of discriminating variants in the edited progenies that are inherited, naturally generated, or induced by genetic modification. Three family trios were re-sequenced at a high average depth of genomic coverage (~ 25.8×). After developing a pipeline to comprehensively analyze the sequence data for de novo single nucleotide variants, indels and structural variations from the genome; we only found a single unintended event in the form of a 2.4 kb inversion induced by site-specific double-strand breaks between two sgRNA targeting sites at the MSTN locus with a low incidence. Conclusions We provide the first report on the fidelity of CRISPR-based modification for sheep genomes targeted simultaneously for gene breaks at three coding sequence locations. The trio-based sequencing approach revealed almost negligible off-target modifications, providing timely evidences of the safe application of genome editing in vivo with CRISPR/Cas9. Electronic supplementary material The online version of this article (10.1186/s12864-018-4712-z) contains supplementary material, which is available to authorized users.

Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.

For two centuries, Jersey cattle were exported globally, adapting to varying climates and production systems, yet the founding population remained genetically isolated on the Island of Jersey. The Island of Jersey formally allowed the importation of pure Jersey cattle in 2008. This study characterized the genetic variation of 49 popular bulls from the Island of Jersey born from 1964 to 2004 and compared them to 47 non-Island Jersey bulls and cows, primarily from the United States In addition, 21 Guernsey cattle derived from the Island of Guernsey and 71 Holstein cattle served as reference populations for genetic comparison. Cattle were genotyped on the Illumina BovineHD Beadchip producing 777,962 SNPs spanning the genome. Principal component analysis revealed population stratification within breed reflective of individual animal’s continental origin. When compared to Holstein and Guernsey, all Jersey clustered together by breed. The Jersey breed demonstrated increased inbreeding in comparison to Holstein or Guernsey with slightly higher estimates of inbreeding coefficients and identity-by-descent. The Island and United States Jersey have relatively similar, yet statistically different inbreeding estimates despite vastly different population sizes and gene flow. Signatures of selection within Island Jersey were identified using genome-wide homozygosity association and marker-based FST that provided population informative single-nucleotide polymorphism (SNPs). Biological significance of the homozygosity association results identified multiple genes on chromosomes 5, 24, and 27, involved in immune function and cellular processes. Overall, genomic variation was identified between the Island and non-Island Jersey cattle producing population informative SNPs and differing runs of homozygosity (ROH) over immune regulation and metabolic genes. Results on inbreeding measures and ROH may reflect varying effective population size or differential selection with grazing systems promoting natural selection for traits such as parasite resistance, whereas confinement systems demonstrate a more intensive artificial selection. More broadly, differences in breed formation, particularly between the two Channel Island breeds, likely contributed to the variation in ROH and inbreeding. This research provides a reference for the Jersey breed based on the genetic foundation of the Island cattle as compared to the intensively selected United States cattle, and identifies regions of the genome for future investigation of immune regulation and metabolic processes.

Several mutations exist in the prolactin receptor gene (PRLR) of cattle that cause a short, sleek hair coat.. The mutation is dominant so slick-haired cattle can have either one or two copies of the mutation. The assay described here detects the most-well studied mutation (SLICK1) that causes translation of a truncated PRLR of 461 amino acids. Originally described in Senepol cattle, this mutation has also been introduced into Holsteins in Puerto Rico, Florida and elsewhere. Note that the assay will not detect other mutations in PRLR that also cause the slick phenotype.

Phylogeny and characteristics of ruminants Ruminants are a diverse group of mammals that includes families containing well-known taxa such as deer, cows, and goats. However, their evolutionary relationships have been contentious, as have the origins of their distinctive digestive systems and headgear, including antlers and horns (see the Perspective by Ker and Yang). To understand the relationships among ruminants, L. Chen et al. sequenced 44 species representing 6 families and performed a phylogenetic analysis. From this analysis, they were able to resolve the phylogeny of many genera and document incomplete lineage sorting among major clades. Interestingly, they found evidence for large population reductions among many taxa starting at approximately 100,000 years ago, coinciding with the migration of humans out of Africa. Examining the bony appendages on the head—the so-called headgear—Wang et al. describe specific evolutionary changes in the ruminants and identify selection on cancer-related genes that may function in antler development in deer. Finally, Lin et al. take a close look at the reindeer genome and identify the genetic basis of adaptations that allow reindeer to survive in the harsh conditions of the Arctic. Science , this issue p. eaav6202 , p. eaav6335 , p. eaav6312 ; see also p. 1130

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.

Genomic selection has revolutionized dairy cattle breeding. Since 2000, assays have been developed to genotype large numbers of single-nucleotide polymorphisms (SNPs) at relatively low cost. The first commercial SNP genotyping chip was released with a set of 54,001 SNPs in December 2007. Over 15,000 genotypes were used to determine which SNPs should be used in genomic evaluation of US dairy cattle. Official USDA genomic evaluations were first released in January 2009 for Holsteins and Jerseys, in August 2009 for Brown Swiss, in April 2013 for Ayrshires, and in April 2016 for Guernseys. Producers have accepted genomic evaluations as accurate indications of a bull's eventual daughter-based evaluation. The integration of DNA marker technology and genomics into the traditional evaluation system has doubled the rate of genetic progress for traits of economic importance, decreased generation interval, increased selection accuracy, reduced previous costs of progeny testing, and allowed identification of recessive lethals.

Prospects of high throughput technology in animal genetics makes easy to investigate hidden genetic variation in farm animal?s genetic resources. However, many SNPs technologies are currently practicing in animal genetics. In this study, we investigated genome wide SNPs variations and its distribution across the indigenous cattle population in Pakistan using Illumina Bovine HD (777K) SNPs bead chip. A total of 136 individuals from ten different breeds were genotyped and after filtration 500, 939 SNPs markers were used for further analysis. The mean minor allele frequency (MAF) was 0.23, 0.20, 0.22, 0.22, 0.20, 0.18, 0.20, 0.22, 0.21 and 0.18 observed for Achi, Bhagnari, Cholistani, Dhanni, Dajal, Kankraj, Lohani, Red sindi, Sahiwal and Tharparkar cattle, respectively. Significant difference (P0.05) within breeds and remaining 36% were considered as monomorphic markers. Average observed (Ho) and expected (HE) heterozygosity values 0.662 and 0.640 were estimated among these breeds. In conclusion, this preliminary study results revealed that these SNPs variation level could potentially be used for genetic characterization of zebu cattle breeds and could also be used to estimate genetic potential of these cattle breeds for livestock improvement in country.

The HH1 haplotype on chromosome 5 is associated with a reduced conception rate and a deficit of homozygotes at the population level in Holstein cattle. The source HH1 haplotype was traced to the bull Pawnee Farm Arlinda Chief (Chief), who was born in 1962 and has sired more than 16,000 daughters. We identified a nonsense mutation in APAF1 (apoptotic protease activating factor 1;APAF1 p.Q579X) within HH1 using whole-genome resequencing of Chief and 3 of his sons. This mutation is predicted to truncate 670 AA (53.7%) of the encoded APAF1 protein that contains a WD40 domain critical to protein-protein interactions. Initial screening revealed no homozygous individuals for the mutation in 758 animals previously genotyped, whereas all 497 HH1 carriers possessed 1 copy of the mutant allele. Subsequent commercial genotyping of 246,773 Holsteins revealed 5,299 APAF1 heterozygotes and zero homozygotes for the mutation. The causative role of this mutation is also supported by functional data in mice that have demonstrated Apaf1 to be an essential molecule in the cytochrome-c-mediated apoptotic cascade and directly implicated in developmental and neurodegenerative disorders. In addition, most Apaf1 homozygous knockouts die by day 16.5 of development. We thus propose that the APAF1 p.Q579X nonsense mutation is the functional equivalent of the Apaf1 knockout. This mutation has caused an estimated 525,000 spontaneous abortions worldwide over the past 35 years, accounting for approximately $420 million in losses. With the mutation identified, selection against the deleterious allele in breeding schemes has aided in eliminating this defect from the population, reducing carrier frequency from 8% in past decades to 2% in 2015.

Due to climate change, cattle can experience heat stress more frequently in traditionally temperate, non-tropical environments. Because of this and the fact that most of the world’s inefficient cattle reside in tropical zones, we set out to demonstrate our ability to adapt Angus animals to heat stress through a single gene edit in the prolactin receptor (PRLR). We selected PRLR, because it is known that the SLICK phenotype results from 1 of 3 different mutations in PRLR and therefore is related to heat stress regulation. The overall project was initiated through a partnership between Acceligen and BluePrint Genetics (BPG). BPG harvested 1415 oocytes from a total of 9 ovum pickup rounds from 7 different Angus donors. These oocytes were graded, selected, and put in maturation medium for shipping to Acceligen. Matured oocytes were fertilized in Fert-TALP medium and co-incubated with frozen/thawed semen from 3 different reproductive certified Angus bulls. Consequently, targeted editing was done on a single cell in the zygotes 12h after fertilization by introduction of guide (g)RNA/Cas9 (250ng μL−1 of each) through intracytoplasmic microinjection. Then, treated zygotes (n=1341) were cultured in synthetic oviductal fluid with amino acids (SOFaa) culture medium under a controlled atmosphere until on Day 6, when 277 (20%) grade 1 embryos were selected and 39 returned to Blueprint Genetics for transfer. Because the number of available recipients was limited, only 4 rounds of fresh embryo transfer were completed, and the remaining embryos (n=190) were vitrified for future transfers. Pregnancy checks by ultrasound on Day 30 revealed a 23% (9/39) rate of pregnancy, which decreased to 13% (5/39) by Day 60. In total, 4 animals reached term and delivered healthy calves. Genetic testing of the PRLR target site was done by amplicon sequencing, which showed 3 edited SLICK animals (75%) and one wild-type. Thus, the SLICK zygote editing by microinjection was demonstrated to be an efficient method to produce bovine beef animals and is currently being prepared for regulatory review in multiple countries and commercialization.

Since its emergence, CRISPR/Cas9-mediated base editors (BEs) with cytosine deaminase activity have been used to precisely and efficiently introduce single-base mutations in genomes, including those of human cells, mice, and crop species. Most production traits in livestock are induced by point mutations, and genome editing using BEs without homology-directed repair of double-strand breaks can directly alter single nucleotides. The p.96R>C variant of Suppressor cytokine signaling 2 (SOCS2) has profound effects on body weight, body size, and milk production in sheep. In the present study, we successfully obtained lambs with defined point mutations resulting in a p.96R>C substitution in SOCS2 by the co-injection of Base Editor 3 (BE3) mRNA and a single guide RNA (sgRNA) into sheep zygotes. The observed efficiency of the single nucleotide exchange in newborn animals was as high as 25%. Observations of body size and body weight in the edited group showed that gene modification contributes to enhanced growth traits in sheep. Moreover, targeted deep sequencing and unbiased family trio-based whole genome sequencing revealed undetectable off-target mutations in the edited animals. This study demonstrates the potential for the application of BE-mediated point mutations in large animals for the improvement of production traits in livestock species.

The ability to alter single bases without homology directed repair (HDR) of double-strand breaks provides a potential solution for editing livestock genomes for economic traits, which are often multigenic. Progress toward multiplex editing in large animals has been hampered by the costly inefficiencies of HDR via microinjection of in vitro manipulated embryos. Here, we designed sgRNAs to induce nonsense codons (C-to-T transitions) at four target sites in caprine FGF5, which is a crucial regulator of hair length in mammals. Initial transfections of the third generation Base Editor (BE3) plasmid and four different sgRNAs into caprine fibroblasts were ineffective in altering FGF5. In contrast, all five progenies produced from microinjected single-cell embryos had alleles with a targeted nonsense mutation. The effectiveness of BE3 to make single base changes varied considerably based on sgRNA design. In addition, the rate of mosaicism differed between animals, target sites, and tissue type. The phenotypic effects on hair fiber were characterized by hematoxylin and eosin, immunofluorescence staining, and western blotting. Differences in morphology were detectable, even though mosaicism was probably affecting the levels of FGF5 expression. PCR amplicon and whole-genome resequencing analyses for off-target changes caused by BE3 were low at a genome-wide scale. This study provided the first evidence of base editing in large mammals produced from microinjected single-cell embryos. Our results support further optimization of BEs for introgressing complex human disease alleles into large animal models, to evaluate potential genetic improvement of complex health and production traits in a single generation.

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non‐European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole‐genome sequencing data. Additionally, we also employed unlinked and phased SNP‐based approaches on high‐density SNP array data to characterize non‐European cattle ancestry in several southern European cattle breeds. Using heterozygosity‐based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross‐bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non‐European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non‐European cattle ancestry in these cattle breeds.

AdaptMap consortium., [Background]: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds., [Results]: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments., [Conclusions]: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide., Authors are grateful to all breeders and AdaptMap members who provided data to the initiative (http://www.goatadaptmap.org/) that are described in Stella et al.. The authors from the University of Milan are grateful to Stefano Frattini who was supported by the GenHome project, for supporting coordinating meetings. Support for Francesca Bertolini was provided by State of Iowa, hatch and Ensminger funds. Financial support provided in part by the Illumina Greater Good grant is appreciated.

The prolactin receptor (PRLR) have been described as a candidate gene with a variant allele containing a nonsense/dominant mutation causative of the slick coat (SC) phenotype (chromosome 20:39136558GC>G; p.L462*) in Senepol and SC Holstein cattle of Puerto Rico (PR). However, inconsistencies between p.L462* genotypes and SC phenotype had been observed in Senepol. Therefore, a total of 661 animals [Holstein (230), Senepol (357), Charolais (4), Senepol x Charolais (13), Jersey (34), and Creole (23)] were genotyped by DNA sequencing of a 645 bp PRLR exon 11 fragment that includes 5 reported polymorphic positions. A non-reported cytosine by thymine single nucleotide polymorphism (SNP) was identified at the chromosome 20:39136612 position; 53 bp downstream of the reported p.L462* cytosine insertion/deletion (InDel), also resulting in a nonsense mutation. This SNP incorporates 16 amino acids to the shortened PRLR. Five genotype combinations (CC/CC, CC/CT, C-/CC, C-/CT and --/CC) resulting from both PRLR exon 11 polymorphisms were observed and allelic heterogeneity resulting in SC phenotype was exclusively present in Senepol and Senepol x Charolais. The PRLR InDel/SNP genotype combination CC/CC, were present in non-slick: Senepol x Charolais (3), Charolais (4), Holstein (127), and Jersey (33) cattle with an overall frequency of 0.25. Heterozygote SC animals, genotypes combination CC/CT [Senepol (4), Senepol x Charolais (2)] and C-/CC [Senepol (49), Senepol x Charolais (7), Holstein (103), Jersey (1), and Creole (23)] had frequencies of 0.01 and 0.28, respectively. Meanwhile, homozygous SC animals, C-/CT [Senepol (45) and Senepol x Charolais (1)] and --/CC [Senepol (259)] presented frequencies of 0.07 and 0.39, individually. The novel pyrimidine transition reported herein in SC Senepol that do not possess the PRLR p.L462* responsible InDel suggest a possible more accurate scenario for slick genotype calling within such tropically adapted breed if selection is to be made in favor of such coat type.

The Double Muscle (DM) phenotype was recently identified in purebred Senepol, a tropically adapted beef cattle breed with short hair phenotype (SH). Initial gene variants were identified: DM, 11 bp deletion in exon 3 of myostatin (MSTN-NT821), and SH, cytosine deletion in exon 11 of prolactin receptor (PRLR). Since MSTN-NT821 results in a non-functional protein, we studied the promoter of both MSTN and its receptor, activin receptor II b (ACVRIIB). The purpose of this study was to determine any interactions between genotypes responsible for DM and SH and ACVRIIB and MSTN, and marker associations with molecular breeding values (MBV; Igenity®, Neogen Corp.) for twelve economic relevant traits and five growth traits. A total of 79 Senepol cows segregating DM and SH alleles were genotyped for reported polymorphisms: insertion/deletion (InDel) of three nucleotides [adenine-guanine-guanine (AGG)] in ACVRIIB promoter (ACVRIIB-P), and adenine/thymine transversion (DraI-RFLP) in MSTN promoter (MSTN-P). The genotypic proportions observed for ACVRIIB-P InDel: CC: 19=homozygous for AGG insertion; CG: 39=heterozygous and GG: 21=homozygous for AGG deletion (P

Unintended off-target mutations induced by CRISPR/Cas9 nucleases may result in unwanted consequences, which will impede the efficient applicability of this technology for genetic improvement. We have recently edited the goat genome through CRISPR/Cas9 by targeting MSTN and FGF5, which increased muscle fiber diameter and hair fiber length, respectively. Using family trio-based sequencing that allow better discrimination of variant origins, we herein generated offspring from edited goats, and sequenced the members of four family trios (gene-edited goats and their offspring) to an average of ∼36.8× coverage. This data was to systematically examined for mutation profiles using a stringent pipeline that comprehensively analyzed the sequence data for de novo single nucleotide variants, indels, and structural variants from the genome. Our results revealed that the incidence of de novo mutations in the offspring was equivalent to normal populations. We further conducted RNA sequencing using muscle and skin tissues from the offspring and control animals, the differentially expressed genes (DEGs) were related to muscle fiber development in muscles, skin development, and immune responses in skin tissues. Furthermore, in contrast to recently reports of Cas9 triggered p53 expression alterations in cultured cells, we provide primary evidence to show that Cas9-mediated genetic modification does not induce apparent p53 expression changes in animal tissues. This work provides adequate molecular evidence to support the reliability of conducting Cas9-mediated genome editing in large animal models for biomedicine and agriculture.

Aeromonas bestiarum is a Gram-negative mesophilic motile bacterium causing acute hemorrhagic septicemia or chronic skin ulcers in fish. Here, we report the draft genome sequence of A. bestiarum strain GA97-22, which was isolated from rainbow trout in 1997. This genome sequence will improve our understanding of the complex taxonomy of motile aeromonads.

Background The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results This 90K “SNP-Chip” was tested in several river buffalo populations and found to have ∼70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised.

The bovine high density SNPs genotyping array has a wide range of applications including detection of selection signatures, identification of copy number variants (CNVs), genome wide association studies, and dendrogram relationships. This array can also be used to improve the accuracy of genomic predictions for low heritable traits viz. reproductive traits. The effectiveness of this array for genomic selection mainly depends on polymorphism level. In this study, we used 136 individuals from ten different Pakistani cattle breeds, include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14), and Tharparkar (13) using high density SNPs genotyping and this array contained approximately 777, 962 SNPs. The results of this study revealed that approximately 500, 939 SNPs were found polymorphic in these breeds. The results indicate that high density SNPs bead chip would offer an informative genotyping platform for quantitative trait loci (QTL) mapping in indigenous Pakistani cattle breeds. Keywords: Copy number variants; Genotyping; Polymorphism; Quantitative trait loci; SNPs http://dx.doi.org/10.19045/bspab.2018.70026

Made available in DSpace on 2018-11-26T15:47:33Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-02-23 USDA, ARS projects USDA-NIFA award Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Evolutionary adaptations are occasionally convergent solutions to the same problem. A mutation contributing to a heat tolerance adaptation in Senepol cattle, a New World breed of mostly European descent, results in the distinct phenotype known as slick, where an animal has shorter hair and lower follicle density across its coat than wild type animals. The causal variant, located in the 11th exon of prolactin receptor, produces a frameshift that results in a truncated protein. However, this mutation does not explain all cases of slick coats found in criollo breeds. Here, we obtained genome sequences from slick cattle of a geographically distinct criollo breed, namely Limonero, whose ancestors were originally brought to the Americas by the Spanish. These data were used to identify new causal alleles in the 11th exon of the prolactin receptor, two of which also encode shortened proteins that remove a highly conserved tyrosine residue. These new mutations explained almost 90% of investigated cases of animals that had slick coats, but which also did not carry the Senepol slick allele. These results demonstrate convergent evolution at the molecular level in a trait important to the adaptation of an animal to its environment. CSIRO Agr & Food, St Lucia, Qld, Australia ARS, US Dairy Forage Res Ctr, USDA, Madison, WI USA Univ Zulia, Fac Ciencias Vet, Unidad Invest Zootecn, Maracaibo, Venezuela Sao Paulo State Univ, Sch Agr & Vet Sci, Dept Prevent Vet Med & Anim Reprod, Sao Paulo, Brazil Collaborating Ctr Anim Genom & Bioinformat, Int Atom Energy Agcy, Aracatuba, Brazil Univ Puerto Rico, Dept Anim Sci, Mayaguez, PR USA Univ Florida, Dept Anim Sci, Gainesville, FL 32611 USA Uludag Univ, Dept Anim Sci, Fac Vet Med, Bursa, Turkey ARS, Anim Genom & Improvement Lab, USDA, Beltsville, MD USA Recombinet Inc, St Paul, MN 55104 USA South China Agr Univ, Coll Anim Sci, Guangzhou, Guangdong, Peoples R China Sao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, Sao Paulo, Brazil Sao Paulo State Univ, Sch Agr & Vet Sci, Dept Prevent Vet Med & Anim Reprod, Sao Paulo, Brazil Sao Paulo State Univ, Sch Vet Med, Dept Support Prod & Anim Hlth, Sao Paulo, Brazil USDA, ARS projects: 1245-31000-104-00D USDA, ARS projects: 5090-31000-024-00-D USDA-NIFA award: 1008017/(2015-07176) FAPESP: 2014/01095-8

The linkage disequilibrium (LD) is an important tool to study quantitative trait locus (QTL) mapping and genetic selection. In this study, we identified the extent of linkage disequilibrium (LD) in Sahiwal (n = 14) cattle using the bovine high density single-nucleotide polymorphisms (SNPs) BeadChip. After data filtering, 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior allele frequency (MAF) was 0.21 in a substantial proportion of SNPs and mean distance between adjacent markers was 4.77 ± 2.83 kb. The overall mean LD between adjacent markers was 0.18 (r 2 ) and 0.55 (|D'|), respectively. The LD (r 2 ) values reduced with the increase in distance between adjacent markers from 1 kb (0.35) to 100 kb (0.12) and |D'| specified distinct decay of the LD. Chromosomes 1, 27, 28 and 29 presented the LD at some distance between markers. The extent of LD was higher, except these four chromosomes, for markers separated by 20 kb. At < 3 kb distance, the upper value of the linkage disequilibrium (LD) was observed at 0.30. High level of the linkage disequilibrium (LD) between markers was observed at high minor allele frequency (MAF) threshold (0.15), at the short distance between markers. The results of this study revealed that the Bovine high density SNPs BeadChip will be informative for the estimation of breeding value in Sahiwal cattle. Keywords: Breeding value, linkage disequilibrium, minor allele frequency, molecular marker

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats., Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows., Conclusions: After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

Age-dependent decline in skeletal muscle function leads to several inherited and acquired muscular disorders in elderly individuals. The levels of microRNAs (miRNAs) could be altered during muscle maintenance and repair. We therefore performed a comprehensive investigation for miRNAs from five different periods of bovine skeletal muscle development using next-generation small RNA sequencing. In total, 511 miRNAs, including one putatively novel miRNA, were identified. Thirty-six miRNAs were differentially expressed between prenatal and postnatal stages of muscle development including several myomiRs (miR-1, miR-206 and let-7 families). Compared with miRNA expression between different muscle tissues, 14 miRNAs were up-regulated and 22 miRNAs were down-regulated in the muscle of postnatal stage. In addition, a novel miRNA was predicted and submitted to the miRBase database as bta-mir-10020. A dual luciferase reporter assay was used to demonstrate that bta-mir-10020 directly targeted the 3'-UTR of the bovine ANGPT1 gene. The overexpression of bta-mir-10020 significantly decreased the DsRed fluorescence in the wild-type expression cassette compared to the mutant type. Using three computational approaches - miranda, pita and rnahybrid - these differentially expressed miRNAs were also predicted to target 3609 bovine genes. Disease and biological function analyses and the KEGG pathway analysis revealed that these targets were statistically enriched in functionality for muscle growth and disease. Our miRNA expression analysis findings from different states of muscle development and aging significantly expand the repertoire of bovine miRNAs now shown to be expressed in muscle and could contribute to further studies on growth and developmental disorders in this tissue type.

Made available in DSpace on 2018-12-11T17:16:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-12-01 The recent evolution of cattle is marked by fluctuations in body size. Height in the Bos taurus lineage was reduced by a factor of ∼1.5 from the Neolithic to the Middle Ages, and increased again only during the Early Modern Ages. Using haplotype analysis, we found evidence that the bovine PLAG1 mutation (Q) with major effects on body size, weight and reproduction is a >1,000 years old derived allele that increased rapidly in frequency in Northwestern European B. taurus between the 16th and 18th centuries. Towards the 19th and 20th centuries, Q was introgressed into non-European B. taurus and Bos indicus breeds. These data implicate a major role of Q in recent changes in body size in modern cattle, and represent one of the first examples of a genomic sweep in livestock that was driven by selection on a complex trait. São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal Department of Preventive Veterinary Medicine and Animal Reproduction International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Istituto di Zootecnica BioDNA Centro di Ricerca sulla Biodiversità e sul DNA Antico Università Cattolica del Sacro Cuore São Paulo State University (Unesp) School of Veterinary Medicine Araçatuba Department of Support Production and Animal Health Recombinetics Inc. UFPI - Universidade Federal do Piauí Animal Genomics and Improvement Laboratory Agricultural Research Service USDA Escola de Veterinária e Zootecnia (EVZ) Universidade Federal de Goiás - UFG Campus Samambaia São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal Department of Animal Science GenSys Consultores Associados Centro Universitário Católico Salesiano Department of Anthropology University of Maryland Dipartimento di Storia Archeologia e Storia dell'Arte Facoltà di Lettere e Filosofia Università Cattolica del Sacro Cuore Società Friulana di Archeologia Istituto di Genomica Applicata Dipartamento di Scienze Agrarie ed Ambientali Università di Udine BOKU University of Natural Resources and Life Sciences Department of Sustainable Agricultural Systems Division of Livestock Sciences São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal Department of Preventive Veterinary Medicine and Animal Reproduction São Paulo State University (Unesp) School of Veterinary Medicine Araçatuba Department of Support Production and Animal Health São Paulo State University (Unesp) School of Agricultural and Veterinarian Sciences Jaboticabal Department of Animal Science

We investigated diverse genomic selections using high-densit ys ingle nucleotide polymorphism data of fi ve distinct cattle breeds. Based on allele frequency differences, we detected hundreds of candidate regions under positive selection across Holstein, Angus, Charolais, Brahman, and N’Dama. In addition to well-known genes such as KIT, MC1R, ASIP, GHR, LCORL, NCAPG, WIF1 ,a ndABCA12, we found evidence for a variety of novel and less-known genes under selection in cattle, such as LAP3, SAR1B, LRIG3, FGF5 ,a ndNUDCD3. Selective sweeps near LAP3 were then validated by next-generation sequencing. Genome-wide association analysis involving 26,362 Holsteins confirmed that LAP3 and SAR1B were related to milk production traits, suggesting that our candidate regions were likely functional. In addition, haplotype network analyses further revealed distinct selective pressures and evolution patterns across these five cattle breeds. Our results provided a glimpse into diverse genomic selection during cattle domestication, breed formation, and recent genetic improvement. These findings will facilitate genome-assisted breeding to improve animal production and health.

Genomic selection (GS) has profoundly changed dairy cattle breeding in the last decade and can be defined as the use of genomic breeding values (GEBV) in selection programs. The GEBV is the sum of the effects of dense DNA markers across the whole genome, capturing all the quantitative trait loci (QTL) that contribute to variation in a trait. This technology was successfully implemented in the United States, Canada, New Zealand, Australia, and several European countries with very promising results. The GEBV reliability depends on estimation procedures and models. The different methodologies to estimate SNP effects and GEBV have been extensively tested for many research groups with very promising results. Although GS is a success, many challenges still remain, including integration of GEBV into genetic evaluation programs and increasing GEBV reliability. The aim of this review is to discuss the main aspects involved with GS, including different methodologies of imputation, SNP effect estimation, and the most important impacts of GS implementation in dairy cattle.

Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD. This study analyzes levels of LD assessed through the r 2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions. The results show higher levels of LD than previously reported, especially at short inter- marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r 2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub) species when applying LD-dependent methods, as compared to most taurine breeds.

peer-reviewed Bovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per annum. Because disease susceptibility is a multi-factorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach, using next generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time-points (0, 12, 24, 36 and 48h) in both milk and blood FACS-isolated CD14+ monocytes from animals infected in vivo with Streptococcus uberis. More than 3,700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Up-regulated genes were significantly enriched for inflammatory pathways, while down-regulated genes were enriched for non-glycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes up-regulated in blood-isolated-monocytes (BIMs) showed a significant association with interferon and chemokine signalling. Furthermore, twenty-six miRNAs were differentially expressed in MIMs and three in BIMs. Pathway analysis revealed that predicted targets of down-regulated miRNAs were highly enriched for roles in innate immunity (FDR < 3.4E-8) in particular TLR signalling, while up-regulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways. This study was funded in part by Teagasc RMIS 6018 and United States Department of Agriculture ARS funding 3625-32000-102-00. NL is supported by a Teagasc Walsh Fellowship.

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

The domestication of cattle from the now-extinct wild aurochs (Bos primigenius) involved selection for physiological and behavioral traits, with underlying genetic factors that remain largely unknown. Non-coding microRNAs have emerged as key regulators of the spatio-temporal expression of target genes controlling mammalian growth and development, including in livestock species. During the domestication process, selection of mutational changes in miRNAs and/or miRNA binding sites could have provided a mechanism to generate some of the traits that differentiate domesticated cattle from wild aurochs. To investigate this, we analyzed the open reading frame (ORF) DNA sequence of 19,994 orthologous protein-coding gene pairs from extant Bos taurus genomes and a single extinct B. primigenius genome. Using this data from 19,994 gene pairs, we identified miRNA binding site polymorphisms in the 3' UTRs of 1,620 orthologous genes. These 1,620 genes with altered miRNA binding sites between the B. taurus and B. primigenius lineages represent candidate domestication genes. Using a novel Score Site ratio (SSr) metric we have ranked these miRNA-regulated genes according to the extent of divergence between miRNA binding site presence, frequency and copy number between the orthologous genes from B. taurus and B. primigenius. This provides an unbiased approach to identify cattle genes that have undergone the most changes in miRNA binding (i.e. regulation) between the wild aurochs and modern-day cattle breeds. In addition, we demonstrate that these 1,620 candidate domestication genes are enriched for roles in pigmentation, fertility, neurobiology, metabolism, immunity and production traits (including milk quality and feed efficiency). Our findings suggest that directional selection of miRNA regulatory variants was important in the domestication and subsequent artificial selection that gave rise to modern taurine cattle.

Aeromonas hydrophila is a Gram-negative bacterium that is particularly adapted to freshwater environments and can cause severe infections in fish and humans. Here, we report the draft genomes of three A. hydrophila catfish and tilapia isolates.

Made available in DSpace on 2018-12-11T16:49:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-10-01 Ministero dell’Istruzione, dell’Università e della Ricerca Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here. Methods: The genomes of 73 buffaloes of 4 different breeds were sequenced and aligned against the bovine genome, which facilitated the identification of 22 million of sequence variants among the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome, inferred from the bovine genome sequence, 90,000 putative single nucleotide polymorphisms were selected to create an Axiom® Buffalo Genotyping Array 90K. Results: This 90K “SNP-Chip” was tested in several river buffalo populations and found to have *70% high quality and polymorphic SNPs. Of the 90K SNPs about 24K were also found to be polymorphic in swamp buffalo. The SNP chip was used to investigate the structure of buffalo populations, and could distinguish buffalo from different farms. A Genome Wide Association Study identified genomic regions on 5 chromosomes putatively involved in milk production. Conclusion: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes. This SNP Chip could also be used to analyse swamp buffalo, but many loci are not informative and creation of a revised SNP set specific for swamp buffalo would be advised. AIA-LGS Associazione Italiana Allevatori–Laboratorio Genetica e Servizi Fondazione Parco Tecnologico Padano Bioinformatics core Parco Tecnologico Padano Animal Genomics and Improvement Laboratory BARC USDA-ARS Department of Animal Science Iowa State University Institute of Zootechnics Università Cattolica del S. Cuore ANASB-Associazione Nazionale Allevatori Specie Bufalina Universidade Estadual Paulista (UNESP) Câmpus de Araçatuba COMSATS Institute of Information Technology Dipartimento di Scienze Zootecniche ed Ispezione degli Alimenti Facoltà di Agraria Università degli Studi di Napoli Federico II Universidade Federal De Minas Gerais (UFMG) Affymetrix UK Ltd Davies Research Centre School of Animal and Veterinary Sciences University of Adelaide Department of Animal Science University of Arkansas Recombinetics Inc. Council on Dairy Cattle Breeding, 4201 Northview Dr. One Town Centre Universidade Estadual Paulista (UNESP) Câmpus de Araçatuba

The GeneSeek Genomic Profiler (GGP) BeadChip (GeneSeek, Lincoln, NE), which became available commercially in February 2012, is based on the Illumina BovineLD Genotyping BeadChip (Illumina Inc., San Diego, CA), with 1,745 additional single nucleotide polymorphisms (SNP) for genomic evaluation and SNP for proprietary single-gene tests. The BovineLD chip with 6,909 SNP, which replaced the Illumina GoldenGate Bovine3K Genotyping BeadChip, has been available since October 2011. The GGP's additional SNP for genomic evaluation were selected to improve imputation by filling SNP gaps on chromosomes and including more Bovine3K SNP than were on the BovineLD chip and to impute microsatellite alleles to facilitate parentage validation. The SNP for single-gene tests were included to minimize the number of separate tests required for those genes, particularly for bulls. The September 2012 US national genomic evaluation included genotypes from BovineLD and GGP chips for 82,510 animals. For those data, BovineLD and GGP performance was similar. The call rate for SNP on these chips that were used in genomic evaluation was 99.6%. The 9 Y-chromosome SNP in common on the BovineLD and GGP chips were highly effective in sex validation (call rate of 99% for males and 0.01% for females). For both chips, the rate of parent–progeny conflicts on a SNP basis (≤0.004%) was similar to that for SNP on the Illumina BovineSNP50 Genotyping BeadChip. Imputation accuracy for 45,187 BovineSNP50 SNP averaged 99.4% for Holsteins. Imputation accuracy was slightly higher for the GGP chip compared with the BovineLD chip because of its additional SNP. Reliability for genomic evaluations using BovineLD and GGP genotypes was 3 percentage points higher than that for Bovine3K genotypes.

Genomic evaluations for 161,341 Holsteins were computed by using 311,725 of 777,962 markers on the Illumina BovineHD Genotyping BeadChip (HD). Initial edits with 1,741 HD genotypes from 5 breeds revealed that 636,967 markers were usable but that half were redundant. Holstein genotypes were from 1,510 animals with HD markers, 82,358 animals with 45,187 (50 K) markers, 1,797 animals with 8,031 (8 K) markers, 20,177 animals with 6,836 (6 K) markers, 52,270 animals with 2,683 (3 K) markers, and 3,229 nongenotyped dams (0 K) with >90% of haplotypes imputable because they had 4 or more genotyped progeny. The Holstein HD genotypes were from 1,142 US, Canadian, British, and Italian sires, 196 other sires, 138 cows in a US Department of Agriculture research herd (Beltsville, MD), and 34 other females. Percentages of correctly imputed genotypes were tested by applying the programs findhap and FImpute to a simulated chromosome for an earlier population that had only 1,112 animals with HD genotypes and none with 8 K genotypes. For each chip, 1% of the genotypes were missing and 0.02% were incorrect initially. After imputation of missing markers with findhap, percentages of genotypes correct were 99.9% from HD, 99.0% from 50 K, 94.6% from 6 K, 90.5% from 3 K, and 93.5% from 0 K. With FImpute, 99.96% were correct from HD, 99.3% from 50 K, 94.7% from 6 K, 91.1% from 3 K, and 95.1% from 0 K genotypes. Accuracy for the 3 K and 6 K genotypes further improved by approximately 2 percentage points if imputed first to 50 K and then to HD instead of imputing all genotypes directly to HD. Evaluations were tested by using imputed actual genotypes and August 2008 phenotypes to predict deregressed evaluations of US bulls proven after August 2008. For 28 traits tested, the estimated genomic reliability averaged 61.1% when using 311,725 markers vs. 60.7% when using 45,187 markers vs. 29.6% from the traditional parent average. Squared correlations with future data were slightly greater for 16 traits and slightly less for 12 with HD than with 50 K evaluations. The observed 0.4 percentage point average increase in reliability was less favorable than the 0.9 expected from simulation but was similar to actual gains from other HD studies. The largest HD and 50 K marker effects were often located at very similar positions. The single-breed evaluation tested here and previous single-breed or multibreed evaluations have not produced large gains. Increasing the number of HD genotypes used for imputation above 1,074 did not improve the reliability of Holstein genomic evaluations.

Since 2009, a clonal group of virulent Aeromonas hydrophila strains has been causing severe disease in the catfish aquaculture industry in the southeastern United States. Here, we report draft genomes of four A. hydrophila isolates from catfish aquaculture that represent this clonal group.

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

Made available in DSpace on 2018-12-11T17:03:58Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-07-06 We compared CNV region (CNVR) results derived from 1,682 Nellore cattle with equivalent results derived from our previous analysis of Bovine HapMap samples. By comparing CNV segment frequencies between different genders and groups, we identified 9 frequent, false positive CNVRs with a total length of 0.8 Mbp that were likely caused by assembly errors. Although there was a paucity of lineage specific events, we did find one 54 kb deletion on chr5 significantly enriched in Nellore cattle. A few highly frequent CNVRs present in both datasets were detected within genomic regions containing olfactory receptor, ATP-binding cassette, and major histocompatibility complex genes. We further evaluated their impacts on downstream bioinformatics and CNV association analyses. Our results revealed pitfalls caused by false positive and lineage-differential copy number variations and will increase the accuracy of future CNV studies in both taurine and indicine cattle. Animal Genomics and Improvement Laboratory BARC USDA-ARS College of Animal Science and Technology Northwest AandF University Shaanxi Key Laboratory of Agricultural Molecular Biology Departamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP - Univ Estadual Paulista Institute of Animal Science Chinese Academy of Agricultural Science Departamento de Apoio Produção e Saúde Animal Faculdade de Medicina Veterinária de Araçatuba UNESP - Univ Estadual Paulista Recombinetics Inc. Departamento de Medicina Veterinária Preventiva e Reprodução Animal Faculdade de Ciências Agrárias e Veterinárias UNESP - Univ Estadual Paulista Departamento de Apoio Produção e Saúde Animal Faculdade de Medicina Veterinária de Araçatuba UNESP - Univ Estadual Paulista

Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by the absence of a variable distal portion of the hindlimbs. The limited genomic resources available for water buffalo, in conjunction with an unconfirmed inheritance pattern, required an original approach to identify genetic variants associated with this disease. The genomes of 4 bilaterally affected cases, 7 unilaterally affected cases, and 14 controls were sequenced. Variant calling identified 19.8 million high confidence single nucleotide polymorphisms (SNPs) and 2.8 million insertions/deletions (INDELs). A concordance analysis of SNPs and INDELs requiring all unilateral and bilateral cases and none of the controls to be homozygous for the same allele, revealed two genes,WNT7AandSMARCA4, known to play a role in embryonic hindlimb development. Additionally, SNP alleles inNOTCH1andRARBwere homozygous exclusively in the bilaterally affected cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genomede novoassembly was then used to identify large contigs representing regions of homozygosity in the cases. This also supported an oligogenic mode of inheritance; implicating 13 genes involved in aberrant hindlimb development in the bilateral cases and 11 in the unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Results from these analyses suggest that mutations inSMARCA4andWNT7Aare required for expression of TH, while several other loci includingNOTCH1act as modifiers and increase the severity of the disease phenotype. Although our data show that the inheritance of TH is complex, we predict that homozygous variants inWNT7AandSMARCA4are necessary for the expression of TH and selection against these variants and avoidance of carrier-to-carrier matings should eradicate TH.Author SummaryGenetic diseases often occur and are spread through small populations under strong selection where rates of inbreeding can be significant. The use of a limited number of water buffalo males via artificial insemination for genetic improvement of milk and milk composition has increased the frequency of the genetic disease, transverse hemimelia (TH). Transverse hemimelia affected calves are normally developed except for malformation of one or both hindlimbs or both hindlimbs and one or both forelimbs. Little is known about the inheritance pattern of TH. We discovered genetic variants present in cases where both hindlimbs and one forelimb were affected, cases were both hindlimbs were affected, cases where only one hindlimb was affected, and in non-affected water buffalo that predict TH to be inherited as an oligogenic disease with two driver loci necessary for disease expression and several additional modifier genes that are responsible for the severity of the disease phenotype. We predict that selection against mutations in the two major loci and the avoidance of mating animals that are heterozygous for these mutations will eliminate TH from water buffalo.

Made available in DSpace on 2018-12-11T17:28:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-06-15 The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1. Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future. USDA-ARS Animal Genomics and Improvement Laboratory Department of Animal and Avian Sciences University of Maryland Universidade Estadual Paulista (UNESP) Division of Animal Sciences University of Missouri Informatics Institute University of Missouri Department of Evolution and Ecology University of California Universidade Estadual Paulista (UNESP)

Made available in DSpace on 2018-12-11T17:28:22Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-06-01 Background: Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). Results: We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894bp to 4,855,088bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. Conclusion: This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12. BARC USDA-ARS Animal Genomics and Improvement Laboratory, BARC-East Northwest A and F University College of Animal Science and Technology Faculdade de Ci�ncias Agr�rias e Veterin�rias UNESP - Univ Estadual Paulista Departamento de Medicina Veterin�ria Preventiva e Reprodu��o Animal Institute of Animal Science Chinese Academy of Agricultural Science College of Animal Science and Food Engineering University of S�o Paulo Department of Veterinary Medicine UNESP - Univ Estadual Paulista Departamento de Zootecnia Faculdade de Ci�ncias Agr�rias e Veterin�rias UNESP - Univ Estadual Paulista Departamento de Apoio Produ��o e Sa�de Animal Faculdade de Medicina Veterin�ria de Ara�atuba Recombinetics Inc. International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics Faculdade de Ci�ncias Agr�rias e Veterin�rias UNESP - Univ Estadual Paulista Departamento de Medicina Veterin�ria Preventiva e Reprodu��o Animal UNESP - Univ Estadual Paulista Departamento de Zootecnia Faculdade de Ci�ncias Agr�rias e Veterin�rias UNESP - Univ Estadual Paulista Departamento de Apoio Produ��o e Sa�de Animal Faculdade de Medicina Veterin�ria de Ara�atuba

Beef represents a major dietary component and source of protein in many countries. With an increasing demand for beef, the industry is currently undergoing changes towards naturally produced beef. However, the true differences between the feeding systems, especially the biochemical and nutritional aspects, are still unclear. Using transcriptome and metabolome profiles, we identified biological pathways related to the differences between grass- and grain-fed Angus steers. In the latissimus dorsi muscle, we have recognized 241 differentially expressed genes (FDR β-oxidation have been observed. The anti-inflammatory n3 polyunsaturated fatty acids are enriched in grass finished beef, while higher levels of n6 PUFAs in grain finished animals may promote inflammation and oxidative stress. Furthermore, grass-fed animals produce tender beef with lower total fat and a higher omega3/omega6 ratio than grain-fed ones, which could potentially benefit consumer health. Most importantly, blood cortisol levels strongly indicate that grass-fed animals may experience less stress than the grain-fed individuals. These results will provide deeper insights into the merits and mechanisms of muscle development.

Aeromonas hydrophila is an opportunistic pathogen residing in freshwater environments that causes infection in fish and mammals. Here, we report the draft genome sequence of A. hydrophila strain TN97-08 isolated from a diseased bluegill ( Lepomis macrochirus ) in 1997.

Reproductive efficiency is of economic importance in commercial beef cattle production, since failure to achieve pregnancy reduces the number of calves marketed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of females and avoid inefficiencies associated with sub-fertile cows. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome-wide association approach based on the >700,000 SNP marker assay. To include the largest number of individuals possible under the available budget, cows from several populations were assigned to extremes for reproductive efficiency, and DNA was pooled within population and phenotype before genotyping. Surprisingly, pools prepared from DNA of low reproductive cattle returned fluorescence intensity data intermediate between fertile females and males for SNP mapped to the Y chromosome (i.e., male sex chromosome). The presence of Y-associated material in low reproductive heifers or cows was confirmed by Y-directed PCR, which revealed that 21 to 29% of females in the low reproductive category were positive by a Y chromosome PCR test normally used to sex embryos. The presence of the Y chromosome anomaly was further confirmed with application of additional Y-specific PCR amplicons, indicating the likelihood of the presence of some portion of male sex chromosome in female cattle in various beef cattle herds across the U.S. Discovery of this Y anomaly in low reproductive females may make an important contribution to management of reproductive failures in beef cattle operations.

The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa , a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment size) at three different stringency levels and then assembling each data set with Velvet. A simple approach was devised to determine which filter stringency was “best.” Venn diagrams identified the regions containing reads that were used in an assembly but were of a low-enough quality to be removed by a filter. By plotting base quality histograms of reads in this region, we judged whether a filter was too stringent or not stringent enough. Our best assembly had a genome size of 33.6 Mb, an N50 of 65.8 kb for a k -mer of 51, and a maximum contig length of 347 kb. Using GeneMark, 9,262 genes were predicted. TargetP and SignalP analyses showed that among the 1,213 genes with secreted products, 986 had motifs for signal peptides and 227 had motifs for signal anchors. Blast2GO analysis provided functional annotation for 5,407 genes. We identified 29 genes with putative roles in copper tolerance and 73 genes for lignocellulose degradation. A search for homologs of these 102 genes showed that F. radiculosa exhibited more similarity to Postia placenta than Serpula lacrymans . Notable differences were found, however, and their involvements in copper tolerance and wood decay are discussed.

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence—476 of which (∼38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ2 test; P-value CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.