Epitopes Of Tilapia Red Blood Cells. I. Species-Specific Antibodies For The Control Of Tilapia Breeding Stocks

Specific antisera against red blood cells of some tilapia species were obtained by reciprocal inter- specific and intergeneric immunizations. The antisera were used to confirm co-dominant expres- sion of epitopes in F1 interspecific hybrids and to identify the parental origin of three red tilapia strains. The antisera in all hybrids (Oreochromis niloticus x O. mossambicus, O. aureus x O. horno- rum, O. niloticus x S. galilaeus and O. niloticus x O. aureus) were positive to both parental strains. However, while all F1 hybrids of O. mossambicus x O. hornorum were positive to anti-O. mossambi- cus antiserum, only 50% were positive to anti-O. hornorum antiserum. In most cases, these results point to co-dominant expression of the species-specific epitopes in hybrids. In addition, the triple parental origins of the Philippine red tilapia (positive for O. aureus, O. mossambicus and O. niloticus epitopes) and of mossambicus red tilapia (positive for O. hornorum, O. mossambicus and O. niloticus epitopes) were assessed. The O. niloticus red tilapia, described as a purebred red variant of O. niloticus, was positive for both anti-O. niloticus and anti-O. aureus antibodies, with a significantly more intense reaction to the latter. A possible genetic basis of this last finding is discussed

Analysis of copy loss and gain variations in Holstein cattle autosomes using BeadChip SNPs

<p>Abstract</p> <p>Background</p> <p>Copy number variation (CNV) has been recently identified in human and other mammalian genomes, and there is a growing awareness of CNV's potential as a major source for heritable variation in complex traits. Genomic selection is a newly developed tool based on the estimation of breeding values for quantitative traits through the use of genome-wide genotyping of SNPs. Over 30,000 Holstein bulls have been genotyped with the Illumina BovineSNP50 BeadChip, which includes 54,001 SNPs (~SNP/50,000 bp), some of which fall within CNV regions.</p> <p>Results</p> <p>We used the BeadChip data obtained for 912 Israeli bulls to investigate the effects of CNV on SNP calls. For each of the SNPs, we estimated the frequencies of occurrence of loss of heterozygosity (LOH) and of gain, based either on deviation from the expected Hardy-Weinberg equilibrium (HWE) or on signal intensity (SI) using the <it>PennCNV </it>"detect" option. Correlations between LOH/CNV frequencies predicted by the two methods were low (up to r = 0.08). Nevertheless, 418 locations displayed significantly high frequencies by both methods. Efficiency of designating large genomic clusters of olfactory receptors as CNVs was 29%. Frequency values for copy loss were distinguishable in non-autosomal regions, indicating misplacement of a region in the current BTA7 map. Analysis of BTA18 placed major quantitative trait loci affecting net merit in the US Holstein population in regions rich in segmental duplications and CNVs. Enrichment of transporters in CNV loci suggested their potential effect on milk-production traits.</p> <p>Conclusions</p> <p>Expansion of HWE and <it>PennCNV </it>analyses allowed estimating LOH/CNV frequencies, and combining the two methods yielded more sensitive detection of inherited CNVs and better estimation of their possible effects on cattle genetics. Although this approach was more effective than methodologies previously applied in cattle, it has severe limitations. Thus the number of CNVs reported here for the Holstein breed may represent as little as one-tenth of inherited common structural variation.</p

SNPmplexViewer--toward a cost-effective traceability system

<p>Abstract</p> <p>Background</p> <p>Beef traceability has become mandatory in many regions of the world and is typically achieved through the use of unique numerical codes on ear tags and animal passports. DNA-based traceability uses the animal's own DNA code to identify it and the products derived from it. Using <it>SNaPshot</it>, a primer-extension-based method, a multiplex of 25 SNPs in a single reaction has been practiced for reducing the expense of genotyping a panel of SNPs useful for identity control.</p> <p>Findings</p> <p>To further decrease <it>SNaPshot</it>'s cost, we introduced the Perl script <it>SNPmplexViewer</it>, which facilitates the analysis of trace files for reactions performed without the use of fluorescent size standards. <it>SNPmplexViewer </it>automatically aligns reference and target trace electropherograms, run with and without fluorescent size standards, respectively. <it>SNPmplexViewer </it>produces a modified target trace file containing a normalised trace in which the reference size standards are embedded. <it>SNPmplexViewer </it>also outputs aligned images of the two electropherograms together with a difference profile.</p> <p>Conclusions</p> <p>Modified trace files generated by <it>SNPmplexViewer </it>enable genotyping of <it>SnaPshot </it>reactions performed without fluorescent size standards, using common fragment-sizing software packages. <it>SNPmplexViewer</it>'s normalised output may also improve the genotyping software's performance. Thus, <it>SNPmplexViewer </it>is a general free tool enabling the reduction of <it>SNaPshot</it>'s cost as well as the fast viewing and comparing of trace electropherograms for fragment analysis. <it>SNPmplexViewer </it>is available at <url>http://cowry.agri.huji.ac.il/cgi-bin/SNPmplexViewer.cgi</url>.</p

Bos taurus–indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle

Crossover localization during meiotic recombination is mediated by the fast-evolving zinc-finger (ZnF) domain of gene PRDM9. To study its impact on dairy cattle performance, we compared its genetic variation between the relatively small Israeli (IL) Holsteins and the North American (US) Holsteins that count millions.https://doi.org/10.1186/s12863-019-0773-

Full-Sib Mating Can Reduce Deleterious Effects Associated With Residual Sperm Inheritance In Gynogenotes

Fertilization of Oreochromis aureus eggs with UV-irradiated sperm from the closely related species O. niloticus, followed by diploidy restoration, produced offspring with lower embryo viability and higher skeletal deformation rates than siblings generated with sperm from a genetically distant species (Tilapia zillii). Results showed that: (a) deleterious effects due to O. niloticus sperm accu- mulate in gynogenetic fish over generations; (b) such effects are eliminated when using T. zillii sperm to fertilize eggs from gynogenetic mothers produced by full-sib matings. These results sug- gest that: (a) deleterious effects are associated with residual male DNA fragments which may be passed on to descendent offspring; (b) such fragments are significantly purged following full-sib mating. These findings suggest that biparental reproduction may play an important role in the con- trol of genome integrality by purging supernumerary chromosome fragments

DNA Barcoding of Israeli Indigenous and Introduced Cichlids

The objectives of this study were barcoding and taxonomic analysis of the five tilapiine species (Oreochromis aureus, O. niloticus, O. mossam- bicus, Sarotherodon galilaeus, and Tilapia zillii), two tilapia hybrid strains (Florida red tilapia and Philippine red tilapia), and two endemic wild cichlids (Tristramella simonis and Astatotilapia flaviijosephi) available in Israel, as well as O. urolepis hornorum. Cytochrome oxidase subunit I (COI) 619 bp sequence traces of 104 individuals were assembled, aligned, and compared (GenBank project GI 209553463). The DNA sequences of two hybrid strains were identical to those of O. hornorum and O. aureus. Absence of intra-specific variability was detected in the commercially used species, O. aureus, S. galilaeus, O. mossambicus, and O. urolepis horno- rum. Two DNA sequence variants were detected in O. niloticus originating from Ghana and Egypt. In contrast, 2-3 variants were detected in the DNA of each of the non-commercial species. Amino-acid sequences were identical in all “true tilapias” and different from the sequences in the endemic cichlids. As a whole, the protein phylogenetic tree fitted the expected conventional taxonomy as opposed to the respective DNA-based tree. Sequences FJ348047-FJ348150 were submitted to GenBank via the BOLD database (identical to FISH001-08 - FISH104-08 in this database)

Comparing BeadChip and WGS Genotyping: Non-Technical Failed Calling Is Attributable to Additional Variation within the Probe Target Sequence

Microarray-based genomic selection is a central tool to increase the genetic gain of economically significant traits in dairy cattle. Yet, the effectivity of this tool is slightly limited, as estimates based on genotype data only partially explain the observed heritability. In the analysis of the genomes of 17 Israeli Holstein bulls, we compared genotyping accuracy between whole-genome sequencing (WGS) and microarray-based techniques. Using the standard GATK pipeline, the short-variant discovery within sequence reads mapped to the reference genome (ARS-UCD1.2) was compared to the genotypes from Illumina BovineSNP50 BeadChip and to an alternative method, which computationally mimics the hybridization procedure by mapping reads to 50 bp spanning the BeadChip source sequences. The number of mismatches between the BeadChip and WGS genotypes was low (0.2%). However, 17,197 (40% of the informative SNPs) had extra variation within 50 bp of the targeted SNP site, which might interfere with hybridization-based genotyping. Consequently, with respect to genotyping errors, BeadChip varied significantly and systematically from WGS genotyping, introducing null allele-like effects and Mendelian errors (&lt;0.5%), whereas the GATK algorithm of local de novo assembly of haplotypes successfully resolved the genotypes in the extra-variable regions. These findings suggest that the microarray design should avoid polymorphic genomic regions that are prone to extra variation and that WGS data may be used to resolve erroneous genotyping, which may partially explain missing heritability

Master-Key Regulators of Sex Determination in Fish and Other Vertebrates&mdash;A Review

In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches