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We have previously reported significant linkage between markers on 11q13.5 and Usher syndrome type 1 (USH1B) in a large Samaritan kindred. USH1B is an autosomal recessive disease characterized by profound congenital sensorineural deafness, vestibular dysfunction and progressive visual loss. A unique haplotype found only in all USH1B carriers and affected individuals implied that the disease-causing mutation probably entered the community from a single founder. Screening for mutations in a gene called GARP, which was mapped to the same genetic interval as USH1B, revealed a base substitution in the coding region of the gene, in a homozygous state in all affected individuals. This base substitution, which results in an arginine to tryptophane change, is not found in control individuals and occurs at an amino acid residue that is conserved across species, including mouse, gorilla, chimpanzee and macaque. This study emphasizes the strength of using an isolated inbred population for efficient identification of the primary linkage and for narrowing the disease interval, but also demonstrates its limitations in distinguishing between mutations causing the disease and those representing unique and private polymorphisms. KEY WORDS consanguineous families; linkage; recessive deafness; Samaritan isolate

The Lake Tiberias (Sea of Galilee) grey mullet (Mugil cephalus) population originates from translocated wild-caught, or hatchery-reared, fish. The aim of the study was to identify the taxonomic status and stock origin of a sample of 32 mullet individuals caught in the Sea of Galilee, based on the mitochondrial Cytochrome Oxidase I (COI) sequence analysis and nuclear microsatellite markers. A total of 13 microsatellite markers were selected from nine different linkage groups with a number of alleles ranging from 5-23, with an average of 9.85 alleles/locus. By using COI sequences and the Barcode of Life Data (BOLD) identification system, seven individuals were taxonomically classified as Thinlip grey mullet (Liza ramda) and the remaining 25 as M. cephalus. Of 663 nucleotides, 122 (18.4%) differed between the COI sequences of the two distinct mullet species. A preliminary parentage analysis of the hatchery-reared stocking batch, based on 13 markers, assigned them as progeny of three mating pairs. These three mating pairs only were tested as potential parents of the 25 M. cephalus individuals captured from the lake. Marker-based comparison showed that a parent-offspring relationship was rejected for 17 M. cephalus individuals by at least four genetic markers. Eight of 25 M. cephalus individuals (32%), were identified as progeny of the three parental pairs with the overall probability of 3.88 x 10-7 for correspondence by chance to any of these three parental pairs. The 13 markers used has high statistical power to reject a putative parent-offspring relationship obtained by chance thus resulting in familial identification. This approach represents an accurate method of genetic stock identification and should also be applicable to populations of other species. The results confirm that the mullet hatcheryreared fingerlings survived in the Sea of Galilee when released alongside wildcaught fingerlings. [ABSTRACT FROM AUTHOR]

Based on pairwise identity-by-state ( IBS) distances and whole-genome SNP data, kinship was investigated in the Israeli Holstein population. A total of 789 bulls, including most of the artificial insemination sires in service since 1987, were genotyped by the Bovine SNP50 BeadChip. This sample included up to five generations. For each bull-by-bull combination, three states are possible for each marker: no match, a single match and both alleles match. Summing over all markers, the 932 598 IBS scores (three match frequencies*310 866 bull-by-bull combinations) were visualized using three-dimensional coordinates that corresponded to the frequencies of the three possible states. Results were reduced to two dimensions using the transformations x' = 0.7071(1 + freq1−freq2) and y' = 1.2247freq0. Bull-by-bull pairs were grouped according to their level of kinship, and canonical scores were calculated using discriminant analysis and the x' and y' features. Of the 474 pairs of recorded maternal grandsire-grandson with both individuals genotyped, the probability for 28 pairs to belong to this level of kinship was low ( P < 0.05), suggesting an error rate of around 3% per generation in pedigree determination. [ABSTRACT FROM AUTHOR]

Offspring of a highly inbred gynogenetic line of Oreochromis aureus displayed 12-fold increase in twinning rate compared to the outbred population. Asymmetric conjoined twins, which consist of a normal embryo attached to a malformed-atrophic twin, were frequently encountered in both gynogenetic (90·7%) and outbred (38·2%) embryos. The monozygotic origin of these twins was determined using five microsatellite markers. Progeny of heterozygous parents for the microsatellite UNH159 were separated into sub-sets of twins and normal full-sibs. Consistent with previous reports, the normal embryo sub-set exhibited elimination of both types of homozygotes for the UNH159 genetic marker at 2-8 days after fertilization. Unexpectedly, this elimination was less frequent in twins. The UNH159 marker as well as RNA-binding motif protein, X-linked ( rbmx), SRY-box containing gene 3 ( sox3) and alpha-thalassemia/mental retardation syndrome X-linked ( atrx) genes were mapped to linkage group 2. These gene orthologues are all located on the mammalian X chromosome and atrx is necessary for the X-chromosome inactivation. [ABSTRACT FROM AUTHOR]

Twelve bull calves were produced by mating elite Israeli cows to‘Glenhapton Enhancer’, a Canadian Holstein bull. The frequency of umbilical hernia (UH) in the progeny of the sons ranged from 1 to 21%, consistent with the hypothesis that Enhancer is the carrier of major dominant or codominant gene with partial penetrance for UH. Five sons of Enhancer produced progeny with>10% frequency of UH including sire 3259, whereas progeny of three sons had<3% UH. A total of 116 grand-progeny of Enhancer, all progeny of 3259, were genotyped for 59 microsatellites spanning the 29 bovine autosomes. Of these offspring, 41 were affected. Significant differences in paternal allele frequencies between the affected and unaffected progeny groups were found for markerBMS1591on bovine chromosome 8 (BTA8). The UH-associated paternal allele originated from Enhancer. The chromosomal segment associated with UH was more precisely mapped betweenUWCA47, on the centromeric end of BTA8 andRM321, 12 cM from the centromere. A maximum LOD score of 3.84 was obtained 2.5 cM from the centromere with a support interval of 8 cM. Haplotype analysis of eight sons of Enhancer suggested that the UH gene is located in the centromeric end of BTA8 beyondARO71/ARO72. Thus, by integrating the results from progeny of sire 3259 and sons of Enhancer the location of the UH gene was further refined to the BTA8 segment betweenARO71/ARO72andUWCA47. [ABSTRACT FROM AUTHOR]

The satiety hormone leptin has a key role in the control of energy homeostasis in mammals. Leptin is produced almost exclusively by the adipose tissue and signals the amount of fat stores primarily to the hypothalamus, but also to peripheral tissues. Recently, we identified the long sought leptin (SEROUSSI et al., 2016), in the "dark side of the chicken genome", meaning extremely GC-rich regions that have been difficult to sequence and assemble. Expression profiling of the avian leptins showed a different pattern compared to mammals, surprisingly with no expression in the adipose tissue. Nevertheless, we found that leptin and leptin receptor (LEPR) genes are expressed in tissues that are implicated in the response to leptin signalling in mammals, and their expression pointed to an autocrine/paracrine instead of endocrine mode of action. Therefore, the role of avian leptins may be relevant to the control of reproduction, stress response and metabolism, but in a different way than in mammals, as it is not the signal of the adipose tissue. Following the success of the identification of chicken leptin and realizing its presence in RNA-seq data rather than genomic assemblies, we asked if other missing genes in chicken could be identified using the RNA-seq approach. Extensive RNA-seq analysis of visceral fat, hypothalamus and pituitary, followed by transcript assembly and bioinformatic analysis led to the identification of 191 novel genes in chickens (BORNELOV et al., 2017), all with very high GC content (~70%). These included the tumour necrosis factor (TNF, also known as TNF-alpha) and nephrin (NPHS1), which were long sought after in the chicken genome. Interestingly, 25 of our novel genes were mapped to the chicken genome in the most recent genome assembly Galgal5. This mapping showed that about 70% of the genes were mapped to chicken microchromosomes, which are known to be GC-rich. The same proportion of genes were mapped in gene blocks demonstrating that the indication that missing genes arranged in gene clusters in other vertebrates cannot be taken as an indication for their evolutionary loss. Altogether, these findings suggest that other missing genes in chickens may be positioned in GC-rich gene clusters in the chicken genome. Among our novel chicken genes, we found five genes belonging to the leptin synteny group in vertebrates: RBM28, SND1, LRRC4, and FLNC. We used this identification to map the chicken leptin gene and its syntenic genes to chicken chromosome 1p (SEROUSSI et al., 2017), thus providing the final proof for the correct identification of the chicken leptin gene. [ABSTRACT FROM AUTHOR]

Examines the mapping of the GATA4, NEIL2, FDFT1 genes and CTSB-associated microsatellites to the centromeric region of BTA8. Alignment of their bovine genomic sequences with the human counterparts; Use of the expressed sequence tag to deduced their structure; Determination of locus polymorphisms.