All-male production by marker-assisted selection for sex determining loci of admixed Oreochromis niloticus and Oreochromis aureus stocks.

Crossing Oreochromis niloticus (On) females with Oreochromis aureus (Oa) males results in all-male progeny that are essential for effective tilapia farming. However, a reproductive barrier between these species limits mating and mass-fry production. One approach to overcoming this barrier is to select parental stocks of mixed genetic backgrounds, which allow interspecific reproductive recognition, while closely maintaining the genetic profiles for sex-determination (SD) of the respective purebred species. Here, we test this approach in a data set of 160 On × Oa spawns of 109 male and 100 female parents randomly collected from admixed stocks, and genotyped for microsatellite markers representing the known SD loci on linkage groups (LGs) 1, 3, and 23. Following crossbreeding, the most significant paternal effects on male proportions in progeny were found for LG1-BYL018 (P < 2 × 10-32 ) and for LG3-UNH168 × LG23-UNH898 interaction (P < 1 × 10-17 ; R2  = 0.98). Furthermore, a maternal effect for LG3-UNH168 (P < 9 × 10-7 ) was associated with low female proportions in progeny (<7%), indicating a non-Mendelian effect on SD. Eighty-four males (77%) and 30 females (30%) were selected as parents, based on their genetic profiles for the SD loci that were associated with male production. Of these, 51 of 53 crosses produced all-male progeny, while two crosses had low female proportions in their progeny (<4%). This suggests that selection could be improved using the causative sequence variation underlying SD on LG3, since the large non-recombining block of the SD region in purebred Oa readily breaks down in hybrids. Nevertheless, marker-assisted selection for sex determining loci of admixed parental stocks may be used for all-male production.

A duplication of the Anti-Müllerian hormone gene is associated with genetic sex determination of different Oreochromis niloticus strains.

Sex determination (SD) mechanisms are ancient and conserved, yet much diversity is exhibited in primary sex-determining signals that trigger male or female development. In O. niloticus, SD is associated with a male-specific locus on linkage group (LG) 23 which harbors the Y-linked Anti-Müllerian hormone (amh) gene, and a truncated duplication, denoted amhΔy. We have evaluated the possible role of identified indels and SNPs in the amh gene on SD, based on conservation in different O. niloticus strains. A fluorescent assay for the detection of a 5 bp insertion in amhΔy exon VI, efficiently discriminated between XX, XY, and YY genotypes. Concordance rate between amhΔy and sex varied in six Oreochromis strains, from 100% (Ghana) through 90% (Swansea) to 85% (Thai-Chitralada). The association of amhΔy with sex was found to be conserved in all tested O. niloticus strains, and thus supports its key role in SD. However, the previously identified missense SNP (C/T) in amh exon II was found only in the Swansea strain, thus excluding its candidacy for the causal variation of SD across all strains. Effects of markers on LGs 1, 3, and 23 (amhΔy) fully explained sex distribution in one Thai-Chitralada family (R2 = 1.0), whereas in another family only the major effect of LG23 (amhΔy) was significant (R2 = 0.37). Thus, amhΔy on LG23 is associated with genetic SD, either as a single causal gene in different O. niloticus strains, or in combination with segregating genes on LGs 1 and 3 in the Thai-Chitralada hybrid strain.

Identification of the sex-determining region in flathead grey mullet (Mugil cephalus).

Elucidation of the sex-determination mechanism in flathead grey mullet (Mugil cephalus) is required to exploit its economic potential by production of genetically determined monosex populations and application of hormonal treatment to parents rather than to the marketed progeny. Our objective was to construct a first-generation linkage map of the M. cephalus in order to identify the sex-determining region and sex-determination system. Deep-sequencing data of a single male was assembled and aligned to the genome of Nile tilapia (Oreochromis niloticus). A total 245 M. cephalus microsatellite markers were designed, spanning the syntenic tilapia genome assembly at intervals of 10 Mb. In the mapping family of full-sib progeny, 156 segregating markers were used to construct a first-generation linkage map of 24 linkage groups (LGs), corresponding to the number of chromosomes. The linkage map spanned approximately 1200 cM with an average inter-marker distance of 10.6 cM. Markers segregating on LG9 in two independent mapping families showed nearly complete concordance with gender (R2  = 0.95). The sex determining locus was fine mapped within an interval of 8.6 cM on LG9. The sex of offspring was determined only by the alleles transmitted from the father, thus indicating an XY sex-determination system.

Pegylated leptin antagonist with strong orexigenic activity in mice is not effective in chickens.

A chicken gene orthologous to human leptin receptor (LEPR) has been characterized and found to be active in leptin signaling in vitro in response to a variety of recombinant leptins and leptin-containing blood samples. However, the endogenous ligand of chicken LEPR (cLEPR) - the putative chicken leptin - has been reported by us and others to be undetectable at the DNA, mRNA, protein and activity levels. These reports have raised questions as to cLEPR's role. Here we analyzed the effects of a pegylated superactive mouse leptin antagonist (PEG-SMLA) in chicken. We showed that the leptin antagonist efficiently and specifically blocks leptin signaling through the cLEPR in vitro. The effect of the leptin antagonist was then studied in vivo by daily administration of 10 mg kg(-1) for 10 consecutive days to white leghorn female chickens (Gallus gallus) at the age of 2 weeks. Despites the efficient attenuation of the cLEPR in vitro, no effect was observed on body mass, feed intake, feed efficiency or fat accumulation in the treated birds. Because similar treatment in rodents leads to a highly pronounced increase in appetite and body mass that are observed from the first day of treatment, it is concluded that the cLEPR is not implicated in the control of appetite or adipose homeostasis in chickens.

Maternity validation using sire-only BovineSNP50 BeadChip data.

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 BovineSNP50 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.

A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of blue tilapia Oreochromis aureus.

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.

Signatures of contemporary selection in the Israeli Holstein dairy cattle.

Strong selection in the Israeli Holstein dairy cattle population over the last three decades should have left clear signatures of selection. Two experimental approaches were applied to detect evidence of contemporary selection based on the 54K BeadChip genotypes of ~1000 Israeli Holstein bulls: (i) the long-range haplotype test, which searches for structural evidence resulting from selective sweep, and (ii) direct analysis of the changes in haplotypes frequencies over time combined with linkage disequilibrium blocks haplotype-based association analysis. Ten traits were analyzed: the PD07 Israeli selection index, milk, milk fat, % fat, milk protein, % protein, somatic cell score, female fertility, milk production persistency and herd life. The long-range haplotype test detected ~15% of the 3288 haplotypes that showed significant positive frequency trends (P < 0.05) and was significantly correlated with the substitution effects of the haplotypes and the selection intensities for the different traits. Thirty signatures of recent selection, which correspond to both approaches and affect the Israeli PD07 selection index, were identified on 17 of the 29 autosomes. The second experimental approach also was used to estimate the selection intensity of the different traits. The correlation between the selection intensities for the traits analyzed, derived from changes in haplotype frequencies in the population of bulls, and those derived from trait-based analysis of the cow population was 0.93 over all traits. Thus, the changes in haplotypes frequencies in the bulls' population accurately estimate genetic trends in the general cow population and can be used to detect signatures of recent selection.

Short communication: Long-term survival of flag eartags on an Israeli dairy farm.

Two-plated self-piercing eartags were first developed in the 19th century, but information on their retention rates is scarce. A method is presented that facilitates estimation of eartag retention rate by using a random sample of cows that initially had 2 tags (1 on each ear) placed for identification and at least 1 of which survived. Striving to adopt the European Union standard for cattle ear tagging, the Israeli veterinary service conducted a field test to evaluate the performance of plastic eartags under the conditions of a typical Israeli dairy farm. The initial sample (n=900 cows) was tagged on a single farm. Retention rates were estimated based on the ratio between the observed numbers of cows with 1 or 2 eartags in the surviving group (n=97 cows). Based on this long-term (>3 yr) field test, the highest yearly retention of flag eartags (0.89±0.03) was lower than expected (0.98). Tag design and on-farm management were key factors affecting tag retention. A better design of the feedline yoke system in the feeding area, avoiding slits that can entangle the eartags, would help increase tag retention.

Differential expression of ruminant ZNF496 variants: Association with quantitative trait locus affecting bovine milk concentration and fertility.

A single nucleotide polymorphism in the intergenic region upstream of the ZNF496 gene on Bos taurus chromosome 7 displayed significant population-wide linkage disequilibrium with milk protein percentage in the Israeli Holstein population. The frequency of the allele associated with increased protein concentration was 10%. This single nucleotide polymorphism was located in the promoter region from which a 10-exon transcript of the bovine and the ovine ZNF496 genes are transcribed. The gene architecture was similar to the mouse ortholog Zkscan17. A 5-exon murine antisense transcript was complementary to the 5' untranslated Zkscan17 region that included a sequence domain conserved between mouse and ruminants, suggesting a regulatory function. In the bovine ZNF496 chromosomal region, segregation of a quantitative trait locus (QTL) for milk protein percentage was confirmed in a daughter design sire family. Concordance was not obtained between QTL status of bulls and any of the polymorphisms in the functional elements of ZNF496. This excludes these variations as the causative polymorphism under the assumption of no epigenetic effect for this locus. However, ZNF496 variants were differentially expressed in bovine ovaries, and only the paternal variant was expressed in liver and kidney in a sheep family with polymorphic ZNF496 sequence. Thus, the search for the mutation underlying the minor QTL allele, which is a top economically favorable allele in Israeli Holstein cattle, may be complicated by the presence of an imprinting center in this QTL confidence interval.

Paternity validation and estimation of genotyping error rate for the BovineSNP50 BeadChip.

Incorrect paternity assignment in cattle can have a major effect on rates of genetic gain. Of the 576 Israeli Holstein bulls genotyped by the BovineSNP50 BeadChip, there were 204 bulls for which the father was also genotyped. The results of 38 828 valid single nucleotide polymorphisms (SNPs) were used to validate paternity, determine the genotyping error rates and determine criteria enabling deletion of defective SNPs from further analysis. Based on the criterion of >2% conflicts between the genotype of the putative sire and son, paternity was rejected for seven bulls (3.5%). The remaining bulls had fewer conflicts by one or two orders of magnitude. Excluding these seven bulls, all other discrepancies between sire and son genotypes are assumed to be caused by genotyping mistakes. The frequency of discrepancies was >0.07 for nine SNPs, and >0.025 for 81 SNPs. The overall frequency of discrepancies was reduced from 0.00017 to 0.00010 after deletion of these 81 SNPs, and the total expected fraction of genotyping errors was estimated to be 0.05%. Paternity of bulls that are genotyped for genomic selection may be verified or traced against candidate sires at virtually no additional cost.

The concordance test emerges as a powerful tool for identifying quantitative trait nucleotides: lessons from BTA6 milk yield QTL.

The lack of conventions for confirming the discovery of quantitative trait nucleotides in livestock was evidenced by the proposals of mutations in two different genes (SPP1 and ABCG2) as the underlying functional mutation for a major quantitative trait locus (QTL) for milk concentration on bovine chromosome 6 (BTA6). Of these conflicting candidates, SPP1 was excluded by follow-up studies and by the data described here. A simple test for concordance of the zygosity state between QTL segregation status and the candidate polymorphism was shown, in this case, to be a critical step towards establishing the proof. If a given sample effectively represents the genetic variation across the QTL region, haplotype-based concordance may further enhance the functionality and resolution power of this test, allowing identification of the causative gene.

Development of a 25-plex SNP assay for traceability in cattle.

Single nucleotide polymorphisms (SNPs) are amenable to automation and therefore have become the marker of choice for DNA profiling. SNaPshot, a primer extension-based method, was used to multiplex 25 SNPs that have been previously validated as useful for identity control. Detection of extended products was based on four different fluorochromes and extension primers with oligonucleotide tails of differing lengths, thus controlling the concise length of the entire chromatogram to 81 bases. Allele frequencies for Holstein, Simmental, Limousin, Angus, Charolais and Tux Cattle were estimated and significant positive Pearson-correlation coefficients were obtained among the analysed breeds. The probability that two randomly unrelated individuals would share identical genotypes for all 25 loci varied from 10(-8) to 10(-10) for these breeds. For parentage control, the exclusion power was found to be 99.9% when the genotypes of both putative parents are known. A traceability test of duplicated samples indicated a high genotyping precision of >0.998. This was further corroborated by analysis of 60 cases of parent-sib pairs and trio families. The 25-plex SNaPshot assay is adapted for low- and high-throughput capacity and thus presents an alternative for DNA-based traceability in the major commercial cattle breeds.

Copy number variation of lipocalin family genes for male-specific proteins in tilapia and its association with gender.

Lipocalins are involved in the binding of small molecules like sex steroids. We show here that the previously reported tilapia male-specific protein (MSP) is a lipocalin encoded by a variety of paralogous and homologous genes in different tilapia species. Exon-intron boundaries of MSP genes were typical of the six-exon genomic structure of lipocalins, and the transcripts were capable of encoding 200 amino-acid polypeptides that consisted of a putative signal peptide and a lipocalin domain. Cysteine residues are conserved in positions analogous to those forming the three disulfide bonds characteristic of the ligand pocket. The calculated molecular mass of the secreted MSP (20.4 kDa) was less than half of that observed, suggesting that it is highly glycosylated like its homologue tributyltin-binding protein. Analysis of sequence variations revealed three types of paralogs MSPA, MSPB and MSPC. Expression of both MSPA and MSPB was detected in testis. In haploid Oreochromis niloticus embryos, each of these types consisted of two closely related paralogs, and asymmetry between MSP copy numbers on the maternal (six copies) and the paternal (three copies) chromosomes was observed. Using this polymorphism we mapped MSPA and MSPC to linkage group 12 of an F(2) mapping family derived from a cross between O. niloticus and Oreochromis aureus. Females with high MSP copy number were more frequent by more than twofold than males. Gender-MSPC combinations showed significant deviation from expected Mendelian segregation (P=0.009) suggesting elimination of males with MSPC copies. We discuss different hypotheses to explain this elimination, including possibility for allelic conflict resulted by the hybridization.

Detection and analysis of quantitative trait loci affecting production and secondary traits on chromosome 7 in Israeli Holsteins.

A total of 5,459 Israeli Holstein cows, daughters of 11 sires, were genotyped for 29 microsatellites spanning chromosome 7 and analyzed by the daughter design for 9 economic traits: milk, fat, and protein yield, fat and protein percentage, somatic cell score, female fertility, herd life, and milk persistency. Quantitative trait loci at chromosome-wise 0.05 significance were obtained for fat and protein yield, fat percentage, somatic cell score, and female fertility. Peak F-values were obtained at 29 cM for fat and protein yield and fat percentage, at 60 cM for somatic cell score, at 74 cM for herd life, and at 11 cM for female fertility. The 0.95 confidence intervals for quantitative trait loci locations were 20 cM for kilograms of fat, 27 cM for fertility, and 51 cM for somatic cell score. Two loci affecting fertility at opposite ends of the chromosome are apparently segregating in the population. A quantitative trait locus for fertility near the centromere was confirmed by application of the modified granddaughter design to a single family. Estimated frequency of the economically favorable allele in the Israeli Holstein cattle was less than 0.5. Significant genetic gain for fertility seems possible by marker-assisted selection.

Detection of quantitative trait loci affecting twinning rate in Israeli Holsteins by the daughter design.

Twinning rate was analyzed in the Israeli Holstein dairy cattle population by the multiple-trait animal model, and a daughter design genome scan for quantitative trait loci was performed. Each parity was considered a separate trait. Heritabilities of twinning rate were very low, but increased by parity from 0.01 in first parity to 0.03 in fifth parity. All genetic correlations among parities were >0.77, but all environmental correlations were <0.07. Genetic correlations between twinning rate and female fertility (measured as the inverse of the number of inseminations to conception) in the first 3 parities were negative for all 9 parity-by-trait combinations. All environmental correlations were very small, but generally negative. The overall genetic trend since 1985 was positive at 0.02% twinning/yr, whereas the phenotypic trends were positive for parities 3 and 4 and negative for the other parities, but all trends were quite small. A total of 5,221 cows, daughters of 11 sires, were genotyped for 73 markers spanning all 29 autosomes. There were 9 markers with significant effects on twinning rate at P < 0.05, for a false discovery rate of 0.4; thus, about 5 of these probably represent true effects. Significant effects were found on chromosomes 1, 6, 7, 8, 14, 15, and 23. Of these, 3 effects were significant at P < 0.01, for a false discovery rate of 0.24. All 11 families were analyzed by interval mapping of chromosome 7. Only 2 families showed nominally significant effects, but chromosome-wise significance at P < 0.05 was not obtained for either family. Suggestive evidence of quantitative trait loci near the beginning of the chromosome and near position 50 cM were found in both families. Sire 3070 also had a significant effect for female fertility near the beginning of the chromosome. There was also evidence for a third quantitative trait loci at the end of the chromosome for sire 2357.

Uniquely conserved non-translated regions are involved in generation of the two major transcripts of protein phosphatase 2Cbeta.

Partial cDNAs of different isoforms of protein phosphatase 2Cbeta (PP2Cbeta or PPM1B) have been characterized in mammals. We disclose here the full cDNAs of two major PP2Cbeta isoforms from human, rat and mouse. These cDNAs (2.6 and 3.3 kb) are able to encode 53 kDa (PP2Cbetal) and 43 kDa (PP2Cbetas) polypeptides, respectively. The isoforms are co-expressed ubiquitously with the highest level in skeletal muscle, as assessed by Northern-blot analysis. Western and in situ analyses using monoclonal antibodies against PP2Cbeta confirmed the existence of two isoforms in the cytoplasm. Comparative sequence analysis revealed that both cDNAs consist of six exons with an alternate usage of the 3' exons that underlies the differences between them. The genomic structure of PP2Cbeta is similar to that of other PP2C paralogs and includes a non-coding first exon followed by a large intron and a large second exon that encoded most of the catalytic domain. Both variants of the ending exon include large non-coding regions. All non-translated regions (NTRs) are highly conserved between the orthologous genes, indicating their regulatory function. The 5'-NTR is long (379 bp), includes upstream start codons and is predicted to contain stable secondary structures. Such features inhibit translation initiation by the scanning mechanism. Introduction of this NTR element into a bi-luciferase expression-cassette enabled expression of the second cistron, suggesting that it might serve as an internal ribosome entry site, or it contains a cryptic promoter. Overexpression of PP2Cbeta under CMV-promoter in 293 cells led to cell-growth arrest or cell death.

Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design.

Nine Israeli Holstein sire families with 2978 daughters were analyzed for quantitative trait loci effects on chromosome 6 for five milk production traits by a daughter design. All animals were genotyped for 2 markers. The three families with significant effects were genotyped for up to 10 additional markers spanning positions 0-122 cM of BTA6. Two sires were segregating for a locus affecting protein and fat percentage near position 55 cM with an estimated substitution effect of 0.18% protein, which is equivalent to one phenotypic standard deviation. This locus was localized to a confidence interval of 4 cM. One of these sires was also heterozygous for a locus affecting milk, fat, and protein production near the centromere. The hypothesis of two segregating loci was verified by multiple regression analysis. A third sire was heterozygous for a locus affecting milk and protein percentage near the telomeric end of the chromosome. Possible candidates for the major quantitative gene near position 55 cM were determined by comparative mapping. IBSP and SSP1 were used as anchors for the orthologous region on human chromosome 4. Twelve genes were detected within a 2-Mbp sequence. None of these genes have been previously associated with lactogenesis.

Characterization of the human NIPSNAP1 gene from 22q12: a member of a novel gene family.

Rapid progress in sequencing of human and other genomes allows high-resolution analysis of their gene content on the basis of comparison between species. We have used a combined computer and biochemical approach to characterize 135 kb of human genomic sequence from 22q12 and discovered a new 10 exon gene, termed NIPSNAP1, located between the neurofibromatosis type 2 and the pK1.3 genes. The NIPSNAP1 gene spans 26 kb of genomic sequence and shows to large introns in the 5'-region. All exon-intron junctions contain the gt/ag consensus splice site. The putative promoter of the NIPSNAP1 gene is TATA-less and resides in a GC-rich island characteristic of housekeeping genes. The NIPSNAP1 mRNA is 2.1 kb, is expressed ubiquitously at variable levels, with the highest expression in liver, is terminated by an uncommon ATTAAA polyadenylation site, and is capable of encoding a 284-amino-acid protein. This NIPSNAP1 protein has a strong sequence similarity limited to the central portion of a hypothetical protein (acc. P34492) from chromosome III of C. elegans, in which the other portions resemble a 4-nitrophenylphosphatase domain and non-neuronal SNAP25-like protein. Thus, the NIPSNAP1 gene is a member of an evolutionarily well conserved, novel gene family with two members in human and mouse that have now been characterized, and one member in C. elegans. The second human gene, NIPSNAP2, is localized in the vicinity of marker D7S499 on chromosome 7. Although the function of the NIPSNAP protein family is unknown, clues about its role may reside in the co-expression of the C. elegans orthologue, within an operon encoding protein motifs known to be involved in vesicular transport.

Predictive ability of selected subsets of single nucleotide polymorphisms (SNPs) in a moderately sized dairy cattle population.

Several studies have shown that computation of genomic estimated breeding values (GEBV) with accuracies significantly greater than parent average (PA) estimated breeding values (EBVs) requires genotyping of at least several thousand progeny-tested bulls. For all published analyses, GEBV computed from the selected samples of markers have lower or equal accuracy than GEBV derived on the basis of all valid single nucleotide polymorphisms (SNPs). In the current study, we report on four new methods for selection of markers. Milk, fat, protein, somatic cell score, fertility, persistency, herd life and the Israeli selection index were analyzed. The 972 Israeli Holstein bulls genotyped with EBV for milk production traits computed from daughter records in 2012 were assigned into a training set of 844 bulls with progeny test EBV in 2008, and a validation set of 128 young bulls. Numbers of bulls in the two sets varied slightly among the nonproduction traits. In EFF12, SNPs were first selected for each trait based on the effects of each marker on the bulls' 2012 EBV corrected for effective relationships, as determined by the SNP matrix. EFF08 was the same as EFF12, except that the SNPs were selected on the basis of the 2008 EBV. In DIFmax, the SNPs with the greatest differences in allelic frequency between the bulls in the training and validation sets were selected, whereas in DIFmin the SNPs with the smallest differences were selected. For all methods, the numbers of SNPs retained varied over the range of 300 to 6000. For each trait, except fertility, an optimum number of markers between 800 and 5000 was obtained for EFF12, based on the correlation between the GEBV and current EBV of the validation bulls. For all traits, the difference between the correlation of GEBV and current EBV and the correlation of the PA and current EBV was >0.25. EFF08 was inferior to EFF12, and was generally no better than PA EBV. DIFmax always outperformed DIFmin and generally outperformed EFF08 and PA. Furthermore, GEBV based on DIFmax were generally less biased than PA. It is likely that other methods of SNP selection could improve upon these results.

Ovine mitochondrial DNA sequence variation and its association with production and reproduction traits within an Afec-Assaf flock.

Polymorphisms in mitochondrial DNA (mtDNA) protein- and tRNA-coding genes were shown to be associated with various diseases in humans as well as with production and reproduction traits in livestock. Alignment of full length mitochondria sequences from the 5 known ovine haplogroups: HA (n = 3), HB (n = 5), HC (n = 3), HD (n = 2), and HE (n = 2; GenBank accession nos. HE577847-50 and 11 published complete ovine mitochondria sequences) revealed sequence variation in 10 out of the 13 protein coding mtDNA sequences. Twenty-six of the 245 variable sites found in the protein coding sequences represent non-synonymous mutations. Sequence variation was observed also in 8 out of the 22 tRNA mtDNA sequences. On the basis of the mtDNA control region and cytochrome b partial sequences along with information on maternal lineages within an Afec-Assaf flock, 1,126 Afec-Assaf ewes were assigned to mitochondrial haplogroups HA, HB, and HC, with frequencies of 0.43, 0.43, and 0.14, respectively. Analysis of birth weight and growth rate records of lamb (n = 1286) and productivity from 4,993 lambing records revealed no association between mitochondrial haplogroup affiliation and female longevity, lambs perinatal survival rate, birth weight, and daily growth rate of lambs up to 150 d that averaged 1,664 d, 88.3%, 4.5 kg, and 320 g/d, respectively. However, significant (P < 0.0001) differences among the haplogroups were found for prolificacy of ewes, with prolificacies (mean ± SE) of 2.14 ± 0.04, 2.25 ± 0.04, and 2.30 ± 0.06 lamb born/ewe lambing for the HA, HB, and the HC haplogroups, respectively. Our results highlight the ovine mitogenome genetic variation in protein- and tRNA coding genes and suggest that sequence variation in ovine mtDNA is associated with variation in ewe prolificacy.