Genome-wide association study for female fertility in Nordic Red cattle.

BACKGROUND: The Nordic Red Cattle (NRC) consists of animls belonging to the Danish Red, Finnish Ayrshire, and Swedish Red breeds. Compared to the Holstein breed, NRC animals are smaller, have a shorter calving interval, lower mastitis incidence and lower rates of stillborn calves, however they produce less milk, fat and protein. Female fertility is an important trait for the dairy cattle farmer. Selection decisions in female fertilty in NRC are based on the female fertility index (FTI). FTI is a composite index including a number of sub-indices describing aspects of female fertility in dairy cattle. The sub-traits of FTI are: number of inseminations per conception (AIS) in cows (C) and heifers (H), the length in days of the interval from calving to first insemination (ICF) in cows, days from first to last insemination (IFL) in cows and heifers, and 56-day non-return rate (NRR) in cows and heifers. The aim of this study was first to identify QTL for FTI by conducting a genome scan for variants associated with fertility index using imputed whole genome sequence data based on 4207 Nordic Red sires, and subsequently analyzing which of the sub-traits were affected by each FTI QTL by associating them with the sub-traits. RESULTS: A total 17,388 significant SNP markers (-log10(P) > 8.25) were detected for FTI distributed over 25 chromosomes. The chromosomes with the most significant markers were tested for associations with the underlying sub-traits: BTA1 (822 SNP), BTA2 (220 SNP), BTA3 (83 SNP), BTA5 (195 SNP), two regions on BTA6 (503 SNP), BTA13 (980 SNP), BTA15 (23 SNP), BTA20 (345 SNP), and BTA24 (104 SNP). The fertility traits underlying the FTI peak area were: BTA1 (IFLC, IFLH), BTA2 (AISH, IFLH, NRRH), BTA3 (AISH, NRRH), BTA5 (AISC, AISH, IFLH), BTA6 (region 1: AISH, NRRH; region 2: AISH, IFLH), BTA13 (IFLH, IFLC), BTA15 (IFLC, NRRH), and BTA24 (AISH, IFLH). For BTA20 all sub-traits had SNP markers with a -log10(P) > 10. Furthermore the genes assigned to the most significant SNP for FTI were located on BTA6 (GPR125), BTA13 (ANKRD60), BTA15 (GRAMD1B), and BTA24 (ZNF521). CONCLUSION: This study 1) shows that many markers within FTI QTL regions were significantly associated with both AISH and IFLH, and 2) identified candidate genes for FTI located on BTA6 (GPR125), BTA13 (ANKRD60), BTA15 (GRAMD1B), and BTA24 (ZNF521). It is not known how the genes/variants identified in this study regulate female fertility, however the majority of these genes were involved in protein binding, 3) a SNP in a QTL region for FTI on BTA20 was previously validated in three cattle breeds.

Identification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data.

BACKGROUND: Female fertility is an important trait in cattle breeding programs. In the Nordic countries selection is based on a fertility index (FTI). The fertility index is a weighted combination of four female fertility traits estimated breeding values for number of inseminations per conception (AIS), 56-day non-return rate (NRR), number of days from first to last insemination (IFL), and number of days between calving and first insemination (ICF). The objective of this study was to identify associations between sequence variants and fertility traits in Jersey cattle based on 1,225 Jersey sires from Denmark with official breeding values for female fertility traits. The association analyses were carried out in two steps: first the cattle genome was scanned for quantitative trait loci using a sire model for FTI using imputed whole genome sequence variants; second the significant quantitative trait locus regions were re-analyzed using a linear mixed model (animal model) for both FTI and its component traits AIS, NRR, IFL and ICF. The underlying traits were analyzed separately for heifers (first parity cows) and cows (later parity cows) for AIS, NRR, and IFL. RESULTS: In the first step 6 QTL were detected for FTI: one QTL on each of BTA7, BTA20, BTA23, BTA25, and two QTL on BTA9 (QTL9-1 and QTL9-2). In the second step, ICF showed association with the QTL regions on BTA7, QTL9-2 QTL2 on BTA9, and BTA25, AIS for cows on BTA20 and BTA23, AIS for heifers on QTL9-2 on BTA9, IFL for cows on BTA20, BTA23 and BTA25, IFL for heifers on BTA7 and QTL9-2 on BTA9, NRR for heifers on BTA7 and BTA23, and NRR for cows on BTA23. CONCLUSION: The genome wide association study presented here revealed 6 genomic regions associated with FTI. Screening these 6 QTL regions for the underlying female fertility traits revealed that different female fertility traits showed associations with different subsets of the individual FTI QTL peaks. The result of this study contributed to a better insight into the genetic control of FTI in the Danish Jersey.

Loci associated with adult stature also affect calf birth survival in cattle.

BACKGROUND: Understanding the underlying pleiotropic relationships among quantitative traits is necessary in order to predict correlated responses to artificial selection. The availability of large-scale next-generation sequence data in cattle has provided an opportunity to examine whether pleiotropy is responsible for overlapping QTL in multiple economic traits. In the present study, we examined QTL affecting cattle stillbirth, calf size, and adult stature located in the same genomic region. RESULTS: A genome scan using imputed whole genome sequence variants revealed one QTL with large effects on the service sire calving index (SCI), and body conformation index (BCI) at the same location (~39 Mb) on chromosome 6 in Nordic Red cattle. The targeted region was analyzed for SCI and BCI component traits. The QTL peak included LCORL and NCAPG genes, which had been reported to influence fetal growth and adult stature in several species. The QTL exhibited large effects on calf size and stature in Nordic Red cattle. Two deviant haplotypes (HAP1 and HAP2) were resolved which increased calf size at birth, and affected adult body conformation. However, the haplotypes also resulted in increased calving difficulties and calf mortality due to increased calf size at birth. Haplotype locations overlapped, however linkage disequilibrium (LD) between the sites was low, suggesting that two independent mutations were responsible for similar effects. The difference in prevalence between the two haplotypes in Nordic Red subpopulations suggested independent origins in different populations. CONCLUSIONS: Results of our study identified QTL with large effects on body conformation and service sire calving traits on chromosome 6 in cattle. We present robust evidence that variation at the LCORL and NCAPG locus affects calf size at birth and adult stature. We suggest the two deviant haplotypes within the QTL were due to two independent mutations.

Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data.

BACKGROUND: Female fertility is important for the maintenance of the production in a dairy cattle herd. Two QTL regions on BTA04 and on BTA13 previously detected in Nordic Holstein (NH) and validated in the Danish Jersey (DJ) and Nordic Red (NR) were investigated further in the present study to further refine the QTL locations. Refined QTL regions were imputed to the full sequence data. The genes in the regions were then studied to ascertain their possible effect on fertility traits. RESULTS: BTA04 was screened for number of inseminations (AIS), 56-day non-return rate (NRR), days from first to last insemination (IFL), and the interval from calving to first insemination (ICF) in the range of 38,257,758 to 40,890,784 bp, whereas BTA13 was screened for ICF only in the range from 21,236,959 to 46,150,079 with the HD bovine SNP array for NH, DJ and NR. No markers in the DJ and NR breeds reached significance. By analyzing imputed sequence data the QTL position on BTA04 was narrowed down to two regions in the NH. In these two regions a total of 9 genes were identified. BTA13 was analyzed using sequence data for the NH breed. The highest -log10(P-value) was 19.41 at 33,903,159 bp. Two regions were identified: Region 1: 33,900,143-33,908,994 bp and Region 2: 34,051,815-34,056,728 bp. SNPs within and between these two regions were annotated as intergenic. CONCLUSION: Screening BTA04 and BTA13 for female fertility traits in NH, NR and DJ suggested that the QTL for female fertility were specific for NH. A missense mutation in CD36 showed the strongest association with fertility traits on BTA04. The annotated SNPs on BTA13 were all intergenic variants. It is possible that BTA13 at this stage is poorly annotated such that the associated polymorphisms are located in as-yet undiscovered genes. Fertility traits are complex traits as many different biological and physiological factors determine whether a cow is fertile. Therefore it is not expected that there is a simple explanation with an obvious candidate gene but it is more likely a network of genes and intragenic variants that explain the variation of these traits.

Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle.

BACKGROUND: The results obtained from genome-wide association studies (GWAS) often show pronounced disagreements. Validation of association studies is therefore desired before marker information is incorporated in selection decisions. A reliable way to confirm a discovered association between genetic markers and phenotypes is to validate the results in different populations. Therefore, the objective of this study was to validate single nucleotide polymorphism (SNP) marker associations to female fertility traits identified in the Nordic Holstein (NH) cattle population in the Nordic Red (NR) and Jersey (JER) cattle breeds. In the present study, we used data from 3,475 NH sires which were genotyped with the BovineSNP50 Beadchip to discover associations between SNP markers and eight female fertility-related traits. The significant SNP markers were then tested in NR and JER cattle. RESULTS: A total of 4,474 significant associations between SNP markers and eight female fertility traits were detected in NH cattle. These significant associations were then validated in the NR (4,998 sires) and JER (1,225 sires) dairy cattle populations. We were able to validate 836 of the SNPs discovered in NH cattle in the NR population, as well as 686 SNPs in the JER population. 152 SNPs could be confirmed in both the NR and JER populations. CONCLUSIONS: The present study presents strong evidence for association of SNPs with fertility traits across three cattle breeds. We provide strong evidence that SNPs for many fertility traits are concentrated at certain areas on the genome (BTA1, BTA4, BTA7, BTA9, BTA11 and BTA13), and these areas would be highly suitable for further study in order to identify candidate genes for female fertility traits in dairy cattle.

Analyzes of genome-wide association follow-up study for calving traits in dairy cattle.

BACKGROUND: There is often a pronounced disagreement between results obtained from different genome-wide association studies in cattle. There are multiple reasons for this disagreement. Particularly the presence of false positives leads to a need to validate detected QTL before they are optimally incorporated or weighted in selection decisions or further studied for causal gene. In dairy cattle progeny testing scheme new data is routinely accumulated which can be used to validate previously discovered associations. However, the data is not an independent sample and the sample size may not be sufficient to have enough power to validate previous discoveries. Here we compared two strategies to validate previously detected QTL when new data is added from the same study population. We compare analyzing a combined dataset (COMB) including all data presently available to only analyzing a validation dataset (VAL) i.e. a new dataset not previously analyzed as an independent replication. Secondly, we confirm SNP detected in the Reference population (REF) (i.e. previously analyzed dataset consists of older bulls) in the VAL dataset. RESULTS: Clearly the results from the combined (COMB) dataset which had nearly twice the sample size of other two subsets allowed the detection of far more significant associations than the two smaller subsets. The number of significant SNPs in REF (older bulls) was about four times higher compare to VAL (younger bulls) though both had similar sample sizes, 2,219 and 2,039 respectively. A total of 424 SNP-trait combinations on 22 chromosomes showed genome-wide significant association involving 284 unique SNPs in the COMB dataset. In the REF data set 101 associations (73 unique SNPs) and in the VAL 24 associations (18 unique SNPs) were found genome-wide significant. Sixty-eight percent of the SNPs in the REF dataset could be confirmed in the VAL dataset. Out of 469 unique SNPs showing chromosome-wide significant association with calving traits in the REF dataset 321 could be confirmed in the VAL dataset at P < 0.05. CONCLUSIONS: The follow-up study for GWAS in cattle will depend on the aim of the study. If the aim is to discover novel QTL, analyses of the COMB dataset is recommended, while in case of identification of the causal mutation underlying a QTL, confirmation of the discovered SNPs are necessary to avoid following a false positive.

18F-ML-10, a PET tracer for apoptosis: first human study.

UNLABELLED: Clinical PET of apoptosis may have substantial value in advancing patient care. We report here the first-in-humans study with (18)F-labeled 2-(5-fluoropentyl)-2-methyl malonic acid ((18)F-ML-10), a small-molecule PET tracer for apoptosis. Presented are the dosimetry, biodistribution, stability, and safety profiles of this PET tracer in healthy human volunteers. Also reported is tracer binding to targeted apoptotic cells in testicular tissue, where a relative abundance of apoptotic cells is normally observed. METHODS: (18)F-ML-10 (233 ± 90 MBq) was intravenously administered to 8 healthy subjects, followed by whole-body PET/CT for 220 min. Serial blood and urine samples were collected for radioactivity measurement, and plasma tracer stability was assessed by high-performance liquid chromatography. Dosimetry calculations were performed using OLINDA/EXM software. RESULTS: (18)F-ML-10 manifested high stability in vivo and rapid distribution followed by fast clearance, with an elimination half-life of 1.3 ± 0.1 and 1.1 ± 0.2 h from the blood and from all other organs, respectively, and excretion through the urine. Dosimetry showed an average effective whole-body dose of 15.4 ± 3.7 µSv/MBq, with the urinary bladder being the dose-limiting organ. Selective accumulation and retention of the tracer in the testes was observed in all male subjects, a finding also demonstrated in mice using both small-animal PET and histopathology, confirming binding to apoptotic cells. Administration of (18)F-ML-10 was safe, without adverse effects. CONCLUSION: (18)F-ML-10 administered to healthy humans demonstrated a favorable dosimetry, biodistribution, stability, and safety profile. Binding to apoptotic sites was also demonstrated. These data support further development of this small-molecule probe for clinical PET of apoptosis.

Cellular processing in the SW1222 cell line of mAb A33 directly and indirectly radiohalogenated.

Investigations into the cellular processing of radiolabeled monoclonal antibodies (mAbs) for their further use in radioimmunodiagnosis and cancer therapy are needed in order to understand the fate of internalized and catabolized mAbs. The anti-colorectal cancer mAb, A33, was labelled with 76Br and 125I using the direct Chloramine-T method, or by labelling N-succinimidyl para-(tri-methylstannyl) benzoate and its further conjugation to the mAb. The cellular processing of the four conjugates was investigated in SW1222 cells in vitro. Uptake of mAb was rapid, peaking after 14-16 h. Intracellular degradation was slow and the early loss of radioactivity was due to dissociation of cell-surface bound mAb. The indirect labelling resulted in stronger binding of the mAb as well as prolonged intracellular retention of the radiolabel. Direct and indirect halogen radiolabelling results in different cell-processing patterns of radiolabels, and radioactive catabolic products follow different routes of cellular excretion. The results of this cellular study indicate that indirect labelling is preferable to the direct Chloramine-T method.

Comparative biodistribution of the radiohalogenated (Br, I and At) antibody A33. Implications for in vivo dosimetry.

The alpha-emitter astatine-211 (T(1/2) = 7.2 h) has great potential for use in targeted radionuclide therapy. Its potent alpha-radiation makes (211)At unsuitable for dose planning. Its x-rays can be used for gamma-camera monitoring of the radioactivity distribution during therapy but not for accurate estimation of absorbed dose in critical organs. This study was intended to establish whether the absorbed dose delivered by astatinated antibody could be accurately determined by analogue labeling with radiohalogens, better suited for quantitative measurements in vivo. PET facilitates quantitative pharmacokinetics; possible halogen labels are, e.g., (76)Br (T(1/2) = 16.2 h) and (124)I (T(1/2) = 4.18 d). Antibody A33 was labeled with (76)Br, (125)I and (211)At using N-succinimidyl-p-halobenzoates. The conjugates were co-injected into Sprague-Dawley rats. Radioactivity concentrations in different organs and tissues were measured at three time points. Pharmacokinetic data were used to calculate absorbed doses. (125)I and (76)Br reflected the biokinetics of astatine reasonably well. The absorbed doses in bladder, kidney, pancreas, liver, bone and brain were determined with 10% accuracy. The absorbed doses in stomach, spleen and thyroid were underestimated by a factor 2-3. Positron-emitting analogues can be used to predict the astatine-derived dose in critical organs. Correction factors should be used for stomach, spleen and thyroid.