Use of single nucleotide polymorphisms in candidate genes associated with daughter pregnancy rate for prediction of genetic merit for reproduction in Holstein cows

Whole-genome resequencing deciphers patterns of genetic diversity, phylogeny, and evolutionary dynamics in Kashmir cattle

Kashmir cattle, which were kept by local pastoralists for centuries, are exceptionally resilient and adaptive to harsh environments. Despite its significance, the genomic characteristics of this cattle breed remain elusive. This study utilized whole genome sequences of Kashmir cattle (n = 20; newly sequenced) alongside published whole genomes of 32 distinct breeds and seven core cattle populations (n = 135). The analysis identified ~25.87 million biallelic single nucleotide polymorphisms in Kashmir cattle, predominantly in intergenic and intron regions. Population structure analyses revealed distinct clustering patterns of Kashmir cattle with proximity to the South Asian, African and Chinese indicine cattle populations. Genetic diversity analysis of Kashmir cattle demonstrated lower inbreeding and greater nucleotide diversity than analyzed global breeds. Homozygosity runs indicated less consanguineous mating in Kashmir cattle compared with European taurine breeds. Furthermore, six selection sweep detection methods were used within Kashmir cattle and other cattle populations to identify genes associated with vital traits, including immunity (BOLA-DQA5, BOLA-DQB, TNFAIP8L, FCRL4, AOAH, HIF1AN, FBXL3, MPEG1, CDC40, etc.), reproduction (GOLGA4, BRWD1, OSBP2, LEO1 ADCY5, etc.), growth (ADPRHL1, NRG2, TCF12, TMOD4, GBP4, IGF2, RSPO3, SCD, etc.), milk composition (MRPS30 and CSF1) and high-altitude adaptation (EDNRA, ITPR2, AGBL4 and SCG3). These findings provide essential genetic insights into the characteristics and establish the foundation for the scientific conservation and utilization of Kashmir cattle breed.

Identifying Regions of the Genome Associated with Conception Rate to the First Service in Holstein Heifers Bred by Artificial Insemination and as Embryo Transfer Recipients

Heifer conception rate to the first service (HCR1) is defined as the number of heifers that become pregnant to the first breeding service compared to the heifers bred. This study aimed to identify loci associated and gene sets enriched for HCR1 for heifers that were bred by artificial insemination (AI, n = 2829) or were embryo transfer (ET, n = 2086) recipients, by completing a genome-wide association analysis and gene set enrichment analysis using SNP data (GSEA-SNP). Three unique loci, containing four positional candidate genes, were associated (p < 1 × 10-5) with HCR1 for ET recipients, while the GSEA-SNP identified four gene sets (NES ≥ 3) and sixty-two leading edge genes (LEGs) enriched for HCR1. While no loci were associated with HCR1 bred by AI, one gene set and twelve LEGs were enriched (NES ≥ 3) for HCR1 with the GSEA-SNP. This included one gene (PKD2) shared between HCR1 AI and ET services. Identifying loci associated or enriched for HCR1 provides an opportunity to use them as genomic selection tools to facilitate the selection of cattle with higher reproductive efficiency, and to better understand embryonic loss.

Identification of genetic variants affecting reproduction traits in Vrindavani cattle

Genome-wide association studies (GWAS) are one of the best ways to look into the connection between single-nucleotide polymorphisms (SNPs) and the phenotypic performance. This study aimed to identify the genetic variants that significantly affect the important reproduction traits in Vrindavani cattle using genome-wide SNP chip array data. In this study, 96 randomly chosen Vrindavani cows were genotyped using the Illumina Bovine50K BeadChip platform. A linear regression model of the genome-wide association study was fitted in the PLINK program between genome-wide SNP markers and reproduction traits, including age at first calving (AFC), inter-calving period (ICP), dry days (DD), and service period (SP) across the first three lactations. Information on different QTLs and genes, overlapping or adjacent to genomic coordinates of significant SNPs, was also mined from relevant databases in order to identify the biological pathways associated with reproductive traits in bovine. The Bonferroni correction resulted in total 39 SNP markers present on different chromosomes being identified that significantly affected the variation in AFC (6 SNPs), ICP (7 SNPs), DD (9 SNPs), and SP (17 SNPs). Novel potential candidate genes associated with reproductive traits that were identified using the GWAS methodology included UMPS, ITGB5, ADAM2, UPK1B, TEX55, bta-mir-708, TMPO, TDRD5, MAPRE2, PTER, AP3B1, DPP8, PLAT, TXN2, NDUFAF1, TGFA, DTNA, RSU1, KCNQ1, ADAM32, and CHST8. The significant SNPs and genes associated with the reproductive traits and the enriched genes may be exploited as candidate biomarkers in animal improvement programs, especially for improved reproduction performance in bovines.

Genome-wide association study for stayability at different calvings in Nellore beef cattle

BACKGROUNDING

Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life.

RESULTS

The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant.

CONCLUSION

Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

Polymorphism and expression of GLUD1 in relation to reproductive performance in Jining Grey goats

Understanding the molecular mechanism of mammalian reproduction (puberty and prolificacy) will play a part in improving animal reproductive performance. GLUD1 (glutamate dehydrogenase 1) is important for mammalian reproduction, as shown in previous studies; however, its roles in puberty and prolificacy have rarely been reported. In this study, we designed seven pairs of primers (P1 to P7) for cloning and sequencing genomic DNA of Jining Grey goats and Liaoning Cashmere goats. Primer 8 (P8) was designed to detect single nucleotide polymorphism (SNP) of the GLUD1 in both sexually precocious and high-fecundity breeds (Jining Grey, Nanjiang Brown and Matou goats) and sexually late-maturing and low-fecundity breeds (Liaoning Cashmere, Inner Mongolia Cashmere and Taihang goats) by PCR-RFLP (restriction fragment length polymorphism). The real-time quantitative polymerase chain reaction (RT-qPCR) technique was used to detect the expression of GLUD1 in a variety of tissues. The results showed that the A197C mutation was only found in the amplification product of P6. For this SNP locus, only two genotypes (AA and AC) were detected in Nanjiang Brown goats, while three genotypes (AA, AC and CC) were detected in the other five breeds. In Jining Grey goats, the frequency of genotypes AA, AC and CC was 0.69, 0.26 and 0.05, respectively. In Jining Grey goats, AA genotype had 0.54 (P < 0.05 ) and 0.3 (P < 0.05 ) more kids than the CC and AC genotype, respectively, and no significant difference (P > 0.05 ) was found in kidding number between the AC and CC genotype. GLUD1 was expressed in five tissues of different developmental stages. The expression level of GLUD1 in the hypothalamus was higher than that in the other four tissues except during puberty of Liaoning Cashmere goats. In puberty in goats, GLUD1 expression was significantly higher in ovaries than that in the juvenile period (P < 0.01 ). RT-qPCR results showed that the expression of GLUD1 in ovaries may relate to the puberty of goats. The present study preliminarily indicated that there might be an association between the 197 locus of GLUD1 and sexual precocity in goats, and allele A of GLUD1 was a potential DNA marker for improving kidding number in Jining Grey goats.

Association between single-nucleotide polymorphism in PIK3CD gene and litter size in Small Tail Han sheep

The p110δ isoform of the PI3K catalytic subunit (encoded by the PIK3CD gene) is a key component of the PI3K pathway for follicle growth in mammalian ovarian granulosa cells. Nevertheless, little is known about the association of its polymorphisms with ovine litter size. In this study, the distribution of different genotypes of two SNPs in the PIK3CD gene was calculated in more than forty sheep breeds, and the associations between SNPs and litter size in Small Tail Han (STH) sheep were also analyzed. Besides, the mRNA expression of the PIK3CD gene was also detected in some reproduction-related tissues. The results showed that the "A" allele frequency was higher in rs412889931 (g.41926327G > A) in a typical polytocous sheep breed (p < 0.01). The association's analysis showed rs412889931 was correlated with ovine fecundity as assessed by three parity litter sizes (p < 0.05). Finally, we found the expression of PIK3CD in the ovary had significant differences in different fecundity sheep breeds, indicating that SNP may regulate the litter size by influencing the PIK3CD gene expression. The present results demonstrated that rs412889931 could be used in the marker-assisted selection of the litter size in sheep breeding.

Effect of LHCGR and FSHR gene polymorphisms on fertility traits and milk yield of cross-bred dairy cows in Sri Lanka

Single nucleotide polymorphism (SNP) analysis of fertility genes will be useful in improving the genetic potential of dairy cows. A population of 142 cross-bred dairy cows was screened for SNPs in bovine luteinizing hormone choriogonadotropin receptor (LHCGR) and bovine follicle stimulating hormone receptor (FSHR) genes. The effect of reported SNPs on selected fertility traits (average calving interval, average number of services per conception and age at first calving) and milk yield was determined. Altogether six SNPs were detected in animals screened under the present study. Among them, four SNPs (rs41256848, rs41256850, rs465790244, and rs45463781) were located in the exon 11 region of the LHCGR gene and two SNPs (rs43676359 and G-278-A (GU253337) were located in the five upstream region of the FSHR gene. Minor alleles identified for SNPs in the FSHR gene in the studied small population of cows differed from those reported in other research. In this study, only rs45463781 SNP at exon 11 of the LHCGR gene significantly affected the average milk yield in cross-bred cows. The nucleotide change from "G" to "A" negatively affected the average milk yield. Further investigations are needed to confirm the reported association with a larger sample size.

Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data

Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing >5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, FST, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (HCN1, KATNA1, FSTL1, GRIK2, and CPLX2), immune (CD244, SLAMF1, LY9, and CD48), and reproduction (AKR1C1, AKR1C3, AKR1C4, and TUSC3). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.

Population Genetic Analysis of Six Chinese Indigenous Pig Meta-Populations Based on Geographically Isolated Regions

The diversification of indigenous pig breeds in China has resulted from multiple climate, topographic, and human cultural influences. The numerous indigenous pig breeds can be geographically divided into six meta-populations; however, their genetic relationships, contributions to genetic diversity, and genetic signatures remain unclear. Whole-genome SNP data for 613 indigenous pigs from the six Chinese meta-populations were obtained and analyzed. Population genetic analyses confirmed significant genetic differentiation and a moderate mixture among the Chinese indigenous pig meta-populations. The North China (NC) meta-population had the largest contribution to genetic and allelic diversity. Evidence from selective sweep signatures revealed that genes related to fat deposition and heat stress response (EPAS1, NFE2L2, VPS13A, SPRY1, PLA2G4A, and UBE3D) were potentially involved in adaptations to cold and heat. These findings from population genetic analyses provide a better understanding of indigenous pig characteristics in different environments and a theoretical basis for future work on the conservation and breeding of Chinese indigenous pigs.

Weighted genomic prediction for growth and carcass-related traits in Nelore cattle

This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass-related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24 480 for marbling (MAR) and 82 981 for subcutaneous backfat thickness (BFT) and rump fat thickness (RFT). The pedigree harbored information from 244 254 animals born between 1977 and 2016, including 6283 sires and 50 742 dams. Animals (n = 7769) were genotyped with the low-density panel (Clarifide® Nelore 3.0), and the genotypes were imputed to a panel containing 735 044 markers. A linear animal model was applied to estimate the genetic parameters and to perform the weighted single-step genome-wide association study (WssGWAS). A total of seven models for genomic prediction were evaluated combining the SNP weights obtained in the iterations of the WssGWAS and the candidate QTL. The heritability estimated for W450 (0.35) was moderate, and for carcass-related traits, the estimates were moderate for REA (0.27), MAR (0.28) and RFT (0.28), and low for BFT (0.18). The prediction accuracy for W450 incorporating reported QTL previously described in the literature along with different SNPs weights was like those described for the default ssGBLUP model. The use of the ssGWAS to weight the SNP effects displayed limited advantages for the REA prediction accuracy. Comparing the ssGBLUP with the BLUP model, a meaningful improvement in the prediction accuracy from 0.09 to 0.63 (700%) was observed for MAR. The highest prediction accuracy was obtained for BFT and RFT in all evaluated models. The application of information obtained from the WssGWAS is an alternative to reduce the genomic prediction dispersion for growth and carcass-related traits, except for MAR. Furthermore, the results obtained herein pointed out that is possible to improve the prediction accuracy and reduce the genomic prediction dispersion for growth and carcass-related traits in young animals.

Genomic Diversity and Selection Signatures for Weining Cattle on the Border of Yunnan-Guizhou

Weining cattle is a Chinese indigenous breed influenced by complex breeding and geographical background. The multi-ethnic breeding culture makes Weining cattle require more attention as livestock resources for its genetic diversity. Here, we used 10 Weining cattle (five newly sequenced and five downloaded) and downloaded another 48 genome data to understand the aspects of Weining cattle: genetic diversity, population structure, and cold-adapted performance. In the current study, a high level of genetic diversity was found in Weining cattle, and its breed comprised two potential ancestries, which were Bos taurus and Bos indicus. The positive selective sweep analysis in Weining cattle was analyzed using composite likelihood ratio (CLR) and nucleotide diversity (θπ), resulting in 203 overlapped genes. In addition, we studied the cold adaptation of Weining cattle by comparing with other Chinese cattle (Wannan and Wenshan cattle) by three methods (FST, θπ-ratio, and XP-EHH). Of the top 1% gene list, UBE3D and ZNF668 were analyzed, and these genes may be associated with fat metabolism and blood pressure regulation in cold adaptation. Our findings have provided invaluable information for the development and conservation of cattle genetic resources, especially in southwest China.

Genetic architecture of a composite beef cattle population

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, 25% Tarentaise. A total of 248 animals were used in this study CGC (n=79), Red Angus (n=61), Charolais (n=79) and Tarentaise (n=29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57% while Charolais decreased to approximately 5%, and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.

Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, F_ST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.

Genetic diversity in reproductive traits of Braunvieh cattle determined with SNP markers

Braunvieh is an important dual‐purpose breed in the Mexican tropics. The study of its genetic diversity is key to implementing genetic improvement programs. This study was conducted to determine genetic diversity of reproductive traits in a Mexican Braunvieh beef cattle population using single nucleotide polymorphisms in candidate genes. Information from 24 genes with 52 intra‐genic loci reported in literature to be associated with productive life, pregnancy rate and cow and heifer conception rate of 150 Braunvieh males and females was considered. Observed heterozygosity (Ho) revealed high genetic diversity for the studied traits, Ho = 0.42 ± 0.087, relative to that of other populations of the same breed. Cluster analyses were carried out using the Ward and K‐means algorithms. These analyses revealed high genetic diversity that was observed in the biplot of non‐metric multi‐dimensional scaling. It was found that clustering strategy allowed visualisation of distant groups by genotype but not by favourable alleles in all the loci. We found that the genes CSNK1E, DNAH11, DSC2, IBSP and OCLN affected most of the traits in our study and they were highly informative. Therefore, they represent a potential resource for selection and crossbreeding programs of the traits studied in Braunvieh. The analyses showed that the Mexican Braunvieh population has a high level of genetic diversity, arguably due to decades‐long adaptation to the Mexican tropics.

Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes

Background

Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic.

Results

There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits.

Conclusions

These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08555-z.

Identification of SSTR5 Gene Polymorphisms and Their Association With Growth Traits in Hulun Buir Sheep

The aim of this study was to locate SSTR5 polymorphisms and evaluate their association with growth traits in Hulun Buir sheep. The study followed up 884 Hulun Buir sheep from birth to 16 months of age, which were born in the same pasture and the same year, and a consistent grazing management strategy was maintained. The birth weight (BRW) was recorded at birth, and body weight (BW), body height (BH), body length (BL), chest circumference (ChC), chest depth (ChD), chest width (ChW), hip width (HW), and cannon circumference (CaC) were measured at 4 and 9 months of age. BW, BH, BL, ChD, HW, and CaC were also recorded at 16 months of age. Based on the growth traits, 233 sheep were selected as experimental animals. Sanger sequencing was performed, and seven single-nucleotide polymorphisms (SNPs) were identified. Association analyses of the SNPs and the growth traits were then conducted. Seven SNPs of the SSTR5 exhibited moderate polymorphism (0.25 Collapse

Key Words

• Hulun Buir sheep
• SSTR5
• association
• growth traits
• haplotypes

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Affiliation(s)

Xue Li Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China University of Chinese Academy of Sciences, Beijing, China
Ning Ding Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China University of Chinese Academy of Sciences, Beijing, China
Zhichao Zhang Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China University of Chinese Academy of Sciences, Beijing, China
Dehong Tian Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
Buying Han Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China University of Chinese Academy of Sciences, Beijing, China
Dehui Liu Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China University of Chinese Academy of Sciences, Beijing, China
Sijia Liu Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
Fei Tian Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
Dejun Fu Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
Xiaoliang Song Inner Mongolia Daxing 'anling Agricultural Reclamation Group Co. LTD., Hulun Buir, China
Kai Zhao Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China

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Frequency of genotypic markers for genetic disorders, colour, polledness, and major genes in Blanco Orejinegro cattle

The purpose of this work was to establish DNA marker frequencies for genetic disorders, colour, horned/polled trait, and major genes of importance for productive and reproductive traits in Blanco Orejinegro (BON) cattle. The Blanco Orejinegro breed is a Colombian creole breed characterized by a white hair coat on black skin with black ears, black hair on the middle part of the legs, and absence of horns. We genotyped 420 animals of Colombia, 70 with the GGP-Bovine 150 K chip and 350 with the GGP-Bovine 50 K chip. The markers were associated with 50 genetic diseases, 52 major gene variants related to productive traits, and 12 variants related to coat coloration, presence of horns, and adaptation, selected from the information contained in the chips. Genotype frequencies were estimated using the R statistical program. Genetic disorder annotations were derived using the Online Mendelian Inheritance in Animals tool (OMIA) and the average inbreeding coefficient (F) (n = 7799) using the MTDFNRM program. Carriers were found for 16 of the genetic disorders evaluated but with low frequencies (0.24 to 2.46%); no homozygous animals were found for the disorders. Carriers were associated with disorders such as bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), syndactyly, and epidermolysis bullosa (EB). The F was 4.41%. Concerning the genes associated with colour (TYR, MC1R, and PMEL), alleles related to black pigmentation, the absence of horns (polledness), and slick coat (an adaptive trait) were highly frequent (> 81.90%). Markers associated with milk production and quality, yellow fat, and fertility showed variable frequencies, indicating selection potential. Allele frequency of genetic disorders in BON cattle was low, suggesting few genetic disorder problems, with syndactyly being the most frequent condition. The markers associated with colour and polledness were almost fixed, with a frequency at or near 100%. Production and reproduction markers showed variability for selection.

Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

Background

Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows.

Results

In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits.

Conclusions

We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08042-x.

Genome-wide association study of economically important traits in Charolais and Limousin beef cows

Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.

Analysis of single nucleotide polymorphisms related to heifer fertility in Hanwoo (Korean cattle)

Genome-wide association studies (GWAS) have accelerated the identification of functional trait loci in cattle and identified single nucleotide polymorphisms (SNPs) in candidate genes associated with fertility and production traits in high milk yield dairy cattle. The fertility of Hanwoo (Korean native beef cattle) has declined after the adaptation of a selection program for high quantity and quality meat. However, there are few GWAS studies of fertility in beef cattle. We performed a genome-wide association study of 40 Korean native beef cattle heifers with imputed 770 K genotype and identified 12 significant SNPs within seven regions on three chromosomes (BTA 8, BTA 16 and BTA 24) associated with services per conception (SPC). Five SNPs were located in the ABCA1, BRINP3 and ESRRG genes, which are involved in early embryo development. In addition, 27 proximal genes were identified within 1 Mb of the candidate SNPs, which are involved in muscle cell differentiation and muscle structure development. However, we did not find any previously reported SNPs related to fertility in Holstein cows. Taken together, we identified SNPs associated with SPC and their proximal genes using gene-based analysis and the candidates were different from SNPs associated with subfertility of dairy cattle.

Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

Fertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.

Effect of COQ9 and STAT5A polymorphisms on reproductive performance in a Holstein cow herd in Mexico

Coenzyme Q9 (COQ9), a coenzyme Q (CoQ) precursor, is an essential component of the mitochondrial electron transport chain that drives adenosine triphosphate production. COQ9 polymorphism 18:25527339 is characterized by substitution of guanine (allele G) for adenine (allele A), which modifies the function of the protein encoded by the gene. In Holsteins, allele A has been associated with better reproductive performance in terms of the conception rate, number of services per conception (SPC) and days open (DO). The signal transducer and activator of transcription (STAT) protein is a transcription factor activated in the presence of cytokines and growth factors. STAT5A polymorphism 19:42407732 in exon 8 has been associated with higher fertility and embryonic survival rates. The objective of this study was to determine the relationship of COQ9 and STAT5A polymorphisms with reproductive parameters [calving to first heat interval (CFHI), DO and SPC]. Blood samples were taken from 112 lactating Holstein from a herd in México for allele genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). To estimate the association between reproductive parameters and genotypes, a linear mixed-effect model was performed. The COQ9 AG genotype was associated significantly with lower SPC (P<0.05) but not with DO or CFHI. No significant association with any reproductive parameter was found for STAT5A. Our findings suggest that the COQ9 18:25527339 polymorphism is a useful molecular marker for improvement of reproductive performance in dairy herds.

Identification of Loci and Pathways Associated with Heifer Conception Rate in U.S. Holsteins

Heifer conception rate (HCR) is defined as the percentage of inseminated heifers that become pregnant at each service. The genome-wide association analyses in this study focused on identifying the loci associated with Holstein heifer (n = 2013) conception rate at first service (HCR1) and the number of times bred (TBRD) to achieve a pregnancy. There were 348 unique loci associated (p < 5 × 10⁻⁸) with HCR1 and 615 unique loci associated (p < 5 × 10⁻⁸) with TBRD. The two phenotypes shared 302 loci, and 56 loci were validated in independent cattle populations. There were 52 transcription factor binding sites (TFBS) and 552 positional candidate genes identified in the HCR1- and TBRD-associated loci. The positional candidate genes and the TFBS associated with HCR1 and TBRD were used in the ingenuity pathway analysis (IPA). In the IPA, 11 pathways, 207 master regulators and 11 upstream regulators were associated (p < 1.23 × 10⁻⁵) with HCR1 and TBRD. The validated loci associated with both HCR1 and TBRD make good candidates for genomic selection and further investigations to elucidate the mechanisms associated with subfertility and infertility.

Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle

In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.

Genetic dissection of reproductive performance of dairy cows under heat stress

Heat stress negatively impacts the reproductive performance of dairy cows. The main objective of this study was to dissect the genetic basis underlying dairy cow fertility under heat stress conditions. Our first goal was to estimate genetic components of cow conception across lactations considering heat stress. Our second goal was to reveal individual genes and functional gene‐sets that explain a cow’s ability to conceive under thermal stress. Data consisted of 74 221 insemination records on 13 704 Holstein cows. Multitrait linear repeatability test‐day models with random regressions on a function of temperature–humidity index values were used for the analyses. Heritability estimates for cow conception under heat stress were around 2–3%, whereas genetic correlations between general and thermotolerance additive genetic effects were negative and ranged between −0.35 and −0.82, indicating an unfavorable relationship between cows’ ability to conceive under thermo‐neutral vs. thermo‐stress conditions. Whole‐genome scans identified at least six genomic regions on BTA1, BTA10, BTA11, BTA17, BTA21 and BTA23 associated with conception under thermal stress. These regions harbor candidate genes such as BRWD1, EXD2, ADAM20, EPAS1, TAOK3, and NOS1, which are directly implicated in reproductive functions and cellular response to heat stress. The gene‐set enrichment analysis revealed functional terms related to fertilization, developmental biology, heat shock proteins and oxidative stress, among others. Overall, our findings contribute to a better understanding of the genetics underlying the reproductive performance of dairy cattle under heat stress conditions and point out novel genomic strategies for improving thermotolerance and fertility via marker‐assisted breeding.

Proteomics Recapitulates Ovarian Proteins Relevant to Puberty and Fertility in Brahman Heifers (Bos indicus L.)

High fertility and early puberty in Bos indicus heifers are desirable and genetically correlated traits in beef production. The hypothalamus-pituitary-ovarian (HPO) axis synthesizes steroid hormones, which contribute to the shift from the pre-pubertal state into the post-pubertal state and influence subsequent fertility. Understanding variations in abundance of proteins that govern steroid synthesis and ovarian signaling pathways remains crucial to understanding puberty and fertility. We used whole ovaries of six pre-pubertal and six post-pubertal Brahman heifers to conduct differential abundance analyses of protein profiles between the two physiological states. Extracted proteins were digested into peptides followed by identification and quantification with massspectrometry (MS) by sequential window acquisition of all instances of theoretical fragment ion mass spectrometry (SWATH-MS). MS and statistical analysis identified 566 significantly differentially abundant (DA) proteins (adjusted p < 0.05), which were then analyzed for gene ontology and pathway enrichment. Our data indicated an up-regulation of steroidogenic proteins contributing to progesterone synthesis at luteal phase post-puberty. Proteins related to progesterone signaling, TGF-β, retinoic acid, extracellular matrix, cytoskeleton, and pleiotrophin signaling were DA in this study. The DA proteins probably relate to the formation and function of the corpus luteum, which is only present after ovulation, post-puberty. Some DA proteins might also be related to granulosa cells signaling, which regulates oocyte maturation or arrest in ovaries prior to ovulation. Ten DA proteins were coded by genes previously associated with reproductive traits according to the animal quantitative trait loci (QTL) database. In conclusion, the DA proteins and their pathways were related to ovarian activity in Bos indicus cattle. The genes that code for these proteins may explain some known QTLs and could be targeted in future genetic studies.

Association of lipid-related genes implicated in conceptus elongation with female fertility traits in dairy cattle

Elongation of the preimplantation conceptus is a requirement for pregnancy success in ruminants, and failures in this process are highly associated with subfertility in dairy cattle. Identifying genetic markers that are related to early conceptus development and survival and utilizing these markers in selective breeding can improve the reproductive efficiency of dairy herds. Here, we evaluated the association of 1,679 SNP markers within or close to 183 candidate genes involved in lipid metabolism of the elongating conceptus with different fertility traits in US Holstein cattle. A total of 27,371 bulls with predicted transmitting ability records for daughter pregnancy rate, cow conception rate, and heifer conception rate were used as the discovery population. The associations found in the discovery population were validated using 2 female populations (1,122 heifers and 2,138 lactating cows) each with 4 fertility traits, including success to first insemination, number of services per conception, age at first conception for heifers, or days open for cows. Marker effects were estimated using a linear mixed model with SNP genotype as a linear covariate and a random polygenic effect. After multiple testing correction, 39 SNP flagging 27 candidate genes were associated with at least one fertility trait in the discovery population. Of these 39 markers, 3 SNP were validated in the heifer population and 4 SNP were validated in the cow population. The 3 SNP validated in heifers are located within or near genes CAT, MYOF, and RBP4, and the 4 SNP validated in lactating cows are located within or close to genes CHKA, GNAI1, and HMOX2. These validated genes seem to be relevant for reducing pregnancy losses, and the SNP within these genes are excellent candidates for inclusion in genomic tests to improve reproductive performance in dairy cattle.

Correlation analysis of candidate gene SNP for high-yield in Liaoning cashmere goats with litter size and cashmere performance

This study was designed to identify the relationship of four genes (GDF9, BMPR-IB, FecB and ESR) polymorphisms in the 3'UTR region with litter size and cashmere performance of Liaoning cashmere goats (LCG, n = 1140). The ESR C463T and T575G loci of LCG were genotyped. The results of correlation analysis showed that five effective single nucleotide polymorphisms (SNPs) loci (C47T, C94T, C299T, C463T and T575G) were found in the four genes. The lambing number of CC and CT genotypic individuals at FecB C94T locus was significantly higher than that of TT genotypic individuals (45.7 and 46.8%, respectively); the lambing number of CC genotypic individuals at ESR C463T locus was significantly higher than that of CT, TT genotypic individuals (9 and 15%, respectively); There was a positive correlation between CC genotype at C463T locus and cashmere fineness. In this study, the relationship between FecB C94T and ESR C463T loci C alleles and lambing number in LCG was preliminarily revealed. These results further confirmed that FecB and ESR genes may be significantly correlated with high fecundity of LCG.

Across-breed validation study confirms and identifies new loci associated with sexual precocity in Brahman and Nellore cattle

The aim of this study was to identify candidate regions associated with sexual precocity in Bos indicus. Nellore and Brahman were set as validation and discovery populations, respectively. SNP selected in Brahman to validate in Nellore were from gene regions affecting reproductive traits (G1) and significant SNP (p ≤ 10^-3 ) from a meta-analysis (G2). In the validation population, early pregnancy (EP) and scrotal circumference (SC) were evaluated. To perform GWAS in validation population, we used regression and Bayes C. SNP with p ≤ 10^-3 in regression and Bayes factor ≥3 in Bayes C were deemed significant. Significant SNP (for EP or SC) or SNP in their ±250 Kb vicinity region, which were in at least one discovery set (G1 or G2), were considered validated. SNP identified in both G1 and G2 were considered candidate. For EP, 145 SNP were validated in G1 and 41 in G2, and for SC, these numbers were 14 and 2. For EP, 21 candidate SNP were detected (G1 and G2). For SC, no candidate SNP were identified. Validated SNP and their vicinity region were located close to quantitative trait loci or genes related to reproductive traits and were enriched in gene ontology terms related to reproductive success. These are therefore strong candidate regions for sexual precocity in Nellore and Brahman.

Single Nucleotide Polymorphisms in SLC5A1, CCNA1, and ABCC1 and the Association with Litter Size in Small-Tail Han Sheep

Simple Summary

Litter size is one of the most important reproductive traits in sheep. Four single nucleotide polymorphisms (SNPs), g.70067210 T > C in SLC5A1, g.25350431 C > T and g.25360220 T > C in CCNA1, and g.14413132 C > T in ABCC1, were identified by mass spectrometry and may be associated with litter size in sheep. Four SNPs were genotyped in Small-Tail Han, Hu, Cele Black, Suffolk, Sunite, Prairie Tibetan, and Tan sheep, and the expression patterns of SLC5A1, CCNA1, and ABCC1 were determined in Small-Tail Han sheep with different fecundities. Furthermore, we also studied the FecB mutation’s association with litter size in Small-Tail Han sheep. The results indicated that all genes included in this study were differentially expressed in the ovary and uterus of polytocous and monotocous Small-Tail Han sheep. Furthermore, association analysis indicated that both g.70067210 T > C in SLC5A1 and the FecB mutation in BMPR-IB were significantly associated with litter size in Small-Tail Han sheep. Linear regression analysis of the association of multiple markers (FecB and g.70067210 T > C in SCL5A1) with litter size indicated that homozygous ewes carrying the BB/TT genotype had a larger litter size than any other genotype.

Abstract

SLC5A1, CCNA1, and ABCC1 have been extensively studied as candidate genes because of their great influence on the reproductive traits of animals. However, little is known about the association between polymorphisms of the SLC5A1, CCNA1, and ABCC1 genes and litter size in Small-Tail Han sheep. In this study, the expression levels of SLC5A1, CCNA1, and ABCC1 in HPG (hypothalamic–pituitary–gonadal) axis tissues of polytocous and monotocous Small-Tail Han sheep were analyzed by qPCR. To better understand the effects of four single nucleotide polymorphisms (SNPs) comprising of g.70067210 T > C in SLC5A1, g.25350431 C > T and g.25360220 T > C in CCNA1, and g.14413132 C > T in ABCC1, a population genetic analysis was conducted using data obtained from genotyping in 728 sheep from seven breeds. The results indicated that all genes included in this study were differentially expressed in the pituitary and uterus of polytocous and monotocous Small-Tail Han sheep (p < 0.05). The associations of these four SNPs and the FecB mutation with litter size in 384 Small-Tail Han sheep were analyzed, therefore, and it was found that both g.70067210T > C and the FecB mutation were significantly associated with litter size (p < 0.05). The linear regression analysis of the association of multiple markers (FecB and g.70067210 T > C in SCL5A1) with litter size indicated that homozygous ewes carrying the BB/TT genotype had larger litter size than any ewes with any other genotype. In conclusion, the SLC5A1 SNPs significantly affect litter size in sheep and are useful as genetic marker for litter size.

Genomic merit for reproductive traits. I: Estrous characteristics and fertility in Holstein heifers

Genetic selection of dairy cattle in the United States has included reproductive traits (daughter pregnancy rate, DPR; heifer conception rate, HCR), which is believed to have partly contributed to halting the decline in reproductive performance. The objectives of the current study were to evaluate the association among genomic merit for DPR (GDPR) and HCR (GHCR) with estrous characteristics measured by an automated device. Holstein heifers (n = 1,005) were genotyped at 2 mo of age and were classified into quartiles (Q1 = lowest, Q4 = highest) according to the GDPR and GHCR values of the study population. At 10 to 11 mo of age, heifers were fitted with a collar that recorded activity and rumination and determined the occurrence of estrus according to changes in activity and rumination compared with the individual's baseline values. Estrous characteristics of spontaneous estruses (SPE) and PGF_2α-synchronized estruses (PGSE) were recorded. Heifers had their estrous cycle synchronized with PGF_2α and following detection of estrus received either artificial insemination or embryo transfer according to the herd's genetic selection program. Heifers in Q2 (17.7 ± 0.3 h) of GHCR tended to have longer SPE than heifers in Q4 (16.7 ± 0.3 h). The interaction between GDPR and GHCR was associated with the likelihood of activity peak (0 = no estrus, 100 = maximum activity) ≥80 at SPE because, among heifers in Q3 and Q4 of GHCR, those in Q1 of GDPR were less likely to have an activity peak ≥80. Heifers in Q1 and Q2 of GDPR had reduced hazard of estrus within 7 d of the first PGF_2α treatment compared with heifers in Q4 of GDPR. Heifers in Q1 (16.1 ± 0.4 h) of GDPR had shorter PGSE than heifers in Q2 (17.6 ± 0.4 h) and Q4 (17.4 ± 0.4 h) and tended to have shorter PGSE than heifers in Q3 (17.4 ± 0.4 h). Rumination nadir on the day of PGSE was greater for heifers in Q1 (-30.1 ± 0.9 min/d) of GDPR compared with heifers in Q4 (-33.7 ± 0.9 min/d). Among heifers receiving only artificial insemination, those in Q1 of GHCR (adjusted hazard ratio = 0.65; 95% confidence interval = 0.48-0.88) became pregnant at a slower rate than heifers in Q4. Genomic merit for HCR was negatively associated with SPE but tended to be positively associated with hazard of pregnancy, whereas GDPR was positively associated with PGSE and hazard of estrus. Selection of dairy cattle for DPR and HCR may improve reproductive performance through different pathways, namely estrous characteristics and pregnancy establishment.

Genomic merit for reproductive traits. II: Physiological responses of Holstein heifers

Fertility traits were recently added to the evaluation of genetic merit, allowing for the selection of Holstein cattle with improved reproductive performance. In the current study, we investigated the associations among genomic merit for daughter pregnancy rate (GDPR) and heifer conception rate (GHCR) and physiological responses during proestrus and diestrus. Holstein heifers (n = 99) were classified based on GDPR [high = 3.26 ± 0.76 (1.6 to 5.3), n = 48; low = -0.17 ± 0.75 (-1.8 to 1.0), n = 51] and GHCR [high = 2.75 ± 0.77 (1.5 to 5.5), n = 49; low = 0.06 ± 0.67 (-2.1 to 1.2), n = 50]. Heifers were fitted with an automated estrous detection device, were treated with PGF_2α for synchronization of estrus, and received either artificial insemination or embryo transfer at detected estrus. Blood was sampled at the time of PGF_2α treatment, within 24 h of the onset of estrus (d 0), and on d 7, 14, 19 ± 2, 28, and 35. Blood samples from all heifers were analyzed for concentrations of estradiol (d 0) and progesterone (on the day of PGF_2α treatment and d 0, 7, and 14). Blood samples from heifers pregnant on d 38 ± 3 were analyzed for concentrations of progesterone (d 0, 7, 14, 19 ± 2, 28, and 35), pregnancy-specific protein B (d 19 ± 2, 28, and 35), and insulin-like growth factor 1 (d 0, 7, 14, 19 ± 2, 28, and 35). Expression of mRNA for interferon-stimulated gene 15 in peripheral leukocytes isolated from blood collected on d 19 ± 2 was determined. Ovaries were scanned by ultrasound daily from d 0 to 4 or until ovulation was detected. Heifers with low GHCR tended to be less likely to be detected in estrus (78.0 vs. 91.8%). Estradiol concentration on d 0 was greater for heifers with high GDPR (4.53 ± 0.23 vs. 3.79 ± 0.23 pg/mL). The ovulatory follicle was larger for heifers with high GDPR (16.28 ± 0.33 vs. 14.55 ± 0.35 mm), whereas heifers with high GHCR tended to have smaller ovulatory follicles (15.00 ± 0.31 vs. 15.83 ± 0.37 mm). Heifers with high GDPR tended to be more likely to ovulate within 96 h of the onset of estrus (90.7 vs. 75.0%). Among heifers pregnant on d 38 ± 3, GDPR and GHCR were not associated with mRNA expression for interferon-stimulated gene 15. Heifers with high GDPR had greater concentration of pregnancy-specific protein B from d 28 to 35 (3.03 ± 0.15 vs. 2.48 ± 0.1 ng/mL). Heifers with high GHCR tended to have greater insulin-like growth factor 1 concentration from d 7 to 35 (108.0 ± 3.2 vs. 97.7 ± 4.2 ng/mL). Our results suggest that selection for Holstein cattle for GDPR may have positive effects on reproductive performance through changes in ovarian follicle development and steroidogenesis. Although selection of Holstein cattle for GHCR may negatively affect estrous expression by affecting ovarian follicle growth, selection for GHCR may improve reproductive performance by altering the somatotropic axis.

Fucosyltransferase gene expression in goat endometrium during the estrous cycle and early pregnancy

Regulation of the expression of the alpha(1,2)fucosyltransferase (FUT) genes and their enzymatic products, including the H-type 1 antigen (HT1), on the luminal surface of the uterus is believed to be critical for establishment of pregnancy in mammals. The FUT1 gene is a marker for conception rates in dairy cows and HT1 is a marker for uterine receptivity in rodents. To determine the spatiotemporal expression patterns of FUT1 and FUT2 genes in goats, endometrial tissues were obtained on six days spanning the estrous cycle (Days 5, 11, 13, 15, 17 and 19) and seven days spanning early pregnancy (Days 5, 11, 13, 15, 17, 19 and 25). In all data, we found no effect of status (cyclic or pregnant; P > 0.1) and pooled data where appropriate. We cloned FUT1 cDNA from goat endometrium and made probes from it for Northern and slot blot analyses. The analyses indicated that FUT1 gene expression was high until Day 13, and then declined. In situ hybridization revealed a change in the cell-specificity of FUT1 gene expression over the estrous cycle and early pregnancy. In situ hybridization signal intensity scores indicated that FUT1 expression by uterine epithelium was high on Day 5, moderate on Day 11, and minimal on subsequent days. In situ hybridization signals in uterine glandular epithelial cells remained high from Day 5 to Day 13, with weaker signals thereafter. Quantitative reverse transcription-PCR (RT-qPCR) assays were used for quantitation of FUT1 and FUT2 mRNAs. Quantitative RT-qPCR data were generated from endometrium collected from cyclic and pregnant animals on Days 5, 11 and 17. Relative levels of FUT1 mRNA were high on Days 5 and 11, but then fell 5-fold by Day 17 (P < 0.01). FUT2 mRNA concentrations were below the accurate detectable limit of the assay. High levels of HT1 were observed on the apical surface of uterine luminal epithelia on Days 5, 15, 17 and 19, with much lower levels on Days 11 and 13. Thus, data suggests that FUT1 is the primary enzyme responsible for the high levels of HT1 antigen present on the uterine luminal epithelium between Days 5 and 11 of the estrous cycle and early pregnancy. But changes in the expression of the FUT1 gene does not directly correlate to HT1 staining, which increased from Day 13-15. Future studies are required to understand the regulation of the HT1 antigen on the luminal surface of endometrium.

Single nucleotide polymorphisms in BMP2 and BMP7 and the association with litter size in Small Tail Han sheep

Although it has been investigated for many years, the physiological processes regulating prolificacy in sheep remains unclear because of regulation by many genes. To better understand the effects of three single nucleotide polymorphisms (SNPs) comprising g.48462350C>T in BMP2, g.58171856C>G and g.58171886A>C in BMP7, a population genetic analysis was conducted using data obtained from genotyping in 768 sheep from six breeds (three polytocous and three monotocous). The results indicate that all the sheep breeds were considered to conform to the Hardy-Weinberg equilibrium (P > 0.05). The associations of these three SNPs with litter size in 384 Small Tail Han sheep were analyzed, therefore, and found to be correlated with fecundity as assessed by mean litter size (P < 0.05). Bioinformatic analysis indicated there was a transmembrane domain change that occurred after a mutation in BMP2 at g.48462350C>T, and changes involving transcription factors such as USF1, USF2 and INMS1 in the BMP7 promoter region might be involved in greater sheep prolificacy.

Symposium review: The choice and collection of new relevant phenotypes for fertility selection

In dairy production, high fertility contributes to herd profitability by achieving greater production and maintaining short calving intervals. Improved management practices and genetic selection have contributed to reversing negative trends in dairy cow fertility, but further progress is still required. Phenotypes included in current genetic evaluations are largely interval and binary traits calculated from insemination and calving date records. Several indicator traits such as calving, health, variation in body condition score, and longevity traits also apply to genetic improvement of fertility. Several fertility traits are included in the selection indices of many countries, but for improved selection, the development of novel phenotypes that more closely describe the physiology of reproduction and limit management bias could be more effective. Progesterone-based phenotypes can be determined from milk samples to describe the heritable interval from calving to corpus luteum activity, as well as additional measures of cow cyclicity. A fundamental component of artificial insemination practices is the observation of estrus. Novel phenotypes collected on estrous activity could be used to select for cows clearly displaying heat, as those cows are more likely to be inseminated at the right time and therefore have greater fertility performance. On-farm technologies, including in-line milk testing and activity monitors, may allow for phenotyping novel traits on large numbers of animals. Additionally, selection for improved fertility using traditional traits could benefit from refined and accurate recording and implementation of parameters such as pregnancy confirmation and reproductive management strategy, to differentiate embryonic or fetal loss, and to ensure selection for reproductive capability without producer intervention. Opportunities exist to achieve genetic improvement of reproductive efficiency in cattle using novel phenotypes, which is required for long-term sustainability of the dairy cattle population and industry.

Multitrait meta-analysis identified genomic regions associated with sexual precocity in tropical beef cattle

Multitrait meta-analyses are a strategy to produce more accurate genome-wide association studies, especially for complex phenotypes. We carried out a meta-analysis study for traits related to sexual precocity in tropical beef cattle (Nellore and Brahman) aiming to identify important genomic regions affecting these traits. The traits included in the analyses were age at first calving (AFC), early pregnancy (EP), age at first corpus luteum (AGECL), first postpartum anoestrus interval (PPAI), and scrotal circumference (SC). The traits AFC, EP, and SCN were measured in Nellore cattle, while AGECL, PPAI, and SCB were measured in Brahman cattle. Meta-analysis resulted in 108 significant single-nucleotide polymorphisms (SNPs), at an empirical threshold P-value of 1.39 × 10-5 (false discovery rate [FDR] < 0.05). Within 0.5 Mb of the significant SNP, candidate genes were annotated and analyzed for functional enrichment. Most of the closest genes to the SNP with higher significance in each chromosome have been associated with important roles in reproductive function. They are TSC22D2, KLF7, ARHGAP29, 7SK, MAP3K5, TLE3, WDR5, TAF3, TMEM68, PPP1R15B, NR2F2, GALR1, SUFU, and KCNU1. We did not observe any significant SNP in BTA5, BTA12, BTA17, BTA18, BTA19, BTA20, BTA22, BTA23, BTA25, and BTA28. Although the majority of significant SNPs are in BTA14, it was identified significant associations in multiple chromosomes (19 out of 29 autosomes), which is consistent with the postulation that reproductive traits are complex polygenic phenotypes. Five proposed association regions harbor the majority of the significant SNP (76%) and were distributed over four chromosomes (P < 1.39 × 10-5, FDR < 0.05): BTA2 (5.55%) from 95 to 96 Mb, BTA4 (5.55%) from 94.1 to 94.8 Mb, BTA14 (59.26%) from 24 to 25 Mb and 29 to 30 Mb, and BTA21 (5.55%) from 6.7 Mb to 11.4 Mb. These regions harbored key genes related to reproductive function. Moreover, these genes were enriched for functional groups associated with immune response, maternal-fetal tolerance, pregnancy maintenance, embryo development, fertility, and response to stress. Further studies including other breeds and precocity traits could confirm the importance of these regions and identify new candidate regions for sexual precocity in beef cattle.

Interactions of human chorionic gonadotropin with genotype and parity on fertility responses of lactating dairy cows

Fertility-promoting effects of treatment of lactating dairy cattle with human chorionic gonadotropin (hCG) after artificial insemination (AI) have been variable. Here, we tested whether fertility response to hCG in lactating Holstein cows interacts with genotype and parity. Primiparous (n = 538) and multiparous (n = 613) cows were treated with hCG (3,300 IU) or vehicle 5 d after AI. Pregnancy was diagnosed on d 32 and 60 after AI. A subset of cows (n = 593-701) was genotyped for 4 single nucleotide polymorphisms (SNP) previously associated with fertility. Treatment with hCG increased progesterone concentration on d 12 after AI regardless of genotype or parity. Pregnancy per AI was improved by hCG in primiparous cows but not in multiparous cows. Moreover, hCG treatment interacted with a SNP in coenzyme Q9 (COQ9) to affect fertility. Fertility of cows treated with vehicle was greatest for the AA allele, whereas fertility was lowest for the same genotype among cows treated with hCG. Pregnancy per AI was also affected by genotype for heat shock protein A1-like (HSPA1L) and progesterone receptor (PGR), but no interactions were observed with treatment. Genotype for a SNP in prostate androgen-regulated mucin-like protein 1 (PARM1) was not associated with fertility. Overall, results show that variation in response to hCG treatment on fertility depends on parity and interacts with a SNP in COQ9.

Development and validation of a small SNP panel for feed efficiency in beef cattle

The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.

Evaluation of environmental effects on reproductive characteristics of Mangalarga Marchador mares in a commercial embryo transfer program

The objective of this study was to evaluate the environmental effects on embryo recovery rate and pregnancy rate of Mangalarga Marchador mares. The reproductive characteristics of donor and recipient mares were evaluated during five years in Brazilian tropical environment. The mares were used throughout the year and seasons were classified as: October to April (breeding season - BS); May (autumn transition out of the breeding season - ATBS); June to August (non-breeding season - nBS); and September (vernal transition into the breeding season - VTBS). Daily temperature rainfall and hours of daylight (photoperiod) were measured during all months and years of evaluation. The embryo recovery rate (ERR) and the pregnancy rate (PR) were observed and frequencies were calculated. The effect of environmental variables, day of flushing, and hormonal treatments (estradiol benzoate and progesterone) were determined for the reproductive measures using the Chi-square and Kruskal-Wallis tests. Significant effects were noted of the year, season and temperature on ERR (P < 0.05), but no significant effects were observed of the environmental parameters (year, season, hormone treatment, rainfall and photoperiod) on PR (P > 0.05). The day of uterine flush affected ERR (P < 0.05) but did not affect PR (P > 0.05). In addition, hormone treatment also supported favorable results of PR in recipient mares during nBS. The conclusion is that mares of this breed can be used in reproduction all year long, with good pregnancy rates, in Brazil's tropical environment. The hormone treatment also supported favorable pregnancy rates in recipient mares during the non-breeding season. It seems that mares can have good pregnancy rates throughout the year in Brazil´s tropical environment.

Single Nucleotide Polymorphisms in the HIRA Gene Affect Litter Size in Small Tail Han Sheep

Simple Summary

Litter size is one of the most important reproductive traits in sheep. Two single nucleotide polymorphisms (SNPs), g.71874104G>A and g.71833755T>C, in the Histone Cell Cycle Regulator (HIRA) gene, were identified by whole-genome sequencing (WGS) and may be correlated with litter size in sheep. The two SNPs were genotyped and expression patterns of HIRA was determined in sheep breeds with different fecundity and in groups of Small Tail Han sheep producing large or small litters. Association analysis indicated that both SNPs were significantly correlated with litter size in Small Tail Han sheep. Furthermore, high levels of HIRA expression may have a negative effect on litter size in Small Tail Han sheep.

Abstract

Maintenance of appropriate levels of fecundity is critical for efficient sheep production. Opportunities to increase sheep litter size include identifying single gene mutations with major effects on ovulation rate and litter size. Whole-genome sequencing (WGS) data of 89 Chinese domestic sheep from nine different geographical locations and ten Australian sheep were analyzed to detect new polymorphisms affecting litter size. Comparative genomic analysis of sheep with contrasting litter size detected a novel set of candidate genes. Two SNPs, g.71874104G>A and g.71833755T>C, were genotyped in 760 Small Tail Han sheep and analyzed for association with litter size. The two SNPs were significantly associated with litter size, being in strong linkage disequilibrium in the region 71.80–71.87 Mb. This haplotype block contains one gene that may affect litter size, Histone Cell Cycle Regulator (HIRA). HIRA mRNA levels in sheep with different lambing ability were significantly higher in ovaries of Small Tail Han sheep (high fecundity) than in Sunite sheep (low fecundity). Moreover, the expression levels of HIRA in eight tissues of uniparous Small Tail Han sheep were significantly higher than in multiparous Small Tail Han sheep (p < 0.05). HIRA SNPs significantly affect litter size in sheep and are useful as genetic markers for litter size.

Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants

BACKGROUND

Increasing marker density was proposed to have potential to improve the accuracy of genomic prediction for quantitative traits; whole-sequence data is expected to give the best accuracy of prediction, since all causal mutations that underlie a trait are expected to be included. However, in cattle and chicken, this assumption is not supported by empirical studies. Our objective was to compare the accuracy of genomic prediction of feed efficiency component traits in Duroc pigs using single nucleotide polymorphism (SNP) panels of 80K, imputed 650K, and whole-genome sequence variants using GBLUP, BayesB and BayesRC methods, with the ultimate purpose to determine the optimal method to increase genetic gain for feed efficiency in pigs.

RESULTS

Phenotypes of average daily feed intake (ADFI), average daily gain (ADG), ultrasound backfat depth (FAT), and loin muscle depth (LMD) were available for 1363 Duroc boars from a commercial breeding program. Genotype imputation accuracies reached 92.1% from 80K to 650K and 85.6% from 650K to whole-genome sequence variants. Average accuracies across methods and marker densities of genomic prediction of ADFI, FAT, LMD and ADG were 0.40, 0.65, 0.30 and 0.15, respectively. For ADFI and FAT, BayesB outperformed GBLUP, but increasing marker density had little advantage for genomic prediction. For ADG and LMD, GBLUP outperformed BayesB, while BayesRC based on whole-genome sequence data gave the best accuracies and reached up to 0.35 for LMD and 0.25 for ADG.

CONCLUSIONS

Use of genomic information was beneficial for prediction of ADFI and FAT but not for that of ADG and LMD compared to pedigree-based estimates. BayesB based on 80K SNPs gave the best genomic prediction accuracy for ADFI and FAT, while BayesRC based on whole-genome sequence data performed best for ADG and LMD. We suggest that these differences between traits in the effect of marker density and method on accuracy of genomic prediction are mainly due to the underlying genetic architecture of the traits.

Symposium review: Building a better cow-The Australian experience and future perspectives

Genomic selection has led to opportunities for developing new breeding values that rely on phenotypes in dedicated reference populations of genotyped cows. In Australia, it has been applied to 2 novel traits: feed efficiency, which was released in 2015 as feed saved breeding values, and heat tolerance genomic breeding values, released for the first time in 2017. Feed saved is already included in the national breeding objective, which is focused on profitability and designed to be in line with farmer preferences. Our future focus is on traits associated with animal health, either directly or in combination with predictor traits, such as mid-infrared spectral data and, into the future, automated data capture. Although it is common for many evaluated traits to have genomic reliabilities ranging between 60 and 75%, many new, genomic information-only traits are likely to have reliabilities of less than 50%. Pooling of phenotype data internationally and investing in maintenance of reference populations is one option to increase the reliability of these traits; the other is to apply improved genomic prediction methods. For example, advances in the use of sequence data, in addition to gene expression studies, can lead to improved persistence of genomic breeding values across breeds and generations and potentially lead to greater reliabilities. Lower genomic reliabilities of novel traits could reduce the overall index reliability. However, provided these traits contribute to the overall breeding objective (e.g., profit), they are worth including. Bull selection tools and personalized genetic trends are already available, but increased access to economic and automatic capture farm data may see even better use of data to improve farm management and selection decisions.

Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers

Zebu animals () are known to take longer to reach puberty compared with taurine animals (), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being -0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant ( < 0.05) terms associated with HP-"Munc18 Proteins," "Fucose," and "Hemoglobins"-and with NF-"Cathepsin B," "Receptors, Neuropeptide," and "Palmitic Acid." This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.

Identification of copy number variation in French dairy and beef breeds using next-generation sequencing

Background

Copy number variations (CNV) are known to play a major role in genetic variability and disease pathogenesis in several species including cattle. In this study, we report the identification and characterization of CNV in eight French beef and dairy breeds using whole-genome sequence data from 200 animals. Bioinformatics analyses to search for CNV were carried out using four different but complementary tools and we validated a subset of the CNV by both in silico and experimental approaches.

Results

We report the identification and localization of 4178 putative deletion-only, duplication-only and CNV regions, which cover 6% of the bovine autosomal genome; they were validated by two in silico approaches and/or experimentally validated using array-based comparative genomic hybridization and single nucleotide polymorphism genotyping arrays. The size of these variants ranged from 334 bp to 7.7 Mb, with an average size of ~ 54 kb. Of these 4178 variants, 3940 were deletions, 67 were duplications and 171 corresponded to both deletions and duplications, which were defined as potential CNV regions. Gene content analysis revealed that, among these variants, 1100 deletions and duplications encompassed 1803 known genes, which affect a wide spectrum of molecular functions, and 1095 overlapped with known QTL regions.

Conclusions

Our study is a large-scale survey of CNV in eight French dairy and beef breeds. These CNV will be useful to study the link between genetic variability and economically important traits, and to improve our knowledge on the genomic architecture of cattle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0352-z) contains supplementary material, which is available to authorized users.

Selecting sequence variants to improve genomic predictions for dairy cattle

Background

Millions of genetic variants have been identified by population-scale sequencing projects, but subsets of these variants are needed for routine genomic predictions or genotyping arrays. Methods for selecting sequence variants were compared using simulated sequence genotypes and real July 2015 data from the 1000 Bull Genomes Project.

Methods

Candidate sequence variants for 444 Holstein animals were combined with high-density (HD) imputed genotypes for 26,970 progeny-tested Holstein bulls. Test 1 included single nucleotide polymorphisms (SNPs) for 481,904 candidate sequence variants. Test 2 also included 249,966 insertions-deletions (InDels). After merging sequence variants with 312,614 HD SNPs and editing steps, Tests 1 and 2 included 762,588 and 1,003,453 variants, respectively. Imputation quality from findhap software was assessed with 404 of the sequenced animals in the reference population and 40 randomly chosen animals for validation. Their sequence genotypes were reduced to the subset of genotypes that were in common with HD genotypes and then imputed back to sequence. Predictions were tested for 33 traits using 2015 data of 3983 US validation bulls with daughters that were first phenotyped after August 2011.

Results

The average percentage of correctly imputed variants across all chromosomes was 97.2 for Test 1 and 97.0 for Test 2. Total time required to prepare, edit, impute, and estimate the effects of sequence variants for 27,235 bulls was about 1 week using less than 33 threads. Many sequence variants had larger estimated effects than nearby HD SNPs, but prediction reliability improved only by 0.6 percentage points in Test 1 when sequence SNPs were added to HD SNPs and by 0.4 percentage points in Test 2 when sequence SNPs and InDels were included. However, selecting the 16,648 candidate SNPs with the largest estimated effects and adding them to the 60,671 SNPs used in routine evaluations improved reliabilities by 2.7 percentage points.

Conclusions

Reliabilities for genomic predictions improved when selected sequence variants were added; gains were similar for simulated and real data for the same population, and larger than previous gains obtained by adding HD SNPs. With many genotyped animals, many data sources, and millions of variants, computing strategies must efficiently balance costs of imputation, selection, and prediction to obtain subsets of markers that provide the highest accuracy.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0307-4) contains supplementary material, which is available to authorized users.