Rate Of Inbreeding Research Articles

Mechanisms of Inbreeding Avoidance in a Wild Primate

The deleterious effects of inbreeding have been well-documented in both captive and wild populations. Hence, animals are expected to engage in inbreeding avoidance. However, one recent meta-analysis of mate-choice experiments indicates that animals of many species do not avoid mating with kin in experimental settings, and another reports that behavioral inbreeding avoidance is likely to evolve only when kin encounter each other regularly and inbreeding costs are high. These important results call for more detailed data on the patterns and processes of encounter frequency and mating behavior between kin within natural animal populations. Here, we present the first detailed assessment of encounter frequency and behavioral inbreeding avoidance in multiple kin classes in a wild mammal population, the baboons of the Amboseli ecosystem in Kenya. We find that death and dispersal are very effective at separating opposite-sex pairs of close adult kin. Nonetheless, adult kin pairs do sometimes coreside, and we find strong evidence for inbreeding avoidance via mate choice in kin classes with relatedness ≥ 0.25. Notably, maternal kin avoid inbreeding more effectively than paternal kin despite having identical coefficients of relatedness, pointing to the problem of kin discrimination as a potential constraint on effective inbreeding avoidance. Overall, demographic and behavioral processes ensure that inbred offspring are rare in undisturbed social groups (1% of offspring). However, in an anthropogenically disturbed social group with reduced male dispersal, we find inbreeding rates 10x higher. Our study reinforces the importance of demographic and behavioral contexts for understanding the evolution of inbreeding avoidance.

A decade of molecular diagnosis of Mucolipidosis II and III in Brazil: a pooled analysis of 32 patients

Abstract GlcNAc-1-phosphotransferase is a hexameric complex formed by subunits α, β, and γ, where the first two are encoded by the GNPTAB gene and the third by the GNPTG gene. Pathogenic variants identified in the GNPTAB gene cause the diseases Mucolipidosis II and III alpha/beta, which are severe and characterized by an overflow of lysosomal hydrolases into the extracellular environment, and their absence in lysosomal compartments causes an accumulation of non-degraded macromolecules. Methodology: a retrospective study that included 32 unrelated Brazilian patients with a clinical and genetic diagnosis of Mucolipidosis II/III alpha/beta. The regional frequency of the altered alleles was determined. Results: The patients were from all regions of Brazil. The most prevalent variants were c.3503_3504del, associated with the severe form of the disease, and c.1208T>C, associated with the milder form. Variant c.3503_3504del is the most frequently found in the Midwest, Northeast, and Southeast regions of Brazil. In the South, 42.8% of the alleles present the c.1196C>T variant. Conclusions: From the perspective of all patients diagnosed with Mucolipidosis II/III in Brazil, it is possible to conclude that different regions present allelic frequencies of specific pathogenic variants, which can be explained by the occurrence of a founding effect or high inbreeding rates.

Mandible morphology as a tool to investigate origin, adaptation and stress in invasive alien species: first insights into Callosciurus erythraeus (Rodentia: Sciuridae) in Europe

When an alien species is introduced in a new area, the new population may be genetically and phenotypically different from the parent population because of the population bottleneck, increased inbreeding rate and adaptation to the new environment. In this study we investigated the variation in shape and size of the mandible among and within three populations of the invasive Pallas’s squirrel introduced in Italy, Belgium and France. Significant differences in both size and shape of the mandible were found among all population pairs, with France being the most distinct. French squirrels showed a larger and slenderer mandible with a broad angular process, a restricted condyle, and a backward-oriented coronoid process. The Italian and the Belgian population also differed significantly but to a lesser extent, the Italian squirrels having a lower coronoid process, a broader angular apophysis, and a restricted condyle. Size explained 15% of the total shape variation, but the slope of allometric trajectories did not reveal any significant difference among populations. A significantly high fluctuating and directional asymmetries were found respectively in the French and the Italian squirrels. Results are discussed in terms of different selective pressures in the invaded areas and possible effects of developmental instability.

An Analysis of the Genetic Relationships and Inbreeding in Tatra Shepherd Dogs Depending on the Type of Breeding

The aim of the study was the analysis of the structure of the population, relationship coefficients, and inbreeding trends in terms of: sex, breeding system, and inbreeding degree of Tatra Shepherd dogs. The breed's inbreeding rate was 6.34%, and for a standardised 4-generation population was 6.68%. The highest inbreeding rate was found in "non-champion-dogs" and in "Polish dog" groups consisting of males and females. The limit value FX was exceeded for 25.65% of Tatra dogs, and the critical value was exceeded for 11.52%. An increasing ancestor loss coefficient (AVK) was found, which may result in an increased number of inbred animals. In particular, this referred to female dogs in the nCH, PL, and Z groups, whereas a significant increase of AVK was observed in the group of male dogs from foreign kennels. The resulting COR values were 55.58% for males and 55.44% for females.

Population Structure Analysis of Javan Rhinoceros at Ujung Kulon National Park, West Java

<p>Javan rhino (Rhinoceros sondaicus) is one of the rare animals with critically endangered status. The Ujung Kulon National Park (UKNP) is one of javan rhino habitat in Indonesia. Every year the monitoring program for javan rhino in UKNP was performed to identify the animals. This research was aimed to analyze the population structure of javan rhino based on the records data from 2011 to 2019 in UKNP. Research showed that the natural increase (NI) and birth rate (BR) values were 17.34% (moderate) and 67.33% (high) respectively. The net return rate (NRR) value was 15.38% (male) and 14.28% (female). The NRR value in the present study was lower than 100% and caused by less number of animals in a population for 30 years of breeding length. Despite this, the inbreeding rate of javan rhino at UKNP in 2019 was 0.01 (low). It was concluded that the natural increase of javan rhino at UKNP showed a good parameter but the population number needs to be increased.</p>

Gingival health condition among children of inbreeding parents compared to children of outbreeding parents in Babylon governorate / Iraq

Background: Consanguineous marriage is a relationship between biologically related individuals. Genetic factors have a role in gene environment interactions that takes the center stage. The evidence of oral disease (gingivitis and periodontitis) may depend on genetic syndromes, inherited diseases, familial studies etc. The present study aims at assessing dental plaque and gingival health condition in children of inbreeding parents compared with children of outbreeding parents among primary schools in Al-Qasem city/ Babylon governorate in Iraq. Materials and methods: this comparative study included three hundred ninety eight (398) students, 6-12 years old, from 4 primary schools; 199 children had their parents of inbreeding marriage with first level of inbreeding, and the other 199 children had parents of outbreeding marriage. Plaque status was assessed according to index of Silness and Loe (1964), gingival health status according to index of Loe and Silness (1963). Results: Children of inbreeding parents showed significantly higher plaque index and gingival index mean values than children of outbreeding parents. Mild gingivitis was found as the most prevalent type among both groups. A highly significant positive correlation was found between gingival and plaque indices. Conclusion: Inbreeding rates have an effect on oral health, as the children of outbreeding parents had significantly better oral hygiene and gingival health condition than children of inbreeding parents.
 

The maintenance of genetic diversity in a local cattle breed through optimal contribution selection

The maintenance of genetic diversity in a local cattle breed through optimal contribution selection

Inbreeding evaluation in Latvian local cattle breeds

Submitted 2020-06-26 | Accepted 2020-08-18 | Available 2020-12-01 https://doi.org/10.15414/afz.2020.23.mi-fpap.52-57 In this study, inbreeding and effective population size of the Latvian gene conservation cattle breeds Latvian Brown (LB) and Latvian Blue (LZ) were analysed. The study was based on the pedigree data of 319 LB and 712 LZ cows that were alive at the time of data selection. The inbreeding level in LB and LZ has been increasing during the last decade and at the end of the year 2019, it was 2.61% and 5.20% for LB and LZ, respectively. The average increase of inbreeding from 2010 to 2019 was 1.80% for LB and 2.26% for LZ. The proportions of inbred animals with an inbreeding level greater than 10% were 0.60% and 2.14% in LB and LZ, respectively. Effective population size based on the rate of inbreeding decreased and was close or within the minimum range of recommended effective population size. The current study demonstrates that the inbreeding has increased, and the effective population size decreased in both populations. Therefore, the breeding organizations have to monitor and control the rate of inbreeding in LB and LZ populations over time. Keywords: inbreeding, Latvian Brown, Latvian Blue, native breed References Addo, S., Schäler, J., Hinrichs, D. and Thaller, G. E. (2017). Genetic diversity and ancestral history of the German Angler and the Red-and-White dual-purpose cattle breeds assessed through pedigree analysis. Agricultural Sciences, 8, 1033-1047. https://doi.org/10.4236/as.2017.89075 Doekes, H. P., Veerkamp, R. F., Bijma, P., de Jong, G., Hiemstra, S. J. and Windig, J. J. (2019). Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle. Genetics Selection Evolution, 51(1), 54. https://doi.org/10.1186/s12711-019-0497-z FAO. ©2019. Domestic Animal Diversity Information System (DAD-IS). Retrieved May 2, 2020 from http://www.fao.org/dad-is. GrÄ«slis, Z. (2006). Blue cows in Vidzeme. Jelgava. BÅ SA “Zilā govs”, 1–36. In Latvian. GrÄ«slis, Z. and Å imkevica, D. (2018). Latvian Blue selection. BÅ SA “Zilā govs”, Jelgava, 1–43. In Latvian. GrÄ«slis, Z., Markey, L. and Zutere, R. (2005). The inbreeding analysis in Latvian Blue cow population. Proceedings of the 11th Baltic animal breeding and genetics conference, Lithuania, 65–69. Groeneveld, E., Westhuizen, B.v.d., Maiwashe, A., Voordewind, F. and Ferraz, J. B. S. (2009). POPREP: a generic report for population management. Genetics and Molecular Research, 8(3), 1158–1178. https://doi.org/10.4238/vol8-3gmr648 Jonkus, D., Paura, L. and Cielava, L. (2020). Longevity and milk production efficiency of Latvian local breeds during last decades. Agronomy Research, 18(S2), 1316–1322. https://doi.org/10.15159/ar.20.064 LDC. (2019). Latvian brown cow conservation program from 2019 and nearest future. Retrieved May 26, 2020 from https://www.ldc.gov.lv/upload/doc/doc20.pdf. In Latvian Mäki-Tanila, A., Fernandez, J., Toro, M. and Meuwissen, T. (2010) Assessment and management or genetic variation. In Mäki-Tanila, A. et al. (eds.) Local cattle breeds in Europe. Development of policies and strategies for self-sustaining breeds. The Netherlands: Wageningen Academic Publishers (pp. 98–119) Mc Parland, S., Kearney, F. and Berry, D. P. (2009). Purging of inbreeding depression within the Irish Holstein-Friesian population. Genetics Selection Evolution, 41, 16. https://doi.org/10.1186/1297-9686-41-16 Mc Parland, S., Kearney, J. F., Rath, M. and Berry, D. P. (2007). Inbreeding effects on milk production, calving performance, fertility, and conformation in Irish Holstein-Friesians. Journal of Dairy Science, 90(9), 4411–4419. https://doi.org/10.3168/jds.2007-0227 Oldenbroek, K. and Van der Waaij, L. (2015). Animal Breeding and Genetics for BSc students. Centre for Genetic Resources and Animal Breeding and Genomics Group, Wageningen University and Research Centre, the Netherlands. Retrieved May 26, 2020 from https://wiki.groenkennisnet.nl/display/TAB/ Sørensen, A. C., Sørensen, M. K. and Berg, P. (2005). Inbreeding in Danish dairy cattle breeds. Journal of Dairy Science, 88(5), 1865–1872. https://doi.org/10.3168/jds.S0022-0302(05)72861-7 Zutere, R., GrÄ«slis, Z. and Sjakste, T. 2006. Breeding programs in Latvian livestock. Proceedings of the 12th Baltic animal breeding conference. Jurmala, Latvia, 6–13.   Â

30 Inbreeding in American Angus cattle before and after the implementation of genomic selection

Abstract The aim of this study was to characterize the American Angus cattle population in terms of changes to the inbreeding rate (ΔF) and effective population size (Ne) before and after the implementation of genomic selection (GS). Genomic information (89,206 SNPs) was obtained for 25,960 bulls and 134,962 cows born between the years 2000 and 2017. Bulls and cows were independently grouped into two groups based on year of birth, pre-GS (2000–2009), and post-GS (2010–2017). Genomic inbreeding (FGRM) was calculated assuming fixed allele frequencies (0.5). Inbreeding based on runs of homozygosity (FROH) was calculated using software SNP1101 (Sargolzaei, 2014). The yearly ΔF for each group was estimated by regressing the inbreeding coefficients on year of birth. The generation intervals (L) were calculated for each of the four pathways of selection at both time periods (pre-GS and post-GS), where the mean of the sires of sires and dams of sires pathways was taken to be the generation interval for the bulls and the mean of the sires of dams and dams of dams pathways was taken to be the generation interval for the cows. The L and ΔF of the three inbreeding coefficients were used to estimate the Ne. Estimates of ΔF and Ne for both sexes at the two time periods can be found in table 1. In both sexes, ΔFROH decreased and NeROH increased from pre-GS to post-GS. For bulls, ΔFGRM and NeGRM did not change, and for cows, ΔFGRM decreased and NeGRM increased from pre-GS to post-GS. These results suggest that the implementation of genomic selection in Angus cattle has not caused the increased inbreeding rates and reduced effective population sizes seen in other species, but instead has been beneficial for the preservation of genetic diversity.

277 Phenotypic and genetic differences in Rambouillet lines divergently selected for reproductive rate over 50 years

Abstract A long-term selection experiment was conducted in a Rambouillet flock from 1969 to 2017. The high (HL) and low lines (LL) were divergently selected based on a maternal reproductive index, and an unselected control line (CL) was also maintained. Adult ewe traits considered were NLB, greasy fleece weight (GFW), and body weight after fall weaning of their lambs (BW). Results indicated that NLB was greatest for HL (1.67 ± 0.01), intermediate for CL (1.48 ± 0.02), and least for LL (1.28 ± 0.01; P < 0.001). Ewe GFW was greatest for LL (3.9 ± 0.02 kg; P ≤ 0.01) but not different between HL (3.82 ± 0.02 kg) and CL (3.88 ± 0.02 kg; P = 0.08); whereas, BW was least for HL (61.7 ± 0.19 kg; P ≤ 0.01) and not different between LL (62.9 ± 0.21 kg) and CL (62.6 ± 0.25 kg; P = 0.58). Heritability was estimated to be low for NLB (0.13 ± 0.02) and moderate for GFW (0.55 ± 0.03) and BW (0.46 ± 0.04). Genetic correlations were estimated to be near zero between NLB and GFW (-0.07 ± 0.08) and NLB and BW (0.12 ± 0.08) and low between GFW and BW (0.29 ± 0.06). Trends for NLB predicted breeding value differed among all 3 lines (P < 0.01) and was positive for HL (0.012 ± 0.0002 lambs/birth year), negative for LL (-0.005 ± 0.0002), and small but positive for CL (0.002 ± 0.0002). Inbreeding rates were positive in all lines but greatest for HL (0.45 ± 0.005 %/birth year), intermediate in LL (0.37 ± 0.006), and lowest in CL (0.28 ± 0.006). Results indicated long-term phenotypic selection for reproductive rate was effective and not genetically antagonistic with wool production or mature BW.

THE STATE OF BROWN CARPATHIAN AND BROWN CAUCASIAN CATTLE BREEDS ON FAO PROJECT TCP/RER/3604 “CONSERVATION AND DEVELOPMENT OF DUAL-PURPOSE CATTLE BREEDS IN EASTERN EUROPE”

During 2018–2019 Ukraine took part in the project of Food and Agriculture Organization (FAO) «Conservation and development of double-purpose cattle breeds in Eastern Europe» (TCP/RER/3604). The project covered Brown Carpathian and Brown Caucasian breeds of Armenia, Georgia and Ukraine. On the results of the project, experts from the FAO Regional Office for Europe and Central Asia, international experts prepared reports on gender, social and economic characteristics of the studied regions, genomic analysis of samples and provided recommendations for breeding in the regions with the breeds. It was considered expedient to present these results to the general scientific community.
 At each country FAO have chosen service-provider (organization), which should make survey on productive environment of targeted breed (in Ukraine – Brown Carpathian), conclude the general state of the breed, visit at least 100 farms where Caucasian/Carpathian Brown cattle breed was kept, collect information from 300 cows and 20 bulls, and genetic samples from at least 100 cows and 20 bulls kept for breeding. Service-provider in Ukraine was M.V.Zubets Institute of Animal Breeding and Genetics, NAAS.
 Scientists of M.V.Zubets Institute of Animal Breeding and Genetics and other sub-contracting organizations during February-June, 2019 investigated 265 heads of cattle in 31 villages 5 districts of the Transcarpathian region, phenotypically classified as Brown Carpathian breed, including 6 breeding bulls of mating age (1.5–2 years). Each animal was photographed, linearly descriptive features of the exterior were evaluated, the necessary body measurements were taken with the help of appropriate tools, live weight and constitutional features were determined, and samples were taken for genetic testing.
 A total of 554 hair samples were taken from the project (123 – from Armenia, 141 – from Georgia and 290 – from Ukraine).
 The basis for classifying the animals as Brown Carpathian was phenotypic examination and strict compliance with the main characteristics of the breed: uniform grey or brown colour with different shades of it, general conformation typical for the breed, lighter belt along the back, black muzzle with lighter hair around it, black hooves and horn tips, lighter "glasses" around the eyes, thick light hair inside outer ears.
 To form the genetic passport of the population, hair was selected from the tail switch of selected animals using equipment provided by FAO, sent to the laboratories of the International Atomic Energy Agency, Austria. In the laboratory in the district of Siebersdorf, DNA was isolated from the obtained samples, the genetic diversity of populations, the degree of inbreeding and their effective number, kinship between populations were assessed and the genetic structure and level of influence of other breeds were analysed.
 DNA was extracted from each hair follicle using a MasterPure kit (Biozym, Illumina, USA) according to the protocol of the Association of Public Health Laboratories (APHL). The isolated DNA was subjected to a two-step quality control procedure before preparation for wide-genome typing. DNA samples were measured using a Nanodrop spectrophotometer to obtain a concentration with a ratio of 260/280 and 260/230. According to the results obtained using a spectrophotometer, DNA samples were diluted to measure high-quality double-stranded DNA (dsDNA) by PicoGreen Assay. The final working DNA was prepared based on PicoGreen measurements and stored at – 20°C for further processing.
 Sample genotyping was performed using a third-generation 384-cell matrix to assess Bovine individuals on the Affymetrix-Axiom platform (Axiom Bovine Genotyping v3 array). Within the project, 48 individuals of Austrian Simmental and 18 – Ayrshire breeds were also genotyped for comparison. The matrix included 64.000 SNPs, providing a high probability of covering genomic variations of the Bos taurus and Bos indicus breeds.
 Intra-breed genetic diversity was assessed using PLINK v1.09 to calculate actual heterozygosity (H0) and inbreeding coefficient (FIS).
 Analysis of genetic parameters of population diversity evidenced a rather low inbreeding rate of Brown Carpathian breed and a fairly high effective population size compared to European breeds, which can indicate a very limited practice of artificial insemination and lack of selection among bulls.
 Analysis of genetic differentiation and relationship between populations, principal components analysis and determination of admixtures of other breeds proved the uniqueness of the Brown Carpathian breed from a genetic point of view.
 Based on the conducted genomic analysis of populations, consultations with project participants, reports of service providers of each country, an international consultant on animal genetic resources, chairman of the ICAR working group on functional traits, formed a breeding program for the studied populations. The breeding program included proposals for further selection work, calculation of basic selection-genetic parameters, selection effect, number of bulls and heifers for selection nucleus, number of doses to maintain genetic diversity of the population, cost of population restoration, breeding work of breeding centre and work plan by years to implement a breeding program.
 Gender analysis of service providers' reports showed some gender differentiation in livestock care, processing and everyday life of owners of Brown Carpathian cattle.

Population structure, diversifying selection, and local adaptation in Pinus patula.

Climate change is predicted to affect natural and plantation forests. The responses of conifers to overcome changing environments will depend on their adaptation to local conditions; however, intraspecific adaptive genetic variation is unknown for most gymnosperms. Studying genetic diversity associated with phenotypic variability along environmental gradients will enhance our understanding of adaptation and may reveal genetic pools important for conservation and management. We used target enrichment and genome skimming to obtain single nucleotide polymorphisms (SNPs) from 61 individuals of Pinus patula, a pine tree native to Mexico widely used in plantation forestry. We investigated the adaptive genetic variation of two varieties with morphological and distributional differences potentially related to genetic and adaptive divergence. Population structure and haplotype network analyses revealed that genetic diversity between P. patula var. patula and P. patula var. longipedunculata was structured, even within populations of P. patula var. longipedunculata. We observed high genetic diversity, low inbreeding rate, and rapid linkage disequilibrium (LD) decay in the varieties. Based on outlier tests, loci showing signatures of natural selection were detected in geographically distant P. patula var. longipedunculata populations. For both varieties, we found significant correlations between climate-related environmental variation and SNP diversity at loci involved in abiotic stress, cell transport, defense, and cell wall biogenesis, pointing to local adaptation. Overall, significant intraspecific adaptive genetic variation in P. patula was detected, highlighting the presence of different genetic pools and signs of local adaptation that should be considered in forestry and conservation.

Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis.

Simple SummaryThe conservation and maintenance of genetic diversity is one of the priorities of the Convention of Biological Diversity and is included in the United Nations (UN’s) Sustainable Development Goals. The evaluation of the genetic variability of a breed is fundamental for its future use in a sustainable way, being indispensable to outline a successful conservation or improvement strategy. Preserving genetic diversity in a population is one of the main objectives for a breed conservation program. Nevertheless, the correct management of genetic diversity is also essential for the adaptation of a population to a new environment, production system or genetic improvement. For the purpose of population monitoring, assessing changes in genetic variability and genetic erosion in animal populations, many methodologies based on pedigree analyses of inbreeding and relationships, and on the probability of genetic origin from different herds, founders and ancestors, have been used. This study presents several genetic diversity indicators in a Portuguese native cattle breed, Mertolenga, assessed by pedigree analysis, and demonstrates the usefulness of these indicators and how they can be used in the genetic management of a breed.The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and genetic diversity and to investigate the major factors affecting genetic erosion in the breed, based on the pedigree herdbook information collected since the 1950s, including records on 221,567 animals from 425 herds. The mean generation intervals were 6.4 years for sires and 7.1 years for dams, respectively. The rate of inbreeding per year was 0.183% ± 0.020% and the correspondent effective population size was 38.83. In the reference population (35,017 calves born between 2015 and 2019), the average inbreeding and relatedness were 8.82% ± 10% and 2.05% ± 1.26%, respectively. The mean relationship among animals from the same and from different herds was 29.25% ± 9.36% and 1.87% ± 1.53%, respectively. The estimates for the effective number of founders, ancestors, founding herds and herds supplying sires were 87.9, 59.4, 21.4 and 73.5, respectively. Although the situation of the Mertolenga breed is not alarming, these results indicate the need to adopt measures to maintain the genetic variability of the population.

Intensified Use of Reproductive Technologies and Reduced Dimensions of Breeding Schemes Put Genetic Diversity at Risk in Dairy Cattle Breeds.

In the management of dairy cattle breeds, two recent trends have arisen that pose potential threats to genetic diversity: the use of reproductive technologies (RT) and a reduction in the number of bulls in breeding schemes. The expected outcome of these changes, in terms of both genetic gain and genetic diversity, is not trivial to predict. Here, we simulated 15 breeding schemes similar to those carried out in large French dairy cattle breeds; breeding schemes differed with respect to their dimensions, the intensity of RT use, and the type of RT involved. We found that intensive use of RT resulted in improved genetic gain, but deteriorated genetic diversity. Specifically, a reduction in the interval between generations through the use of ovum pick-up and in vitro fertilization (OPU-IVF) resulted in a large increase in the inbreeding rate both per year and per generation, suggesting that OPU-IVF could have severe adverse effects on genetic diversity. To achieve a given level of genetic gain, the scenarios that best maintained genetic diversity were those with a higher number of sires/bulls and a medium intensity of RT use or those with a higher number of female donors to compensate for the increased intensity of RT.

Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed.

With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genotyping Array-670k SNP (Thermo Fisher), 192 horses were genotyped. Our results showed different estimates: inbreeding from genomic coefficients (FROH )=0.16; pedigree-based (FPED )=0.008; and a method based on excess homozygosity (FHOM )=0.010. The correlations between the inbreeding coefficients were low to moderate, and some comparisons showed negative correlations, being practically null. In total, 85,295 runs of homozygosity (ROH) and 10,016 runs of heterozygosity (ROHet) were characterized for the 31 horse autosomal chromosomes. The class with the highest percentage of ROH was 0-2Mbps, with 92.78% of the observations. In the ROHet results, only the 0-2 class presented observations, with chromosome 11 highlighted in a region with high genetic variability. Three regions from the ROHet analyses showed genes with known functions: tripartite motif-containing 37 (TRIM37), protein phosphatase, Mg2+ /Mn2+ dependent 1E (PPM1E) and carbonic anhydrase 10 (CA10). Therefore, our findings suggest moderate inbreeding, possibly attributed to breed formation, annulling possible recent inbreeding. Furthermore, regions with high variability in the MM genome were identified (ROHet), associated with the recent selection and important events in the development and performance of MM horses over generations.

Genomic mating as sustainable breeding for Chinese indigenous Ningxiang pigs.

An important economic reason for the loss of local breeds is that they tend to be less productive, and hence having less market value than commercial breeds. Nevertheless, local breeds often have irreplaceable values, genetically and sociologically. In the breeding programs with local breeds, it is crucial to balance the selection for genetic gain and the maintaining of genetic diversity. These two objectives are often conflicting, and finding the optimal point of the trade-off has been a challenge for breeders. Genomic selection (GS) provides a revolutionary tool for the genetic improvement of farm animals. At the same time, it can increase inbreeding and produce a more rapid depletion of genetic variability of the selected traits in future generations. Optimum-contribution selection (OCS) represents an approach to maximize genetic gain while constraining inbreeding within a targeted range. In the present study, 515 Ningxiang pigs were genotyped with the Illumina Porcine SNP60 array or the GeneSeek Genomic Profiler Porcine 50K array. The Ningxiang pigs were found to be highly inbred at the genomic level. Average locus-wise inbreeding coefficients were 0.41 and 0.37 for the two SNP arrays used, whereas genomic inbreeding coefficients based on runs of homozygosity were 0.24 and 0.25, respectively. Simulated phenotypic data were used to assess the utility of genomic OCS (GOCS) in comparison with GS without inbreeding control. GOCS was conducted under two scenarios, selecting sires only (GOCS_S) or selecting sires and dams (GOCS_SD), while kinships were constrained on selected parents. The genetic gain for average daily body weight gain (ADG) per generation was between 18.99 and 20.55 g with GOCS_S, and between 23.20 and 28.92 with GOCS_SD, and it varied from 25.38 to 48.38 g under GS without controlling inbreeding. While the rate of genetic gain per generation obtained using GS was substantially larger than that obtained by the two scenarios of genomic OCS in the beginning generations of selection, the difference in the genetic gain of ADG between GS and GOCS reduced quickly in latter generations. At generation ten, the difference in the realized rates of genetic gain between GS and GOCS_SD diminished and ended up with even a slightly higher genetic gain with GOCS_SD, due to the rapid loss of genetic variance with GS and fixation of causative genes. The rate of inbreeding was mostly maintained below 5% per generation with genomic OCS, whereas it increased to between 10.5% and 15.3% per generation with GS. Therefore, genomic OCS appears to be a sustainable strategy for the genetic improvement of local breeds such as Ningxiang pigs, but keeping mind that a variety of GOCS methods exist and the optimal forms remain to be exploited further.

Identificação de doenças genéticas na Atenção Primária à Saúde

Problema: Embora individualmente raras, somadas, as doenças genéticas têm prevalência global estimada de 31,5 a 73,0 por 1.000 indivíduos. Além disto, doenças genéticas e defeitos congênitos representam a segunda causa de mortalidade infantil no Brasil. Diante deste cenário, foi instituída a Política Nacional de Atenção Integral às Pessoas com Doenças Raras no Sistema Único de Saúde. Esta política prevê funções específicas para Atenção Primária à Saúde (APS) que incluem diagnóstico precoce e mapeamento de pessoas com ou sob-risco de desenvolver doenças genéticas raras e/ou defeitos congênitos para encaminhamento regulado. Essa experiência objetivou colaborar com o desenvolvimento de métodos para o reconhecimento de indivíduos com ou sob-risco de desenvolver doenças genéticas na APS. Métodos: Através de visitas domiciliares e por meio do preenchimento de uma ficha específica, realizou-se busca ativa de casos de doença genética e/ou defeito congênito em uma amostra probabilística aleatória, representativa de uma Unidade de Saúde da Família de um município brasileiro de porte médio. Resultados: Foram investigados 295 domicílios, totalizando 1.160 indivíduos e 238 casais. A média de filhos por casal foi de 2,7, a frequência de consanguinidade foi 3,8% e de abortamento espontâneo foi 8,7%. Foram identificadas 29 pessoas (2,5%) com doenças congênitas, 11 (0,9%) com deficiências auditivas, 10 (0,9%) com deficiência mental e 6 (0,5%) com déficits visuais importantes. Atraso no desenvolvimento neuropsicomotor foi relatado em 8,8% das crianças e adolescentes. Doze indivíduos (1%) possuíam câncer e 9,6% relataram história familiar positiva para câncer. Conclusão: Os profissionais da APS estão em posição privilegiada para identificar e organizar uma rede de cuidados para indivíduos com doenças genéticas e/ou defeitos congênitos. A utilização sistemática de instrumentos que facilitem o reconhecimento de fatores de risco e de situações suspeitas pode ser uma estratégia útil a ser incorporada pela APS.

Management of Genetic Diversity in the Era of Genomics.

Management of genetic diversity aims to (i) maintain heterozygosity, which ameliorates inbreeding depression and loss of genetic variation at loci that may become of importance in the future; and (ii) avoid genetic drift, which prevents deleterious recessives (e.g., rare disease alleles) from drifting to high frequency, and prevents random drift of (functional) traits. In the genomics era, genomics data allow for many alternative measures of inbreeding and genomic relationships. Genomic relationships/inbreeding can be classified into (i) homozygosity/heterozygosity based (e.g., molecular kinship matrix); (ii) genetic drift-based, i.e., changes of allele frequencies; or (iii) IBD-based, i.e., SNPs are used in linkage analyses to identify IBD segments. Here, alternative measures of inbreeding/relationship were used to manage genetic diversity in genomic optimal contribution (GOC) selection schemes. Contrary to classic inbreeding theory, it was found that drift and homozygosity-based inbreeding could differ substantially in GOC schemes unless diversity management was based upon IBD. When using a homozygosity-based measure of relationship, the inbreeding management resulted in allele frequency changes toward 0.5 giving a low rate of increase in homozygosity for the panel used for management, but not for unmanaged neutral loci, at the expense of a high genetic drift. When genomic relationship matrices were based on drift, following VanRaden and as in GCTA, drift was low at the expense of a high rate of increase in homozygosity. The use of IBD-based relationship matrices for inbreeding management limited both drift and the homozygosity-based rate of inbreeding to their target values. Genetic improvement per percent of inbreeding was highest when GOC used IBD-based relationships irrespective of the inbreeding measure used. Genomic relationships based on runs of homozygosity resulted in very high initial improvement per percent of inbreeding, but also in substantial discrepancies between drift and homozygosity-based rates of inbreeding, and resulted in a drift that exceeded its target value. The discrepancy between drift and homozygosity-based rates of inbreeding was caused by a covariance between initial allele frequency and the subsequent change in frequency, which becomes stronger when using data from whole genome sequence.

Comparison of long-term effects of genomic selection index and genomic selection using different Bayesian methods

Aggregate genotype in selection programs commonly includes multiple traits, and response to individual traits have importance in addition to their inclusion in the aggregate genotype. The availability of the effect of all markers on genomic selection is an opportunity to select animals based on the desired marker alleles that affect different traits. Genomic selection index (GSI) method divides markers into different groups based on their effects on different traits. It combines and weighs the genomic breeding value of each marker group into an overall index such that maximize response in the aggregate genotype. The primary purpose of this study was to evaluate the long-term effect of GSI compared to genomic selection on genetic progress of a two-trait aggregate genotype and its constituent traits using different Bayesian methods. The results showed that when the correlation between traits was negative, the GSI method yielded higher gain than the genomic selection for the low heritable trait and the aggregate genotype. However, the GSI superiority was decreased as the correlation between the traits increased and a similar response to the genomic selection was obtained for the correlation of 0.5. A higher reduction in genetic variance was observed for scenarios that cause a more significant response to selection. The inbreeding rate was relatively low in all scenarios. The results of this study suggest the use of GSI rather than genomic selection, especially when traits with low heritability are present in the aggregate genotype, and have a negative correlation with other high heritability traits.

A genome-wide scan for candidate lethal variants in Thoroughbred horses

Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having high frequencies of heterozygotes in Thoroughbreds and other domestic horse breeds. Variant analysis of whole-genome sequence data identified two SNPs in the 3′UTR of the LY49B gene that may result in loss of function. Analysis of transcriptomic data from equine embryonic tissue revealed that LY49B is expressed in the trophoblast during placentation stage of development. These findings suggest that LY49B may have an essential, but as yet unknown function in the implantation stage of equine development. Further investigation of this region may allow for the development of a genetic test to improve fertility rates in horse populations. Identification of other lethal variants could assist in improving natural levels of fertility in horse populations.