Complete Pedigree Research Articles

Pedigree-based analysis of population structure and genetic diversity in high-milch Vrindavani crossbred cattle of India.

The present study aimed to elucidate the population structure and genetic diversity along with the estimation of genealogical parameters in Vrindavani cattle using pedigree data. The study was based on pedigree data on 12,718 animals, spread across multiple generations during a 52-year period (between 1971 and 2023). The pedigree data was used to estimate different population genealogical parameters including the generation interval; pedigree completeness; rate and level of inbreeding; effective population size; and parameters characterizing the probabilities of gene origin. The ENDOG program was used for estimation of different parameters while using population after 2010as reference cohort. The results revealed the maximum number of generations (MG) to be 13, while the numbers of completed (CG) and equivalent generations (EqG) were 3.23 and 1.95, respectively. The mean generation interval for the population was 6.9years. The average inbreeding coefficient of animals in the whole and reference population was 1.11 and 3.44%, respectively; with 0.68% rate of inbreeding per generation. The average additive relationship among all the animals and those in the reference population was 1.16 and 5.49%, respectively. The average effective population sizes for the maximum, equivalent, and complete generations were 115.56, 56.42, and 46.02, respectively. The effective population size on the basis of regression and log-regression on birth date was 77.40 and 71.24, respectively. The probabilities of gene origin were estimated by the effective number of founders (fe) and ancestors (fa), which was 115 and 78, respectively. The fe/fa ratio in the reference population was 1.20, indicating that occasional bottlenecks may have occurred in the population. The analysis revealed a loss of 5.3% of total heterozygosity as compared to base population, though significant variability exists in the latest generations. The results revealed that considerable genetic variability exists within the population that may be exploited through appropriate breed improvement programs targeting various economic traits.

Assessing the population structure and genetic variability of Kenyan native goats under extensive production system

Indigenous goats are important to many livelihoods. Despite this, they are subjected to indiscriminate crossbreeding. This affects their genetic variability which is needed to survive in current regime of climate change. The study assessed population structure and genetic diversity of Galla and Small East African goats (SEA) using pedigree information. A total of 7384 animals, 5222 of the Galla and 2162 of the SEA breeds, born between the years 1983 and 2022, were utilized. Individuals with known parents were defined as reference population. From the results, the maximum generation traced for Galla and SEA populations was 14.6 and 14.5, respectively. However, only 6 and 5 generations for Galla and SEA were complete. Pedigree completeness increased with the increasing number of generations. The average generation interval (GI) for Galla and SEA was 3.84 ± 0.04 and 4.4 ± 0.13 years. The average increase in the rate of inbreeding per generation for Galla and SEA was 0.04 and 0.05, with the effective ancestors and founders (fa/fe) ratio being same (1.00) for both breeds. Fifty percent (50%) of the genetic variability in the populations was contributed by 3 and 1 ancestor for Galla SEA, respectively. The effective population size (Ne) was 5.19 and 4.77 for Galla and SEA. Therefore, the current breeding programs should be changed to avoid future genetic bottlenecks in this population. These findings offer an opportunity to enhance the current genetic status and management of Kenyan native goats and other regions with similar production systems.

Pedigree analysis of Korean native chickens: unraveling inbreeding and genetic diversity

This study assessed the trends in inbreeding, effective population size, and genetic diversity across six Korean native chicken lines using pedigree records from 54,383 chickens. Understanding these genetic parameters is significantly important for maintaining healthy and viable chicken populations. The primary objective was to analyze the pedigree data to assess the levels of inbreeding and genetic diversity and to evaluate the effective population size across the different lines. Pedigree analysis revealed that pedigree completeness peaked in the first generation and declined in subsequent generations for all lines. Line A exhibited a mean inbreeding coefficient of 0.0201, whereas the other lines displayed lower mean values ranging from 0.0009 to 0.0098, indicating that inbreeding levels were within an acceptable range and considered safe from extinction. Average relatedness consistently increased with time. Individual increases in inbreeding were the highest in Line A (0.62%), with smaller increases in the other lines ranging from 0.02 to 0.23%. Effective population sizes varied from 81 to 2500, with average coancestry within parental populations ranging from 0.0032 to 0.0290. The fe/fa ratio between 1.00 and 1.69 in the 6 lines suggested a moderate impact during bottleneck events, with subsequent populations recovering well. The genetic diversity loss due to genetic drift and unequal founder contributions ranged from 0.66-3.15%, indicating that considerable genetic variability remains within the populations. The results of this study have practical applications in the management and conservation of genetic resources in poultry breeding programs. By highlighting the importance of monitoring inbreeding and maintaining genetic diversity, the findings can help develop strategies to ensure the long-term sustainability of these chicken lines. This study provides valuable insights into the genetic management of Korean native chicken lines, emphasizing the need for strategic breeding practices to preserve genetic health and diversity.

Exploring unknown parent groups and metafounders in single-step genomic best linear unbiased prediction: Insights from a simulated cattle population

This study explores how the metafounder (MF) concept enhances genetic evaluations in dairy cattle populations using single-step genomic best linear unbiased prediction (ssGBLUP). By improving the consideration of relationships among founder populations, MF ensures accurate alignment of pedigree and genomic relationships. The research aims to propose a method for grouping MF based on genotypic information, assess different approaches for estimating the gamma matrix, and compare unknown parent groups (UPG) and MF methodologies across various scenarios, including those with low and high pedigree completeness based on a simulated dairy cattle population. In the scenario where unknown ancestors are rare, the impact of UPG or MF on breeding values is minimal but MF still performs slightly better compared with UPG. The scenario with lower genotyping rates and more unknown parents shows significant differences in evaluations with and without UPG and also compared with MF. The study shows that ssGBLUP evaluations where UPG are considered via Quaas-Pollak-transformation in the pedigree-based and genomic relationship matrix (UPG_fullQP) results in double counting and subsequently in a pronounced bias and overdispersion. Another focus is on the estimation of the gamma matrix, emphasizing the importance of crossbred genotypes for accuracy. Challenges emerge in classifying animals into subpopulations and further into MF or UPG, but the method used in this study, which is based on genotypes, results in predictions which are comparable to those obtained using the true subpopulations for the assignment. Estimated validation results using the linear regression method confirm the superior performance of MF evaluations, although differences compared with true validations are smaller. Notably, UPG_fullQP's extreme bias is less evident in routine validation statistics.

Pathogenic germline variants among Thai patients with colorectal cancer: A study in Genomics Thailand Project.

e22534 Background: Germline variant testing in colorectal cancer (CRC) patients (pts) has been applied in many countries. Limited data is known regarding germline CRC prevalence in Thailand and other low to middle-income countries in Southeast Asia. Identifying the variants in different ethnicities may show the variety in frequency of the pathogenic germline variants (PGVs) and their relationship with clinical characteristics. Our study reports on the distribution of PGVs and their clinical findings in Thai CRC pts. Methods: We use the germline testing results from the Genomics Thailand Project during 2020-2023, which performed next-generation sequencing on 50,000 pts in 5 disease groups. CRC pts in our institution with a potential risk of carrying PGVs were sent to a geneticist to obtain a family history prior to undergoing germline testing with 25-96 cancer-predisposing genes. Pts with complete pedigree data and germline testing results were enrolled in our retrospective cohort to analyze the variants and clinical findings from chart reviews. Descriptive statistics, the Cox proportion hazards model, and the Kaplan-Meier method were used to evaluate the results. Results: We included 137 CRC pts with a mean age of 47 years at diagnosis, and 58.4% were male. Of these, 38/137 (27.8%) pts were identified as pathogenic/likely pathogenic(P/LP). 26/38 (68.4%) were pathogenic Lynch syndrome (LS), 16 (42.1%) MLH1, 6 (15.8%) MSH2, 2 (5.3%) MSH6, and 2 (5.3%) PMS2. Among pathogenic non-LS, the most frequent variant was 4 (10.5%) APC, followed by 3 (7.9%) ATM, 2 (5.3%) BRCA2, 1 (2.6%) PTEN, 1 (2.6%) BARD1, and 1 (2.6%) monoallelic MUTYH. The LS group was significantly associated with a family history of CRC (p < 0.001), endometrial cancer (p = 0.001), and a synchronous/metachronous CRC (p = 0.003) compared to the non-PGVs group. Likewise, the presence of CRC in a first-degree relative (p = 0.025), more than one CRC pts in the family (p = 0.027), or early onset CRC (p = 0.012) in a first-degree relative was also significantly higher in the pathogenic non-LS group compared to the non-PGVs group. CRC pts who had more than one primary cancer in a lifetime were not significant in the LS or non-LS group compared to the non-PGVs group. At a median follow-up time of 60 (range 7-453) months, Pts in the PGVs group tended to have a shorter median time from the first CRC diagnosis to a second event defined as any of metachronous/synchronous CRC, recurrent CRC, or second cancer in a different organ compared to the non-PGVs group (135 vs. 228 months, p = 0.11). Conclusions: 27.8% pts in our cohort carried P/LP germline variants. The PGVs group was associated with a shorter time to the second event and a higher rate of familial cancer. Our study supports the benefits of genetic cancer screening. [Table: see text]

Genomic Diversity of the Retinta Breed Derived from Two Ancestral Bovine Lineages.

The Retinta breed, an autochthonous type of Spanish beef cattle, is highly adapted to breeding in its natural environment, which is characterized by a Mediterranean climate. The origins of this breed can be traced to two ancestral bovine stocks, which gave rise to distinct morphotypes differentiated primarily by coat color, alongside other significant traits such as growth, morphological conformation and temperament. Specifically, one morphotype comprises blond animals (Rubia Andaluza), genetically resembling the ancestral Bos taurus Aquitanicus, while the other encompasses brown- and red-colored animals (Retinta Extremeña) originating from Bos taurus Turdenatus stock. Over decades, these populations have undergone hybridization, leading to a unified population, albeit with the original subpopulations largely maintaining their genetic integrity. The objective of this study was to undertake genealogical and genomic characterization of these genetic lines, including a particular subpopulation within the blond animals (Tamarona cow). To achieve this, the genealogical records of 22,004 active animals were analyzed, and over 63,000 SNPs from a total of 1030 animals were examined for genomic characterization. Genealogical analysis revealed pedigree completeness and a high level of effective population size (Ne) across the entire population, yet relatively low Ne values within each pure line (ranging from 28.38 to 34.47). These findings underscore the ongoing efforts of the National Association of Retinta Breeders (ACRE) over the past decades to mitigate the loss of variability in this breed. The genomic characterization highlights the persistent differences within the original population and the predominant influence of the Retinto line within the current breed, as evidenced by principal component analysis (PCA) and admixture analysis. Furthermore, the identification of the Tamarona subpopulation within the blond lineage underlines its unique genetic composition, warranting its recognition as an official genetic line within the current Retinta breed. Given the small population size of these lines, particularly the Tamarona subpopulation, protective measures are imperative to preserve this distinct gene pool. Such measures would enhance the genetic diversity of the Retinta breed, which is essential for sustainable breeding practices in its natural habitats.

Lifetime reproductive characteristics of gray wolves

Abstract Female and male cooperative breeders can use different strategies to maximize reproduction and fitness over their lifetimes. Answering questions about fitness in cooperative breeders requires long-term studies as well as complete data on group composition and size which can be exceedingly difficult to obtain. Using a long-term genetic data set of complete group pedigrees, I asked how lifetime reproductive characteristics of female and male gray wolves (Canis lupus) differed. I predicted that genetic relatedness to helpers would be higher for females than males due to philopatric behavior of female wolves, group size would be similar between the sexes, females would inherit breeding positions from within groups more often than males due to differences in dispersal strategies between the sexes, males would have more lifetime mates and produce more young than females because of polygamy, and females would breed for more years than males due to the likelihood that females would still breed (with a new partner) after a mate died or was expelled from the group. I documented complete lifetime breeding histories for 11 male and 18 female wolves in Idaho, United States, 2008 to 2018. Genetic relatedness to helpers, group size, number of mates, pups, and years breeding did not differ between the sexes. Females, however, inherited breeding positions within groups far more often than males. Individuals who secured breeding positions generally reproduced for 2 seasons and commonly had more than 1 partner during their lifetimes if they were able to maintain their breeding position longer. Direct fitness varied greatly within female and male breeding wolves.

Качествена оценка на педигрето на Среднородопската овца 2005-2023

The aim of this study was to estimate the quality of the Central Rhodope Sheep pedigree data in years 2005-2023. The data was provided by the Association for breeding Central Rhodope sheep, Karakachan sheep and Rhodope Cigay sheep, which is keeping the breed’s herdbook. The herdbook has 18 720 records for the studied period. Along with the individuals registered only as sires or dams, there were 22686 individuals in total in the pedigree file. The pedigree was processed by the OptiSel software package and then checked for errors with the PedigreeViewer software. All the inconsistencies found in the pedigree, cycles and the gender discrepancies, were solved by erasing the conflicting data. In total 565 sires and 12 156 dams were identified in the pedigree file. The maximum number of generations traced for an animal in the pedigree were six. Since 2014, the average pedigree completeness index is over 98% for the first generation, and for second and third increases from 58% to 100%, and from 38% to 94%, respectively. In the recent five years, the average number of equivalent generations by year of birth is between 2.145 to 3.159, and the average number of full generations 1.839 to 2.537. These results indicate that the cumulated pedigree data might be used for analyses of the population structure and genetic diversity of the Central Rhodope Sheep breed.

Population structure and genetic diversity of Polish Arabian horses based on pedigree data

With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the dataset of 12 254 individuals (total population). We traced their genealogy to assess inbreeding coefficients (F), founder effects, and genetic variability measures such as the effective number of founders (fe), ancestors (fa), or founder genome equivalents (fge). The results indicated a good pedigree quality with an average of 28.1 maximum traced generations, revealing high pedigree completeness for initial generations with a decline beyond the seventh generation. The genetic diversity parameters showed a considerable bottleneck effect, with an effective number of founders at 73, which reflects a substantial loss of genetic diversity over time. Despite the vast total number of founders (852), only a few have had a lasting impact on the current population, signaling the need for revised breeding strategies to maintain diversity. The study identified a slight but consistent rise in inbreeding over the last century, with a marginal recent decline, and a significant difference in the contribution of various founders. The average F was 5.8%, with 99.6% of the reference population being inbred. The analysis of effective population size (Ne) highlighted potential risks for genetic diversity, urging for revision of breeding goals to consider a wider array of founder lineages. The study indicated that stallions belonging to RP can be attributed to 15 distinct sirelines, whereas mares to 45 unique damlines, more than considered in the current breeding program (8 and 15, respectively). Conclusively, the study underlines the need for ongoing monitoring and strategic breeding to maintain and enhance the genetic diversity of Polish Arabians, considering the breed's historical significance and contemporary genetic challenges.

Pedigree analysis in the mhorr gazelle (Nanger dama mhorr): Genetic variability evolution of the captive population.

Breeding programs have an essential role in the recovery of threatened populations through optimal genetic management and mating strategies. The dama gazelle (Nanger dama) is a North African ungulate listed as critically endangered. The mhorr subspecies is extinct in the wild and currently survives thanks to the creation in 1971 of an ex situ breeding program. The aim of the present study was to assess the evolution of genetic variability in this mhorr gazelle captive population, as well as the mating strategy used in two reference populations studied (Almeria and Europe). The entire pedigree, with 2739 animals, was analyzed to measure demographic characters, pedigree completeness level, probability of gene origin, level of relatedness and genetic structure of the population. The population size has been progressively increasing, with up to 264 individuals alive in Europe at the time of the study. The average number of equivalent complete generations was 5.55. The effective number of founders and ancestors was both 3, and the founder genome equivalent was 1.99. The genetic contributions of the four main ancestors were unbalanced. The average values of inbreeding and average relatedness for the whole pedigree were, respectively, 28.34% and 50.14%. The effective population size was 8.7 by individual increase in inbreeding and 9.8 by individual increase in coancestry. F-statistics evidenced a very small level of population subdivision (F ST = 0.033370). The mating strategy used, based on the minimum coancestry of the individuals, has minimized the losses of genetic variability and helped to balance the genetic contributions between ancestors. The strategy also avoided large subdivisions within the population and the appearance of new bottlenecks. This study shows how pedigree analysis can both be used to determine the genetic variability of the population and to assess the influence of the mating strategy used in the breeding program on such variability.

Pedigree diversity and implications for genetic selection of Katahdin sheep.

The Katahdin hair breed gained popularity in the United States as low input and prolific, with a propensity to exhibit parasite resistance. With the introduction of genomically enhanced estimated breeding values (GEBV) to the Katahdin genetic evaluation, defining the diversity present in the breed is pertinent. Utilizing pedigree records (n = 92,030) from 1984 to 2019 from the National Sheep Improvement Program, our objectives were to (i) estimate the completeness and quality of the pedigree, (ii) calculate diversity statistics for the whole pedigree and relevant reference subpopulations and (iii) assess the impact of current diversity on genomic selection. Reference 1 was Katahdins born from 2017 to 2019 (n = 23,494), while reference 2 was a subset with at least three generations of Katahdin ancestry (n = 9327). The completeness of the whole pedigree, and the pedigrees of reference 1 and reference 2, were above 50% through the fourth, fifth and seventh generation of ancestors, respectively. Effective population size (Ne) averaged 111 animals with a range from 42.2 to 451.0. The average generation interval was 2.9 years for the whole pedigree and reference 1, and 2.8 years for reference 2. The mean individual inbreeding and average relatedness coefficients were 1.62% and 0.91%, 1.74% and 0.90% and 2.94% and 1.46% for the whole pedigree, reference 1, and reference 2, respectively. There were over 300 effective founders in the whole pedigree and reference 1, with 169 in reference 2. Effective number of ancestors were over 150 for the whole pedigree and reference 1, while there were 67 for reference 2. Prediction accuracies increased as the reference population grew from 1k to 7.5k and plateaued at 15k animals. Given the large number of founders and ancestors contributing to the base genetic variation in the breed, the Ne is sufficient to maintain diversity while achieving progress with selection. Stable low rates of inbreeding and relatedness suggest that incorporating genetic conservation in breeding decisions is currently not of high priority. Current Ne suggests that with limited genotyping, high levels of accuracy for genomic prediction can be achieved. However, intense selection on GEBV may cause loss of genetic diversity long term.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations.

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

Elucidating genetic diversity and population structure of Alpine x Beetal goats using pedigree analysis

Pedigree analysis is essential for effective management of the breeding program and to keep the inbreeding under acceptable limits. Alpine x Beetal is a crossbred population of goats, bred at National Dairy Research Institute (NDRI) Karnal for last five decades. This germplasm is adapted to the tropical climate and has high milk potential as well as prolificacy. Objective of this study was to elucidate the genetic diversity and population structure in the flock of the Alpine x Beetal goats. The data were collected from the Animal Genetics and Breeding Division of ICAR-NDRI, Karnal for 5656 animals from the year 1971–2021. Animals born between 2014 and 2017 were 283, considered as reference cohort. Results revealed that the average generation interval was 3.40 years for the complete pedigree. The average inbreeding coefficient and the average relatedness for the whole population were 4.77% and 7.84%, respectively, and 9.65% and 11.98% respectively, for the reference population. High inbreeding coefficient and average relatedness in the reference cohort demonstrated the impact of closed gene pool and demands immediate intervention for management of genetic diversity in the closed nucleus under study. Ancestors contributing 50% of the gene pool were 8 for the complete pedigree which illustrates that few ancestors were responsible for genetic diversity in the flock. This resulted in the decline of effective population size (51.39). Effective number of founders (fe), ancestors (fa), and founder genomes equivalents (fg) were 24, 12, and 4.17, respectively. The (fe/fa) ratio in the reference population was 2 indicating the occurrence of the bottleneck effect in the flock. To lessen inbreeding and augment genetic diversity in the flock, the use of sires with lower average relatedness and the use of appropriate mating strategies are recommended.

Analysis of genetic variability and population structure of the Mangalica pig breed using pedigree data

The maintenance of genetic diversity (GD) and low rate of inbreeding are two main goals for any conservation programs, especially in a small, closed population which is likely to violate these conservation targets in a long run. Among the conservation programs in Hungary probably the most characterizing is that of the Mangalica pigs, which is an autochthonous Hungarian pig breed group that has been preserved for biological diversity since 1973. The current study aimed to expose the evolution of population structure, GD and inbreeding coefficient with different approaches by analysing the pedigree of these breeds in the context of the conservation program. Genealogy analysis used the data of 12,808, 2393 and 3963 Blonde, Swallow-Belly and Red breeding animals born between 1980 and 2021, respectively. The reference populations (REF2021) were defined as breeding animals born between 2016 and 2021. Pedigree completeness was more than 90% in the fifth generation and the complete generation equivalent ranged from 4.29 to 7.08 and from 6.87 to 9.73 for the whole and the reference populations (REF2021), respectively. Generation interval on average was vary from 3.06 to 3.45 years with the longer pathways to the son. Most of different estimated inbreeding coefficient showed increased trends through pedigrees except for the Kalinowski new inbreeding coefficient (FNew) which decreased in all breeds in the last decade. The mean Wright inbreeding coefficient (Fw) was low, being 5.50%, 4.30% and 7.54% for the Blonde, Swallow-Belly, and Red reference populations (REF2021), respectively. Fw showed strong correlation with FNew but low correlation with FBal while the two types of ancestral inbreeding coefficients (FBal and FKal) were ranging from moderate strong to strong correlation in every breed. Effective population size of the reference populations (REF2021) was 85.57, 76.91, and 57.56, respectively. Based on the predicted future inbreeding for the next 25 years only the Red Mangalica breed was predicted to be “Transitional” in the endangerment categories. The GD loss in these three breeds was 5.6%, 5.7% and 8.7%, respectively, in which the loss due to genetic drift was decisive compared to the unequal founder contributions. In conclusion, the three populations at the present and in the next few generations are having optimistic perspective in terms of GD. These populations should be focused on reducing new inbreeding in mating plans and the Red population need to be monitored more carefully because of its current highest GD loss, smallest effective population size and highest inbreeding coefficient.

Comprehensive analysis of three female patients with different types of X/Y translocations and literature review

BackgroundX/Y translocations are highly heterogeneity in terms of clinical genetic effects, and most patients lack complete pedigree analysis for clinical and genetic characterization.ResultsThis study comprehensively analyzed the clinical and genetic characteristics of three new patients with X/Y translocations. Furthermore, cases with X/Y translocations reported in the literature and studies exploring the clinical genetic effects in patients with X/Y translocations were reviewed. All three female patients were carriers of X/Y translocations with different phenotypes. The karyotype for patient 1 was 46,X,der(X)t(X;Y)(p22.33;q12)mat, patient 2 was 46,X,der(X)t(X;Y)(q21.2;q11.2)dn, and patient 3 was 46,X,der(X)t(X;Y)(q28;q11.223)t(Y;Y)(q12;q11.223)mat. C-banding analysis of all three patients revealed a large heterochromatin region in the terminal region of the X chromosome. All patients underwent chromosomal microarray analysis, which revealed the precise copy number loss or gain. Data on 128 patients with X/Y translocations were retrieved from 81 studies; the phenotype of these patients was related to the breakpoint of the chromosome, size of the deleted region, and their sex. We reclassified the X/Y translocations into new types based on the breakpoints of the X and Y chromosomes.ConclusionX/Y translocations have substantial phenotypic diversity, and the genetic classification standards are not unified. With the development of molecular cytogenetics, it is necessary to combine multiple genetic methods to obtain an accurate and reasonable classification. Thus, clarifying their genetic causes and effects promptly will help in genetic counseling, prenatal diagnosis, preimplantation genetic testing, and improvement in clinical treatment strategies.

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds.

The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.

Insight into the Complex Genetic Relationship of Chinese Fir (Cunninghamia lanceolata (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets

Accurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted to employ different molecular markers to address the genetic architecture of their target population, but the power of an advanced parent tree population with a complex pedigree relationship is still rather limited. In this study, a partly known pedigree map combined with marker-derived (SSRs and SNPs) information was implemented for the first time in the assessment of the genetic relatedness of a complex advanced parent tree population (n = 50) in Chinese fir. The bivariate analysis showed that relatedness coefficients between individuals based on SSRs were significantly correlated with SNPs (r = 0.690, p &lt; 0.01). Moreover, the heatmap generated by the SSR-based coefficient matrix was largely consistent with that derived from the SNP-based matrix. Additionally, STRUCTURE and ADMIXTURE analyses based on the two markers showed an analogical genetic clustering result. When compared to the recorded pedigree information, the genetic relationships estimated by the two molecular markers were broadly parallel with pedigree relatedness. These results indicated that SSRs and SNPs can be used as effective tools to clarify genetic relationships when complete pedigree records are not available in Chinese fir. Based on the two markers, the present study revealed a relatively wide genetic variation (SSRs: PIC = 0.573; SNPs: PIC = 0.231) in the selected parent trees. This investigation provides important input into the progress of Chinese fir advanced-generation breeding.

Population dynamics of a long-term selection experiment in White Plymouth Rock chickens selected for low or high body weight

The population dynamics of 2 lines of chickens from a long-term (59 generations) selection experiment were assessed based on pedigree data. These lines were propagated from phenotypic selection for low and high 8-wk BW in White Plymouth Rock chickens. Our objective was to determine whether the 2 lines maintained similar population structures over the selection horizon to allow meaningful comparisons of their performance data. A complete pedigree of 31,909 individuals, consisting of 102 founders, 1,064 from the parental generation, and 16,245 low weight (LWS) and 14,498 high weight (HWS) select chickens, was available. Inbreeding (F) and average relatedness (AR) coefficients were computed. Average F per generation and AR coefficients were 1.3 (SD 0.8) % and 0.53 (SD 0.001) for LWS, and 1.5 (SD 1.1) % and 0.66 (SD 0.001) for HWS. Mean F for the entire pedigree was 0.26 (0.16) and 0.33 (0.19), and maximum F was 0.64 and 0.63, in LWS and HWS, respectively. Based on Wright's fixation index, at generation 59, substantial genetic differences were established between lines. The effective population size was 39 in LWS and 33 in HWS. The effective number of founders was 17 and 15, effective number of ancestors were 12 and 8, and genome equivalents were 2.5 and 1.9 in LWS and HWS, respectively. About 30 founders explained the marginal contribution to both lines. By generation 59, only 7 male and 6 female founders contributed to both lines. Moderately high levels of inbreeding and low effective population sizes were inevitable, as this was a closed population. However, effects on the fitness of the population were expected to be less substantial because founders were a combination of 7 lines. The effective numbers of founders and ancestors were relatively low compared to the actual number of founders, as few ancestors contributed to descendants. Based on these evaluations, it can be inferred that LWS and HWS had similar population structures. Comparisons of selection responses in the 2 lines therefore should be reliable.

The genetic and phenotypic associations between lamb survival outcomes and other traits recorded at lambing

Context Australian sheep breeding values (ASBVs) for lambing ease (LE) are estimated by Sheep Genetics, by using a threshold animal model at the lamb level, in a tri-variate analysis that includes data on birth weight, gestation length and lambing ease score. The implications of these traits for lamb survival, or the use of other indirect traits to improve accuracy of ASBVs for LE, are not currently being considered. Ultimately, it is desirable to extend the analysis to outcomes for individual lamb survival. Aim The present study investigated implications of LE for lamb survival outcomes, accounting for litter size, and examined associations with other traits recorded at or shortly after lambing in maternal sheep breeds. Methods Equivalent linear models were used to compare lamb- and ewe-level models with various combinations of additional random effects. In particular, lambing ease was treated as a different trait for single-born and twin-born lambs, to identify changes in genetic correlations associated with litter size between LE and other traits. Other traits included lambs recorded dead at birth, survival to weaning, lamb birth weight, gestation length and maternal behaviour score. Key results Individual lamb survival outcomes inferred from field data and dead at birth lambs, are lowly heritable traits influenced by both direct and maternal effects. Lamb survival is positively correlated with birth weight, but negatively correlated with gestation length, lambing ease score (increasing lambing difficulty) and dead at birth lambs. Genetic and phenotypic correlations demonstrated that birth weight and lambing ease are antagonistic traits, more so for single-born lambs. Genetic correlations were moderate between dead at birth lambs and LE (0.40–0.45 singles; 0.15–0.36 including data from twins) or lamb survival (−0.63 to −0.81 singles; −0.00 to −0.23 including data from twins) and can add to the accuracy of genetic evaluation for these traits. In contrast, maternal behaviour score was predominantly an ewe trait, and will therefore add to accuracy of evaluation only for maternal effects. Lamb-level models appeared to underestimate heritability, sometimes compensated for by larger variance, and over-estimate genetic correlations for some traits relative to ewe-level models. Conclusions Expanding the current lambing ease analysis to include dead at birth records and lamb survival outcomes would provide more detailed options for breeders to develop breeding goals to improve outcomes for both ewes and lambs. Further work is required to expand analyses to include threshold and continuous traits and understand genetic contributions to ewe survival traits. Implications Relative selection emphasis on LE and birth weight must be considered in light of the expected litter size in which lambs will be born, to ensure favourable outcomes for lamb survival overall. Accuracy of genetic evaluation for LE can be improved using data on dead at birth. Equivalent ewe model analyses are possible. Completeness of pedigree, availability of informative lamb level data and integration with other traits are also factors to consider for the choice between operational lamb- versus ewe-level models for genetic evaluation systems.

Identifying influential sires and distinct clusters of selection candidates based on genomic relationships to reduce inbreeding in the US Holstein.

High relatedness in the US Holstein breed can be attributed to the increased rate of inbreeding that resulted from strong selection and the extensive use of a few bulls via reproductive biotechnology. The objectives of this study were to determine whether clustering could separate selected candidates into genetically different groups and whether such clustering could reduce the expected inbreeding of the next generation. A genomic relationship matrix composed of 1,145 sires with the most registered progeny in the breed born after 1985 was used for principal component analysis and k-means clustering. The 5 clusters reduced the variance by 25% and contained 171 (C1), 252 (C2), 200 (C3), 244 (C4), and 278 (C5) animals, respectively. The 2 most predominant families were C1 and C2, while C4 contained the most international animals. On average, C1 and C5 contained older animals; the average birth year per cluster was 1988 (C1), 1996 (C2 and C3), 1999 (C4), and 1990 (C5). Increasing to 10 clusters allowed the separation of the predominant sons. Statistically significant differences were observed for indices (net merit index, cheese merit index, and fluid merit index), daughter pregnancy rate, and production traits (milk, fat, and protein), with older clusters having lower merit for production but higher for reproduction. K-means clustering was also used for 20,099 animals considered as selection candidates. Based on the reduction in variance achieved by clustering, 5 to 7 clusters were appropriate. The number of animals in each cluster was 3,577 (C1), 3,073 (C2), 3,302 (C3), 5,931 (C4), and 4,216 (C5). The expected inbreeding from within or across cluster mating was calculated using the complete pedigree, assuming the mean inbreeding of animals born in the same year when parents are unknown. Generally, inbreeding was highest within cluster mating and lowest across cluster mating. Even when 10 clusters were used, one cluster always gave low inbreeding in all scenarios. This suggests that this cluster contains animals that differ from all other groups but still contains enough diversity within itself. Based on lower across cluster inbreeding, up to 7 clusters were appropriate. Statistically significant differences in genomic estimated breeding values were found between clusters. The rankings of clusters for different traits were mostly the same except for reproduction and fat. Results show that diversity within the population exists and clustering of selection candidates can reduce the expected inbreeding of the next generations.