Mean Inbreeding Coefficient Research Articles

A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population.

Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.

Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca).

Pikeperch (Sander lucioperca) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size (N e ), and assessed relatedness among parental individuals. A mean of 2,235 ± 526 and 1,841 ± 363 ROH segments per individual, resulting in a mean inbreeding coefficient of 0.33 ± 0.06 and 0.25 ± 0.06 were estimated for the progeny and parents, respectively. N e was about 12 until four generations ago and at most 106 for 63 generations in the past, with varying genetic relatedness amongst the parents. This study shows the importance of genomic information when family relationships are unknown and the need of selective breeding programs for reproductive management decisions in the aquaculture industry.

PLUM VARIETIES USED AS PARENTS IN ROMANIAN BREEDING PROGRAM

There are about three thousand varieties belonging to Prunus domestica available at present worldwide that can be used as genitors in plum breeding activity. An analysis of the pedigrees of plum cvs. developed in Romanian breeding programs shows that the most are descended from ‘Tuleu gras’, ‘Renclod Althan’, ‘Anna Späth’, ‘Stanley’ and ‘Early Rivers’, called 'ancestors'. That means the majority of plum cvs. have at least one of the ancestors as parent or grandparent. For those 40 plum cvs. registered in Romania in 60 years an increased number of crosses with these 'ancestors' has led to what we call 'inbreeding'. According to data presented in this paper, ‘Tuleu gras’ cv. was the most frequently used parent in the cross combinations, giving origin to 23 cvs. Among the other frequently used genitors were: ‘Renclod Althan’ (7 cvs.), ‘Anna Späth’ (3 cvs.) and ‘Stanley’ (1 cv.). Many of the cultivars – 32 altogether (80%) have originated from hybridization, whereas 4 cvs. have originated from open pollination, others 3 cvs. from mutagenesis and 1 cv. from clonal selection. The goal of this work is to measure genetic diversity presently use in Romanian plum breeding. Pedigrees of each cv. were used to study the genetic contributions of ancestor. Of the 40 cvs. analyzed, 33 had an inbreeding coefficient other than zero. The overall mean inbreeding coefficient was 0.419 for all cvs., where their parentages were known. For cvs. with unknown parentage (nonrelated with known parentage) the inbreeding coefficient is zero. The mean coefficient of coancestry of 40 plum cvs. are 0.081 with ‘Tuleu gras’ cv., 0.019 with ‘Renclod Althan’ and ‘Anna Späth’ cvs., 0.017 with ‘Early Rivers’ cv., 0.014 with ‘d’Agen’ and ‘Renclod Violet’ cvs. and 0.005 with Stanley cv. In conclusion, plum breeders have worked with populations of greatly reduced genetic diversity and this strategy becomes a problem because it leads to genetic impoverishment, and, also, the loss of the genetic resistance to different diseases.

Insights Into the Genetic Diversity of Nordic Red Clover (Trifolium pratense) Revealed by SeqSNP-Based Genic Markers.

Red clover (Trifolium pratense) is one of the most important fodder crops worldwide. The knowledge of genetic diversity among red clover populations, however, is under development. This study provides insights into its genetic diversity, using single nucleotide polymorphism (SNP) markers to define population structure in wild and cultivated red clover. Twenty-nine accessions representing the genetic resources available at NordGen (the Nordic gene bank) and Lantmännen (a Swedish agricultural company with a red clover breeding program) were used for this study. Genotyping was performed via SeqSNP, a targeted genotype by sequencing method that offers the capability to target specific SNP loci and enables de novo discovery of new SNPs. The SNPs were identified through a SNP mining approach based on coding sequences of red clover genes known for their involvement in development and stress responses. After filtering the genotypic data using various criteria, 623 bi-allelic SNPs, including 327 originally targeted and 296 de novo discovered SNPs were used for population genetics analyses. Seventy-one of the SNP loci were under selection considering both Hardy-Weinberg equilibrium and pairwise FST distributions. The average observed heterozygosity (HO), within population diversity (HS) and overall diversity (HT) were 0.22, 0.21 and 0.22, respectively. The tetraploids had higher average HO (0.35) than diploids (0.21). The analysis of molecular variance (AMOVA) showed low but significant variation among accessions (5.4%; P < 0.001), and among diploids and tetraploids (1.08%; P = 0.02). This study revealed a low mean inbreeding coefficient (FIS = −0.04) exhibiting the strict outcrossing nature of red clover. As per cluster, principal coordinate and discriminant analyses, most wild populations were grouped together and were clearly differentiated from the cultivated types. The cultivated types of red clover had a similar level of genetic diversity, suggesting that modern red clover breeding programs did not negatively affect genetic diversity or population structure. Hence, the breeding material used by Lantmännen represents the major genetic resources in Scandinavia. This knowledge of how different types of red clover accessions relate to each other and the level of outcrossing and heterozygosity will be useful for future red clover breeding.

Genetic diversity and population structure of the long-tailed hamster Cricetulus longicaudatus in Shanxi Province, China.

The long-tailed hamster Cricetulus longicaudatus is a dominant rodent in farmland of Shanxi Province, China, but little is known about its genetic diversity and population structure. In this study, the genomic DNAs of individuals from 13 populations captured in different fields of Shanxi were extracted and amplified by six pairs of microsatellite primers and by universal primers for mtDNA COI gene sequences. Our data revealed significant departure from Hardy-Weinberg equilibrium in four of the 13 populations. In all 13 populations, the mean observed heterozygosity was significantly lower than the expected heterozygosity. Meanwhile, the mean inbreeding coefficient was statistically significant, which indicated non-random mating within populations. The pairwise genetic distance and natural logarithm of linear geographical distance were not significantly correlated for any C. longicaudatus populations. However, the correlation between genetic distance and resistance distance based on mountain landscape was significant, suggesting that the mountain landscape is an important factor affecting gene flow of C. longicaudatus. Pairwise FST analysis of population structure showed moderate to high genetic differentiation among populations, and all individuals could be divided into two gene clusters. Phylogenetic analysis based on COI sequences also showed that many individuals originated from a single haplotype, suggesting the existence of gene exchange among these populations at some time in the past. Our research should provide a scientific basis for the analysis of genetic differentiation and gene flow among populations of C. longicaudatus.

SNP-based parentage analyses over two successive generations demonstrates the feasibility of efficient production of inbred lines in the Pacific oyster (Crassostrea gigas) by self-fertilization of simultaneous hermaphrodites despite severe inbreeding depression

The Pacific oyster, Crassostrea gigas, is a species in which true male and true female well as hermaphrodite individuals have been reported. Among the latter, most are sequential, with one or more sex changes throughout their live, while a few (<2%) are simultaneous hermaphrodites (SH) which may self-fertilize. Sex determinism and its functional bases remain unclear is this species. In this study, one SH oyster was found among a mature broodstock and used to produce a progeny by self-fertilization. Several thousand offspring were obtained for this family (SF1) but only 73 SF1 oysters survived following an episode of mass mortality at the spat stage. Six of them were conditioned for reproduction and three were found to be SH, and one produced a limited but viable progeny by self-fertilization (SF2). Oysters were sampled and genotyped with 226 SNP markers, confirming that the SF1 and the SF2 oysters were produced by self-fertilization over two successive generations. To our knowledge, it is the second study reporting the feasibility of production on an inbred line of Pacific oysters by self-fertilization using a simultaneous hermaphrodite as primary genitor, and the first study to generate two successive generations of selfing. Observed mean inbreeding coefficient of SF2 oysters produced by selfing for two generations was 0.61, ranging from 0.46 to 0.80. This coefficient was lower than the expected theoretical value (0.8125), suggesting that the most homozygous offspring died at early stages due to inbreeding depression. Our study demonstrates that inbred lines of Pacific oysters can be produced by self-fertilization but may exhibit higher heterozygosity than theoretically expected due to better survival of the most heterozygous offspring.

Development of polymorphic microsatellite markers for the Trichoglossus haematodus and cross-species amplification in Trichoglossus moluccanus.

Trichoglossus haematodus is the most popular parrots globally and one of the most bred species in Korea's zoos. However, despite its popularity, there are limited studies on the population genetics of this species. In this study, 10 polymorphic microsatellite markers were developed for T. haematodus. The number of alleles ranged from 6 to 9 (mean 7.9). Null alleles were present in two loci (TH-07 and TH-08). The observed heterozygosity ranged from 0.4444 to 1.0000 (mean 0.7000). One locus (TH-08) indicated a significant deviation from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.005). The mean inbreeding coefficient (FIS) of the 10 loci was positive, suggesting that there is inbreeding in the population. Since the polymorphism information content (PIC) values were more than 0.7 in all loci, all markers developed in this study were classified as informative. The parentage exclusion probabilities considering all loci were higher than 0.99 in all three cases (P1, P2, and P3). The cross-species amplification of the 10 markers was tested in T. moluccanus, a close relative species of T. haematodus. These markers were also informative for T. moluccanus with PIC values higher than 0.7 in all loci. Additionally, the parentage exclusion probabilities (P1, P2 and P3) for T. moluccanus were above 0.99. However, due to the small number of T. haematodus and T. moluccanus investigated in this study, the 10 microsatellite markers should be analyzed with more individuals of these two species in future studies. The markers developed in this study might be helpful for investigations of genetic diversity and parentage analysis of T. haematodus and T. moluccanus.

The Nero Lucano Pig Breed: Recovery and Variability.

Simple SummaryThe reduction of biodiversity determines the loss of species and breeds, with the consequent disappearance of production systems, knowledge, cultures and local traditions. The Nero Lucano pig is a native breed of Southern Italy (Basilicata region) recovered, starting from 2001, because of the high quality of its cured meat products. This study gives a picture of the low genetic variability of this breed. Knowledge of individual inbreeding levels allows for planning of interventions to reduce the negative effects of the low effective population size and, then, improve the efficiency of the actual recovery project.The Nero Lucano (NL) pig is a black coat colored breed characterized by a remarkable ability to adapt to the difficult territory and climatic conditions of Basilicata region in Southern Italy. In the second half of the twentieth century, technological innovation, agricultural evolution, new breeding methods and the demand for increasingly lean meat brought the breed almost to extinction. Only in 2001, thanks to local institutions such as: the Basilicata Region, the University of Basilicata, the Regional Breeders Association and the Medio Basento mountain community, the NL pig returned to populate the area with the consequent possibility to appreciate again its specific cured meat products. We analyzed the pedigrees recorded by the breeders and the Illumina Porcine SNP60 BeadChip genotypes in order to obtain the genetic structure of the NL pig. Results evidenced that this population is characterized by long mean generation intervals (up to 3.5 yr), low effective population size (down to 7.2) and high mean inbreeding coefficients (FMOL = 0.53, FROH = 0.39). This picture highlights the low level of genetic variability and the critical issues to be faced for the complete recovery of this population.

Inbreeding in Holstein Fresian Cattle Population in Turkey

Inbreeding is generally associated with a reduction in production and profitability. Therefore, it is essential that it be monitored and kept under control. The purpose of this study was to calculate the inbreeding coefficient for Holstein Friesian cattle registered in the database of the Cattle Breeders' Association of Turkey (TDSYMB). The TDSYMB database is comprised of two elements: (i) pre-herdbook and (ii) herdbook, including information about, for example, ownership, breeding, and some production traits. In this study, the two databases were combined. The database consisted of 6,935,005 individuals born in 1962-2012. Inbreeding coefficients were calculated using Wright's method, and ranging from zero to 43.75% with a mean of 0.0012 and standard deviation (SD) of 0.01273 for all animals, considering the inbred animals, the mean inbreeding coefficient was 0.0106 and standard deviation (SD) was 0.03272. The average inbreeding of all animals born in the population in 2012 was found to be 0.0022. In the population, the proportion and number of inbred individuals increased over the years, while the mean inbreeding coefficient decreased. This could be due to the fact that gene flow in the population from other countries was quite high, and pedigree information was taken into account while importing sperm and live animals (both heifers and bulls).

Genetic diversity of Matrinxã breeding stocks: implications for management and conservation

The formation of fish breeding stocks for fish farming or conservation programs is commonly carried out from the capture of fish in natural environments. Information on the geographic and genetic origin of these stocks is important to guide actions that allow correct management in captivity and, when lost, harm production and genetic conservation. In this sense, the objective of this study was to evaluate the genetic diversity and origin of two breeding stocks of matrinxã, Brycon amazonicus (INPA, Amazonas - INPA and Nova Motum, Mato Grosso - NM). A total of 68 caudal fin samples were collected, including 33 INPA samples and 35 NM samples. Twenty pairs of microsatellite primers were tested, but only seven primers showed satisfactory amplification, amplifying 41 alleles ranging from 187-318 bp. The polymorphic information content ranged from 0.135 (Borg25) to 0.782 (Bh6). Exclusive alleles were observed for both populations (INPA: 04 and NM: 18). Allelic richness results revealed that there was increased loss of genetic variation in NM, indicating a lower evolutionary potential of this stock. The average values of the observed heterozygosity corroborated this statement; however, there were high values for INPA (0.545) and NM (0.475), signifying an adequate genetic variability. An imbalance was found in the Hardy-Weinberg equilibrium at the Borg59 locus in INPA (P &lt; 0.05), possibly due to the effect of null alleles, but was attributed to a founder effect. For NM, an imbalance in the Hardy-Weinberg equilibrium was observed at loci BoM13 and Bh6, which together with the results of the mean inbreeding coefficient values demonstrated the presence of genetic drift. The analysis of molecular variance showed greater variation within populations than between them, and was confirmed by the genetic differentiation value (0.086 - moderate genetic differentiation) and by the distance and genetic identity values (0.273 and 0.761, respectively). Bayesian analysis designated a value of K = 2, with the presence of structuring for NM and INPA; however, with correlated allelic frequencies, confirming a common origin. This origin was corroborated by the presence of gene flow through the number of migrants (5.691). Based on these results, there was a moderate genetic variability for INPA and NM and their common origin was confirmed. Recommendations are also included to minimize the probability of inbreeding processes or genetic drift in the studied stocks.

Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls.

Beta distributions are characterized by two determining parameters and a parameter space from 0 to 1, and may be useful for examining population genetic parameters such as the relationship or inbreeding coefficients. Often subpopulations exist within breeds that are congregated around particular lineages of cattle or ancestors that breeders value. These subpopulations are more related to each other than to the majority of other animals; they may have higher inbreeding as well. Value may be added to these subpopulations because of their relatedness with important or renowned ancestors. The objectives of this work were to compare the relatedness and inbreeding of a group of 26 modern bulls from a subpopulation of the American Hereford breed relative to 1) 30 males with the most descendants present in the pedigree, 2) 15 renowned American Hereford bulls considered important individuals in the breed’s history, and 3) 19 prominent subpopulation male ancestors. Conformance of the mean relationship coefficients of the bulls with the three groups and the mean inbreeding coefficient with all pedigree animals to beta distributions was assessed by 1) visually determining the parameters of the beta distributions based on the entire pedigree, 2) testing the mean relationship coefficient or inbreeding coefficient of the group of subpopulation bulls for its positional inclusion in those distributions, and 3) bootstrap sampling methodology. The mean relationship coefficients of the 26 Trask bulls with the 30 bulls with the most descendants, the 15 renowned ancestors, and the 19 Trask male ancestors were 0.15, 0.132, and 0.208, respectively. Testing of these means in beta distributions indicated that the group of 26 Trask bulls were no more related to the three groups of bulls than all of the animals in the pedigree (0.06 < P < 0.25). Bootstrap sampling indicated that the 26 bulls were more related to the three groups of male ancestors than the remainder of the animals in the pedigree (P < 0.0001). The mean inbreeding coefficient of the 26 bulls (0.13) did not differ from the overall inbreeding coefficient (0.056) when tested using a beta distribution; however, bootstrap sampling indicated otherwise (P < 0.0001). Results may indicate the inadequacy of visually parameterizing a beta distribution. Quantification of pedigree relatedness of a group of animals to key ancestors, especially with no DNA available, may add value to that group and individuals.

Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

Loss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

Outcrossing Mating System of the Early-Divergent Moonwort Fern (Botrychium lunaria, Ophioglossaceae) Revealed in the European Alps

Premise of research. Vascular plants depend on sexual recombination for generating new genetic variability to meet environmental needs. Nevertheless, members of the early-divergent fern genus Botrychium (Ophioglossaceae) typically maintain gametophytic selfing and show strong inbreeding within populations. To explain this evolutionary anomaly, the existence of previous or current but undiscovered outcrossing, genetically rich precursors of the existing genetically depauperate taxa, has been hypothesized.Methodology. Using allele expression at 13 independently assorting enzyme loci, we compared allelic diversity and levels of heterozygosity in 471 B. lunaria individuals across 16 populations in the Alps and Jura Mountains of Switzerland. We examined habitat characteristics influencing mating systems and investigated population genetic structure on the basis of a discriminant analysis of principal components (DPAC) and a graph-theoretic framework. We tested the pattern of isolation by distance and explored the biological processes favoring or limiting spore dispersal at a regional scale.Pivotal results. We found high genetic diversity within and among populations and similar observed heterozygosity (HO) and expected heterozygosity (HS) across loci (HO = 0.020–0.450 and HS = 0.040–0.590, respectively). Estimates of HO (0.050–0.272) were lower than those of HS (0.144–0.305) across individuals, indicating a weak deficit in heterozygotes. Mean values of departure (D) from expected heterozygosity were close to what would be expected with random mating (DL=0.061 and DP=0.059 across loci and populations, respectively). The mean inbreeding coefficient (FIS) was low (FIS=0.247), and the overall genetic differentiation (FST) was moderate (global FST=0.083).Conclusions. Together, the DAPC and the population graph revealed a complex population genetic structure and weak genetic differentiation, with substantial gene flow among most populations. One population (Arosa), sampled from a site recently released from permafrost, demonstrated a probable founder effect not correlated with geographical isolation. The topology of the population graph identified three subgroups with several key populations (Bosco Gurin, Chandolin Low, Grand St. Bernard, San Bernardino, and Val Roseg) that maintained genetic connectivity of populations from distant locations.

Determination of Chromosome Number and Genetic Diversity using SSR and RAPD Markers in Ziziphus jujuba Mill.

The jujube is very important in Iran’s horticultural sector, and its value-added is very high for per cubic meter of water consumed. The chromosome number and genetic diversity of 25 jujube trees from different regions of South Khorasan Province were assessed using 24 simple sequence repeat (SSR) and 16 random amplified polymorphic DNA (RAPD) markers. The polymorphism percentage was 100% and 67.59% with SSR and RAPD, respectively. The Shannon’s information index (I), Nei’s gene diversity (H), and effective allele (Ae) were higher for SSR (1.44, 0.72 and 4.21, respectively) than for RAPD (0.46, 0.30 and 1.49, respectively). A high level of genetic differentiation and low level of gene flow were detected by SSR (Fst = 0.29, Nm = 0.61) and RAPD (Gst = 0.47, Nm = 0.85). SSR identified 26 genotype-specific alleles, while RAPD identified 3 unique bands. In SSR markers, the mean observed heterozygosity (0.67) was higher than mean expected heterozygosity (0.51), and the mean inbreeding coefficient was negative (− 0.33), which indicated heterozygosity excess in the investigated samples. The cluster analysis classified the samples into 3, 5, and 3 groups based on SSR, RAPD, and SSR + RAPD, respectively. Although some of the examined samples were suckers from the same genotypes, they were distinguished by both markers, revealing a somatic mutation occurrence among them. In general, SSR had a better ability than RAPD to accommodate the suckers belonging to the same genotypes in the same groups. The chromosome number in all samples was diploid.

Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers.

Simple SummaryWe investigated the genetic diversity of Polish Konik in sire lines. The Polish Konik horse is a Polish native horse breed of a primitive type and is one of the breeds managed via a conservation program. Due to the small number of breed founders (six male lines) and paternal lineages with unknown representation, the genetic diversity and structure of the population should be monitored regularly. This is the first characterization of the genetic diversity of Polish Konik paternal lines based on microsatellite markers (STRs). The fixation index (FST), which measures population differentiation, was low for all the studied markers and its mean value was 0.0305. Our analysis also revealed that there has been no inbreeding in the Polish Konik population for the studied group. This monitoring of genetic diversity could be helpful for the Polish Konik breeding and conservation programs and also for making informed decisions in the management of paternal lineages.The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.

Pedigree relatedness and pseudo-phenotypes as a first approach to assess and maintain genetic diversity of the Walloon Piétrain pig population

The breeding of pure Piétrain animals is currently performed in two different contexts: industrial lines and individual breeders. As one of the four main pig breeds worldwide, the Piétrain breed might not be considered to be endangered. However, in Wallonia (southern Belgium), even though the Belgian Piétrain programme aims to preserve the Walloon Piétrain population through cryopreservation of semen of relevant boars, only 10 pure Piétrain breeders remain and produce traditional breeding stock. Current breeders are retiring and no new breeders are replacing them. Moreover, the genetic diversity of the pigs from these individual breeders may highly contribute to the global gene pool of the breed, therefore it is important to assess this diversity. This was done on a local level by using pedigree relatedness but also differences in phenotypes. Pedigree parameters such as effective population size (Ne), genetic diversity and inbreeding coefficients were estimated for 219 boars from which offspring performances were recorded at the Walloon test station. A multi-dimensional scaling (MDS) was performed based on genetic distances. Considering the current owners of the boars, a principal component analysis (PCA) was made on deregressed breeding values (pseudo-phenotypes) based on the performances of their crossbred offspring at the test station. The Ne was 223, the genetic diversity parameter was 97.96%, while the mean inbreeding coefficient was 2.74%. The MDS identified four main clusters of boars. Two principal components indicated two major directions of selection: growth or meat traits. Genetically close boars did not necessarily show similar performances in their offspring. Different performances for genetically linked animals should reflect the breeding objectives of their owner, a practice that was confirmed by most owners during interviews. Pedigree, phenotypes and genotypes provide complementary information and therefore should be used simultaneously in the implementation of conservation programmes. These first results also showed that the genetic diversity of the Walloon Piétrain population is so far well preserved. However, recommendations need to be developed in order to maintain it. For example, boars provided to the progeny-testing scheme should come from equally contributing breeders, allowing the Belgian Piétrain programme to sample boars from a larger variety of animals taking into account genetic and phenotypic diversity. Finally, in-situ preservation of Piétrain diversity will require the development of new tools and mating schemes.

Population Structure of a Remnant Quilombo Community: An Analysis of the Inbreeding and Ethnic Admixture

The histories and oral traditions identify rural communities them as quilombos and that are currently denominated quilombo remnants in Brazil. The formation of these communities was usually carried out by a small number of individuals who remained isolated for generations. This study is an analysis of the effects of inbreeding and ethnic admixture in the remaining quilombo community Tucum in the South-Center region of the State of Bahia, in Brazil. The inbreeding values were obtained through inbreeding coefficients and genealogical database. The admixture analysis was conducted by phenotypic and cultural index. Other demographic genetic parameters were evaluated in the search for the better understanding of the population structure. A total of 489 individuals were analyzed for effective population size (Nef), inbreeding coefficient expected (O), inbreeding coefficient (F) and mean inbreeding coefficient (F) resulting in 384, 0, 0.144, 0.0086, respectively. The community presents 20.64% of consanguineous marriages and an inbreeding coefficient (r) of 0.288. These data are larger than those found in the total Brazilian population and to other traditional communities analyzed in the country. The admixture analysis revealed a Negroid Phenotypic Index (NPI) of 0.60 and the Negroid Cultural Index (NCI) of 0.33, lower than that found in other remnants. The isolation index (i) helps to understand this pattern of population structure, and the community studied was not a genetic isolate (i = 22.4) demonstrating a large migratory flow. Based on the data presented, it is possible to conclude that the community is not a genetic isolate, transcending the initial implications of the founding effect. However, the high migration does not prevent inbreeding and high rates of consanguineous marriages, influenced by cultural ethnic characters, which may change evolutionary mechanisms, as genetic drift, alleles fixation, natural selection (for preferential selection) and an increase in genetic diseases.

FACTORS ASSOCIATED WITH INBREEDING IN CHAROLLAISLAMBS

Inbreeding within sheep populations is a relatively understudied area due to limited pedigree information. This study assessed the level of inbreeding within a Charollais sheep population. Data were obtained from35,220 Charollais lambs between the years2000 to 2018 from performance-recorded flocks in the UK. Differences among flocks, study years, lamb eight-week body weight categories and if embryo transfer lambs were assessed. Mean inbreeding value for Charollaislambswas2.8% (s.e. ± 0.1), with a range of 0% to 31%. While the proportion of lambs with an inbreeding value of >7% has been relatively stable at 0.1 or less since 2006, the general trend is an increasing mean inbreeding coefficient for the population in recent years. After adjusting lamb inbreeding coefficient for fixed and random effects, the average inbreeding coefficient was found to be lower for lambs in the heavier eight-week body weight category (>32kg), for certain flocks (mean ranged from 0.4% to 14.6%), and for embryo transfer lambs. Monitoring of inbreeding and approaches used for genetic selection in flocks can help minimise poor lamb performance(i.e. potentially lower growth and body weight) associated with inbreeding.

Population structure of Simmental beef cattle using pedigree analysis.

The purpose of this study was to estimate parameters related to the population structure and genetic diversity in the Simental breed based on the pedigree information of 77,553 animals. The individual coefficients of inbreeding and average relatedness, number of complete generations, coefficient of change of inbreeding, effective size, effective number of founders, number of ancestors and generation interval were calculated. Using the Simmental cattle information, the mean inbreeding and average relatedness coefficients were 1.49% and 0.99%, respectively. The effective number of founders and ancestors was 163 and 132, respectively, and the effective population size was 48.03. Despite the relatively small inbreeding coefficient, some of the estimated population parameters indicated the need to adopt measures to maintain the genetic variability of the population.

Consanguineous marriages among Andalusian Gitanos/Calé: a genealogical analysis (1925-2006).

Using data from the family and genealogical reconstitutions of the Gitano population of 22 contiguous localities in eastern Andalusia, Spain, this study analysed the intensity, structure and historical evolution of consanguinity in 3056 couples formed from 1925 to 2006. Of these unions, 54.8% were consanguineous, and 28.7% involved relatives up to and including second cousins, resulting in a mean coefficient of inbreeding up to the third degree α3 = 12.4 × 10-3. The rest of the consanguineous unions (26.1% of all) involved more-distant relatives, such as third cousins, fourth cousins and so forth. When all consanguinity degrees found in the genealogical reconstitution were considered, the total mean coefficient of inbreeding was αt = 14.8 × 10-3. The merging of families and pedigrees generated a complex genealogical network with many inbreeding loops and important founder effects. This network revealed a high rate (62%) of Multiple Consanguineous Marriages (MCMs) in which second and subsequent consanguineous ties increased inbreeding levels by a fifth (20.5%). The accumulation of multiple degrees of distant relatedness, many of which had little social or biological importance, has contributed to a significant increase in inbreeding rates. Among Gitano people, intra-family marriages have remained common in the last decades, in sharp contrast to other Spanish populations. Hence the highest rates of close consanguinity (34%) and inbreeding (α3 = 14.6 × 10-3) were found in the 1960s, the decade that saw the onset of Spain's socioeconomic modernization, internationalization and massive migration. These are among the highest rates of inbreeding found in any European population, including the most endogamous Spanish isolates. They reveal marriage strategies not constrained primarily by geographical barriers, but by ethnocultural separation. Interestingly, in recent decades mixed marriages have been increasing rapidly in this minority, although they are compatible with high rates of consanguinity. Gitano secular endogamy is breaking up, but not uniformly.