Coancestry Coefficient Research Articles

Evaluating different genomic coancestry matrices for managing genetic variability in turbot

In population management, the most efficient method to control the increase of inbreeding and the associated loss of genetic variability is the Optimal Contributions method. This method optimizes the contributions of breeding candidates by minimizing the weighted global coancestry. Traditionally, coancestry coefficients have been estimated from pedigree data but the current availability of genome-wide information allows us to estimate them with higher precision. In recent years, developments of genomic tools in aquaculture species have been very significant. For turbot, a species with an increasing aquaculture value, the whole genome has been recently assembled and genetic and physical maps have been refined. Although several measures of genomic coancestry have been proposed, their relative efficiency for maintaining genetic variability is unknown. The objectives of this study were to compare different measures of genomic coancestry for turbot, and to evaluate their efficiency for retaining genetic variability when using the Optimal Contributions method. We used genomic data obtained through 2b-RAD technology for a domesticated population to achieve the objectives. The different genome-wide coancestry matrices compared were based on: i) the proportion of shared alleles; ii) deviations of the observed number of alleles shared by two individuals from the expected number; iii) the realized relationship matrix obtained by VanRaden's method 1; iv) the realized relationship matrix obtained by VanRaden's method 2; v) the realized relationship matrix obtained by Yang's method; and vi) identical by descent segments. The amount of genetic variability retained when using each coancestry matrix was measured as the expected heterozygosity in the next generation. Results revealed that coancestry coefficients showing high correlations between them gave similar results from the optimization. The genetic variability retained was about 5% higher when using the matrices based on the proportion of shared alleles, deviations of the observed number of alleles shared or segments than when using the three genomic relationship matrices. Matrices retaining more variability showed a higher ability to discriminate relationships between individuals. The higher the diversity achieved the lower was the number of fish selected to contribute to the next generation.

Estimating the inbreeding level and genetic relatedness in an isolated population of critically endangered Sichuan taimen (Hucho Bleekeri) using genome-wide SNP markers.

Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF‐seq)‐based genotyping was performed for Sichuan taimen with 43 yearling individuals from three locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome‐wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (2.6 × 10−3 ± 0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < .001), and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic‐relatedness‐guided breeding and conservation strategy for wild fish species without pedigree information records.

Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses.

We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; FIS was -0.07, indicating that the analyzed animals reflected frequent outbreeding and had maintained genetic variation. Based on genetic structural analysis, the number of genetic subpopulations of the animals was estimated to be as 6, and the majority (more than 50%) of each subpopulation corresponded to the progeny of one of the sires used in the breeding farm; these observations suggested that genetic variation in the analyzed animals reflected the genetic differences among sires. Pedigree records indicated that the average co-ancestry coefficient between sires used in the breeding farm was 0.015 corresponding to second cousin. This level of kinship among sires is acceptable for producing HKDs that maintain genetic variation.

Optimized grouping to increase accuracy of prediction of breeding values based on group records in genomic selection breeding programs

BackgroundPhenotypic records of group means or group sums are a good alternative to individual records for some difficult to measure, but economically important traits such as feed efficiency or egg production. Accuracy of predicted breeding values based on group records increases with increasing relationships between group members. The classical way to form groups with more closely-related animals is based on pedigree information. When genotyping information is available before phenotyping, its use to form groups may further increase the accuracy of prediction from group records. This study analyzed two grouping methods based on genomic information: (1) unsupervised clustering implemented in the STRUCTURE software and (2) supervised clustering that models genomic relationships.ResultsUsing genomic best linear unbiased prediction (GBLUP) models, estimates of the genetic variance based on group records were consistent with those based on individual records. When genomic information was available to constitute the groups, genomic relationship coefficients between group members were higher than when random grouping of paternal half-sibs and of full-sibs was applied. Grouping methods that are based on genomic information resulted in higher accuracy of genomic estimated breeding values (GEBV) prediction compared to random grouping. The increase was ~ 1.5% for full-sibs and ~ 11.5% for paternal half-sibs. In addition, grouping methods that are based on genomic information led to lower coancestry coefficients between the top animals ranked by GEBV. Of the two proposed methods, supervised clustering was superior in terms of accuracy, computation requirements and applicability. By adding surplus genotyped offspring (more genotyped offspring than required to fill the groups), the advantage of supervised clustering increased by up to 4.5% compared to random grouping of full-sibs, and by 14.7% compared to random grouping of paternal half-sibs. This advantage also increased with increasing family sizes or decreasing genome sizes.ConclusionsThe use of genotyping information for grouping animals increases the accuracy of selection when phenotypic group records are used in genomic selection breeding programs.

GENETIC DIVERSITY AND MATING SYSTEM OF Rhizophora mangle L. (RHIZOPHORACEAE) IN NORTHERN BRAZIL REVEALED BY MICROSATELLITE ANALYSIS

ABSTRACT Rhizophora mangle L. (Rhizophoraceae) grows on aerial roots, which emerge above the water level, giving stands of this tree the characteristic “mangrove” appearance. To produce in situ and ex situ information for genetic conservation programs for this species, we investigated the genetic diversity and mating system of one R. mangle population. We sampled 30 adult trees and a total of 349 seeds in Northern Brazil. We genotyped all adult trees and seeds with four microsatellite loci. The average fixation index was -0.222 for adult trees and 0.030 for seeds. The multilocus outcrossing rate (t m =0.921) was significantly lower than unity (1.0). There was no substantial evidence of null alleles nor genotypic disequilibrium among the loci. The combined power to exclude the first parent probability was 0.921. The average coancestry coefficient (=0.180) was similar to that expected for half-sib progenies (=0.125). Thus, the number of adult trees necessary for seed collection to obtain progeny arrays with an effective size of 150 was estimated to be 62. In conclusion, this study produced important information for the management and conservation of R. mangle and will contribute to conservation and management programs for this species.

Small ad hoc versus large general training populations for genomewide selection in maize biparental crosses.

For genomewide selection in each biparental population, it is better to use a smaller ad hoc training population than a single, large training population. In genomewide selection, different types of training populations can be used for a biparental population made from homozygous parents (A and B). Our objective was to determine whether the response to selection (R) and predictive ability (rMP) in an A/B population are higher with a large training population that is used for all biparental crosses, or with a smaller ad hoc training population highly related to the A/B population. We studied 969 biparental maize (Zea mays L.) populations phenotyped at four to 12 environments. Parent-offspring marker imputation was done for 2911 single nucleotide polymorphism loci. For 27 A/B populations, training populations were constructed by pooling: (1) all prior populations with A as one parent (A/*, where * is a related inbred) and with B as one parent (*/B) [general combining ability (GCA) model]; (2) A/* or */B crosses only; (3) all */* crosses (same background model, SB); and (4) all */*, A/*, and */B crosses (SB + GCA model). The SB model training population was 450-6000% as large as the GCA model training populations, but the mean coefficient of coancestry between the training population and A/B population was lower for the SB model (0.44) than for the GCA model (0.71). The GCA model had the highest R and rMP for all traits. For yield, R was 0.22Mgha-1 with the GCA model and 0.15Mgha-1 with the SB model. We concluded that it is best to use an ad hoc training population for each A/B population.

Forest inventory and the genetic diversity of the remaining fragment of Hymenaea courbaril L.

ABSTRACT Hymenaea courbaril is a rare species in the riparian areas of the state of Sergipe, Brazil. This species is known as Brazilian cherry or Brazilian copal and it occurs in fragments of the Rainy Forest and in the transition zones between the Rainy Forest and the Caatinga Biomes. This work was carried out, in order to quantify the genetic diversity of the remaining population of Brazilian cherry, by RAPD markers. In a studied area of 100 ha in the low course of the São Francisco River, only 15 individuals were observed. The analyzed parameters were as follows: Jaccard’s genetic similarity, the number of observed alleles, the number of effective alleles, the genetic diversities of Nei, the percentages of the polymorphic loci, the genetic diversities when using the Shannon index and the coancestry coefficient. There was no correlation between the genetic distances and the geographical distances. Despite the low number of individuals, high genetic diversity was observed, a fact that contributes to the development of strategies for the conservation of the species.

Understanding genetic diversity, spatial genetic structure, and mating system through microsatellite markers for the conservation and sustainable use of Acrocomia aculeata (Jacq.) Lodd. Ex Mart.

Acrocomia aculeata is a native palm distributed widely throughout Brazil that is used in a diverse array of products from the food industry to biodiesel oil production. This study uses nine microsatellite loci to assess the genetic diversity, spatial genetic structure (SGS), and mating system of A. aculeata. A total of 200 samples were collected from four populations (Fusquinha—FU, Padre Josimo—PJ, Gleba XV-GB, and Amparo—AM), in Sao Paulo State, Brazil. We also collected fruits from 20 randomly selected seed trees in the FU population to assess mating patterns, for a total of 246 genotyped embryos. We identified a total of 103 alleles and all loci were polymorphic. The average observed heterozygosity ( $${H_o}$$ ) ranged from 0.410 (AM) to 0.531 (FU) and expected heterozygosity ( $${H_e}$$ ) ranged from 0.547 (PJ) to 0.615 (GB). The average fixation index ( $$F$$ ) ranged from 0.043 to 0.254 for FU and AM populations, respectively. The coancestry coefficient ( $${\theta _{xy}}$$ ) was significant up to 38 m in PJ the population and 71 m in AM. Individual palm outcrossing rates were predominantly high ( $${t_m}$$ = 0.985) and the paternity correlation ( $${r_{{p_{(m)}}}}$$ = 0.02) was significantly low, indicating a high probability of the occurrence of half-sibs. Compared to other palm species, the studied populations show high levels of genetic diversity. Our results confirm that A. aculeata is primarily allogamous, with no significant paternity correlation, and seeds should be harvested from at least 40 trees to ensure high levels of genetic diversity in seed collection programs.

A high level of outcrossing in the vulnerable species Prosopis rubriflora in a Chaco remnant

Prosopis rubriflora Hassl. is a tree species typically found in chaquenian areas, mainly with an arborised phytophysiognomy in the southern region of the Pantanal wetland. This species has become vulnerable in recent decades as a result of considerable increases in anthropogenic activities such as cattle breeding, and this vulnerability has also been observed in several other native species. The goal of this study was to estimate the mating system of P. rubriflora in a Chaco remnant by analysing 10 microsatellite markers. Samples were collected over 2 years (2010–213 seedlings and 2011–180 seedlings), and the results suggest that the mating system of P. rubriflora is preferably allogamous. A progeny array was predominantly composed of half-sibs (from 76 to 79%), full-sibs (from 15%) and self-half-sibs (from 6 to 9%). The outcrossing rate between related individuals was significant in 2011 but not in 2010. The average co-ancestry coefficient () ranged from 0.158 to 0.162, and the variance effective size (Ne) ranged from 3.05 to 3.13. The number of seed trees required for seed collection (m) to retain an effective size of 150 in progeny array samples was 48–49. The high levels of outcrossing of P. rubriflora appear to be related to several mechanisms that avoid selfing and due to the behaviour of native pollinators, which clearly contribute to the gene flow of the species.

Mating patterns of the gum arabic tree (Acacia senegal synonym Senegalia senegal) in two different habitats

Understanding the variation of mating patterns in disturbed habitats provide insight into the evolutionary potential of plant species and how they persist over time. However, this phenomenon is poorly understood in tropical dryland tree species. In the present study, we investigated how Acacia senegal reproduces in two different environmental contexts in Kenya. Open-pollinated progeny arrays of 10 maternal trees from each environmental context were genotyped using 12 nuclear microsatellite markers. Overall, A. senegal displayed a predominantly allogamous mating pattern. However, higher multilocus outcrossing rate (tm) was found in Lake Bogoria (tm = 1.00) than in Kampi ya Moto population (tm = 0.949). Higher biparental inbreeding (t m − t s = 0.116) and correlation of outcrossed paternity (rp = 0.329) was found in Kampi ya Moto than in Lake Bogoria population (t m − t s = 0.074, rp = 0.055), showing the occurrence of mating among relatives. Coefficient of coancestry (Θ = 0.208) showed that full-sibs constitute about 21% of the offspring in Kampi ya Moto population compared to about 14% (Θ = 0.136) in Lake Bogoria population. The results demonstrate that low adult tree density of A. senegal may be promoting seed production through consanguineous mating and suggest that man-made disturbance can affect mating patterns of the species. Despite these mating differences, trees from both populations can contribute as seed source for conservational plans, and to support effective genetic conservation and artificial regeneration programs of A. senegal. We suggest collection of seeds from at least 42 and 63 trees in Lake Bogoria and Kampi ya Moto populations, respectively, to retain a progeny array with a total effective population size of 150.

Diversidad haplotípica del exón XII del gen dopamina β-hidroxilasa en tres razas bovinas

Polymorphisms in the dopamine β-hydroxylase gene (DBH) have been associated with temperament in cattle. In 16 animals of Colombian creole breed Blanco Orejinegro (BON), 20 Brahman (BRA) and 16 fighting bulls (GLI), polymorphisms of exon XII of the DBH gene were evaluated by sequencing. 13 haplotypes were found, 6 in BON, 9 and 2 in BRA and GLI respectively. Haplotype H2 was the most frequent in the whole population (0,615) and it was found in all breeds. Haplotypes H6 and H9 were shared between BON-BRA and BRA-GLI, respectively. The greatest value of genetic(DG: 0.915 ± 0.04) and nucleotide (DN: 0.011 ± 0.006) diversity, was found in BRA, followed by BON (DG: 0.700 ± 0.12; DN: 0.008 ± 0.004) and GLI (DG: 0.350 ± 0.14;DN: 0.0011 ± 0.001). The D-Tajima test was greater than zero, but not significant (P&gt; 0.05) in BON and BRA, GLI presented a value of −1.92 (P &lt; 0.05). The analysis of molecular variance showed a variation between the breeds of 23.9% and a poblacional structure (FST) of 0.23 (P &lt; 0.001). The highest values of the coancestry coefficient were presented between GLI and BRA (0.52) and between GLI and BON (0.22). It is concluded that the GLI race has low diversity in the DBH gene compared to BON and BRA, that there are effects of neutral selection in BON and BRA breeds, whereas, in the GLI and not in favor of temperament.

Inbreeding depression from selfing and mating between relatives in the Neotropical tree Cariniana legalis Mart. Kuntze

Selfing or mating between related individuals in self-compatible hermaphroditic tree species may lead to inbreeding depression (ID) due to homozygosis in recessive, identical by descent alleles. In general, studies of ID in tree species have been based on comparisons of selfed individuals (produced by controlled pollination) with outcrossed individuals for quantitative traits in progeny tests. However, this approach requires a long time to quantify the extent of ID. Thus, we used an approach based on genetic markers to estimate coancestry coefficients between assigned parents from paternity analysis in two populations of the Neotropical tree Cariniana legalis. Using this method, we were able to determine which seedlings in a nursery trial originated from; (i) outcrossing between un-related trees, (ii) mating between related trees and (iii) selfing. We detected a low selfing rate (<10 %), but a substantial quantity of seedlings from mating between related parents (minimum of 35.7 %). In general, the outcrossed seedlings from unrelated parents exhibited significantly greater genetic diversity than those resulting from selfing and mating among relatives. The extent of ID varied among traits and populations. Outcrossed seedlings originating from unrelated trees generally showed greater survival than seedlings originating from selfing and related parents. Inbreeding depression was greater in the selfed seedlings than in those from mating among related parents. The results are discussed in terms of implications for genetic conservation, breeding and environmental restoration using the species.

Genomic Inbreeding and Relatedness in Wild Panda Populations

Inbreeding and relatedness in wild panda populations are important parameters for panda conservation. Habitat loss and fragmentation are expected to increase inbreeding but the actual inbreeding levels in natural panda habitats were unknown. Using 150,025 SNPs and 14,926 SNPs selected from published whole-genome sequences, we estimated genomic inbreeding coefficients and relatedness of 49 pandas including 34 wild pandas sampled from six habitats. Qinling and Liangshan pandas had the highest levels of inbreeding and relatedness measured by genomic inbreeding and coancestry coefficients, whereas the inbreeding levels in Qionglai and Minshan were 28–45% of those in Qinling and Liangshan. Genomic coancestry coefficients between pandas from different habitats showed that panda populations from the four largest habitats, Minshan, Qionglai, Qinling and Liangshan, were genetically unrelated. Pandas between these four habitats on average shared 66.0–69.1% common alleles and 45.6–48.6% common genotypes, whereas pandas within each habitat shared 71.8–77.0% common alleles and 51.7–60.4% common genotypes. Pandas in the smaller populations of Qinling and Liangshan were more similarly to each other than pandas in the larger populations of Qionglai and Minshan according to three genomic similarity measures. Panda genetic differentiation between these habitats was positively related to their geographical distances. Most pandas separated by 200 kilometers or more shared no common ancestral alleles. The results provided a genomic quantification of the actual levels of inbreeding and relatedness among pandas in their natural habitats, provided genomic confirmation of the relationship between genetic diversity and geographical distances, and provided genomic evidence to the urgency of habitat protection.

GlobalFiler® Express DNA amplification kit in South Africa: Extracting the past from the present

In this study, the GlobalFiler® Express amplification kit was evaluated for forensic use in 541 South African individuals belonging to the Afrikaaner, amaXhosa,11Prefixes ama- and isi- are used within Bantu populations to indicate population group and language respectively. amaZulu,1 Asian Indian and Coloured population groups.Allelic frequencies, genetic diversity parameters and forensic informative metrics were calculated for each population. A total of 301 alleles were observed ranging between 5 and 44.2 repeat units, 43 were rarely observed partial repeats and seven were novel. The combined match probability (CMP) ranged from 2.21×10−26 (Coloured) to 5.21×10−25 (AmaZulu), and the combined power of exclusion (CPE) 0.9999999978 (Afrikaaner) to 0.99999999979 (AmaZulu) respectively. No significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction.Strong evidence of genetic structure was detected using the coancestry coefficient θ, Analysis of Molecular Variance (AMOVA) and an unsupervised Bayesian clustering method (STRUCTURE). The efficiency of assignment of individuals to population groups was evaluated by applying likelihood ratios with WHICHRUN, and the individual ancestral membership probabilities inferred by STRUCTURE. Likelihood ratios performed the best in the assignment of individuals to population groups. Signs of positive selection were detected for TH01 and D13S317 and purifying/balancing selection for locus SE33. These three loci also displayed the largest informativeness for assignment (In) values.The results of this study supports the use of the GlobalFiler® STR profiling kit for forensic applications in South Africa with the additional capability to predict ethnicity or continental origin of a random sample.

The use of coancestry based on shared segments for maintaining genetic diversity.

We have evaluated the use of genomic coancestry coefficients based on shared segments for the maintenance of genetic diversity through optimal contributions methodology for populations of three different Austrian cattle breeds. This coancestry measure has been compared with the genomic coancestry coefficient calculated on a SNP-by-SNP basis and with pedigree-based coancestry. The regressions of the shared segments coancestry on the other two coefficients suggest that the former mainly reflect Identity By Descent but with the advantage over pedigree-based coancestry of providing the realized Identity By Descent rather than an expectation. The effective population size estimated from the rate of coancestry based on shared segments was very similar to those obtained with the other coefficients and of small magnitude (from 26.24 to 111.90). This result highlights the importance of implementing active management strategies to control the increase of inbreeding and the loss of genetic diversity in livestock breeds, even when the population size is reasonably large. One problem for the implementation of coancestry based on shared segments is the need of estimating the gametic phases of the SNPs which, given the techniques used to obtain the genotypes, are a priori unknown. This study shows, through computer simulations, that using estimates of gametic phases for computing coancestry based on shared segments does not lead to a significant loss in the diversity maintained. This has been shown to be true even when the size of the population is very small as it is usually the case in populations subjected to conservation programmes.

Genetic Characterization of the North Carolina State University Maize Lines

ABSTRACTSince 1980, 150 North Carolina State University (NCSU) maize (Zea mays L.) inbreds have been developed and released on the basis of superior performance for topcross yield and other traits of agronomic importance. During this time, there has been great emphasis placed on breeding with exotic germplasm, with 86 NCSU inbreds having at least 50% exotic parentage and 40 of those having all‐tropical parentage. Maize germplasm released by NCSU represents a potentially useful resource for increasing maize diversity and performance in the United States. The objectives of this study were to characterize the genetic relationships among inbreds released from this unique breeding program and to compare them genetically with inbreds from other public and private breeding programs. The NCSU maize inbreds can be classified into five germplasm pools: Lancaster, Temperate‐adapted all tropical (TAAT), Lancaster × Tropical, Stiff Stalk, and Southern non‐Stiff Stalk; detailed analysis of pedigree records and molecular marker genotypes reveals additional substructure within each of these pools. There is general agreement among the four cluster analyses performed, three using single nucleotide polymorphism (SNP) data and one using pedigree‐derived coefficients of coancestry. We introduce a novel application of Procrustes analysis to identify disagreements between pedigree and marker similarities. The NCSU maize breeding germplasm includes diverse genetic backgrounds, as evidenced by the number of unique alleles compared with publically available inbreds from both public and off‐protection, private‐sector sources.

The use of genomic information can enhance the efficiency of conservation programs

The development of genomic tools allows for more accurate estimates of genetic relationships between animals (genomic coancestry coefficients) than those obtained with pedigree data (pedigree-based coancestry coefficients) and thus permit better management of genetic diversity. There are different issues relevant to conservation programs that could benefit from the use of genomic data. These include establishing synthetic ex situ populations, maintaining genetic diversity, preserving original genetic structures, and eliminating exogenous genetic information. The use of dense panels of single-nucleotide polymorphism (SNPs) in strategies proposed to deal with all these issues improves the general performance of conservation programs in both farm and wild animal populations.

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient (F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH (FROH) in three local dairy cattle breeds. FROH values were compared with F estimated from the genomic relationship matrix (FGRM), based on the difference between observed v. expected number of homozygous genotypes (FHOM) and the genomic homozygosity of individual i (FMOL i). The molecular coancestry coefficient (fMOL ij) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of FROH, whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between FHOM and FROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among FROH and other estimated F coefficients were generally lower ranged from 0.45 (FMOL i−FROH) in Cinisara to 0.17 (FGRM−FROH) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.

Contribution of microsatellites markers in the clarification of the origin, genetic risk factors, and implications for conservation of Tunisian native sheep breeds.

The genetic diversity and genetic relationship of the two main groups of African sheep, thin-tailed and fat-tailed sheep, represented by the indigenous Tunisian sheep breeds "Barbarine" (BAR, fat-tailed) and "Queue Fine de l'Ouest" (QFO, thin-tailed) were investigated. The genotypes of 110 animals belonging to these two breeds and their crossbreed (CRO) were assessed using 17 microsatellite markers. The results showed high levels of genetic diversity and a total of 256 alleles were identified in the whole population. The mean values of observed and expected heterozygosity were 0.719 and 0.789, respectively, and the mean allelic richness estimate was 10.89. The average FIS (0.112) and FIT (0.118) values over all loci indicated a notable level of inbreeding within the whole population. However, the FST value (0.007) showed a low level of genetic differentiation between these two native breeds. The high level of both gene flow and molecular coancestry coefficient detected between the two breeds and their CRO revealed an old miscegenation between the BAR and QFO breeds. The clustering analysis performed with the STRUCTURE software confirmed gene flow between these two breeds. Results arising from this study provide evidence regarding the genetic structure and variability of the two main local sheep breeds, and the implications of their actual management, which indicates the need for an urgent conservation strategy in order to prevent significant gene flow and preserve the remaining breed specificity for future generations.

Individual, fruit, and annual variation in correlated mating in a Genipa americana population

Abstract In this paper, we use six microsatellite loci to examine a spatially isolated population of Genipa americana in relation to mating system variation at the level of individual and among and within fruits, over two reproductive events. For our analysis, we sampled hierarchically among and within fruits open-pollinated seeds collected from 13 seed trees during the reproductive event in 2010 and 12 seed trees in 2011. The rate of mating among relatives (1-ts) was significantly greater than zero and different between the investigated reproductive events, indicating that some seeds are inbred. The estimate of fixation index (Fo) was significantly higher than zero for seeds from both reproductive events (2010: Fo = 0.258; 2011: Fo = 0.294), confirming that seeds present inbreeding, probably originated from mating among full-sibs. The multilocus paternity correlation within fruits (rp(w)) and among fruits (rp(a)) varied among seed trees and reproductive events. The rp(w) was significantly higher than rp(a) in both reproductive events, suggesting that it is more likely to find full-sibs within fruits (2010: 36.4%; 2011: 72.4%), than among fruits (2010: 18.9%; 2011: 12.8%). Due to the presence of inbreeding, mating among relatives and correlated mating, the within families coancestry coefficient (Θ) was higher and the variance effective size (Ne) lower than expected in open-pollinated families from panmictic populations (Θ = 0.125, Ne = 4). In practical terms for conservation programs, our results show the need to collect seeds from at least 60 seed trees to retain progeny arrays with a total effective size of 150.