Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive,non‐random SNP heterozygosity

Local breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350‐year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high‐density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62–90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r² = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.     

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 (F_ROH) in three local dairy cattle breeds. F_ROH values were compared with F estimated from the genomic relationship matrix (F_GRM), based on the difference between observed v. expected number of homozygous genotypes (F_HOM) and the genomic homozygosity of individual i (F_{MOL i}). The molecular coancestry coefficient (f_{MOL 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 F_ROH, 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 F_HOM and F_ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F_ROH and other estimated F coefficients were generally lower ranged from 0.45 (F_{MOL i}−F_ROH) in Cinisara to 0.17 (F_GRM−F_ROH) 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.     

Multi-step metabolic activation of benzene. Effect of superoxide dismutase on covalent binding to microsomal macromolecules,and identification of glutathione conjugates using high pressure liquid chromatography and field desorption mass spectrometry

Incubation of [¹⁴C]benzene or [¹⁴C]phenol with liver microsomes from untreated rats, in the presence of a NADPH-generating system, gave rise to irreversible binding of metabolites to microsomal macromolecules. For both substrates this binding was inhibited by more than 50% by addition of superoxide dismutase to the incubation mixtures. The decrease in binding was compensated for by accumulation of [¹⁴C]hydroquinone, indicating superoxide-mediated oxidation of hydroquinone as one step in the activation of benzene to metabolites binding to microsomal macromolecules. Since our previous work had shown that binding occurred mainly with protein rather than ribonucleic acid and was virtually completely prevented by glutathione, suggesting identity of metabolite(s) responsible for binding to protein and glutathione, a conjugate was chemically prepared from p-benzoquinone and reduced glutathione (GSH) and identified by field desorption mass spectrometry (FDMS) as 2-(S-glutathionyl) hydroquinone. Microsomal incubations, containing an NADPH-generating system, with benzene, phenol, hydroquinone or p-benzoquinone in the presence of [³H]glutathione or, alternatively, with [¹⁴C]benzene or [¹⁴C]phenol in the presence of unlabeled glutathione, were performed. All of these incubations gave rise to a peak of radioactivity eluting from the high pressure liquid chromatograph (HPLC) at a retention time identical to that of the chemically prepared 2-(S-glutathionyl) hydroquinone, whilst microsomal incubation of catechol in the presence of [³H]glutathione led to a conjugate with a very different retention time which was not observed after incubation of benzene or phenol. The microsomal metabolites of p-benzoquinone, hydroquinone and phenol thus eluting from the HPLC were further identified as the 2-(S-glutathionyl) hydroquinone by field desorption mass spectrometry. The glutathione adduct formed from benzene during microsomal activation eluted from HPLC with the same retention time and its mass spectrum also contained the molecular ion (MH⁺) (m/e 416) of this conjugate as an intense peak, but the fragmentation patterns did not allow definite assignments probably due to the considerably smaller amounts of ultimate reactive metabolites formed from this pre-precursor and thus relatively larger amounts of impurities.The results indicate that rat liver microsomes activate benzene via phenol and hydroquinone to p-benzosemiquinone and/or p-benzoquinone as quantitatively important reactive metabolites.     

Palynology and intergeneric relationships in subtribe Hyoseridinae (CompositaerLactuceae)

Ceratopteris pteridoides is an inbreeding species. Intralocus homozygosity is deduced from the almost total absence of genetic load (recessive deleterious and lethal genes) in sporophytes from natural populations, and from gametangial sequences which indicate intragametophytic selfing. This mating system and the profound capacity of the species for vegetative reproduction, coupled with the small size and geographical isolation of many populations, strongly support the hypothesis of individual homozygosity. However, polymorphism is exhibited both within and between populations in specific, genetically mediated, gametophytic characteristics. The population genetic structure of C. pteridoides is similar to other inbreeding species.     

No inbreeding depression but increased sexual investment in highly inbred ant colonies

Inbreeding can lead to the expression of deleterious recessive alleles and to a subsequent fitness reduction. In Hymenoptera, deleterious alleles are purged in haploid males moderating inbreeding costs. However, in these haplodiploid species, inbreeding can result in the production of sterile diploid males. We investigated the effects of inbreeding on the individual and colony level in field colonies of the highly inbred ant Hypoponera opacior. In this species, outbreeding winged sexuals and nest‐mating wingless sexuals mate during two separate reproductive periods. We show that regular sib‐matings lead to high levels of homozygosity and the occasional production of diploid males, which sporadically sire triploid offspring. On the individual level, inbreeding was associated with an increased body size in workers. On the colony level, we found no evidence for inbreeding depression as productivity was unaffected by the level of homozygosity. Instead, inbred colonies altered their allocation strategies by investing more resources into sexuals than into workers. This shift towards sexual production was due to an increased investment in both males and queens, which was particularly pronounced in the dispersive generation. The absence of inbreeding depression combined with increased reproductive investment, especially in outbreeding sexuals, suggests that these ants have evolved active strategies to regulate the extent and effects of frequent inbreeding.     

What should we weigh to estimate heterozygosity,alleles or loci?

The interest to study the effects of inbreeding in natural populations has increased in the last years. Several microsatellite-derived metrics have recently been developed to infer inbreeding from multilocus heterozygosity data without requiring detailed pedigrees that are difficult to obtain in open populations. Internal relatedness (IR) is currently the most widespread used index and its main attribute is that allele frequency is incorporated into the measure. However, IR underestimates heterozygosity of individuals carrying rare alleles. For example, descendants of immigrants paired with natives (normally more outbred) bearing novel or rare alleles would be considered more homozygous than descendants of native parents. Thus, the analogy between homozygosity and inbreeding that generally is carried out would have no logic in those cases. We propose an alternative index, homozygosity by loci (HL) that avoids such problems by weighing the contribution of each locus to the homozygosity index depending on their allelic variability. Under a wide range of simulated scenarios, we found that our index (HL) correlated better than both IR and uncorrected homozygosity (H(O)), measured as proportion of homozygous loci) with genome-wide homozygosity and inbreeding coefficients in open populations. In these populations, which are likely to prevail in nature, the use of HL instead of IR reduced considerably the sample sizes required to achieve a given statistical power. This is likely to have important consequences on the ability to detect heterozygosity fitness correlations assuming the relationship between genome-wide heterozygosity and fitness traits.     

Genetic signatures of pre-expansion bottleneck in the Choctaw population of Oklahoma

Previous research showed that the Choctaw Indians of Oklahoma exhibit considerable linkage disequilibria (LD) in a number of regions of the genome that has allowed genetic fine mapping for potential susceptibility genes for the autoimmune connective tissue disease scleroderma, or systemic sclerosis (SSc). In principle, such enhanced background LD in the Choctaws could be caused by population bottleneck event(s) followed by recent population expansion. This investigation utilizes genome-scan data on 175 dinucleotide loci from 76 Choctaw individuals to seek genetic evidence of the demographic history of the Choctaw Nation. Of the 175 loci examined, 105 are in Hardy-Weinberg equilibrium. The average unbiased homozygosity over the 105 loci for the Choctaws (29.3%) is significantly higher than that in the European descent group (20.9%); and when adjusted for sample-size differences, the Choctaw also exhibit a significantly smaller number of segregating alleles (6.65 vs. 8.14) at these loci. Both of these observations are consistent with the trend expected in an isolated population. Comparison of the allele size variance and gene diversity yields an imbalance index (lnbeta) of 0.811 in the Choctaw. Of the 105 loci examined, 93 exhibit excess expected homozygosity in comparison to the expectations of a stepwise mutation model in a population of constant size. Taken together, these observations are consistent with a signature of the recent population size expansion of the Choctaws, preceded by bottleneck event(s).     

Does homozygosity contribute to the asymmetry of common white leg markings in the Arabian horse?

Common white and facial markings have a multifactorial mode of inheritance inEquus caballus and result from the absence of melanocytes in the unpigmented areas. Directional asymmetry and fluctuating asymmetry apparently account for the total asymmetry of common white leg markings. Using computerized records obtained from the Arabian Horse Registry of America, Inc., and the International Arabian Horse Association, studies were carried out to determine if homozygosity increases the total asymmetry in common white leg markings by presumably promoting fluctuating asymmetry. The results were as follows: (1) Arabian horses that are symmetrical and asymmetrical for common white leg markings have similar distributions of inbreeding coefficients; (2) Arabian and half-Arabian horses have similar concordance values, in general, for specific white markings in both their forelegs and hind legs. It is concluded that homozygosity does not contribute to the total asymmetry of common white leg markings in the Arabian horse.