Sex-dependent colonic microbiota modulation by hazelnut (Corylus avellana L.) dietary fiber.

Although many efforts have been made to characterize the functional properties of hazelnut constituents (mainly its oil, protein, and phenolics), those of its dietary fiber (DF) have not been elucidated yet. Here, we aimed to investigate the impact of DF of natural and roasted hazelnuts, and hazelnut skin on the colonic microbiota in vivo (C57BL/6J mouse models) by determining their composition through 16S rRNA sequencing and microbial short-chain fatty acids (SCFAs) using gas chromatography. Our results revealed that hazelnut DF generally showed an acetogenic effect in male mice, whereas the same trend was not observed in the female counterparts. The 16S rRNA sequencing results showed that hazelnut DF, especially that of natural hazelnuts, increased the relative abundances of Lactobacillus-related OTUs that have probiotic potential. LEfSe analysis indicated that, for female mice, Lachnospiraceae, Prevotella, Ruminococcaceae, and Lactobacillus were found to be discriminators for DF of natural hazelnuts, roasted hazelnuts, hazelnut skin, and control, respectively, whereas Bacteroides, Lactobacillus, Prevotella, and Lactococcus were the discriminators for the male counterparts, respectively. This study clearly indicates that, although the roasting process slightly alters the functionalities, hazelnut DF favors beneficial microbes and stimulates beneficial microbial metabolites in the colon in a sex-dependent way, which could be a contributing factor to the health-promoting effects of hazelnuts. Furthermore, hazelnut skin, a byproduct of the hazelnut industry, was found to have potential to be utilized to produce functional DF targeting colonic health.

Runs of homozygosity in Swiss goats reveal genetic changes associated with domestication and modern selection.

BACKGROUND: The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic single nucleotide variants (SNVs) were used for the identification of runs of homozygosity (ROH) and the detection of ROH islands. RESULTS: Across the 226 caprine genomes from 11 populations, we detected 344 ROH islands that harbor 1220 annotated genes. We compared the ROH islands between the modern breeds and the Bezoar goats. As a proof of principle, we confirmed a signature of selection, which contains the ASIP gene that controls several breed-specific coat color patterns. In two other ROH islands, we identified two missense variants, STC1:p.Lys139Arg and TSHR:p.Ala239Thr, which might represent causative functional variants for domestication signatures. CONCLUSIONS: We have shown that the information from ROH islands using WGS data is suitable for the analysis of signatures of selection and allowed the detection of protein coding variants that may have conferred beneficial phenotypes during goat domestication. We hypothesize that the TSHR:p.Ala239Thr variant may have played a role in changing the seasonality of reproduction in modern domesticated goats. The exact functional significance of the STC1:p.Lys139Arg variant remains unclear and requires further investigation. Nonetheless, STC1 might represent a new domestication gene affecting relevant traits such as body size and/or milk yield in goats.

Selection signatures in goats reveal copy number variants underlying breed-defining coat color phenotypes.

Domestication and human selection have formed diverse goat breeds with characteristic phenotypes. This process correlated with the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity, so called selection signatures or selective sweeps. Using whole genome sequencing of DNA pools (pool-seq) from 20 genetically diverse modern goat breeds and bezoars, we identified 2,239 putative selection signatures. In two Pakistani goat breeds, Pak Angora and Barbari, we found selection signatures in a region harboring KIT, a gene involved in melanoblast development, migration, and survival. The search for candidate causative variants responsible for these selective sweeps revealed two different copy number variants (CNVs) downstream of KIT that were exclusively present in white Pak Angora and white-spotted Barbari goats. Several Swiss goat breeds selected for specific coat colors showed selection signatures at the ASIP locus encoding the agouti signaling protein. Analysis of these selective sweeps revealed four different CNVs associated with the white or tan (AWt), Swiss markings (Asm), badgerface (Ab), and the newly proposed peacock (Apc) allele. RNA-seq analyses on skin samples from goats with the different CNV alleles suggest that the identified structural variants lead to an altered expression of ASIP between eumelanistic and pheomelanistic body areas. Our study yields novel insights into the genetic control of pigmentation by identifying six functionally relevant CNVs. It illustrates how structural changes of the genome have contributed to phenotypic evolution in domestic goats.

Genetic Diversity of Eight Domestic Goat Populations Raised in Turkey.

The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P < 0.001) pairwise F ST values of each pair of breeds. Exceptionally, F ST values calculated for Honamli and Hair breeds were statistically nonsignificant (P > 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers.

Condition-dependent mate choice and a reproductive disadvantage for MHC-divergent male tiger salamanders.

Major histocompatibility complex (MHC) alleles likely have adaptive value because of overdominance, in which case MHC heterozygous individuals have increased fitness relative to homozygotes. Because of this potential benefit, the evolution of sexual reproduction between MHC-divergent individuals (i.e. negative assortative mating, NAM) may be favoured. However, the strongest evidence for MHC-based NAM comes from inbred animals, and context-dependent mating preferences have rarely been evaluated although they often occur in nature. We assessed the extent MHC-based mating preferences among wild tiger salamanders (Ambystoma tigrinum) using multiple molecular approaches. We genotyped 102 adults and 864 larvae from 36 breeding trials at both microsatellite and MHC loci. Parentage analysis revealed that reproductive success among males was positively associated with increased tail length and that with respect to the focal female, MHC-similar males sired a significantly higher number of offspring than more dissimilar males. This trend was consistent, even under context-dependent scenarios that favour traditional MHC-based NAM. These results suggest that the most MHC-divergent males may be at a reproductive disadvantage in pairwise breeding trials. Our data add to a growing body of evidence that suggests where it exists, MHC-based choice is probably dynamic and mediated by many factors that vary in the wild, notably signals from other indicator traits and by the quality and quantity of potential mates.

Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci.

Microsatellites are commonly used for mapping and population genetics because of their high heterozygosities and allelic variability (i.e., polymorphism). Microsatellite markers are generally more polymorphic than other types of molecular markers such as allozymes or SNPs because the insertions/deletions that give rise to microsatellite variability are relatively common compared to nucleotide substitutions. Nevertheless, direct evidence of microsatellite mutation rates (MMRs) is lacking in most vertebrate groups despite the importance of such estimates to key population parameters (e.g., genetic differentiation or theta = 4N (e)micro). Herein, we present empirical data on MMRs in eastern tiger salamanders (Ambystoma tigrinum tigrinum). We conducted captive breeding trials and genotyped over 1,000 offspring at a suite of microsatellite loci. These data on 7,906 allele transfers provide the first direct estimates of MMRs in amphibians, and they illustrate that MMRs can vary by more than an order of magnitude across loci within a given species (one locus had ten mutations whereas the others had none).

Polymorphism of alternative splicing of major histocompatibility complex transcripts in wild tiger salamanders.

Alternative splicing (AS) of mRNA transcripts is increasingly recognized as a source of transcriptome diversity. To date, most AS studies have focused either on comparisons across taxa or on intragenomic comparisons across gene families. We generated a novel data set that represents one of the first population genetic comparisons of AS across individuals. In ambystomatid salamanders, AS of the major histocompatibility complex (MHC) class IIbeta gene (Amti-DAB) produces two transcripts, one full-length and one truncated. The full-length transcript is functional, but the truncated transcript is missing the critical beta1 domain that forms half of the peptide binding region in the intact MHC class II molecule. We captured wild salamander larvae (Ambystoma tigrinum tigrinum) and genotyped them at Amti-DAB via DNA sequencing. From these same larvae, we extracted RNA from gill and spleen and evaluated the relative expression level of Amti-DAB in each tissue. Across individuals, 21% of the transcripts were truncated (alternatively spliced), and the absolute level of alternative transcript expression was higher in gill. The high level of nucleotide variation among seven Amti-DAB alleles provides the ability to detect substitutions (or linked DNA polymorphisms) that might have influenced AS. The data reveal no correlation between AS and haplotype, allele, or zygosity. However, indirect evidence (comparative expression patterns across 3 million years of evolution) suggests that the truncated Amti-DAB transcript may be functional and maintained by natural selection.