Whole-Genome Resequencing Reveals Genetic Structure and Introgression in Chinese Pudong White Pigs

Background: Pudong white (PDW) pigs originating from Shanghai, are the only Chinese indigenous pigs with white coat color except Rongchang (RC) pigs. However, there is limited information about its overall genetic structure, relationship with other breeds especially the East Chinese (ECN) and European pig due to the white coat of PDW. Whole-genome sequencing provides the effective approach to get the unique information of genome. The high-depth whole-genome sequencing data of 26 global pig breeds, European Wild boars (EWB), Chinese Wild boars (CWB) and out group (OUT) were implemented to detect the genetic structure, signature of selection and potential exotic introgression in PDW pigs.Results: The PDW pigs belonging to ECN pigs based on genetic relationship, and harbor lower genetic diversity and higher inbreeding coefficient compared to other Chinese indigenous pigs. Both the f3 and D-statistics analysis demonstrated that PDW pigs shared apparent alleles with Large White (LW) pigs. Then, two statistics, haplotype heat-map, copy number variation (CNV) and rIBD analysis further revealed that PDW pigs carry the same KIT genotype and share haplotypes at PARG-MARCHF8 locus with LW pigs, suggesting that the lineage of European (EUR) pigs in PDW originated from LW pigs. After detecting the KIT mutations in different pig breeds, PDW was confirmed to be same with LW at DUP1, DUP2 and the splicing mutation on intron 17 of KIT which determine the white coat color phenotype in European white pigs.Conclusions: This study shows that ECN pigs crossed with LW pigs after introduced to China about 110-164 years ago, where the offspring carrying KIT genotype that caused white coat color phenotype, and then were selected due to the rare white coat color in Chinese indigenous pigs, gradually forming PDW pig breed. To our knowledge, this study gives the first thorough description of the genetic structure of PDW pig via whole-genome resequencing data. This study not only advances our understanding of genetic structure, molecular phylogeny, and molecular origin of PDW pigs, but also provides a basis for facilitating the development of a national project for the conservation and utilization of this unique Chinese local population.

Sexual dimorphism of mandibular measures from computed tomographies

ABSTRACT Objetive: The objective of this study was to analyze mandibular measurements obtained from 225 computed tomography scans of the Osteological and CT Biobanks of Faculdade de Odontologia de Piracicaba Universidade Estadual de Campinas, aiming to verify the existence of a relationship between these measures and sexual dimorphism and ancestry. Methods: We sought to establish a mathematical model capable of estimating sex and ancestry. Of these scans, 126 were male, 94 were female and 5 were unidentified, aged 15 to 100 years, and ancestry known for the skin color phenotype (white, black, brown and yellow). Measurements were made between the following points: right lateral condylion and left lateral condylion; right lateral condylion and pogonion; left lateral condylion and pogonion; mesial border of right mental foramen and mesial border of left mental foramen. The area delimited by the triangle formed by the measurements between right lateral condylion and left lateral condylion was also analyzed; right lateral condylion and pogonion; and left lateral condylion and pogonion. Student t test for homogeneous variances showed that there was statistical difference in the means as a function of sex, except for the area measure, which was not used in the model. Results: It was possible to establish a mathematical model with accuracy of 69.2%. There was no statistical difference in the averages as a function of ancestry. Conclusion: It is concluded that the measures investigated help in the process of estimating sex, but were not adequate to estimate ancestry. The proposed methodology should be expanded to other population groups so that it can be improved.

RrGT2, A Key Gene Associated with Anthocyanin Biosynthesis in Rosa rugosa, Was Identified Via Virus-Induced Gene Silencing and Overexpression

In this study, a gene with a full-length cDNA of 1422 bp encoding 473 amino acids, designated RrGT2, was isolated from R. rugosa ‘Zizhi’ and then functionally characterized. RrGT2 transcripts were detected in various tissues and were proved that their expression patterns corresponded with anthocyanins accumulation. Functional verification of RrGT2 in R. rugosa was performed via VIGS. When RrGT2 was silenced, the Rosa plants displayed a pale petal color phenotype. The detection results showed that the expression of RrGT2 was significantly downregulated, which was consistent with the decrease of all anthocyanins; while the expression of six key upstream structural genes was normal. Additionally, the in vivo function of RrGT2 was investigated via its overexpression in tobacco. In transgenic tobacco plants expressing RrGT2, anthocyanin accumulation was induced in the flowers, indicating that RrGT2 could encode a functional GT protein for anthocyanin biosynthesis and could function in other species. The application of VIGS in transgenic tobacco resulted in the treated tobacco plants presenting flowers whose phenotypes were lighter in color than those of normal plants. These results also validated and affirmed previous conclusions. Therefore, we speculated that glycosylation of RrGT2 plays a crucial role in anthocyanin biosynthesis in R. rugosa.

The mutations within MC1R, TYRP1, ASIP genes and their effects on phenotypes of coat color in wild pigs (Sus scrofa ussuricus )

Animal coloration is a powerful model for studying the genetic mechanisms that determine animal phenotypes. But, there has not been comprehensive characterization of the molecular basis of the complex patterns of coat color phenotype variation in wild boars. This study results indicated that the wild-type allele E+ of the MC1R gene was a dominant allele in wild boars and was not responsible for black, brown or other coat color phenotypes. A novel mutation c.695 T > C was identified in the 3¢-UTR of the ASIP gene. The association analysis showed that the C mutation allele was highly significantly associated with wild-type coat colors between wild boars and Western pig breeds (P=1.35E-33). A non-synonymous g.2254 G > A substitution was found in exon 2 of the TYRP1 gene (p.143His>Arg). The association analysis demonstrated that the G mutation allele was also significantly associated with wild-type coat colors between wild boars and Western pig breeds (P = 5.09E-10). In short, a few mutation sites in MC1R, ASIP, and TYRP1 genes were identified and surveyed several polymorphisms molecular variations in Chinese wild boars. In our identified mutations have caused the morphological diversity in wild boars, but did not influence coat color phenotype variation in some domesticated pig breeds. The conclusion was obtained that some mutations in color-associated genes were associated with wild-type coat colors in wild boar population, and that similar coat colorations observed in domesticated pig and wild boars can be the product of underlying differences in the genetic basis of color variants.

Occurrence of leucism in Eira barbara (Carnivora, Mustelidae) in Brazil

The occurrence of anomalous coloration (albinism, leucism and melanism) in mammals is a rare phenomenon in nature, but this phenomenon has been reported for several species of mammals. In this study, we report on the occurrence of leucism in Eira barbara by examining three road-killed individuals and two sightings of live animals in Reserva Particular do Patrimônio Natural Santuário do Caraça, southeastern Brazil. In addition, we examined tayra specimens housed in mammal collections from Brazil and USA. The animals found dead and those sighted had a whitish yellow fur on the body and head, resulting in lighter coloration than the coloring pattern commonly observed in tayras. Despite these lighter color pattern, the specimens showed parts of soft tissue, such as iris and the skin, with pigmentation very similar to that present in individuals with the typical color pattern. This set of factors indicates the specimens recorded were in fact leucistic and not albino. Among the specimens examined in the scientific collections, we found nine individuals from different localities that presented the whitish yellow color pattern. Some studies attribute the higher frequency of cases of leucism due to small populations and / or with some mechanism of reproductive isolation. Thus, analysis of the genetic variability of populations containing individuals with such characteristics should be considered. On the other hand, the occurrence of polymorphic color phenotype in tayras indicates that hypotheses related to the fixation of recessive characteristics, or on possible environmental adaptive advantages of these phenotypes can be tested.