The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia

Ancient DNA identifies elite equids in Bronze Age Mesopotamia as the first human-bred hybrid animals, the enigmatic kungas.

Morphological and microsatellite DNA diversity of Djallonké sheep in Guinea-Bissau

Background The present study aimed at characterizing the Djallonké Sheep (DS), the only local sheep breed raised in Guinea-Bissau. A total of 200 animals were sampled from four regions (Bafatá, Gabú, Oio and Cacheu) and described using 7 visual criteria and 8 measurements. These parameters have been studied by principal components analysis. The genetic diversity and population structure of 92 unrelated animals were studied using 12 microsatellite markers. Results The values of quantitative characters in the Bafatá region were significantly higher than those obtained in the other three regions. A phenotypic diversity of the DS population was observed and three genetic types distinguished: animals with “large traits” in the region of Bafatá, animals with “intermediate traits” in the regions of Gabú and Oio and animals with “small traits” in the Cacheu region. The hair coat colors are dominated by the white color, the shape of the facial head profile is mainly convex and the ears “erected horizontally”. Most of the morphobiometric characteristics were significantly influenced by the “region” and “sex of animals”. The average Polymorphism Information Content (PIC) of 0.65 ± 0.11 supports the use of markers in genetic characterization. Gabú subpopulation had the highest genetic diversity measures (He = 0.716 ± 0.089) while Cacheu DS subpopulation presented the smallest (He = 0.651 ± 0.157). Only Gabú and Bafatá subpopulations presented significant heterozygote deficiency across all loci indicating possible significant inbreeding. Mean values for FIT,FST, FIS and GST statistics across all loci were 0.09, 0.029, 0.063 and 0.043 respectively. The overall genetic differentiation observed between the four DS subpopulations studied was low. Bafatá and Gabú are the most closely related subpopulations (DS = 0.04, genetic identity = 0.96) while Bafatá and Cacheu were the most genetically distant subpopulations (DS = 0.14, genetic identity = 0.87). Using Bayesian approach, the number of K groups that best fit the data is detected between 2 and 3, which is consistent with the morphological analysis and the factorial analysis of correspondence. Conclusions The molecular results on DS population of Guinea-Bissau confirmed the ones obtained with morphological analysis. The three genetic types observed phenotypically might be due to a combination of the agro-ecological differences and the management of breeding rather than genetic factors.

Georeferenced Cartography and Landscape: the Protection of the Monumental Olive Heritage

This research studies the protection of the rural landscape and agri-food heritage, offering a perspective on the role and contribution of research to support land management processes and the development of local resources.This opportunity for reflection was created by a project developed at the request of Regione Campania, in Southern Italy, aimed at preserving the inestimable source of biodiversity represented by olive varieties from the risk of genetic erosion, and at guaranteeing the production of oils with typical and diversified organoleptic qualities and properties.Within the scope of the project, the geo-cartographic section has analyzed, surveyed, georeferenced and represented, for a selected territory, the presence of centuries-old olive trees and allowed the creation of other research sections, more specifically agronomic and legal.The georeferencing map of the millenary olive trees typical of the territory, together with the genetic identity card of each plant, have been inserted in a publicly accessible database, through which it is possible to trace the origins and, consequently, the quality of the oil produced.

Genetic Identity, Diversity, and Population Structure of the Sweetpotato's (I. batatas) Germplasm Collection From International Potato Center's

The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.

Genotyping Analysis by RAD-Seq Reads Is Useful to Assess the Genetic Identity and Relationships of Breeding Lines in Lavender Species Aimed at Managing Plant Variety Protection

Lavender species are widely distributed in their wild forms around the Mediterranean Basin and they are also cultivated worldwide as improved and registered clonal varieties. The economic interest of the species belonging to the Lavandula genus is determined by their use as ornamental plants and important source of essential oils that are destinated to the production of cosmetics, pharmaceuticals and foodstuffs. Because of the increasing number of cases of illegal commercialization of selected varieties, the protection of plant breeders’ rights has become of main relevance for the recognition of breeding companies’ royalties. With this aim, genomic tools based on molecular markers have been demonstrated to be very reliable and transferable among laboratories, and also much more informative than morphological descriptors. With the rising of the next-generation sequencing (NGS) technologies, several genotyping-by-sequencing approaches are now available. This study deals with a deep characterization of 15 varietal clones, belonging to two distinct Lavandula species, by means of restriction-site associated DNA sequencing (RAD-Seq). We demonstrated that this technology screens single nucleotide variants that enable to assess the genetic identity of individual accessions, to reconstruct genetic relationships among related breeding lines, to group them into genetically distinguishable main subclusters, and to assign their molecular lineages to distinct ancestors. Moreover, a number of polymorphic sites were identified within genes putatively involved in biosynthetic pathways related to both tissue pigmentation and terpene production, useful for breeding and/or protecting newly registered varieties. Overall, the results highlighted the presence of pure ancestries and interspecific hybrids for the analyzed Lavandula species, and demonstrated that RAD-Seq analysis is very informative and highly reliable for characterizing Lavandula clones and managing plant variety protection.

Development of Daphnia Magna SSR Markers and Genetic Diversity Analysis Based on RAD-Seq Technology

Daphnia magna belongs to the Cladocera order and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In our research, 26 novel microsatellite (SSR) markers were developed in an artificially domesticated of D. magna and 12 wild population of D. magna using restriction site-associated DNA sequencing (RAD-seq). The results showed that the observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.083 to 0.999 and 0.085 to 0.862, respectively. The PIC ranged from 0.368 to 0.805. These results indicate that the developed SSR marker is highly polymorphic. Nei’s genetic identity (H) ranged from 0.0926 to 0.3462, with a mean of 0.2233. Shannon’s Information index (I) ranged from 0.1333 to 0.4799, with an average of 0.3073; Shanxi province had the highest value and Hunan province had the lowest. Genetic distance and Nei’s genetic identity analysis, NJ tree diagram analysis, and PCoA analysis were conducted on populations of D. magna from different regions. The results show that the D. magna genetic relationship between Liaoning and Shanxi, Hunan and Anhui, and Beijing and Hainan is relatively close, while the genetic structure of D. magna in Guangdong, Jiangsu, and Sichuan is quite different from other sampling sites. An analysis of population genetic structure divided the test D. magna samples into two major groups. These results indicate that the genetic diversity of D. magna is rich, and the genetic structure of D. magna differs considerably in different regions. These research results and the newly developed polymorphic SSR markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated population and conservation genetics research.

Psychological health: values and self-identification of adolescent schoolchildren

The paper is devoted to the study of the phenomenon of “sanitary-genetic identity” of adolescents, which is the value self-determination of a forming personality, coupled with an attitude towards achieving psychological health. In previous works, we presented an integral model of psychological health, which includes emotional, regulatory-volitional, cognitive-creative, reflexive-acmeological and socio-communicative components. Based on the presented model, we have developed and carried out a methodology for studying sanitary-genetic identity, which allows us to study the values of psychological health, the current and prospective sanitary-genetic identity of adolescents. The study involved 119 adolescent schoolchildren of St. Petersburg. It was found that adolescents are aware of the value of psychological health, predominantly identify themselves with a group of peers who exhibit constructive behavioural patterns, and also demonstrate targeted health-forming and health-preserving attitudes. The most problematic for girls are emotional patterns of psychological health, which at the same time have a high value for them. The cognitive-creative component of psychological health (interest in cognition, study, creativity) has a low value for boys in comparison with other components, both in the designation of values and in the structure of sanitary-genetic identification. The conducted factor analysis made it possible to single out the key value-self-identification factors of the psychological health of adolescent schoolchildren.

Recovery, Molecular Characterization, and Ampelographic Assessment of Marginal Grapevine Germplasm from Southern Umbria (Central Italy)

The protection of grapevine biodiversity and the safeguarding of genetic variability are certainly primary and topical objectives for wine research, especially in territories historically devoted to viticulture. To assess the autochthonous germplasm of three different districts of Southern Umbria (Central Italy), the plant material of 70 grapevines retrieved from reforested land plots or old vineyards was collected, and their genetic identity was investigated using 13 microsatellite markers (SSR). The results revealed the presence of 39 unique genotypes, divided into 24 already-known cultivars and 15 never-reported SSR profiles. Most of the grapevine accessions were then vegetatively propagated and cultivated in a vineyard collection both to be protected from extinction and to be evaluated at the ampelographic level. Overall, this work emphasizes the need for recovering the threatened genetic variability that characterizes minor neglected grapevine cultivars or biotypes of Southern Umbria germplasm, and the requirement to revalue and exploit the more valuable genetic resources to enhance the local agri-food economy.

Variasi genetik dan jarak genetik suku Sakai di Provinsi Riau dengan suku Minangkabau di Desa Pagaruyung Sumatera Barat berdasarkan DNA mikrosatelit

Terdapat beberapa versi yang menjelaskan mengenai asal-usul suku Sakai baik secara literatur ataupun cerita-cerita yang berkembang dan diturunkan sejak dahulu. Masyarakat Sakai sendiri meyakini bahwa leluhur mereka berasal dari sebuah nagari bernama Pagaruyung di Provinsi Sumatera Barat. Oleh karena itu, penelitian ini bertujuan untuk mengetahui variasi dan jarak genetik masyarakat suku Sakai di Provinsi Riau dengan suku Minangkabau di Desa Pagaruyung Provinsi Sumatera Barat berdasarkan tiga lokus DNA mikrosatelit (D2S1338, D16S539 dan D13S317). Ditemukan total 10 ragam alel yang tersebar dalam tiga lokus DNA mikrosatelit suku Sakai dan 11 ragam alel pada suku Minangkabau. Hasil analisis data menggunakan software GenAlex 6.503 diperoleh nilai heterozigositas pada suku Sakai dan suku Minangkabau tergolong sedang dengan nilai 0,557 ± 0,062 pada Suku Sakai dan 0,615 ± 0,073 pada suku Minangkabau. Begitu pula dengan nilai diferensiasi genetik (F’ST) pada kedua suku ini juga menunjukkan perbedaan genetik yang sedang (0,088 ± 0,039). Berdasarkan nilai F’ST dan nilai heterozigositas dari tiga lokus DNA mikrosatelit ini maka dapat dikatakan bahwa suku Sakai dan suku Minangkabau memiliki kemiripan secara genetik. Hal ini didukung dengan adanya aliran keluar atau masuknya alel pada suku Sakai dan suku Minangkabau dengan laju migrasi sebanyak empat orang setiap generasi sehingga secara genetik suku Sakai dan suku Minangkabau memiliki kemiripan dengan jarak genetik sebesar 0,269 dan besarnya proporsi gen yang identik (Genetic identity) sebesar 0,764.