Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

Background Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. Results We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264–364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. Conclusions As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

Identification of Fruit Firmness QTL ff2.1 by SLAF-BSA and QTL Mapping in Melon

Fruit firmness is an important target of melon breeding, as it is associated with shelf life and economic value; however, the precise mechanism determining fruit firmness during fruit ripening remains elusive. In the present study, one hundred forty-four F2 plants and F2-3 families derived from the high-firmness melon line M2-10 and the low-firmness melon line ZT091 were used to identify major quantitative trait loci (QTLs) by specific-locus amplified fragment (SLAF) sequencing with bulked segregant analysis (BSA). Simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (Caps) markers based on the resequencing of parental lines were also used to narrow the associated region to identify candidate genes. Two regions associated with fruit firmness were investigated, including a 4.87 Mb region on chr. 2 and a 28.7 Mb region on chr. 5 of the melon genome. SSR and Caps markers were used to construct a genetic map of the associated regions: QTL ff5.1 was located between CmSSR13509 and CmSSR13423 and explained 38.44% of the observed variation, with an LOD threshold of 17.44; ff2.1 was located between CmSSR07709 and SNP22228 and explained 28.14% of the variation, with an LOD threshold of 3.8, and this region included 106 Kb and 10 candidate genes. Quantitative Real-time PCR (qRT-PCR) was used to investigated the investigate candidate gene expression at 15, 20 and 25 days after pollination (DAP) in the parental lines, and significant expression levels were detected for most of the genes, including four genes of unknown function and MELO3C017519, MELO3C017520, MELO3C017522, MELO3C029506, and MELO3C029520. These results revealed a new QTL, ff2.1, for melon fruit firmness-related gene identification.

The Genetic and Environmental Adaptation of the Associated Liana Species Derris trifoliata Lour. (Leguminosae) in Mangroves

Derris trifoliata Lour. is an indigenous and associated liana species of mangroves in China; however, its rapid dispersal is threatening mangrove survival. To explore and evaluate their persistence in past disturbances and their potential resistance to future climate and environmental changes, 120 D. trifoliata samples were collected from three sites in Guangdong Province, China, and they were used to develop single nucleotide polymorphic markers using specific-locus amplified fragment sequencing technology. A total of 351.59 Mb reads and 97,998 polymorphic specific-locus amplified fragment sequencing tags were identified, including 360,672 single nucleotide polymorphisms. The principal component analysis, phylogenetic tree, and genetic structure all clustered the samples according to their geographic positions. The three populations showed medium genetic diversity levels and high clonal diversity, indicating that sexual propagation played vital roles in the populations’ succession, although clonal growth was intense within the populations. An association analysis revealed that 9 out of 16 markers were correlated with nitrogen, which indicated the positive roles of nitrogen in population formation and maintenance. This study provides an ecological and molecular basis for understanding the outbreaks of D. trifoliata in mangroves. To control the further expansion of D. trifoliata in mangroves, preventive and control measures should be taken against clonal growth and sexual propagation, respectively; obstructing the clonal growth, especially that of the stolon, should be mainly considered at the junctions of D. trifoliata and mangroves.

Народная демонология Полесья в контексте восточнославянских традиционных верований

This article studies folk demonological beliefs that are widespread on the territory of Polesye, located on the border of Ukraine, Belarus, and Russia. The traditional culture of this region is of great interest for ethnologists of the broadest profile, since it preserves many archaic elements of all-Slavic significance. In the first part of the study, two blocks of the regional mythological system were considered: spirits of domestic and natural loci, and a group of characters originated from the souls of deceased. The second part of the work considers two groups of mythological characters: spirits not assigned to a specific locus (the devil, spirits of diseases, personification of death, characters for intimidation of children) and different categories of living people endowed with supernatural knowledge (witches, sorcerers, healers, werewolves). The study is based on data from the East-Slavic demonology.

The rs1421085 variant within FTO promotes thermogenesis and is associated with human migration

One lead risk signal of obesity–rs1421085 T > C within the FTO gene–is reported to be functional in vitro but lack of organismal evidence. Here, we established global and the brown-adipocyte specific locus-knock-in mice to recapitulate this homologous variant in humans and discovered that mice carrying the C-alleles showed increased thermogenic capacity and a resistance to high-fat diet-induced adiposity with enhanced FTO transcription, while FTO knockdown or inhibition effectively eliminated the increased thermogenic ability of brown adipocytes. In humans, the C-allele was associated with lower birthweight, and its allele frequency increases following the environmental temperature decreases. Cumulatively, these findings identified rs1421085 T > C as a functional variant promoting whole-body thermogenesis and was associated with early human migration from hot to cold environments.

Guest Editorial: Transforming Borders and the Discretionary Politics of Migration Control

The eight articles in this issue promise us a global journey around transformed borders, multiscalar bordering, and discretionary practices within these migration controls. In doing so, the authors guide us through the Global North and Global South with countries as varied as the US, Mexico, Mali, Poland, Norway, the Netherlands, the United Kingdom (UK), Spain, Italy, Germany, Greece, and Turkey. We also gain insights through these specific research settings from additional Asian and African countries of origin for the migrants involved. By situating their analyses in a specific locus, the authors provide us with a grounded, localized narrative, which they insightfully theorize on and interact with at the global level. Through these glocalized analyses, we not only learn about the importance of multiscalar forms of migration control and the discretion of these actors within these bordering practices, but also gain insights into the immediate and long-term effects of these control efforts on the divergent actors that transform our borders and give meaning to the multiscalar bordering practices.

Strong neutral sweeps occurring during a population contraction

A strong reduction in diversity around a specific locus is often interpreted as a recent rapid fixation of a positively selected allele, a phenomenon called a selective sweep. Rapid fixation of neutral variants can however lead to similar reduction in local diversity, especially when the population experiences changes in population size, e.g., bottlenecks or range expansions. The fact that demographic processes can lead to signals of nucleotide diversity very similar to signals of selective sweeps is at the core of an ongoing discussion about the roles of demography and natural selection in shaping patterns of neutral variation. Here we quantitatively investigate the shape of such neutral valleys of diversity under a simple model of a single population size change, and we compare it to signals of a selective sweep. We analytically describe the expected shape of such neutral sweeps and show that selective sweep valleys of diversity are, for the same fixation time, wider than neutral valleys. On the other hand, it is always possible to parametrize our model to find a neutral valley that has the same width as a given selected valley. We apply our framework to the case of a putative selective sweep signal around the gene Quetzalcoatl in D. melanogaster and show that the valley of diversity in the vicinity of this gene is compatible with a short bottleneck scenario without selection. Our findings provide further insight in how simple demographic models can create valleys of genetic diversity that may falsely be attributed to positive selection.

The rs1421085 variant within FTO promotes but not inhibits thermogenesis and is potentially associated with human migration

Disease-associated GWAS loci are predominantly scattered among noncoding regions of the human genome, which impedes causality estimation. One lead risk signal of obesity-rs1421085 T>C within the FTO gene-is reported to functional in vitro but lack of organismal evidence. Here, we established global and the brown-adipocyte specific locus-knock-in mice to recapitulate this homologous variant in humans, and discovered the minor allele (C-allele) as one candidate thermogenic locus. Mice carrying the C-alleles showed increased thermogenic capacity and a resistance to high-fat diet-induced adiposity. In terms of mechanism, the knock-in models showed enhanced FTO expression, while FTO knockdown or inhibition effectively eliminated the increased thermogenic ability of brown adipocytes. In humans, the C-allele was associated with lower birthweight, and its allele frequency increases following the environmental temperature decreases. Cumulatively, these findings demonstrated rs1421085 T>C as a functional variant regulating whole-body thermogenesis, and this variation was possibly related to early human migration from hot to cold environments.

Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese

Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs’ filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs—which had different allelic frequencies—were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.