Development Of Genetic Markers Research Articles

MicroRNA-875-5p inhibits the growth and metastasis of cervical cancer cells by promoting autophagy and apoptosis and inhibiting the epithelial-mesenchymal transition.

MicroRNA-875-5p (miR-875-5p) is a cancer-related microRNA. It has been demonstrated that miR-875-5p participates in the development of various types of cancer such as hepatocellular carcinoma, gastric carcinoma, prostate and bladder cancer. Previous research suggested that miR-875 is implicated in the development of cervical cancer cells. However, the exact role and function of miR-875-5p in cervical cancer remain unexplored. It is important to examine the role and function of miR-875-5p and the associated signaling pathway, as the findings may have diagnostic and therapeutic significance. Thus, in this study, we investigated the effect of miR-875-5p on the growth and metastasis of cervical cancer cells and the possible underlying mechanisms. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of miR-875-5p in cervical cancer cells and normal cervical epithelium. After overexpression or co-expression of miR-875-5p in cells, the changes in cell function were analyzed. Western blot was used to detect the expression changes of epithelial-mesenchymal transition (EMT) -related proteins and autophagy-related proteins. Functional studies demonstrated that miR-875-5p overexpression significantly inhibited the proliferation, migration, invasion, and EMT, and promotes apoptosis and autophagy of cervical cancer cells., while miR-875-5p knockdown promoted the proliferation, migration, invasion, and EMT, and inhibited apoptosis and autophagy cervical cancer cells. Furthermore, Western blot results showed that overexpression of miR-875-5p downregulated the expressions of N-cadherin, Snail, Vimentin and microtubule-associated protein 1 light chain 3B I (LC3B I). Conversely, miR-875-5p upregulated the expression of E-cadherin. In conclusion, our findings suggest that miR-875-5p functions as a tumor inhibitor suppressing the growth and metastasis of cervical cancer. Overexpression of miR-875-5p inhibits malignant behavior and promotes autophagy and apoptosis in cervical cancer cells. These findings advance our understanding of the role and function of miR-875-5p in cervical cancer and could facilitate the development of early genetic markers or biomarkers and therapeutic targets for cervical cancer.

Genomic regions associated with coat color in Gir cattle.

Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.

Evolution of Endogenous Retroviruses in the Subfamily of Caprinae.

The interest in endogenous retroviruses (ERVs) has been fueled by their impact on the evolution of the host genome. In this study, we used multiple pipelines to conduct a de novo exploration and annotation of ERVs in 13 species of the Caprinae subfamily. Through analyses of sequence identity, structural organization, and phylogeny, we defined 28 ERV groups within Caprinae, including 19 gamma retrovirus groups and 9 beta retrovirus groups. Notably, we identified four recent and potentially active groups prevalent in the Caprinae genomes. Additionally, our investigation revealed that most long noncoding genes (lncRNA) and protein-coding genes (PC) contain ERV-derived sequences. Specifically, we observed that ERV-derived sequences were present in approximately 75% of protein-coding genes and 81% of lncRNA genes in sheep. Similarly, in goats, ERV-derived sequences were found in approximately 74% of protein-coding genes and 75% of lncRNA genes. Our findings lead to the conclusion that the majority of ERVs in the Caprinae genomes can be categorized as fossils, representing remnants of past retroviral infections that have become permanently integrated into the genomes. Nevertheless, the identification of the Cap_ERV_20, Cap_ERV_21, Cap_ERV_24, and Cap_ERV_25 groups indicates the presence of relatively recent and potentially active ERVs in these genomes. These particular groups may contribute to the ongoing evolution of the Caprinae genome. The identification of putatively active ERVs in the Caprinae genomes raises the possibility of harnessing them for future genetic marker development.

A Bibliometric and Visual Analysis of the Current Status and Trends of Forensic Mixed Stain Research.

To explore the context and hotspot changes of forensic mixed stain research through bibliometric approach. The literature of forensic mixed stain included in the core collection of Web of Science database from 2011 to 2022 were collected as the study object, and the annual publication number, countrie (region), institution, journal, keywords, etc. were bibliometrically and visually analyzed using the R-based Bibliometrix 1.1.6 package and VOSviewer 1.6.18 software. A total of 732 articles on forensic mixed stain were included from 2011 to 2022, with the annual number of articles published and the annual citation frequency showing a steady increase year by year. Among the 59 countries (regions) with the most published articles, the United States ranked first with 246 articles, followed by China with 153 articles. The literature came from 104 journals, and the total number of articles published in the top 10 journals was 633. FORENSIC SCI INT GENET ranked first with 307 articles. Visual analysis using VOSviewer software showed that keywords could be divided into four research clusters, namely the genetic marker development group (blue), the mixed stain typing analysis theory group (red), the sequencing analysis group (yellow), and the case sample research group (green). It can be divided into four development stages in terms of different time periods: early development (2011-2013), middle development (2014-2016), rapid development (2017-2020) and latest development (2021-2022). The number of publications by domestic and foreign scholars in the study of mixed stain in forensic science is showing a relatively stable trend. Machine learning, next generation sequencing and other research have been the hottest topics that have attracted the most attention in recent years, which is expected to further develop the theory of mixed stain typing and sequencing analysis in forensic mixed stain research.

Development of genetic markers in Yarrowia lipolytica.

The oleaginous yeast Yarrowia lipolytica represents a potential microbial cell factory for the recombinant production of various valuable products. Currently, the commonly used selection markers for transformation in Y. lipolytica are limited, and successive genetic manipulations are often restricted by the number of available selection markers. In our study, we developed a dominant marker, dsdA, which encodes a D-serine deaminase for genetic manipulation in Y. lipolytica. In Y. lipolytica, this marker confers the ability to use D-serine as a nitrogen source. In addition, the selection conditions of several infrequently used dominant markers including bleoR (zeocin resistance), kanMX (G418 resistance), and guaB (mycophenolic acid resistance) were also analyzed. Our results demonstrated that these selection markers can be used for the genetic manipulation of Y. lipolytica and their selection conditions were different for various strains. Ultimately, the selection markers tested here will be useful to expand the genetic toolbox of Y. lipolytica. KEY POINTS: • The dsdA from Escherichia coli was developed as a dominant marker. • The applicability of several resistance markers in Y. lipolytica was determined. • We introduced the Cre/mutant lox system for marker recycling.

Recent Advances in Breeding of Mango (Mangifera indica): A Review

Mango stands as a significant fruit crop with global importance, thriving primarily in tropical and subtropical regions across the world. (Mangifera indica L.) belongs to the Anacardiaceae family. This evergreen, sizable tree bears a beloved tropical fruit that enjoys local consumption and international trade. The choice of preferred mango varieties varies from one country to another. Generally, mango types from subcontinental Asian regions are monoembryonic, while those from South East Asian regions tend to be polyembryonic. Despite Mangifera indica's prevalence within the Mangifera genus, several other species within this genus share grafting and pollination compatibility with M. indica. These species can serve as valuable rootstocks or sources of novel genetic traits for breeders. Growing mango presents challenges due to the rapid decline in seed viability shortly after fruit maturity, typically within weeks. While a diverse array of mango varieties is available, inherent limitations exist, including extended juvenility, high clonal heterozygosity, the presence of only one seed per fruit, resilient seeds, polyembryony, early post-zygotic auto-incompatibility, and a substantial land requirement for hybrid evaluation. Breeders, however, benefit from the extensive variation and the ease of vegetative hybrid production. A successful mango cultivar must exhibit traits such as dwarfness, precocity, regular and prolific fruit bearing, appealing fruit of good size and quality, resistance to physiological issues, diseases, and insects, and an extended shelf life. A comprehensive understanding of mango phenology, inheritance patterns, and advanced techniques for hybridization has proven invaluable in addressing challenges like irregular fruit bearing, susceptibility to disorders and pests, and issues with taste and quality. The development of genetic markers has further reduced uncertainties in mango breeding and improved the management of hybrid populations.

Comprehensive Organ-Specific Profiling of Douglas Fir (Pseudotsuga menziesii) Proteome.

The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.

Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection.

Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.

Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats. a systematic review

Background: Litter size (LS) is a significant, challenging, and economical aspect of the goat industry in Indonesia. It is influenced by several different factors and genes; consequently, identifying potential genes and loci associated with litter size has become a genetic problem. Several genetic indicators have been found to be associated with litter size in goats. This has prompted the need to discuss candidate genes associated with litter size in goats in Indonesia. Methods: A systematic review was conducted using critical databases including ResearchGate, Google Scholar, PubMed, Google search engine and Science direct. There were any exclusion criteria, they were as follows: articles published in languages other than English, Conference papers, short communication papers and papers not related to animals. After reviewing the abstracts of 42 publications, the remaining 17 investigations were chosen for full paper evaluation. A further eight studies were removed after a comprehensive evaluation of the publications because they did not match our inclusion criteria. Results: These markers include growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), bone morphogenetic protein receptor type IB (BMPR1B), and kisspeptin (KISS1). Single nucleotide polymorphisms in these genes contribute to the development of novel genetic markers that helps in the selection of goats with the most favorable genotypes for litter size. This type of genetic selection is more successful than the traditional way of selecting animals for reproductive traits, particularly litter size. Conclusions: As a result, this study summarizes the genetic impacts of polymorphisms in candidate genes associated with litter size features in Indonesian goats.

Development of microsatellite markers for the invasive mosquito Aedes koreicus

BackgroundAedes koreicus is a mosquito species native to East Asia which has recently invaded several countries in Europe. In Italy, this mosquito was first detected in the North-East in 2011 and is now widely distributed in the entire northern part of the country. The development of specific genetic markers, such as microsatellites, is necessary to uncover the dispersal routes of this mosquito from its native areas and, eventually, to plan future control interventions.MethodsAvailable raw sequences of genomic DNA of Ae. koreicus were screened in silico using BLASTn to identify possible microsatellite-containing sequences. Specific primer pairs were then designed, and their efficiency was determined through polymerase chain reaction (PCR) on 32 individuals of Ae. koreicus collected in Italy. PCR conditions were optimised in three multiplex reactions. Genotyping of individual mosquitoes was performed on both single and multiplex PCR reactions. Finally, analysis of intra-population variation was performed to assess the level of polymorphism of the markers.ResultsMosquito genotyping provided consistent results in both single and multiplex reactions. Out of the 31 microsatellite markers identified in the Ae. koreicus genome raw sequences, 11 were polymorphic in the examined mosquito samples.ConclusionsThe results show that the 11 microsatellite markers developed here hold potential for investigating the genetic structure of Ae. koreicus populations. These markers could thus represent a novel and useful tool to infer the routes of invasion of this mosquito species into Europe and other non-native areas.Graphical

Development of genetic markers for reproductive management of toucans.

Retention of genetic diversity in successive generations is key to successful ex situ programs and will become increasingly important to restore wild populations of threatened animals. When animal genealogy is partly unknown or gaps exist in studbook records, the application of molecular resources facilitates informed breeding. Here, we apply molecular resources to an ex situ breeding population of toucans (Ramphastidae), a bird family zoos commonly maintain. Toucans face population declines from illegal poaching and habitat degradation. We developed novel microsatellite markers using blood samples from 15 Keel-billed Toucans (Ramphastos sulfuratus Lesson 1830). Parentage of two individuals was known a priori, but possible sibship among 13 putative founders-including the parents-was unknown. We compared available avian heterologous and novel microsatellite markers to recover known relationships and reconstruct sibship. Eight of 61 heterologous markers amplified consistently and were polymorphic, but less so than the 18 novel markers. Known sibship (and three sibling pairs whose relatedness was unknown a priori) and paternity-though not maternity except in one case-were well-recovered using both likelihood and pairwise relatedness methods, when incorporating novel but not heterologous markers. Zoo researchers seeking microsatellite primer sets for their breeding toucan populations will likely benefit from our heterologous markers, which can be leveraged both to assess relatedness and select breeding pairs. We recommend that zoo biologists rely on species-specific primers and not optimize heterologous primers for toucan species without molecular resources. We conclude with a brief discussion of modern genotyping methods of interest to zoo researchers.

Genetic diversity and population structure of bermudagrass (Cynodon spp.) revealed by genotyping-by-sequencing.

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. To explore diversity in bermudagrass, a total of 206 Cynodon accessions consisting of 193 common bermudagrass (C. dactylon var. dactylon) and 13 African bermudagrass (C. transvaalensis) accessions of worldwide origin were assembled for genetic characterization. Genotyping-by-sequencing (GBS) was employed for genetic marker development. With a minor allele frequency of 0.05 and a minimum call rate of 0.5, a total of 37,496 raw single nucleotide polymorphisms (SNPs) were called de novo and were used in the genetic diversity characterization. Population structure analysis using ADMIXTURE revealed four subpopulations in this germplasm panel, which was consistent with principal component analysis (PCA) and phylogenetic analysis results. The first three principal components explained 15.6%, 10.1%, and 3.8% of the variance in the germplasm panel, respectively. The first subpopulation consisted of C. dactylon accessions from various continents; the second subpopulation was comprised mainly of C. transvaalensis accessions; the third subpopulation contained C. dactylon accessions primarily of African origin; and the fourth subpopulation represented C. dactylon accessions obtained from the Oklahoma State University bermudagrass breeding program. Genetic diversity parameters including Nei's genetic distance, inbreeding coefficient, and Fst statistic revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs.

Diagnosis of Parkinson's Disease via the Metabolic Fingerprint in Saliva by Deep Learning.

Parkinson's disease (PD) is the second cause of the neurodegenerative disorder, affecting over 6 million people worldwide. The World Health Organization estimated that population aging will cause global PD prevalence to double in the coming 30 years. Optimal management of PD shall start at diagnosis and requires both a timely and accurate method. Conventional PD diagnosis needs observations and clinical signs assessment, which are time-consuming and low-throughput. A lack of body fluid diagnostic biomarkers for PD has been a significant challenge, although substantial progress has been made in genetic and imaging marker development. Herein, a platform that noninvasively collects saliva metabolic fingerprinting (SMF) by nanoparticle-enhanced laser desorption-ionization mass spectrometry with high-reproducibility and high-throughput, using ultra-small sample volume (down to 10 nL), is developed. Further, excellent diagnostic performance is achieved with an area-under-the-curve of 0.8496 (95% CI: 0.7393-0.8625) by constructing deep learning model from 312 participants. In conclusion, an alternative solution is provided for the molecular diagnostics of PD with SMF and metabolic biomarker screening for therapeutic intervention.

Identification of sex-linked codominant markers and development of a rapid LAMP-based genetic sex identification method in channel catfish (Ictalurus punctatus)

Channel catfish (Ictalurus punctatus), a commercially important aquaculture species, is native to North America and has spread worldwide. Channel catfish exhibit sexual size dimorphism, with males growing faster than females. Therefore, the creation of an all-male population is promising for growth improvement in channel catfish. In the process of monosex fish breeding, the development of sex-specific genetic markers is the most critical step. Although sex-linked SSRs and SNPs have been developed in channel catfish, they are polymorphic, unstable, and difficult to use for rapid sex genotyping. In this study, three codominant markers with large size differences between their two alleles were identified by performing a detailed comparison of the region on X and Y chromosomes that enriched male-specific SNPs using preexisting RAD-seq data and genome data. After examination by one wild and three artificially bred populations using electrophoresis on agarose gel, the accuracy rate reached 100%, suggesting that all three codominant markers could be effectively used for genetic sex identification in channel catfish. To achieve genetic sex identification performed in the field without complex equipment, a rapid LAMP-based method was established for the identification of genetic sex in channel catfish based on the codominant markers we identified. Overall, this study established rapid and effective PCR- and LAMP-based methods to identify the genetic sex of channel catfish in the laboratory and in the field.

Integrative genomics analysis highlights functionally relevant genes for equine behaviour.

Behavioural plasticity enables horses entering an exercise training programme to adapt with reduced stress. We characterised SNPs associated with behaviour in yearling Thoroughbred horses using genomics analyses for two phenotypes: (1) handler-assessed coping with early training events [coping] (n=96); and (2) variation in salivary cortisol concentration at the first backing event [cortisol] (n=34). Using RNA-seq derived gene expression data for amygdala and hippocampus tissues from n=2 Thoroughbred stallions, we refined the SNPs to those with functional relevance to behaviour by cross-referencing to the 500 most highly expressed genes in each tissue. The SNPs of high significance (q < 0.01) were in proximity to genes (coping - GABARAP, NDM, OAZ1, RPS15A, SPARCL1, VAMP2; cortisol - CEBPA, COA3, DUSP1, HNRNPH1, RACK1) with biological functions in social behaviour, autism spectrum disorder, suicide, stress-induced anxiety and depression, Alzheimer's disease, neurodevelopmental disorders, neuroinflammatory disease, fear-induced behaviours and alcohol and cocaine addiction. The strongest association (q=0.0002) was with NDN, a gene previously associated with temperament in cattle. This approach highlights functionally relevant genes in the behavioural adaptation of Thoroughbred horses that will contribute to the development of genetic markers to improve racehorse welfare.

Development of genetic sex markers of zig-zag eel (Mastacembelus armatus) by a NGS method

Identifying sex-specific marker with universal applicability is important for the study of unisexual reproduction and sex determination mechanism. In this study, two genetic sex markers of zig-zag eel were identified using a NGS method. Twelve potential male-specific sequences were first obtained by whole genome re-sequencing analysis of three males and three females. After PCR amplification and agarose gel electrophoresis for validation, two male-specific markers were obtained. Moreover, these markers were further verified in different populations in the Pearl River basin, and the accuracy of M2 markers was 100%. In addition, these markers were used to identify the genetic sex of different periods of embryonic development and hatching of juveniles at different time points in the cultured population, and it was found that male to female switching was common in the cultured population. Besides, we also found some embryos with YY genotype. These universal sex-specific markers will lay a good foundation for understanding of sex determination mechanism and development of all-male breeding of zig-zag eel.

Potential prognostic and predictive value of UBE2N, IMPDH1, DYNC1LI1 and HRASLS2 in colorectal cancer stool specimens.

Colorectal cancer (CRC) is the most common gastrointestinal malignancy worldwide. The poor specificity and sensitivity of the fecal occult blood test has prompted the development of CRC-related genetic markers for CRC screening and treatment. Gene expression profiles in stool specimens are effective, sensitive and clinically applicable. Herein, a novel advantage of using cells shed from the colon is presented for cost-effective CRC screening. Molecular panels were generated through a series of leave-one-out cross-validation and discriminant analyses. A logistic regression model following reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry was used to validate a specific panel for CRC prediction. The panel, consisting of ubiquitin-conjugating enzyme E2 N (UBE2N), inosine monophosphate dehydrogenase 1 (IMPDH1), dynein cytoplasmic 1 light intermediate chain 1 (DYNC1LI1) and phospholipase A and acyltransferase 2 (HRASLS2), accurately recognized patients with CRC and could thus be further investigated as a potential prognostic and predictive biomarker for CRC. UBE2N, IMPDH1 and DYNC1LI1 expression levels were upregulated and HRASLS2 expression was downregulated in CRC tissues. The predictive power of the panel was 96.6% [95% confidence interval (CI), 88.1-99.6%] sensitivity and 89.7% (95% CI, 72.6-97.8%) specificity at a predicted cut-off value at 0.540, suggesting that this four-gene panel testing of stool specimens can faithfully mirror the state of the colon. On the whole, the present study demonstrates that screening for CRC or cancer detection in stool specimens collected non-invasively does not require the inclusion of an excessive number of genes, and colonic defects can be identified via the detection of an aberrant protein in the mucosa or submucosa.

Polymorphism studies and candidate genes associated with litter size traits in Indonesian goats. a systematic review

Background: Litter size (LS) is a significant, challenging, and economical aspect of the goat industry in Indonesia. It is influenced by several different factors and genes; consequently, identifying potential genes and loci associated with litter size has become a genetic problem. Several genetic indicators have been found to be associated with litter size in goats. This has prompted the need to discuss candidate genes associated with litter size in goats in Indonesia. Methods: A systematic review was conducted using critical databases including ResearchGate, Google Scholar, PubMed, Google search engine and Science direct. There were any exclusion criteria, they were as follows: articles published in languages other than English, Conference papers, short communication papers and papers not related to animals. After reviewing the abstracts of 42 publications, the remaining 17 investigations were chosen for full paper evaluation. A further eight studies were removed after a comprehensive evaluation of the publications because they did not match our inclusion criteria. Results: These markers include growth differentiation factor 9 (GDF9), bone morphogenetic protein 15 (BMP15), bone morphogenetic protein receptor type IB (BMPR1B), and kisspeptin (KISS1). Single nucleotide polymorphisms in these genes contribute to the development of novel genetic markers that helps in the selection of goats with the most favorable genotypes for litter size. This type of genetic selection is more successful than the traditional way of selecting animals for reproductive traits, particularly litter size. Conclusions: As a result, this study summarizes the genetic impacts of polymorphisms in candidate genes associated with litter size features in Indonesian goats.

Expression of highly conserved developmental phase change regulating miR156 and miR172 microRNAs in silver birch using real-time PCR and high-throughput sequencing methodologies

Silver birch (Betula pendula Roth) is the most significant deciduous tree species in Latvia. Efficient vegetative reproduction methods are crucial for shortening breeding cycles. In many woody tree species, success of vegetative propagation sharply decreases as individuals mature. Development of molecular genetic markers related to phase change has the potential to increase the efficiency of vegetative reproduction methods. Studies in annual model plant species have identified evolutionary highly conserved miRNAs that are involved in phase change – miR156 and miR172. This study compared expression levels of these miRNA families using two approaches – real-time PCR (RT‑PCR) and high-throughput sequencing, in silver birch in vitro shoot samples. High expression of miR156 in juvenile samples was identified by both methods, but increased expression of miR172 was only observed by RT‑PCR. Further studies in long-lived perennial species are needed to fully elucidate the miRNAs involved in developmental phase transition processes.

The Development of Genetic Sex Identification Markers and Evidence of a Male Heterogametic Sex Determination System in Red Shiner

AbstractThe Red Shiner Cyprinella lutrensis is of increasing management interest as an invasive species that negatively impacts many native fishes throughout North America. Trojan sex chromosome (TSC)‐carrying individuals could theoretically control invasive fish populations by skewing the sex ratio to 100% male. The efficacy of TSC‐based control programs requires an understanding of a population's sex determination system, yet such information is lacking for Red Shiner. We used single‐digest restriction site‐associated DNA sequencing to discover sex‐linked single‐nucleotide polymorphisms (SNPs), and we conducted a series of breeding experiments to uncover the sex determination system. All candidate sex‐linked SNPs that fit our selection criteria exhibited a pattern of male heterogamety. We developed two sex‐identification (sex‐ID) marker assays, XY_248 and XY_170, which showed phenotype–genotype concordance scores of 77.00% and 84.35%, respectively. These sex‐ID markers exhibited relatively high phenotype–genotype concordance in females (XY_248 = 96.30%; XY_170 = 98.61%), which allowed for selective breeding of phenotypically feminized genetic males. We observed a 3:1 male : female sex ratio in spawns from feminized males crossed with wild‐type males, indicative of a male heterogametic sex determination system (i.e., XY male/XX female). The discovery of a male heterogametic sex determination system, in combination with our two markers, increases the likelihood of developing an effective TSC eradication strategy for invasive Red Shiner populations.