Search Results (7)

The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S & 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions. Full article

Pets have a crucial role in cancer research. Specifically, dogs and cats share the same environment as their owners and thus may serve as sentinels of naturally occurring tumors that are linked to the exposure to environmental hazards. Quantitative comparison of tumor types may reveal unusual cancer frequencies, providing directions for research and generation of hypotheses of cancer causation in a specific area and identification of risk factors. The aim of this study was to describe the data collected by the pathology-based animal cancer registry, managed by Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM), during 10 years of activity (2014–2023) and to assess its potential epidemiological relevance. Frequencies of tumor topography and morphology in dogs and cats were described, analyzed and compared. Proportional morbidity ratios (PMRs) were calculated, taking into consideration some potential risk factors such as species, breed, sex, diet and living environment. The database comprises 5311 tumors (n = 4719 in dogs and n = 592 in cats), with a higher prevalence in females (67.3% in dogs and 61.2% in cats). The mean age at the first diagnosis of tumors was similar between sexes and slightly lower in dogs compared to cats. PMRs highlighted certain risk and “protective” factors for the development of tumors in specific topography. The risk of developing tumors of the blood and hematopoietic system (PMR = 0.44; 95% CI: 0.21–0.94), skin and subcutaneous tissues (PMR = 0.70; 95% CI: 0.61–0.80), oral cavity and pharynx (PMR = 0.60; 95% CI: 0.24–0.89), urinary organs (PMR = 0.33; 95% CI: 0.11–0.99) and bones, joints and cartilage (PMR = 0.72; 95% CI: 0.22–0.98) was lower in non-neutered male dogs than in neutered male dogs. Non-spayed female dogs had a greater risk of developing tumors of the mammary gland (PMR = 1.75; 95% CI: 1.57–1.96), female sexual organs (PMR = 2.12; 95% CI: 1.01–4.36) and respiratory system (PMR = 2.25; 95% CI: 1.55–6.74) but less risk for cutaneous and subcutaneous tissue tumors (PMR = 0.44; 95% CI: 0.38–0.51) and blood/hematopoietic system tumors (PMR = 0.47; 95% CI: 0.26–0.85) compared to spayed female dogs. Compared with mixed breed, purebred dogs had a significantly greater risk of developing mammary gland tumors (PMR = 1.36; 95% CI: 1.20–1.54) and lower risk for respiratory (PMR = 0.15; 95% CI: 0.07–0.32), gastrointestinal (PMR = 0.63; 95% CI: 0.34–0.94) and oral (PMR = 0.59; 95% CI: 0.36–0.96) neoplasia. Non-neutered male cats had a lower risk of developing skin and subcutaneous tumors (PMR = 0.68; 95% CI: 0.50–0.92) compared with neutered cats. The risk of developing skin and subcutaneous tissues tumors was higher for dogs and cats that lived mostly outdoor (PMR dogs = 1.21; 95% CI: 1.10–1.33; PMR cats = 1.18; 95% CI: 1.08–1.47), while dogs that live mainly indoor had a greater risk to develop mammary gland tumors (PMR = 0.78; 95% CI: 0.68–0.89). Results described herein highlight the fundamental role of animal cancer registration initiatives. These efforts would contribute to the possibility of conducting multicentric collaborative studies to deepen the knowledge of the epidemiology of tumors in dogs and cats from a comparative perspective, thus fulfilling the One Health approach. Full article

Most existing studies on pet breeds classification focus on images with simple backgrounds, leading to the unsatisfactory performance of models in practical applications. This paper investigates training pet breeds classification models using complex images and constructs a dataset for identifying breeds of pet cats and dogs. We use this dataset to fine-tune three SOTA models: ResNet34, DenseNet121, and Swin Transformer. Specifically, in terms of top-1 accuracy, the performance of DenseNet is improved from 89.10% to 89.19%, while that of the Swin Transformer is increased by 1.26%, marking the most significant enhancement. The results show that training with our dataset significantly enhances the models’ classification capabilities in complex environments. Additionally, we offer a lightweight pet breeds identification model based on PBI-EdgeNeXt (Pet Breeds Identification EdgeNeXt). We utilizes the PolyLoss function and Sophia optimizer for model training. Furthermore, we compare our model with five commonly used lightweight models and find that the proposed model achieves the highest top-1 accuracy of 87.12%. These results demonstrate that the model achieves high accuracy, reaching the SOTA level. Full article

Curcuma alismatifolia (Zingiberaceae) is an ornamental species with high economic value due to its recent rise in popularity among floriculturists. Cultivars within this species have mixed genetic backgrounds from multiple hybridization events and can be difficult to distinguish via morphological and histological methods alone. Given the need to improve identification resources, we carried out the first systematic study using plastomic data wherein genomic evolution and phylogenetic relationships from 56 accessions of C. alismatifolia were analyzed. The newly assembled plastomes were highly conserved and ranged from 162,139 bp to 164,111 bp, including 79 genes that code for proteins, 30 tRNA genes, and 4 rRNA genes. The A/T motif was the most common of SSRs in the assembled genomes. The Ka/Ks values of most genes were less than 1, and only two genes had Ka/Ks values above 1, which were rps15 (1.15), and ndhl (1.13) with petA equal to 1. The sequence divergence between different varieties of C. alismatifolia was large, and the percentage of variation in coding regions was lower than that in the non-coding regions. Such data will improve cultivar identification, marker assisted breeding, and preservation of germplasm resources. Full article

The popularity of dogs as human companions explains why these pets regularly come into focus in forensic cases such as bite attacks or accidents. Canine evidence, e.g., dog hairs, can also act as a link between the victim and suspect in a crime case due to the close contact between dogs and their owners. In line with human DNA identification, dog individualization from crime scene evidence is mainly based on the analysis of short tandem repeat (STR) markers. However, when the DNA profile does not match a reference, additional information regarding the appearance of the dog may provide substantial intelligence value. Key features of the dog’s appearance, such as the body size and coat colour are well-recognizable and easy to describe even to non-dog experts, including most investigating officers and eyewitnesses. Therefore, it is reasonable to complement eyewitnesses’ testimonies with externally visible traits predicted from associated canine DNA samples. Here, the feasibility and suitability of canine DNA phenotyping is explored from scratch in the form of a proof of concept study. To predict the overall appearance of an unknown dog from its DNA as accurately as possible, the following six traits were chosen: (1) coat colour, (2) coat pattern, (3) coat structure, (4) body size, (5) ear shape, and (6) tail length. A total of 21 genetic markers known for high predicting values for these traits were selected from previously published datasets, comprising 15 SNPs and six INDELS. Three of them belonged to SINE insertions. The experiments were designed in three phases. In the first two stages, the performance of the markers was tested on DNA samples from dogs with well-documented physical characteristics from different breeds. The final blind test, including dogs with initially withheld appearance information, showed that the majority of the selected markers allowed to develop composite sketches, providing a realistic impression of the tested dogs. We regard this study as the first attempt to evaluate the possibilities and limitations of forensic canine DNA phenotyping. Full article

In Australia, each state and territory authority implements and enforces regulations regarding dog management—including the breeding and sale of dogs online—which is increasingly becoming the most popular method of obtaining pets. The aims for this study included: 1. Benchmarking regulatory compliance in online dog advertisements in Australia, and, 2. Understanding factors associated with regulatory compliance in online advertisements. We collected advertisements for dogs and puppies from Gumtree—one of Australia’s most popular online trading platforms—on two separate days, two weeks apart (25 March and 8 April 2019). A total of 1735 unique advertisements were included in the dataset. Chi-squared tests and multivariable logistic regression models were used to identify risk factors for microchipping, desexing and breeder identification number, and compliance levels. State laws requiring animals to be microchipped prior to sale and the inclusion of chip numbers in advertisements were found to be the biggest factor in increasing likelihood of microchipped animals in Gumtree advertisements, while desexing was more common in microchipped and older animals. The online ad was more likely to include a breeder ID if the dog was young, vaccinated, and advertised by a breeder rather than an owner. The findings from this study will assist regulators to make evidence-based decisions on managing online advertisements for companion animals. In the future, the benchmarking this study has presented will allow future analysis of the effectiveness of regulation changes. Full article

Hybrid breeding in sunflowers based on CMS PET1 requires development of restorer lines carrying, in most cases, the restorer gene Rf1. Markers for marker-assisted selection have been developed, but there is still need for closer, more versatile, and co-dominant markers linked to Rf1. Homology searches against the reference sunflower genome using sequences of cloned markers, as well as Bacterial Artificial Chromosome (BAC)-end sequences of clones hybridizing to them, allowed the identification of two genomic regions of 30 and 3.9 Mb, respectively, as possible physical locations of the restorer gene Rf1 on linkage group 13. Nine potential candidate genes, encoding six pentatricopeptide repeat proteins, one tetratricopeptide-like helical domain, a probable aldehyde dehydrogenase 22A1, and a probable poly(A) polymerase 3 (PAPS3), were identified in these two genomic regions. Amplicon targeted next generation sequencing of these nine candidate genes for Rf1 was performed in an association panel consisting of 27 maintainer and 32 restorer lines and revealed the presence of 210 Single Nucleotide Polymorphisms (SNPs) and 67 Insertions/Deletions (INDELs). Association studies showed significant associations of 10 SNPs with fertility restoration (p-value < 10⁻⁴), narrowing Rf1 down to three candidate genes. Three new markers, one co-dominant marker 67N04_P and two dominant markers, PPR621.5R for restorer, and PPR621.5M for maintainer lines were developed and verified in the association panel of 59 sunflower lines. The versatility of the three newly developed markers, as well as of three existing markers for the restorer gene Rf1 (HRG01 and HRG02, Cleaved Amplified Polymorphic Sequence (CAPS)-marker H13), was analyzed in a large association panel consisting of 557 accessions. Full article