Search Results (6)

Plant breeding is considered to be the science and art of genetically improving plants according to human needs. Breeders in this context oftentimes face the difficult task of selecting among thousands of genotypes for dozens of traits simultaneously. Using a breeder’s selection decisions from a commercial wheat breeding program as a case study, this study investigated the possibility of implementing a recommender system based on the breeder’s preferences to support early-generation selection decisions in plant breeding. The target trait was the retrospective binary classification of selected versus non-selected breeding lines during a period of five years, while the selection decisions of the breeder were predicted by various machine learning models. The explained variance of these selection decisions was of moderate magnitude (${\mathsf{\rho }}_{\mathrm{S}\mathrm{N}\mathrm{P}}^2$ = 0.45), and the models’ precision suggested that the breeder’s selection decisions were to some extent predictable (~20%), especially when some of the pending selection candidates were part of the training population (~30%). Training machine learning algorithms with breeders’ selection decisions can thus aid breeders in their decision-making processes, particularly when integrating human and artificial intelligence in the form a recommender system to potentially reduce a breeder’s effort and the required time to find interesting selection candidates. Full article

Poultry production systems are usually exposed to important infections that could be prevented by vaccination programs. Conventional methods of vaccination such as drinking water; spray, eye, or nose inoculation; and injection are usually given after hatching and have many disadvantages. Therefore, there is a great need for searching of alternative ways for vaccination process. In ovo vaccination technology is now regarded as an alternative approach to post-hatch vaccination in modern poultry operations. This technique is effective, fast, provides uniform vaccine dosing and delivery, is suitable for massive production, and reduces labor costs. Routine in ovo vaccination is applied during the late stage of embryonic development between days 17.5 and 19.25 of egg incubation. The best route of inoculation of the vaccine is in the amniotic fluid or in the embryo’s muscles, without causing any hatchability or chick quality losses. Accordingly, the inoculation site, the age of the embryos and breeders, presence of maternal antibodies, and the sanitation of equipment’s and the environment during the vaccination process affect the efficiency of the in ovo vaccination technique. In ovo vaccination technology is currently applied for vaccination against several economically important viral diseases such as Newcastle, infectious bursal disease, Marek’s disease, infectious laryngotracheitis, infectious bronchitis, avian influenza, and avian metapneumovirus. Moreover, vaccines used for prevention of mycoplasmosis and coccidiosis could be applied in ovo instead of in post-hatching application. It can be concluded that in ovo vaccination is a rapidly growing trend of vaccine technology, and it can replace post-hatching vaccination conventional methods. Full article

Progressive retinal atrophies (PRAs) are a genetically heterogeneous group of inherited eye diseases that affect over 100 breeds of dog. The initial clinical sign is visual impairment in scotopic conditions, as a consequence of rod photoreceptor cell degeneration. Photopic vision degeneration then follows, due to progression of the disease to the cone photoreceptors, and ultimately results in complete blindness. Two full-sibling English Shepherds were diagnosed with PRA at approximately 5 years old and tested clear of all published PRA genetic variants. This study sought to identify the novel PRA-associated variant segregating in the breed. We utilised a combined approach of whole genome sequencing of the probands and homozygosity mapping of four cases and 22 controls and identified a short interspersed nuclear element within an alternatively spliced exon in FAM161A. The XP_005626197.1 c.17929_ins210 variant was homozygous in six PRA cases and heterozygous or absent in control dogs, consistent with a recessive mode of inheritance. The insertion is predicted to extend exon 4 by 39 aberrant amino acids followed by an early termination stop codon. PRA is intractable to treatment, so the development of a genetic screening test, based on the associated variant, is significant, because it provides dog breeders/owners with a means of reducing the frequency of the disease variant within this breed as well as minimising the risk of breeding puppies that will develop this blinding disease. Full article

During the last twenty years, minimal white spotting associated with blue eyes was selected by feline breeders to create the Altai, Topaz, and Celestial breeds. Additionally, certain breeders introduced this trait in their lineages of purebred cats. The trait has been called “dominant blue eyes (DBE)” and was confirmed to be autosomal dominant in all lineages. DBE was initially described in outbred cats from Kazakhstan and Russia and in two purebred lineages of British cats from Russia, as well as in Dutch Maine Coon cats, suggesting different founding effects. We have previously identified two variants in the Paired Box 3 (PAX3) gene associated with DBE in Maine Coon and Celestial cats; however, the presence of an underlying variant remains undetermined in other DBE breeding lines. Using a genome-wide association study, we identified a single region on chromosome C1 that was associated with DBE in British cats. Within that region, we identified PAX3 as the strongest candidate gene. Whole-genome sequencing of a DBE cat revealed an RD-114 retrovirus LTR (long terminal repeat) insertion within PAX3 intron 4 (namely NC_018730.3:g.206975776_206975777insN[433]) known to contain regulatory sequences. Using a panel of 117 DBE cats, we showed that this variant was fully associated with DBE in two British lineages, in Altai cats, and in some other DBE lineages. We propose that this NC_018730.3:g.206975776_206975777insN[433] variant represents the DBE^ALT (Altai Dominant Blue Eye) allele in the domestic cat. Finally, we genotyped DBE cats from 14 lineages for the three PAX3 variants and showed that they were not present in four lineages, confirming genetic heterogeneity of the DBE trait in the domestic cat. Full article

Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using F_ST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy. Full article

This paper introduces GRover (the grapevine rover), an adaptable mobile platform for the deployment and testing of proximal imaging sensors in vineyards for the non-destructive assessment of trunk and cordon volume and pruning weight. A SICK LMS-400 light detection and ranging (LiDAR) radar mounted on GRover was capable of producing precise (±3 mm) 3D point clouds of vine rows. Vineyard scans of the grapevine variety Shiraz grown under different management systems at two separate locations have demonstrated that GRover is able to successfully reproduce a variety of vine structures. Correlations of pruning weight and vine wood (trunk and cordon) volume with LiDAR scans have resulted in high coefficients of determination (R² = 0.91 for pruning weight; 0.76 for wood volume). This is the first time that a LiDAR of this type has been extensively tested in vineyards. Its high scanning rate, eye safe laser and ability to distinguish tissue types make it an appealing option for further development to offer breeders, and potentially growers, quantified measurements of traits that otherwise would be difficult to determine. Full article