Forests are essential resources on a global scale, not only for the ecological benefits, but also for economical and landscape purposes. However, in recent years, a large number of forest species have suffered a serious decline, with maritime pine being one of the most affected. In Portugal, the maritime pine forest has been devastated by the pine wood nematode (PWN), the causal agent of pine wilt disease. In this study, RNA-Seq data was used to characterize the maritime pine response to infection with PWN, by determining the differentially expressed genes and identifying the regulatory networks and pathways associated. The analyses showed clear differences between an early response that occurs immediately after inoculation and a late response that is observed seven days after inoculation. Moreover, differentially expressed genes related to secondary metabolism, oxidative stress and defense against pathogen infection were identified over different time points. These results provide new insights about the molecular mechanisms and metabolic pathways involved in the response of Pinus pinaster against PWN infection, which will be a useful resource in follow-up studies and for future breeding programs to select plants with lower susceptibility to this disease.

Pine wilt disease (PWD) caused by pine wood nematode (PWN), Bursaphelenchus xylophilus, is a serious threat to global forest populations of conifers, in particular Pinus spp. Recently, the presence of PWN was reported in dead Yunnan pine (Pinus yunnanensis) trees under natural conditions. To further understand the potential impact caused by PWN in Yunnan pine populations, a transcriptional profiling analysis was performed over different time points (0 hours (h), 6 h, 24 h, 48 h, and 7 days) after PWN inoculation. A total of 9961 differentially expressed genes were identified after inoculation, which suggested a dynamic response against the pathogen, with a more intense pattern at 48 h after inoculation. The results also highlighted a set of biological mechanisms triggered after inoculation that provide valuable information regarding the response of Yunnan pine to PWN infection. When compared with maritime pine (Pinus pinaster), the Yunnan pine response was less complex and involved a smaller number of differentially expressed genes, which may be associated with the increased degree of resistance to PWN displayed by Yunnan pine. These results revealed different strategies to cope with PWN infection by these two pine species, which display contrasting degrees of susceptibility, especially in the timely perception of the infection and response magnitude.

As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ H_o ≤ .34; .30 ≤ H_e ≤ .35; 1.7 × 10^–3 ≤ π ≤ 3.1 × 10^–3) and the levels of inbreeding were negligible (.005 ≤ F_IS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.

Gastrointestinal nematodes (GIN) are one of the main constraints affecting sheep production worldwide. For decades, control methods based on anthelmintics have been extensively used, which ended up in multiple drug‐resistant helminth strains. Selective breeding for disease resistance is a long‐term and sustainable strategy to improve animal health, welfare and productivity. Therefore, we performed a genome‐wide association study using a customized SNP panel to identify genomic regions and molecular mechanisms associated with GIN resistance/susceptibility among Portuguese Merino and Merino‐related sheep. Two SNPs located within centromere protein K (chr 16; 14 439 999 bp) and NADH: ubiquinone oxidoreductase complex assembly factor 2 (chr 16; 19 366 442 bp) genic regions reached genome‐wide Bonferroni significance ( p = 2.08 × 10 ⁻⁶ ). Additionally, five genome‐wide suggestive SNPs were detected within genic regions of adenomatous polyposis coli regulator of WNT signaling pathway (chr 7; 1 050 994 bp), regulator of G protein signaling 8 (chr 12; 68 278 650 bp) and hypoxia inducible factor 3 subunit alpha (chr 14; 57 059 428 bp), as well as in intergenic regions near calcium binding and coiled‐coil domain 1 and ATP synthase membrane subunit C locus 2 (chr 3 142 391 546 bp) and semaphorin‐6D (chr 7; 65 321 727 bp). Candidate genes located in these regions are involved in intestinal homeostasis, epithelial barrier reinforcement, and regulatory mechanisms of immune response. These results provide new and useful information about the genetic architecture underlying GIN infection in Portuguese Merino sheep. Further analyses are needed to validate these SNPs and assess their contribution to selection strategies focused on breeding animals with enhanced GIN resistance.

The identification of skeletal remains recovered from archaeological contexts is central to the reconstruction of past societies, environments, and human-animal relationships. Among the skeletal el...