Disentangling genotype and environment specific latent features for improved trait prediction using a compositional autoencoder.

In plant breeding and genetics, predictive models traditionally rely on compact representations of high-dimensional data, often using methods like Principal Component Analysis (PCA) and, more recently, Autoencoders (AE). However, these methods do not separate genotype-specific and environment-specific features, limiting their ability to accurately predict traits influenced by both genetic and environmental factors. We hypothesize that disentangling these representations into genotype-specific and environment-specific components can enhance predictive models.

Physiological and phenological adjustments in water and carbon fluxes of Aleppo pine forests under contrasting climates in the Eastern Mediterranean.

The ability of plants to adjust to the adverse effects of climate change is important for their survival and for their contribution to the global carbon cycle. This is particularly true in the Mediterranean region, which is among the regions that are most vulnerable to climate change. Here, we carried out a 2-year comparative ecophysiological study of ecosystem function in two similar Eastern Mediterranean forests of the same tree species (Pinus halepensis Mill.

The Dissemination of Conidia by Females of the Red Palm Weevil, Suggests a New Mechanism for Prevention Practices.

Direct contact between the conidia of entomopathogenic fungi (EPF) and their host is a prerequisite to successful infection; the host can, therefore, be infected by both direct treatment and by transmission of fungal inoculum from infested surfaces. This unique characteristic makes EPF especially relevant for the control of cryptic insects. In the case of the red palm weevil (RPW) , the eggs and larvae are almost inaccessible to direct-contact treatment.

Geographic factors and climatic fluctuation drive the genetic structure and demographic history of (Cycadaceae), an endemic endangered species to Hainan Island in China.

Hainan Island had experienced several cold-warm and dry-humid fluctuations since the Late Pleistocene period, resulting in separating and connecting from the mainland several times with the cyclic rise and fall of sea level. The fluctuations can change the biota and ecological environment in the island. Carruthers is endemic to Hainan Island and is classified as endangered by the International Union for Conservation of Nature (IUCN).

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes.

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation.

Characterization of the complete chloroplast genome of (Cycadaceae), an endemic species in the red river region of China.

In this study, we determined the complete chloroplast genome of (Cycadaceae), one of the first-class protected plants in China. The chloroplast genome is 162,048 bp in length with 133 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content is 39.

Effects of the Noncoding Subgenomic RNA of Red Clover Necrotic Mosaic Virus in Virus Infection.

In recent years, a new class of viral noncoding subgenomic RNA (ncsgRNA) has been identified. This RNA is generated as a stable degradation product via an exoribonuclease-resistant RNA (xrRNA) structure, which blocks the progression of 5'→3' exoribonuclease on viral RNAs in infected cells. Here, we assess the effects of the ncsgRNA of red clover necrotic mosaic virus (RCNMV), called SR1f, in infected plants.

Sex and Regeneration.

Regeneration is usually regarded as a unique plant or some animal species process. In reality, regeneration is a ubiquitous process in all multicellular organisms. It ranges from response to wounding by healing the wounded tissue to whole body neoforming (remaking of the new body).

Leaf Plasmodesmata Respond Differently to TMV, ToBRFV and TYLCV Infection.

Macromolecule and cytosolic signal distribution throughout the plant employs a unique cellular and intracellular mechanism called plasmodesmata (PD). Plant viruses spread throughout plants via PD using their movement proteins (MPs). Viral MPs induce changes in plasmodesmata's structure and alter their ability to move macromolecule and cytosolic signals.

Florigen governs shoot regeneration.

It is widely known that during the reproductive stage (flowering), plants do not root well. Most protocols of shoot regeneration in plants utilize juvenile tissue. Adding these two realities together encouraged us to study the role of florigen in shoot regeneration.

Underground heterosis for yield improvement in melon.

Heterosis, the superiority of hybrids over their parents, is a major genetic force associated with plant fitness and crop yield enhancement. We investigated root-mediated yield heterosis in melons (Cucumis melo) by characterizing a common variety grafted onto 190 hybrid rootstocks, resulting from crossing 20 diverse inbreds in a diallel-mating scheme. Hybrid rootstocks improved yield by more than 40% compared with their parents, and the best hybrid yield outperformed the reference commercial variety by 65% under both optimal and minimal irrigation treatments.

The natural hybridization between species and (Senecioneae, Asteraceae) suggests underdeveloped reproductive isolation and ambiguous intergeneric boundary.

Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between and was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear.

Functional analysis of MYB alleles from Solanum chilense and Solanum lycopersicum in controlling anthocyanin levels in heterologous tobacco plants.

Flavonoids are natural pigments occurring in plants and are present in fruits, leaves, stems, roots, and flowers. Tobacco plants transformed with an MYB regulatory gene from either Solanum chilense (Sc) or S. lycopersicum (Sl) demonstrate that ScANT1 induces a higher level of anthocyanin accumulation in comparison to SlANT1 and that this gene is sufficient to promote increased anthocyanin levels.

Control of translation during the unfolded protein response in maize seedlings: Life without PERKs.

The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2α to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress.

Genetic studies of extra-early provitamin-A maize inbred lines and their hybrids in multiple environments.

Vitamin A deficiency, drought, low soil nitrogen (low-N), and parasitism of maize ( L.) cause malnutrition and food insecurity in sub-Saharan Africa. The objectives of this study were to determine combining abilities of extra-early provitamin A (PVA) lines, classify them into heterotic groups (HGs), identify testers, and determine yield stability of hybrids under contrasting environments in two trials.

Tomato T2 ribonuclease LE is involved in the response to pathogens.

T2 ribonucleases (RNases) are RNA-degrading enzymes that function in various cellular processes, mostly via RNA metabolism. T2 RNase-encoding genes have been identified in various organisms, from bacteria to mammals, and are most diverse in plants. The existence of T2 RNase genes in almost every organism suggests an important biological function that has been conserved through evolution.

High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo.

Melon is an important crop that exhibits broad variation for fruit morphology traits that are the substrate for genetic mapping efforts. In the post-genomic era, the link between genetic maps and physical genome assemblies is key for leveraging QTL mapping results for gene cloning and breeding purposes. Here, using a population of 164 melon recombinant inbred lines (RILs) that were subjected to genotyping-by-sequencing, we constructed and compared high-density sequence- and linkage-based recombination maps that were aligned to the reference melon genome.

Pathways for Carotenoid Biosynthesis, Degradation, and Storage.

Carotenoids are isoprenoid compounds synthesized de novo in all photosynthetic organisms as well as in some nonphotosynthetic bacteria and fungi. In plants, carotenoids are essential for light harvesting and photoprotection. They contribute to the vivid color found in many plant organs.

Genetic mapping of green curd gene Gr in cauliflower.

Gr5.1 is the major locus for cauliflower green curd color and mapped to an interval of 236 Kbp with four most likely candidate genes. Cauliflower with colored curd enhances not only the visual appeal but also the nutritional value of the crop.

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits.

Melon is an economically important fruit crop that has been cultivated for thousands of years; however, the genetic basis and history of its domestication still remain largely unknown. Here we report a comprehensive map of the genomic variation in melon derived from the resequencing of 1,175 accessions, which represent the global diversity of the species. Our results suggest that three independent domestication events occurred in melon, two in India and one in Africa.

Investigation of Substituent Effect in Modified Nature-Sourced Polymers: Rational Side Chain Engineering to Control Yield, Design, and Properties.

"Side chain engineering" research has yielded many promising and beneficial results, with applications in various fields. However, this research did not receive sufficient focus when nature-sourced polymers are concerned. In this study, we have performed side chain engineering on chitosan, a nature-sourced polysaccharide, by coupling it with a number of aliphatic aldehydes of varying chain lengths.

The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon.

Color and pigment contents are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops.

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in .

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors.

Activity of native and commercial strains of Metarhizium spp. against the poultry red mite Dermanyssus gallinae under different environmental conditions.

The poultry red mite (PRM), Dermanyssus gallinae, is a major pest of laying hens with extremely limited control means. To evaluate the potential of natural and commercial entomopathogenic fungi (EPF) for use against D. gallinae, we tested four wild populations of D.

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops.

The Cucurbitaceae family (cucurbit) includes several economically important crops, such as melon, cucumber, watermelon, pumpkin, squash and gourds. During the past several years, genomic and genetic data have been rapidly accumulated for cucurbits. To store, mine, analyze, integrate and disseminate these large-scale datasets and to provide a central portal for the cucurbit research and breeding community, we have developed the Cucurbit Genomics Database (CuGenDB; http://cucurbitgenomics.