Genome analyses and breeding of polyploid crops.

Polyploidization is a common and important evolutionary process in the plant kingdom. Compared with diploid plant species, the intricate genome architecture of polyploid plant species presents substantial challenges in applying multi-omics approaches for crop breeding improvement. In this Review, we summarize the current techniques for analysing polyploid genomes, including constructing reference genomes and pan-genomes, and detecting variants.

Invited Review: Using data from sensors and other precision farming technologies to enhance the sustainability of dairy cattle breeding programs.

The increased uptake of sensor technologies and precision farming tools for the dairy cattle sector is enabling real-time monitoring of animal health, welfare, and productivity. These digital advancements provide high-frequency, objective, and large-scale phenotypic data for breeding purposes. This review explores the potential of sensor-derived data to improve genetic and genomic evaluations in dairy cattle and outlines key challenges, opportunities, and approaches associated with their implementation.

Schmallenberg virus epidemiology and regional control strategies: diagnostics, vaccines, and vector management.

Schmallenberg virus (SBV) is an emerging orthobunyavirus transmitted by midges. It poses a serious global health threat to ruminants, especially during pregnancy, causing abortion, stillbirths, and congenital malformations. Since its first outbreak in 2011, SBV has spread across Europe and other regions.

A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.

Extrachromosomal circular DNA (eccDNA) has been described in several eukaryotic species and has been shown to impact phenomena as diverse as cancer and herbicide tolerance. EccDNA is thought to arise mainly through transposable element (TE) mobilization. Because studies based on short-read sequencing cannot efficiently identify full-length eccDNA forms generated from TEs, we employed the CIDER-Seq pipeline based on long-read sequencing, to obtain full-length eccDNAs from Arabidopsis.

Genetic parameters and relevance for heat stress assessment in dairy cattle of 2 udder health traits: Somatic cell score and differential somatic cell count.

Somatic cell count is widely used for large-scale udder health monitoring and remains a proxy for mastitis incidence still used in many genetic evaluation systems. This trait and its log-transformation, SCS, are thus also available to study the effect of heat stress on mammary gland health. Currently, a new trait called differential somatic cell count (DSCC), which represents the percentage of neutrophils and lymphocytes in the total SCC, is increasingly phenotyped simultaneously with SCC.

A BAC-guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava.

Background: Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging.

Effects of warm-season feeding on yak growth, antioxidant capacity, immune function, and fecal microbiota.

The yak () is of great importance to the local ecosystem and animal husbandry on the Tibetan Plateau. However, the impacts of different feeding practices on yak growth, health, and ecosystem interactions are not fully understood. This study investigates the effects of warm-season grazing and housing-feeding on yak growth performance, antioxidant capacity, immune function, metabolome, and fecal microbiota.

Polyphosphate-Induced Changes in Transcriptome and Root-Functional Traits Elucidate Enhanced Phosphorus Acquisition Mechanisms and Growth of Durum Wheat.

Phosphate (P) fertilization impacts many rhizosphere processes, driving plant P use efficiency. However, less is known about the induced molecular and physiological root-rhizosphere traits in responses to polyphosphates (PolyP), particularly root transcriptome and belowground functional traits responsible for P acquisition. The present study aims to investigate physiological and transcriptomic belowground mechanisms explaining the enhanced durum wheat P acquisition under PolyP (PolyB and PolyC) supply.

Investigating the genetic background of novel behavioral indicators of robotic milking efficiency in North American Holstein cattle.

The adoption of automated milking systems (AMS) across worldwide dairy farms has grown considerably over the last few decades. Automated milking systems contribute to reducing labor costs, increasing milk performance, improving cow welfare, and generating large-scale data on a routine basis that can be used for deriving novel traits for breeding purposes. Therefore, the primary objectives of this study were to (1) derive behavioral traits from AMS data and assess their phenotypic variability during lactation in US Holstein cattle, and (2) estimate variance components and genetic parameters for these traits.

An Agrobacterium-mediated base editing approach generates transgene-free edited banana.

Genome editing for the development of improved varieties is supported by the possibility of segregating out the editor T-DNA cassette after genome editing in many crop species. Removal of the T-DNA cassette prevents potential continuous editing activity in the transformed plant and furthermore facilitates regulatory approval. While transgene outcrossing of exogenous sequences is possible for many crops, this is not the case for vegetatively propagated and sterile crops, such as Cavendish bananas.

A 6.49-Mb inversion associated with the purple embryo spot trait in potato.

Unlabelled: The embryo spot trait leads to a deep purple or reddish coloration at the base of the cotyledons of the embryo, visible on both sides of flat potato () seeds. This trait has long been used by potato researchers and breeders as a morphological marker during dihaploid induction. The formation of embryo spots reflects the accumulation of anthocyanins, but the genetic basis of this trait remains unclear.

Exploring the relationship between predicted negative energy balance and its biomarkers of Holstein cows in first-parity early lactation.

The negative energy balance (NEB) state in dairy cows is a critical factor affecting health, reproduction, and production, particularly during early lactation. Multiple blood and milk biomarkers change when dairy cows are in the NEB state. Direct measurement of NEB is impractical for large-scale use due to costs, necessitating reliance on indirect predictors such as milk mid-infrared (MIR) spectrometry-based predicted biomarkers.

Weighted single-step genomic best linear unbiased predictor enhances the genomic prediction accuracy for milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation.

Previous studies have shown that milk citrate predicted by milk mid-infrared (MIR) spectra is strongly affected by a few genomic regions. This study aimed to explore the effect of weighted single-step GBLUP on the accuracy of genomic prediction (GP) for MIR-predicted milk citrate in early-lactation Holstein cows. A total of 134,517 test-day predicted milk citrate collected within the first 50 DIM on 52,198 Holstein cows from the first 5 parities were used.

Leveraging a phased pangenome for haplotype design of hybrid potato.

The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.) dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement.

Genetic investigations into the use of sensory evaluation: the case of boar taint discrimination in Pietrain sired crossbreds.

Using genetic selection for raising intact boars, which improves growth and feed efficiency, is a promising alternative to castration for mitigating boar taint. Selective breeding has the potential to help to identify and select genetic lines with a reduced risk of boar taint. Common phenotypes are laboratory measurements of skatole (SKA) and androstenone (ANON) i.

Key role played by mesophyll conductance in limiting carbon assimilation and transpiration of potato under soil water stress.

Introduction: The identification of the physiological processes limiting carbon assimilation under water stress is crucial for improving model predictions and selecting drought-tolerant varieties. However, the influence of soil water availability on photosynthesis-limiting processes is still not fully understood. This study aimed to investigate the origins of photosynthesis limitations on potato () during a field drought experiment.

Route Planning Process by the Endangered Black Lion Tamarin in Different Environmental Contexts.

Daily, primates take a variety of decisions to establish why, when, and where to move. However, little is known about the factors influencing and shaping primate daily routes. We investigated the decision-making processes linked to route planning in four groups of black lion tamarins (BLT-Leontopithecus chrysopygus).

Stable Isotopes Analysis of Black Lion Tamarins Reveals Increasing Arthropod Consumption When Fruit Productivity Decreases in Forest Fragments.

Given the cryptic and elusive nature of prey consumption, quantifying its contribution to the diet of free-ranging primates using behavioral methods is challenging. In this context, the use of carbon and nitrogen-stable isotopes represents a promising alternative approach. Here, we used stable isotope analysis to estimate the proportion of arthropods and fruits in the diet of black lion tamarins (Leontopithecus chrysopygus), an endangered primate endemic to the Brazilian Atlantic Forest.

Analyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication.

Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions.

Both GacS-regulated lipopeptides and the type three secretion system contribute to Pseudomonas cichorii induced necrosis in lettuce and chicory.

Pseudomonas cichorii SF1-54, the causal agent of lettuce midrib rot disease, produces lipopeptides cichofactins and cichopeptins which are important virulence factors. The GacS/GacA two-component system is well known to regulate production of lipopeptides in pseudomonads. Additionally, the functions of the type three secretion system (T3SS) in P.

Prediction of body condition score throughout lactation by random regression test-day models.

Regular monitoring of body condition score (BCS) changes during lactation is a crucial management tool in dairy cattle; however, the current BCS measurements are often discontinuous and unevenly spaced in time. The aim of this study was to investigate the ability of random regression test-day models (RR-TDM) to predict BCS for the entire lactation in dairy cows even if the actual scoring is limited to one BCS record. The data consisted of test-day records of milk yield (MY), fat percentage (FP), protein percentage (PP) and BCS (based on a 9-point scale with unit increments; 1-9) collected from 2014 to 2022 in 128 herds in the Walloon Region of Belgium.

Bacillus velezensis: a versatile ally in the battle against phytopathogens-insights and prospects.

The escalating interest in Bacillus velezensis as a biocontrol agent arises from its demonstrated efficacy in inhibiting both phytopathogenic fungi and bacteria, positioning it as a promising candidate for biotechnological applications. This mini review aims to offer a comprehensive exploration of the multifaceted properties of B. velezensis, with particular focus on its beneficial interactions with plants and its potential for controlling phytopathogenic fungi.