Selection For Traits Research Articles

Overcoming challenges to access ecological function: a marine soft-bottom perspective

Ecosystem functioning studies have gained prominence due to concerns about the decline of species. In marine sediments, benthic invertebrates perform important ecological functions. However, the challenges within the field of functional ecology are sparsely discussed. Our aim was to systematize the problems and suggest pathways forward. To achieve this, we review recent articles on functional ecology on marine sediments and identified two main issues. First, the absence of a clear definition of terms. Second, in terms of applicability, we observed a mismatch between the scales of functioning and traits, incomplete information on trait databases, inappropriate selection of traits, subjective measures of traits, overlooked trait variability and data analyses without the link between the taxonomy and the traits associated with functions. We propose some pathways to overcome the challenges, such as (i) reasoning of the concept of function, process and trait, (ii) increasing experiments to measure functions, (iii) clarification of the relationship between traits and functions, (iv) clear procedure for assigning trait scores, (v) experiments for understanding trait variability and function performance, and (vi) analyses that consider the sets of traits of each taxon. Overcoming these challenges will allow us to advance research and fill gaps in knowledge of ecosystem functioning.

Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies

Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578, and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes, and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.

Enhancing Growth of Upland Rice in Low-Phosphorus Soil by Leveraging Root Morphological Traits

Low phosphorus (P) in the upland ecosystems negatively, influence rice growth and causes significant yield losses. In the present study, 9 upland rice genotypes were screened to identify root traits that support the growth in low P soil in a cement tank. Rice genotypes showed significant (p = ≤ 0.05) variation for number of root tips (NRT), number of root branching points (NBP), total root length (TRL), whole root network area (NA), average root diameter, root volume (RV), root surface area (RSA), first order root length (FORL), and second order root length (SORL). BW01 and ITA01 recorded the highest NRT, NBP, TRL, RV, NA, RSA, FORL and SORL while NERICA04 had the lowest representing 5.8, 8.0, 7.6, 6.8, 9.0, 5.8, and 9.3 differences in these traits under low P soil. NRT significantly positively correlated with NBP, TRL, NA, RV, RSA, FORL indicating the role of different root traits in foraging for soil nutrients. The principal component analysis (PCA) showed that the NRT, NBP, TRL, RSA and SORL are important and effective root traits for selection in rice breeding under low P soil supply. BW01 and ITA01 recorded well developed root system indicating that they are P-efficient than P-inefficient NERICA04 under low P soil conditions. Therefore, BW01 and ITA01 can targeted for cultivation in P deficient soils and also used as donor of novel root traits to improve P-inefficient rice cultivars.

Adaptive potential in the face of a transmissible cancer in Tasmanian devils.

Emerging infectious diseases (EIDs) not only cause catastrophic declines in wildlife populations but also generate selective pressures that may result in rapid evolutionary responses. One such EID is devil facial tumour disease (DFTD) in the Tasmanian devil. DFTD is almost always fatal and has reduced the average lifespan of individuals by around 2 years, likely causing strong selection for traits that reduce susceptibility to the disease, but population decline has also left Tasmanian devils vulnerable to inbreeding depression. We analysed 22 years of data from an ongoing study of a population of Tasmanian devils on Freycinet Peninsula, Tasmania, to (1) identify whether DFTD may be causing selection on body size, by estimating phenotypic and genetic correlations between DFTD and size traits, (2) estimate the additive genetic variance of susceptibility to DFTD, and (3) investigate whether size traits or susceptibility to DFTD were under inbreeding depression. We found a positive phenotypic relationship between head width and susceptibility to DFTD, but this was not underpinned by a genetic correlation. Conversely, we found a negative phenotypic relationship between body weight and susceptibility to DFTD, and there was evidence for a negative genetic correlation between susceptibility to DFTD and body weight. There was additive genetic variance in susceptibility to DFTD, head width and body weight, but there was no evidence for inbreeding depression in any of these traits. These results suggest that Tasmanian devils have the potential to respond adaptively to DFTD, although the realised evolutionary response will critically further depend on the evolution of DFTD itself.

The selection traits of mite non-reproduction (MNR) and Varroa sensitive hygiene (VSH) show high variance in subsequent generations and require intensive time investment to evaluate

The honey bee ectoparasite Varroa destructor is the main cause of honey bee colony losses worldwide. Over the last decades, several projects have focused on improving the robustness of Apis mellifera against this parasitic mite. Selection traits, such as mite non-reproduction (MNR) and Varroa sensitive hygiene (VSH), are favored selection factors in Varroa resistance projects. VSH is a trait where adult honey bees remove the Varroa-infested brood. During this process, the female mites are arrested in their reproductive cycle leading to a reduction of the Varroa population within the bee colony. From 2019 to 2022, 1402 queens were instrumentally inseminated with single or multiple drones in a breeding program. Colonies headed by these queens were established annually, and the MNR and VSH levels were analyzed. VSH was evaluated in response to cells artificially infested with Varroa, and colonies with high VSH values were used to generate our selected VSH stock. Despite crossing high VSH drones and queens, we measured a remarkable heterogeneity of MNR and VSH in the next generation(s), most likely due to the well-described, high recombination rate in the honey bee genome. When assessed multiple times in the same colony, great variance between measurements was observed. Detailed evaluations of daughter colonies are thus required if selection programs want to breed colonies with reliable VSH traits. This constant need to evaluate all offspring to ensure the desirable resistance traits are present results in high workloads and great expenses in selection programs. Furthermore, such large-scale breeding programs are inefficient due to high fluctuations between measurements and generations, indicating we need to develop new approaches and improved methods for assessing Varroa resistance.

Thermal response in Boer goats differing in coat colour

Context The coat is the first defense layer protecting animals from direct sunlight, influencing radiant-heat absorption and loss. Dark coat colour may increase animal heat impact because of higher absorption of solar radiation. Aims We investigated the impact of pigmentation intensity on the heads of animals and their thermal responses to solar radiation. Furthermore, we compared the thermal responses between dark and light brown-coloured animals, to determine whether the duration of sun and shade exposure (3 h each) is sufficient to differentiate the heat gain and losses between the two groups. Methods The effect of coat colour on rectal and surface temperatures in Boer goats, classified according to their head pigmentation pattern as dark (DB, N = 11) or light brown (LB, N = 11), exposed to sun and shade, was evaluated. The animals’ body and head surface temperatures were measured the same day before, during, and after sun exposure by using infrared thermography. Individual thermographic images were analysed by body regions (rump, leg, neck) and head areas (eye, ear, upper and lower part of the head, and the muzzle). Key results During solar radiation, all measured variables increased. In the shade, the rump, leg, and neck surfaces remained elevated, whereas the head area cooled down faster, with the highest temperature changes measured for the ear of about 10%. Most surface cooling occurred within 30 min after returning to the shade. Coat colour groups differed only in higher overall muzzle temperature of DB than that of LB goats (P = 0.048). Correlations between rectal and surface temperatures were low to medium, ranging from −0.02 (eye) to 0.31 (muzzle). Conclusions The head area is suggested as the important thermal window for heat dissipation and selective brain cooling. Light brown-headed animals were more efficient in eliminating the heat gained from solar radiation when returned to shade. Implications The colouration of the animal’s head may play an important role for its heat tolerance. As an easy-to-recognise characteristic, coat colour can serve as a selection trait for local goat populations. In view of global warming, selection for lighter coat colour in domestic ruminants may also become important even under temperate climates.

Heritability and Genetic Correlations of Carcass and Meat Quality Traits in White and Brown Strains of Japanese Quail

Successful breeding programs for Japanese quails rely on accurately estimating genetic parameters linked to economically important traits such as body weight, carcass characteristics, and meat quality. The objective of the present study was to evaluate body weight (BW) characteristics, carcass attributes, and their genetic correlations with select meat quality traits in two strains of Japanese quail (white and brown). A total of 530 quail chicks, with 265 from each strain, were included in the analysis. At six weeks of age, the quails were slaughtered, and carcass traits as well as amino acid profiles were measured. For BW traits, the heritability (h2) estimates ranged from 0.27 at d 1 to 0.36 at d 42. The h2 estimated for carcass traits ranged from 0.19 for liver weight, to 0.42 for carcass yield (CY). The h2 estimated for drip loss (DL) of meat quality was 0.21, and the h2 estimate was 0.35 for the meat's ultimate Ph (Phu). White quail quails recorded the heaviest weight of all carcass traits. Also, white quails had the highest water-holding capacity (WHC), yellowness (b*), and lightness (L*) with the lowest level of DL, cooking losses (CL), and redness (a*) in muscles compared with brown quails. A high genetic correlation of 0.32 was noted between CW carcass weight (CW) and b*. For the pHU, a negative correlation of -0.11 was exhibited with BW. In contrast, L* appeared to have a positive but smaller relationship with CW and CY. High negative correlations were noted for b* with BW and CY -0.24 and -0.27, respectively. The CW showed a moderate relationship (0.19) with CL. In conclusion, the current study revealed that the white quail strain had high BW, as well as the finest carcass traits and meat quality. Therefore, white plumage Japanese quail might be preferred as a meat-producing strain. Keywords: Amino acid, Carcass, Genetic correlation, Meat quality, Heritability, Quail

Molecular markers and their importance for pig production and breeding: an overview

The DNA polymorphisms are changes in the sequence of nucleotide bases that result in genetic differences among two or more individuals. These polymorphisms have been used as molecular markers and contribute to studies in swine related to genetic diversity, pedigree analysis, selection, and discovery of genomic regions controlling economically important traits. Among the molecular markers, Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) have been most studied in pigs mainly due to their greater abundance in the genome, ease of detection and possibility of automation. The knowledge and application of information from molecular marker shave contribute to a more efficient and competitive pig production. Furthermore, in pig breeding programs, the molecular markers are especially important to allow higher efficiency in selection for traits with low heritability, difficult or expensive to measure, sex-limited, and that express later in the animal’s life, resulting in a higher prediction accuracy for these traits. Considering the relevance of DNA molecular markers for the development of pig production and the advances in research in this area, we aimed to present an overview of the main research results related to the discovery, contribution and implementation of molecular markers in pig breeding and production. This review contextualizes and summarizes important results and recent findings in order to update the reader and stimulate future research based on the identification and relevance of molecular markers applied to pig production.

Vertical farming goes dynamic: optimizing resource use efficiency, product quality, and energy costs

Vertical farming is considered to be a key enabler for transforming agrifood systems, especially in or nearby urbanized areas. Vertical farming systems (VFS) are advanced indoor cropping systems that allow for highly intensified and standardized plant production. The close control of environmental parameters makes crop production stable and repeatable, ensuring year-round uniform product quality and quantity irrespective of location. However, due to continuous changes in plant physiology and development, as well as frequent changes in electricity prices, the optimum conditions for crop production and its associated costs can change within days or even minutes. This makes it beneficial to dynamically adjust setpoints for light (intensity, spectrum, pattern, and daylength), CO2, temperature, humidity, air flow, and water and nutrient availability. In this review, we highlight the beneficial effects that dynamic growth conditions can have on key plant processes, including improvements in photosynthetic gas exchange, transpiration, organ growth, development, light interception, flowering, and product quality. Our novel findings based on modeling and experimentation demonstrate that a dynamic daily light intensity pattern that responds to frequent changes in electricity prices can save costs without reducing biomass. Further, we argue that a smart, dynamic VFS climate management requires feedback mechanisms: several mobile and immobile sensors could work in combination to continuously monitor the crop, generating data that feeds into crop growth models, which, in turn, generate climate setpoints. In addition, we posit that breeding for the VFS environment is at a very early stage and highlight traits for breeding for this specialized environment. We envision a continuous feedback loop between dynamic crop management, crop monitoring, and trait selection for genotypes that are specialized for these conditions.

Exploring intraspecific and interspecific variation of coral reef algae using a novel trait‐based framework

Abstract The development of trait‐based approaches has accelerated our understanding of how communities assemble, respond to environmental change and may best be managed in the Anthropocene. Understanding the magnitude and pattern of interspecific variability forms a critical underpinning of trait‐based approaches while exploring intraspecific variability can identify the potential of species to adapt to changing environmental drivers. Our work is motivated by the critical need for a novel conceptual framework for understanding the functional ecology of macroalgae, as the current paradigm is still mired in functional group models developed in the 1980s. Our objective was to quantify interspecific and intraspecific functional trait variability in three common and morphologically diverse species of tropical marine macroalgae by exploring traits relating to the ecological functions of resource acquisition, resistance to herbivory, and resistance to physical disturbance and the trade‐offs between them. We quantified intraspecific and interspecific variability of 11 functional traits for three common and morphologically diverse species of tropical macroalgae from five fringing reefs of Mo'orea, French Polynesia that were likely to capture a wide range of environmental variability. Differences in traits among species and sites were determined with PERMANOVA, visualised with non‐metric multidimensional scaling, and trade‐offs between pairs of traits explored with correlation. Finally, spatial patterns among select traits across all species were quantified. Species clustered together in distinctly different trait spaces driven by trade‐offs among suites of functional traits. Two of three species had considerable intraspecific variability, though this variability occurred at different scales, while one clustered tightly. Exploration of individual traits across species and sites revealed trade‐offs between two strategies for resource acquisition, growing tall and strong versus investing in large surface area. Synthesis. We captured novel patterns of interspecific and intraspecific variability for tropical marine macroalgae. We found fundamental differences in traits between species that may represent ecological strategies while considerable intraspecific variability demonstrates a wide range in abilities to respond to environmental drivers. Overall, our work provides novel insights into intra and interspecific trait variation that form an essential underpinning for using a trait‐based framework in a taxon that is increasingly dominant on tropical reefs.

Selection and genetic parameters of sheep of the Aginskaya breed of the Zugalay type

The results of the study of selectable traits, exterior-constitutional features of medium wool sheep of the Aginskaya breed of the Zugalay type are presented. The data of correlation-regression, variance analysis are given, according to the results of which paired and multifactor regression models have been designed. Body weight (6.4–12.6%), down length (19.3–19.7%) and awn length (13.1–16.9%) and cannon bone girth (9.1%) are characterized by the greatest variability in the studied sheep. In terms of physique indices, rams are distinguished by longer legs, better breast development, stronger bones, ewe lambs are distinguished by a more stretched, bunched and massive body with a better developed hind part. Correlation analysis of the breeding traits with external body parts indicates that live weight and wool clip in rams has a closer correlation with linear measurements in comparison with ewe lambs. In both males and females, live weight was more strongly correlated with the width in the dippers, wool clip – with the width at hips in rams, in ewe lambs the relationship was weak or practically absent. Linear regression coefficients indicate that live weight and wool clip gain in rams are predicted by an increase per unit in hip width (4.37 abs. gain; r = 0.824; p < 0.001 and 0.13 abs. gain; r = 0.792; p < 0.001). The coefficient of determination showed that in rams the changes in live weight and wool clip by 67.9 and 62.8% were explained by the width at hips, the influence of other factors – 32.1 and 37.2%, respectively. In multifactor regression models, 90.3 and 78.0% of changes in body weight and wool clip in rams are explained by the influence of a complex of linear measurements, in ewe lambs – by 25.7 and 17.5%, respectively, the remaining share is attributed to the influence of other factors, respectively.

A Synthesis Analysis of the Relationship between Main and Ratoon Crop Grain Yields in Ratoon Rice

Ratoon rice represents a viable means to enhance rice production efficiency in terms of both area and time. Nonetheless, the development of specific varieties tailored for ratoon rice has been hindered by the complexity of trait considerations required during breeding/screening processes. A pivotal step towards advancing ratoon rice breeding programs involves reducing the dimensionality of selection traits. In this study, we performed a comprehensive analysis exploring whether the yield of the main crop could serve as a predictor for ratoon crop yield, thereby simplifying the selection process. Our findings revealed significant variability in the rice yields of both main and ratoon crops, with the ratoon crop yield averaging 51% of the main crop. Importantly, the correlation between grain yields of the main and ratoon crops did not deviate from the identity line, substantiating the feasibility of predicting ratoon crop yield based on the main crop yield. The number of panicles in the ratoon crops was found to be closely linked to that of the main crop; however, the size values of the panicles in the ratoon crops exhibited less of a dependency on the main crop’s panicle size. Additionally, a general decrease in grain weight was observed in the ratoon crops compared to the main crop. In summary, this study elucidates a pathway for the simplification of selection traits, thereby enhancing the efficiency of breeding high-yielding ratoon rice varieties, with the ultimate aim of fostering the sustainable development of ratoon rice.

Combined Genome-Wide Association Studies (GWAS) and Linkage Mapping Identifies Genomic Regions Associated with Seedling Root System Architecture (RSA) under Different Nitrogen Conditions in Wheat (Triticum aestivum L.)

The nitrogen (N) use efficiency (NUE) in the roots of seedlings is beneficial for increasing crop yield. Creating marker-assisted selection for wheat root traits can assist wheat breeders in choosing robust roots to maximize nutrient uptake. Exploring and identifying the effect of different N supply conditions on root system architecture (RSA) is of great significance for breeding N efficient wheat varieties. In this study, a total of 243 wheat varieties native to the Yellow and Huai Valley regions of China were utilized for genome-wide association studies (GWAS). Furthermore, a recombinant inbred line (RIL) population of 123 lines derived from the cross between Avocet and Chilero was utilized for linkage examination. A hydroponic seedling experiment using a 96-well tray was conducted in the lab with two treatments: normal N (NN) and low N (LN). Five RSA traits, including the relative number of root tips (RNRT), relative total root length (RTRL), relative total root surface area (RTRS), relative total root volume (RTRV), and relative average root diameter (RARD), were investigated. GWAS and linkage analysis were performed by integrating data from the wheat 660 k single nucleotide polymorphism (SNP) chip and diversity arrays technology (DArT) to identify genetic loci associated with RSA. The results showed that, based on the ratio of RSA-related traits under two N supply conditions, a total of 497 SNP markers, which are significantly associated with RSA-related traits, were detected at 148 genetic loci by GWAS. A total of 10 QTL loci related to RSA were discovered and identified by linkage mapping. Combining two gene localization methods, three colocalized intervals were found: AX-95160997/QRtrl.haust-3D, AX-109592379/QRnrt.haust-5A, and AX-110924288/QRtrl.haust-7D/QRtrs.haust-7D. According to the physical location of the colocalization of these two sites, between 39.61 and 43.74 Mb, 649.97 and 661.55 Mb, and 592.44 and 605.36 Mb are called qRtrl-3D, qRnrt-5A, and qRtrl-7D. This study has the potential to enhance the effectiveness of selecting root traits in wheat breeding programs, offering valuable insights into the genetic underpinnings of NUE in wheat. These results could help in breeding wheat varieties with higher NUE by implementing focused breeding strategies.

Response of maiden ewes to the ‘ram effect’ is a robust management practice and a candidate selection trait for enhanced reproductive performance in drylands

Management of reproduction that relies on naturally based solutions is extremely important to counter the negative perception around hormone-based interventions. In Mediterranean latitudes and wider regions of non-tropical drylands, sheep do not normally ovulate during spring but exposure to a ram can induce oestrus and ovulation. This study assesses the response of maiden Barbarine ewes in drylands to the ‘ram effect’ during springtime and estimates the genetic parameters of this response. The study uses a database documenting, for 24 consecutive years, the response of nulliparous 18-month-old ewes when mated after stimulation by the ‘ram effect.’ In addition to the oestrous and fertility database, a pedigree database was also available. Nearly half of the maiden ewes responded to the ‘ram effect,’ while 24% exhibited spontaneous reproductive activity and displayed oestrus during the first 14 days following the introduction of rams. Nearly 5% of females did not exhibit oestrus, and these animals are proposed for early culling. Average annual values of Normalised Difference Vegetation Index (NDVI), reflecting vegetation cover, and the percent of maiden ewes spontaneously cycling were positively correlated (P = 0.006). Interestingly, NDVI was negatively correlated with the percentage of anoestrus females that did not respond to the ‘ram effect’ but exhibited oestrus beyond the hypothetical time frame commonly used to describe it. Average fertility was 82.8% and was significantly affected by mating year, live weight at mating, and the response to the ‘ram effect.’ The highest fertility (88.39%) was for females spontaneously cycling at the time of ram introduction, and the lowest (83.35%) was for females coming into oestrus beyond the time frame for a ram-induced oestrus and ovulation. Heritability from a univariate logit-transformed analysis for fertility was 0.10 and the genetic correlation between fertility and the interval between ram introduction and oestrus was 0.26, suggesting that a shorter interval is associated with higher fertility. Thus, the interval between ram introduction and oestrus is a good candidate for selective breeding for high fertility of maiden ewes in drylands mated out-of-season using the ‘ram effect.’

Population structure and selective signature of Kirghiz sheep by Illumina Ovine SNP50 BeadChip.

By assessing the genetic diversity and associated selective traits of Kirghiz sheep (KIR), we aim to uncover the mechanisms that contribute to sheep's adaptability to the Pamir Plateau environment. This study utilized Illumina Ovine SNP50 BeadChip data from KIR residing in the Pamir Plateau, Qira Black sheep (QBS) inhabiting the Taklamakan Desert, and commonly introduced breeds including Dorper sheep (DOR), Suffolk sheep (SUF), and Hu sheep (HU). The data was analyzed using principal component analysis, phylogenetic analysis, population admixture analysis, kinship matrix analysis, linkage disequilibrium analysis, and selective signature analysis. We employed four methods for selective signature analysis: fixation index (Fst), cross-population extended homozygosity (XP-EHH), integrated haplotype score (iHS), and nucleotide diversity (Pi). These methods aim to uncover the genetic mechanisms underlying the germplasm resources of Kirghiz sheep, enhance their production traits, and explore their adaptation to challenging environmental conditions. The test results unveiled potential selective signals associated with adaptive traits and growth characteristics in sheep under harsh environmental conditions, and annotated the corresponding genes accordingly. These genes encompass various functionalities such as adaptations associated with plateau, cold, and arid environment (ETAA1, UBE3D, TLE4, NXPH1, MAT2B, PPARGC1A, VEGFA, TBX15 and PLXNA4), wool traits (LMO3, TRPS1, EPHA5), body size traits (PLXNA2, EFNA5), reproductive traits (PPP3CA, PDHA2, NTRK2), and immunity (GATA3). Our study identified candidate genes associated with the production traits and adaptation to the harsh environment of the Pamir Plateau in Kirghiz sheep. These findings provide valuable resources for local sheep breeding programs. The objective of this study is to offer valuable insights for the sustainable development of the Kirghiz sheep industry.

161 Development, deployment, and calibration of genomic selection tools to improve performance traits for Canadian beef cattle

Abstract Genomic selection has the potential to accelerate the genetic improvement rate for difficult/expensive to measure traits such as feed efficiency and fertility traits in beef cattle. To develop genomic selection tools for Canadian beef cattle, we collected or sourced phenotypic data of feed efficiency along with other traits including carcass merit, female feed intake and fertility related traits, and their genotypes from both research and commercial herds. The phenotypic data were consolidated and recorded for contemporary groups, leading to the development of data sets including 11,292 beef cattle with residual feed intake, dry matter intake, average daily gain, metabolic body weight, 7,299 to 8,081 cattle with carcass merit traits, and 1,802 to 2,792 cows with feed intake and fertility traits after quality controls. Genotype data of the animals from various single nucleotide polymorphisms (SNP) panels were merged to the same allele format of 50K, and then imputed to 770K SNPs, and eventually to whole genome sequence variants. The refined Canadian beef cattle data sets have not only allowed us to investigate genetic architectures of the beef performance traits but also enabled the development of genomic selection tools including molecular breeding values and multiple trait selection indexes with a moderate to moderately high accuracy for the traits through a cross-validation of within reference data set. The genomic selection tools have been successfully deployed to over 10,415 breeding candidates submitted by Canadian beef producers through multiple demonstration projects. The average accuracy of the molecular breeding values and multiple trait selection index of the commercial beef cattle ranged from 0.38 to 0.49 for feed efficiency and carcass merit traits, and from 0.26 to 0.38 for female feed intake and fertility traits. Current research is focusing on calibrating the genomic selection tools with larger data sets and with more advanced genomic prediction methods.

A 3D micro-computed tomography study comparing embryonic skeletal development in layer versus broiler strains of the domestic chicken

Our objective was to analyze the effect of selection for divergent traits in the domestic chicken on embryonic skeletal development, which could affect postnatal bird welfare. Development was compared between the Ross 308 broiler line (fast growth and muscle mass accrual) and Novoponte layers (high laying rate and egg quality). In Study 1 (Initial Conditions), we characterized egg composition prior to incubation and identified the onset of embryonic skeletal mineralization in the 2 strains. In Study 2 (Developmental Dynamics), we used 3D X-ray tomographic imaging (µCT) on incubation days ED11, ED13, ED15 and ED17 to track skeletal maturation trajectories as a pseudo-time series. Results showed that Ross 308 embryos, which are heavier than Novoponte embryos, possess higher levels of yolk nutrients including phosphorus and calcium, but lower eggshell mineral content, than Novoponte embryos. Skeletal mineralization started synchronously in both strains, on ED11. The higher mineral ion content in the larger yolk of Ross 308 eggs compared to Novoponte eggs may partly explain why skeletal mineralization in Ross 308 embryos advances faster: using µCT, we show that the mandible and tibiotarsi in Ross 308 embryos are larger at ED11 and ED13 compared with Novoponte embryos. However, Novoponte embryos catch up from this initial lag in mineralization by ED15. The timing of the Novoponte acceleration coincides with the functional activation of the chorioallantoic membrane in releasing calcium from the inner eggshell. This correlates with a decrease in eggshell thickness from ED11 to ED17 in Novoponte eggs, which was not observed during Ross 308 incubation. To conclude, while some temporal discrepancies exist in early skeletal development between the embryos of Ross 308 and Novoponte strains, overall prenatal skeletal maturation seems to be robustly regulated. Despite selection for antagonist production traits, layer and broiler prehatch skeletal morphology ultimately synchronizes. Practically, since the extent of skeletal maturity equalizes between strains towards the end of incubation, refinements of farming practices, postnatal environment, and diet should be considered for improving domestic fowl welfare.

Whole-genome re-sequencing reveals genetic structure and selection signals of different populations in Megalobrama amblycephala

Characterization of genetic variants is crucial for understanding the molecular mechanisms behind selected traits and enhancing the rate of genetic gain through artificial selection. This study explored the genetic diversity and population structure of blunt snout bream Megalobrama amblycephala, a key freshwater fish in Chinese aquaculture. We conducted whole-genome re-sequencing of individuals from six populations, comprising three natural and three genetically improved strains, to assess genetic diversity, population structure and the impacts of selective breeding. We identified 17,009,590 high-quality biallelic single nucleotide polymorphism (SNP) loci. Genetic diversity assessments revealed low levels of polymorphism across populations, with genetically improved strains showing moderate to high genetic differentiation from their source populations. The study also highlighted runs of homozygosity (ROH) and analyzed linkage disequilibrium (LD) decay, indicating minimal recent inbreeding and diverse recombination events among populations. Selective sweep analyses uncovered significant selection loci associated with growth and hypoxia tolerance traits. Enrichment analyses identified genes involved in olfactory signal transduction, immune response, and metabolism pathways, which are closely related to these selective traits. These findings offer insights into the genetic basis of critical traits in M. amblycephala, contributing to the conservation of germplasm resources and supporting ongoing selective breeding efforts.

Natural Selection Across Three Generations of Americans.

We investigate natural selection on polygenic scores in the contemporary US, using the Health and Retirement Study. Across three generations, scores which correlate negatively (positively) with education are selected for (against). However, results only partially support the economic theory of fertility as an explanation for natural selection. The theory predicts that selection coefficients should be stronger among low-income, less educated, unmarried and younger parents, but these predictions are only half borne out: coefficients are larger only among low-income parents and unmarried parents. We also estimate effect sizes corrected for noise in the polygenic scores. Selection for some health traits is similar in magnitude to that for cognitive traits.

Drivers of diversification in fungal pathogen populations.

To manage and treat chronic fungal diseases effectively, we require an improved understanding of their complexity. There is an increasing appreciation that chronic infection populations are often heterogeneous due to diversification and drift, even within a single microbial species. Genetically diverse populations can contribute to persistence and resistance to treatment by maintaining cells with different phenotypes capable of thriving in these dynamic environments. In chronic infections, fungal pathogens undergo prolonged challenges that can drive trait selection to convergent adapted states through restricted access to critical nutrients, assault by immune effectors, competition with other species, and antifungal drugs. This review first highlights the various genetic and epigenetic mechanisms that promote diversity in pathogenic fungal populations and provide an additional barrier to assessing the actual heterogeneity of fungal infections. We then review existing studies of evolution and genetic heterogeneity in fungal populations from lung infections associated with the genetic disease cystic fibrosis. We conclude with a discussion of open research questions that, once answered, may aid in diagnosing and treating chronic fungal infections.