Variation In Phenotypic Traits Research Articles

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, which are desirable traits for the "steep, cheap, and deep" ideotype. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene coexpression analysis was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies.

Robust hydraulic traits correlation in woody species despite large trait variation along natural and experimental environmental gradients

Abstract Hydraulic traits are major determinants of plant fitness, thus exerting control over vegetation structure, function and distribution. Yet it remains unclear whether and how hydraulic traits respond to environmental stimuli (i.e. phenotypic variation of hydraulic traits; PVHT) and if the coordination between different hydraulic traits and the trait–climate relationship are affected by PVHT. Here, we synthesized data of PVHT (maximum hydraulic conductivity and water potential inducing 50% loss of hydraulic conductivity) and potentially related morphological and anatomical traits (e.g. sapwood density, branch Huber value, mean and hydraulic weighted conduit diameter). We analysed the magnitude, direction and source of variation of the plastic response, as well as the influence of environmental factors on trait coordination. Additionally, we compared the intra‐ and inter‐specific variation between key hydraulic traits and climate metrics (mean annual precipitation and mean annual temperature) at the site of growth, as well as across the population range. PVHT was highly variable in both magnitude and direction, which was contingent on the environmental factor. The variation in PVHT mainly occurred at high taxonomic levels (i.e. family and genus), whereas phenology explained little variation for PVHT. Despite the high variability, trait correlation remained robust in the presence of environmental stimuli. Moreover, trait–climate relationships differed at inter‐specific and intra‐specific levels. The intra‐specific variation of hydraulic traits in most species showed no correlation with climate metrics compared with the high correlation of hydraulic traits with climate metrics across species. Our findings suggest that the high variability of PVHT does not affect the trait correlation which may be valuable in predicting vegetation dynamics under varying environments. The distinct trait–climate relationships highlight the need to unravel the driving force of PVHT, as well as the adaptive strategy across populations. Read the free Plain Language Summary for this article on the Journal blog.

Spatio‐temporal shift in body size and plumage coloration is associated with the magnitude of climate change in a cosmopolitan owl

AbstractAimClimatic gradients shape geographic variation in phenotypic traits that are involved in animal thermoregulation. Therefore, increasing temperatures under global warming are expected to cause change over time in traits that show predictable spatial patterns according to environmental clines (body and appendage size, tegument coloration), as well exemplified by biogeographic rules and shown by increasing literature at a local scale. However, whether temporal shifts in phenotypic traits vary spatially according to the magnitude of the change in local climatic conditions is still unknown.LocationWorld.TaxonBarn owl species complex (Tyto alba group).MethodsBy using thousands of museum specimens collected across the globe from 1901 to 2018, we calculated within‐population change over time in wing length, bill length and melanin‐based plumage coloration and examined whether these trends differed across geographic regions, latitudes and gradients of climate changes.ResultsWe showed that populations exposed to an increasing warmer climate were subjected to a more marked decrease in body size, as gauged by wing length, and also absolute bill length that displayed a similar, although less steep, pattern of shrinking over time. In addition, phaeomelanin‐based ventral plumage colour has become paler in regions where the climate changed into warmer and drier, and darker where both temperature and precipitation increased.Main ConclusionsThese trends are generally coherent with the predictions based on Bergmann's and Gloger's rules, but not Allen's rule, and suggest that temporal shifts in body size and tegument colour depend on the magnitude of the alteration in climatic conditions, with populations living in regions where the climate has changed the most that are subjected to more marked phenotypic changes. Spatio‐temporal variation in climate has driven within‐species phenotypic clines, and it is expected to increase differences among populations according to the predicted further climate change.

Accounting for nuclear and mito genome in dairy cattle breeding - a simulation study

Mitochondria play a significant role in numerous cellular processes through proteins encoded by both the nuclear genome (nDNA) and mito genome (mDNA), and increasing evidence shows that traits of interest might be affected by mito-nuclear interactions. While the variation in nDNA is influenced by mutations and recombination of parental genomes, the variation in mDNA is solely driven by mutations. In addition, mDNA is inherited in a haploid form, from the dam. Cattle populations show significant variation in mDNA between and within breeds. Past research suggests that variation in mDNA accounts for 1–5% of the phenotypic variation in dairy traits. Here we simulated a dairy cattle breeding program to assess the impact of accounting for mDNA variation in pedigree-based and genome-based genetic evaluations on the accuracy of estimated breeding values for mDNA and nDNA components. We also examined the impact of alternative definitions of breeding values on genetic gain, including nDNA and mDNA components that both impact phenotype expression, but mDNA is inherited only maternally. We found that accounting for mDNA variation increased accuracy between +0.01 and +0.03 for different categories of animals, especially for young bulls (+0.03) and females without genotype data (between +0.01 and +0.03). Different scenarios of modeling and breeding value definition impacted genetic gain. The standard approach of ignoring mDNA variation achieved competitive genetic gain. Modeling, but not selecting on mDNA expectedly reduced genetic gain, while optimal use of mDNA variation recovered the genetic gain.

Local adaptation to an altitudinal gradient: The interplay between mean phenotypic trait variation and phenotypic plasticity in Mimulus laciniatus

Organisms can adapt to environmental heterogeneity through two mechanisms: (1) expression of population genetic variation or (2) phenotypic plasticity. In this study we investigated whether patterns of variation in both trait means and phenotypic plasticity along elevational and latitudinal clines in a North American endemic plant, Mimulus laciniatus, were consistent with local adaptation. We grew inbred lines of M. laciniatus from across the species’ range in two common gardens varying in day length to measure mean and plastic trait expression in several traits previously shown to be involved in adaptation to M. laciniatus’s rocky outcrop microhabitat: flowering time, size-related traits, and leaf shape. We tested for phenotypic plasticity and GxE, examined correlations between the mean phenotype and plasticity, and tested for a relationship between trait variation and population elevation and latitude. We did not find a strong correlation between mean and plastic trait expression at the individual genotype level suggesting that they operate under independent genetic controls. We identified multiple traits that show patterns consistent with local adaptation to elevation: critical photoperiod, flowering time, flower size, mean leaf lobing, and leaf lobing plasticity. These trends occur along multiple geographically independent altitudinal clines indicating that selection is a more likely cause of this pattern than gene flow among nearby populations with similar trait values. We also found that population variation in mean leaf lobing is associated with latitude. Our results indicate that both having more highly lobed leaves and greater leaf shape plasticity may be adaptive at high elevation within M. laciniatus. Our data strongly suggest that traits known to be under divergent selection between M. laciniatus and close relative Mimulus guttatus are also under locally varying selection within M. laciniatus.

Accounting for dominance genetic variation in carcass quality traits of Canadian crossbred beef cattle

The objectives of this study were to evaluate the contribution of additive and dominance genetic effects to the phenotypic variation of carcass quality traits and to identify the underlying genetic variants associated with these traits. A total of 3958 Canadian crossbred beef cattle with phenotype and genotype data were used in two models: (1) additive and (2) joint additive and dominance genomic models that included fixed contemporary group, and covariates of slaughter age, and the eigenvectors of five principal components to account for population structure. Variance components and genome-wide association analyses were performed, and a 10% genome-wide false discovery rate (FDR) was applied to declare associations as significant. Genomic heritability ranged from 0.31 ± 0.03 for ultrasound rib eye area to 0.46 ± 0.05 for marbling score. Up to 10% dominance genetic variation was observed for ultrasound rib eye area and marbling score, indicating the contribution of dominance genetic effects to these trait variations. Eleven overlapping significant single-nucleotide polymorphism associations were identified across the studied traits and models. The identified candidate genes (e.g., BTC, SPP1, and SEPSECS) have biological functions related to tissue growth and skeletal muscle development and can be further validated in other cattle populations to determine their usefulness for beef cattle genetic improvement.

Inter- and intra-specific variations in phenotypic traits of Pectobacterium strains isolated from diverse eudicots and monocots in Taiwan.

Pectobacterium spp. are phytopathogenic bacteria whose phylogeny has been continuously revised throughout the years. Previous studies on Pectobacterium's phenotypic diversity often analyzed strains obtained from specific crops or adopted outdated Pectobacterium classification systems. Therefore, a current perspective on trait variations in Pectobacterium species or strains infecting more diverse plant species is limited. This study conducted phylogenetic and phenotypic analyses on strains isolated from 8 eudicot and 4 monocot families in Taiwan. Phylogenetic analysis on 78 strains identified 6 recognized species, namely P. brasiliense, P. aroidearum, P. actinidiae, P. colocasium, P. carotovorum, and P. versatile. Among these, the first two were the most predominant. Patterns suggesting varying host preferences among bacterial species were detected; most P. aroidearum strains were isolated from monocots, whereas P. brasiliense and P. actinidiae tended to exhibit preferences for eudicots. Physiological tests and Biolog analyses conducted on representative strains of each species revealed great within-species phenotypic variation. Despite these strain-level variations, a combination of indole production and phosphatase activity tests was capable of distinguishing all representative strains of P. brasiliense from those of other identified species. Inoculation assays on potato, bok choy, calla lily and onion showed inter- and intra-specific heterogeneities in the tested strains' maceration potentials. Virulence patterns across Pectobacterium species and strains differed depending on the inoculated host. Altogether the findings from this work expand the understanding of Pectobacterium's phenotypic diversity and provide implications for pathogen identification and management.

Temporal phenotypic variation of spinach root traits and its relation to shoot performance

The root system is important for the growth and development of spinach. To reveal the temporal variability of the spinach root system, root traits of 40 spinach accessions were measured at three imaging times (20, 30, and 43 days after transplanting) in this study using a non-destructive and non-invasive root analysis system. Results showed that five root traits were reliably measured by this system (RootViz FS), and two of which were highly correlated with manually measured traits. Root traits had higher variations than shoot traits among spinach accessions, and the trait of mean growth rate of total root length had the largest coefficients of variation across the three imaging times. During the early stage, only tap root length was weakly correlated with shoot traits (plant height, leaf width, and object area (equivalent to plant surface area)), whereas in the third imaging, root fresh weight, total root length, and root area were strongly correlated with shoot biomass-related traits. Five root traits (total root length, tap root length, total root area, root tissue density, and maximal root width) showed high variations with coefficients of variation values (CV ≥ 0.3, except maximal root width) and high heritability (H2 > 0.6) among the three stages. The 40 spinach accessions were classified into five subgroups with different growth dynamics of the primary and lateral roots by cluster analysis. Our results demonstrated the potential of in-situ phenotyping to assess dynamic root growth in spinach and provide new perspectives for biomass breeding based on root system ideotypes.

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice.

Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.

Identification of major QTLs for drought tolerance in soybean, together with a novel candidate gene, GmUAA6.

Drought tolerance is a complex trait in soybean that is controlled by polygenetic quantitative trait loci (QTLs). In this study, wilting score, days-to-wilting, leaf relative water content, and leaf relative conductivity were used to identify QTLs associated with drought tolerance in recombinant inbred lines derived from a cross between a drought-sensitive variety, Lin, and a drought-tolerant variety, Meng. A total of 33 drought-tolerance QTLs were detected. Of these 17 were major QTLs. In addition, 15 were novel drought-tolerance QTLs. The most predominant QTL was on chromosome 11. This was detected in at least three environments. The overlapped mapping interval of the four measured traits was 0.2 cM in genetic distance (about 220 kb in physical length). Glyma.11g143500 (designated as GmUAA6), which encodes a UDP-N-acetylglucosamine transporter, was identified as the most likely candidate gene. The allele of GmUAA6 from Lin (GmUAA6Lin) was associated with improved soybean drought tolerance. Overexpression of GmUAA6Lin in Arabidopsis and soybean hairy roots enhanced drought tolerance. Furthermore, a 3-bp insertion/deletion (InDel) in the coding sequence of GmUAA6 explained up to 49.9% of the phenotypic variation in drought tolerance-related traits, suggesting that this InDel might be used in future marker-assisted selection of drought-tolerant lines in soybean breeding programs.

Genetic variation, genetic advance, heritability and correlation analysis of phenotypic traits in tetraploid wheat (Triticum turgidum spp.) landraces and some improved cultivars of Ethiopia

AbstractTetraploid wheat species from Ethiopia hold ample genetic variation, which could provide a source for improvement of wheat. A total of 196 Ethiopian tetraploid wheat (Triticum turgidum spp.) accessions, including 174 landraces and 22 improved cultivars, were evaluated at Sinana and Debrezeit to assess morphological variation, genetic advance, heritability and correlation based on 11 phenotypic traits. Except for spike length, highly significant variation (P &lt; 0.001) among genotypes for all traits was observed. The observed mean and range values of the phenotypic traits revealed high variability in the accessions. Phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) values were high for grain yield, biomass yield and harvest index. Seed yield showed highly significant (P &lt; 0.001) negative correlation with days to booting and days to maturity and positive correlation with all traits. The estimates of heritability (H2) for grain yield and the number of spikelets per spike respectively ranged from 41.78 to 84.62%. The genetic advance as a percentage of mean was low for the number of seeds per spikelet, days to booting and days to maturity; intermediate for plant height, thousand kernel weight and spike length and high for the number of spikelets per spike, the number of effective tillers per plant, grain yield, biomass yield and harvest index, respectively. The number of spikelets per spike gave a high value of genetic advance and heritability implying high genetic gain from its selection.

Functional differences between Andean oak (Quercus humboldtii Bonpl.) populations: The importance of intraspecific variation.

Monodominant tree communities can have phenotypic trait variation (intraspecific variation) as extreme as the trait variation across a forest with higher species diversity. An example of such forests is those composed of Quercus, an important genus of woody angiosperms in the montane neotropical forest. The Andean oak, or Quercus humboldtii Bonpl., is the sole member of this genus in South America and a characteristic component of montane ecosystems. Although there are several studies on the ecology and genetic structure of this species, there are few studies on the functional trait diversity among populations. Understanding functional traits can improve our comprehension of how organisms respond to various environmental conditions. In this study, we aimed to evaluate differences in six functional traits in individuals of the Andean oak, in two ontogenetic stages (juveniles and adults) from three populations with contrasting environmental conditions. Additionally, using T-statistics, we assessed the impact of external filters (e.g., climate, resource availability, large-scale biotic interactions) on population assembly. We found a remarkable level of functional differentiation among Andean oak forests, with all traits differing between populations and five traits differing between ontogenetic stages. External filters had a stronger influence in populations with more extreme environmental conditions. These findings emphasize the dynamic and context-dependent nature of functional traits in this species. However, given the limited exploration of functional diversity in Andean oak populations, further studies are needed to inform conservation efforts.

Transposon insertion in pmel17 rewired skin and muscle transcriptomes in Mozambique tilapia

The pmel17 gene plays a crucial role in melanin pigmentation. Our previous studies showed that in Mozambique tilapia, a transposon inserted into the 3′ untranslated region (3′ UTR) of pmel17 resulted in the silencing of pmel17 and led to the loss of melanin pigments (golden mutant phenotype). Additionally, the transposon insertion caused reduced growth performance and increased locomotion. In this study, to investigate the mechanisms underlying these phenotypic changes, we sequenced transcriptomes of the skin and muscle samples collected from wildtype and mutant tilapias. A total of 51 and 141 differentially expressed genes (DEGs) were identified in the skin and muscle transcriptomes, respectively. DEGs in the skin were primarily down-regulated in golden genotypes and associated with neural crest development and melanin pigmentation pathways. Besides these DEGs involved in the classic melanin pigmentation pathway of vertebrates, 14 DEGs were also observed to be related to melanogenesis. In muscle transcriptomes, there was an enrichment of GO terms associated with growth factors and cellular lipid catabolic processes. Specifically, DEGs related to growth factor binding exhibited a down-regulation, while those related to lipid metabolism showed an up-regulation in mutant genotypes. These findings agree with observed phenotypic changes. Furthermore, several DEGs associated with muscle function and mobility were up-regulated. Our study sheds light on how a single mutation in a gene can modulate multiple phenotypes by rewiring gene regulation networks. The research also provides valuable insights into the complex genetic mechanisms underlying the regulation of diverse phenotypic traits by a single gene.

The Genetic Dissection of Nitrogen Use-Related Traits in Flax (Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection.

Nitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N-) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N- conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input.

Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population.

Selection in the Iowa Stiff Stalk Synthetic (BSSS) maize population for high yield, grain moisture, and root and stalk lodging has indirectly modified plant architecture traits that are important for adaptation to high plant density. In this study, we developed doubled haploid (DH) lines from the BSSS maize population in the earliest cycle of recurrent selection (BSSS), cycle 17 of reciprocal recurrent selection, [BSSS(R)17] and the cross between the two cycles [BSSS/BSSS(R)C17]. We aimed to determine the phenotypic variation and changes in agronomic traits that have occurred through the recurrent selection program in this population and to identify genes or regions in the genome associated with the plant architecture changes observed in the different cycles of selection. We conducted a per se evaluation of DH lines focusing on high heritability traits important for adaptation to high planting density and grain yield. Trends for reducing flowering time, anthesis-silking interval, ear height, and the number of primary tassel branches in BSSS(R)17 DH lines compared to BSSS and BSSS/BSSS(R)C17 DH lines were observed. Additionally, the BSSS(R)C17 DH lines showed more upright flag leaf angles. Using the entire panel of DH lines increased the number of SNP markers identified within candidate genes associated with plant architecture traits. The genomic regions identified for plant architecture traits in this study may help to elucidate the genetic basis of these traits and facilitate future work about marker-assisted selection or map-based cloning in maize breeding programs.

Dry storage alters intraspecific variation in phenotypic traits at early life stages: evidence from a dominant alpine meadow species

AbstractThe intraspecific variations of phenotypic traits in the early life stages, such as seed germination and seedling establishment, are important components affecting species adaptation and differentiation. As one of the most common ways in which seeds are maintained, dry storage usually affects these traits, by either increasing or decreasing variation among populations. However, little is known about how the interaction between dry storage and population variation of a species affects the performance and adaptability of early life-cycle traits. In this study, we conducted experiments with seeds from ten populations of Elymus nutans along an altitudinal gradient on the eastern Qinghai-Tibet Plateau. Fresh seeds and seeds stored dry for 6 months were used to quantify the temperature thresholds for germination, determine seedling emergence and survival in two common gardens and examine the correlation between these traits and environmental conditions of population provenance. Dry storage increased germination percentage, germination speed and seedling emergence, and decreased intraspecific variation in germination traits of seeds (reduced by 33.36, 52.05 and 20.45% for Tb, θT(50) and σθT, respectively). Dry storage had little effect on the intraspecific variation of seedling emergence and survival. In addition, the temperature threshold for germination cannot be used to predict seedling emergence and survival in either common garden, regardless of whether seeds were stored or not. These results indicated that it is feasible to use dry-stored seeds to evaluate and select suitable provenances in ecological restoration, and using dry-stored seeds in ecological restoration projects is expected to achieve better vegetation restoration results than fresh seeds. On the other hand, the status of seeds (fresh vs. dry stored) should be considered in an evaluation of the adaptive value of plant functional traits, especially in the early life stages, otherwise, inconsistent conclusions may be drawn.

Comprehensive analysis of phenotypic variation and selection strategies for yield-related traits in recombinant inbred lines of soybeans

Comprehensive analysis of phenotypic variation and selection strategies for yield-related traits in recombinant inbred lines of soybeans

Variability of morphology, phytochemical traits and essential oil profile of tea (Camellia sinensis (L.) Kuntze) accessions in the southern region of the Caspian Sea

Abstract Tea (Camellia sinensis (L.) Kuntze) leaves are an important beverage crop due to their high caffeine content. Although the north of Iran is the main region for high-quality tea plants, there is no document on variations of phenotypic traits of different accessions. The present study was to assess the biodiversity of 12 tea accessions originating from four tea main sites in Iran (Langroud, Siahkal, Kobijar and Bazkiaguorab) using multivariate analysis. Two-year-old tea plants were cultivated in a completely randomized design with five replicates in a greenhouse. One year after plant establishment, phenotypic characteristics were studied. The tea accessions showed different responses in chlorophyll and total ash contents. The highest and lowest amount of caffeine in tea accessions was found in Kobijar A7 and Langroud A2, respectively. Epicatechin was obtained in a 6.48–15.44 mg g−1 range, and the maximum variability was found in epigallocatechin gallate (EGCG), differing from 0.94 to 21.03 mg g−1. Langroud A2 and Bazkiaguorab A11 contained the maximum EGCG and the total polyphenolic content in Bazkiaguorab was greater than other accessions. Heat map analysis showed the maximum variability of EGCG, catechin, and GA among the accessions. The main essential oil compounds were 2-pentyl furan followed by hexanal, gamma-terpinene, octane, ortho-cymene, terpinen-4-ol, alpha-copaene and E-caryophyllene. In conclusion, changes in phytochemical traits caused by genetics and origin can significantly alter the quality of tea compounds. The results of this study can be utilized as raw materials in future breeding projects to improve new cultivars with superior characteristics.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

BackgroundDomestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.ResultsTo comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the “hair follicle maturation” Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with “regulation of heart contraction” in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.ConclusionThis accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity.

Many threatened plants have low genetic diversity, which may reduce their capacity for genetically based adaptation, increasing their extinction risk. Non-genetic variation (e.g. epigenomic modifications such as DNA methylation) and plasticity may facilitate the persistence of threatened plants, yet are rarely incorporated into conservation assessments. We present a case study investigating variation and plasticity in DNA methylation and phenotypic traits in four genetically depauperate species of Leavenworthia (Brassicaceae), including one widespread species and one asexual, threatened species. We grew individuals from several maternal lines and populations per species in contrasting watering treatments, measured phenotypic traits and analysed DNA methylation using whole-genome bisulphite sequencing. We addressed four questions: (1) How do patterns of DNA methylation differ within and among species? (2) Within species, how do phenotypic traits and patterns of DNA methylation vary in response to drought? (3) Does variation in DNA methylation correspond to phenotypic variation? (4) What are the implications for conservation? We found that taxa were epigenomically distinct and that each species exhibited variation in DNA methylation among populations that could be relevant for conservation. Within species, the DNA methylation response to environmental stress corresponded to its phenotypic response. Species differed in their DNA methylation and phenotypic responses to environmental stress, with the extent of plasticity possibly related to species geographic range size. We also found phenotypic and DNA methylation variation in the asexual, threatened species that may be relevant for conservation. Our results suggest that variation in DNA methylation may promote the persistence of genetically depauperate threatened plants, highlighting its potential as a novel conservation target to reduce extinction risk.