Variation In Phenotypic Traits Research Articles

Genotyping-by-Sequencing Identifies Historical Breeding Stages of the Recently Domesticated American Cranberry

The cranberry (Vaccinium macrocarpon Ait.) is a North American fruit crop domesticated less than 200 years ago. The USDA began the first cranberry breeding program in response to false-blossom disease in 1929, but after the first generation of cultivars were released in the 1950s, the program was discontinued. Decades later, renewed efforts for breeding cranberry cultivars at Rutgers University and the University of Wisconsin yielded the first modern cultivars in the 2000’s. Phenotypic data suggests that current cultivars have changed significantly in terms of fruiting habits compared to original selections from endemic populations. However, due to the few breeding and selection cycles and short domestication period of the crop, it is unclear how much cultivated germplasm differs genetically from wild selections. Moreover, the extent to which selection for agricultural superior traits has shaped the genetic and phenotypic variation of cranberry remains mostly obscure. Here, a historical collection composed of 362 accessions, spanning wild germplasm, first-, second-, and third-generation selection cycles was studied to provide a window into the breeding and domestication history of cranberry. Genome-wide sequence variation of more than 20,000 loci showed directional selection across the stages of cranberry domestication and breeding. Diversity analysis and population structure revealed a partially defined progressive bottleneck when transitioning from early domestication stages to current cranberry forms. Additionally, breeding cycles correlated with phenotypic variation for yield-related traits and anthocyanin accumulation, but not for other fruit metabolites. Particularly, average fruit weight, yield, and anthocyanin content, which were common target traits during early selection attempts, increased dramatically in second- and third-generation cycle cultivars, whereas other fruit quality traits such as Brix and acids showed comparable variation among all breeding stages. Genome-wide association mapping in this diversity panel allowed us to identify marker-trait associations for average fruit weight and fruit rot, which are two traits of great agronomic relevance today and could be further exploited to accelerate cranberry genetic improvement. This study constitutes the first genome-wide analysis of cranberry genetic diversity, which explored how the recurrent use of wild germplasm and first-generation selections into cultivar development have shaped the evolutionary history of this crop species.

The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen.

Convergent evolution leads to identical phenotypic traits in different species or populations. Convergence can be driven by standing variation allowing selection to favour identical alleles in parallel or the same mutations can arise independently. However, the molecular basis of such convergent adaptation remains often poorly resolved. Pesticide resistance in agricultural ecosystems is a hallmark of convergence in phenotypic traits. Here, we analyse the major fungal pathogen Zymoseptoria tritici causing serious losses on wheat and with fungicide resistance emergence across several continents. We sampled three population pairs each from a different continent spanning periods early and late in the application of fungicides. To identify causal loci for resistance, we combined knowledge from molecular genetics work and performed genome-wide association studies (GWAS) on a global set of isolates. We discovered yet unknown factors in azole resistance including a gene encoding membrane associated functions. We found strong support for the "hotspot" model of resistance evolution with convergent changes in a small set of loci but additional loci showed more population-specific allele frequency changes. Genome-wide scans of selection showed that half of all known resistance loci were overlapping a selective sweep region. Hence, the application of fungicides was one of the major selective agents acting on the pathogen over the past decades. Furthermore, loci identified through GWAS showed the highest overlap with selective sweep regions underlining the importance to map phenotypic trait variation in evolving populations. Our population genomic analyses highlighted that both de novo mutations and gene flow contributed to convergent pesticide adaptation.

Analysis of X chromosome and autosomal genetic effects on growth and efficiency-related traits in sheep

Abstract Context It is believed that the X chromosome plays an important role in influencing quantitative traits. Despite this, until recently, X-linked genetic effects have not been considered in models to estimate genetic parameters for economically important traits of livestock. Aims A large dataset was analysed to quantify autosomal additive genetic, X-linked additive genetic and maternal effects on growth and efficiency-related traits in Baluchi sheep. Methods Traits included bodyweight at birth, weaning (WW), 6 months (W6), 9 months and yearling age, pre- and post-weaning average daily gain, pre- and post-weaning Kleiber ratio, pre- and post-weaning efficiency of growth (EFb), and pre- and post-weaning relative growth rate. Each trait was analysed using the REML procedure fitting a series of eight univariate animal models. For each trait, the most appropriate model was selected by the Akaike information criterion and Bayesian information criterion. Key results The X-linked genetic effect was significant only in models fitted to EFb, where the estimate of X-linked heritability was 0.02 ± 0.01 from the best model. Other traits were not affected significantly by X-linked genetic effects. Estimates of autosomal heritability () for growth traits were between 0.06 ± 0.02 (post-weaning average daily gain, pre-weaning relative growth rate) and 0.22 ± 0.04 (bodyweight at yearling age), and ranged between 0.02 ± 0.01 (EFb) and 0.08 ± 0.02 (pre-weaning Kleiber ratio) for efficiency-related traits. Maternal effects significantly contributed to phenotypic variation of most traits, with larger effects on traits measured early in life. For EFb, the Spearman’s correlation between breeding values including and excluding X-linked effects was 0.95. It was 1.00 for traits that were not affected by X-linked genetic effects. Conclusions Although the proportion of phenotypic variance attributed to X-linked loci for most traits was zero, the importance of X-linked genetic effects should be at least tested in models when estimating variance components for growth and efficiency traits of Baluchi sheep. Implications As estimates of genetic parameters are breed-specific, we recommend for growth and efficiency traits of sheep that the importance of X-linked genetic effects should be evaluated to assess if these effects should be included in models used in genetic evaluation.

Genome-Wide Association Study to Identify Candidate Loci for Biomass Formation Under Water Deficit in Perennial Ryegrass.

Global warming is predicted to impact many agricultural areas, which will suffer from reduced water availability. Due to precipitation changes, mild summer droughts are expected to become more frequent, even in temperate regions. For perennial ryegrass (Lolium perenne L.), an important forage grass of the Poaceae family, leaf growth is a crucial factor determining biomass accumulation and hence forage yield. Although leaf elongation has been shown to be temperature-dependent under normal conditions, the genetic regulation of leaf growth under water deficit in perennial ryegrass is poorly understood. Herein, we evaluated the response to water deprivation in a diverse panel of perennial ryegrass genotypes, employing a high-precision phenotyping platform. The study revealed phenotypic variation for growth-related traits and significant (P < 0.05) differences in leaf growth under normal conditions within the subgroups of turf and forage type cultivars. The phenotypic data was combined with genotypic variants identified using genotyping-by-sequencing to conduct a genome-wide association study (GWAS). Using GWAS, we identified DNA polymorphisms significantly associated with leaf growth reduction under water deprivation. These polymorphisms were adjacent to genes predicted to encode for phytochrome B and a MYB41 transcription factor. The result obtained in the present study will increase our understanding on the complex molecular mechanisms involved in plant growth under water deficit. Moreover, the single nucleotide polymorphism (SNP) markers identified will serve as a valuable resource in future breeding programs to select for enhanced biomass formation under mild summer drought conditions.

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4–10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4–1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

GENOME-WIDE ASSOCIATION STUDY FOR GROWTH TRAITS IN BLANCO OREJINERO (BON) CATTLE FROM COLOMBIA

In the Colombian Creole cattle breed Blanco Orejinegro (BON), the mechanisms involved in growth trait variation are not well characterized. The aim of this work was to identify genomic regions associated with growth traits variability of Colombian BON cattle. The analyzed information included 439 individuals belonging to 14 herds with genotypes for 107,999 SNPs and genealogical and phenotypic information of deregressed genetic values of BON animals for the following growth traits: birth weight (BW), weaning weight (WW), yearling weight (YW), daily weight gain between birth and weaning (DWG), time to reach 120 kg of live weight (T120), and time to reach 60% of adult weight (T60%). A genome-wide association analysis (GWAS) was performed using the Bayes Cπ method. The association tests showed different signals with effect on the phenotypic variation of growth traits in Colombian BON cattle located within genomic regions with genes and metabolic pathways of crucial biological processes related to growth and development, and associated with at least one QTL previously reported, especially in Bos taurus autosome (BTA)1, BTA2, BTA6, BTA10, and BTA20. Two regions with effect on several growth traits were identified; the first in BTA1 with effect on WW, YW, T120, and T60%, and the second in BTA3 with effect on BW, WW, DWG, and T120, showing a genetic correlation between growth traits. These results will improve our biological and genetic understanding of growth traits in Colombian BON cattle.

Phenotypic consequences of maternally selected nests: a cross-fostering experiment in a desert lizard.

Despite the importance of maternally selected nests in shaping offspring phenotypes, our understanding of how the nest environment affects embryonic development and offspring traits of most non-avian reptiles is rather limited largely due to the logistical difficulty in locating their nests. To identify the relative contributions of environmental (temporal [seasonal] and spatial [nest-site]) and intrinsic (clutch) factors on embryonic development and offspring traits, we conducted a cross-fostering experiment by swapping eggs between maternally-selected nests of the toad-headed agama (Phrynocephalus przewalskii) in the field. We found that nest environment explained a large proportion of variation in incubation duration, hatching success, and offspring size and growth. In contrast, clutch only explained a small proportion of variation in these embryonic and offspring traits. More significantly, compared with spatial effects, seasonal effects explained more phenotypic variation in both embryonic development and offspring traits. Eggs laid early in the nesting season had longer incubation durations and produced smaller hatchlings with higher post-hatching growth rates than did later-laid eggs. Consequently, hatchlings from early-laid eggs reached larger body sizes prior to winter. In addition, we found that female toad-headed agama did not select nests specific to reaction norms of their own offspring because hatchlings from original or translocated nests had similar phenotypic traits. Overall, our study demonstrates the importance of seasonal variation in nest environments in determining embryonic development and offspring phenotypes, which has not been widely appreciated at least in non-avian reptiles.

Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits.

Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli.

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits.

Recombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different recombination histories in these regions that significantly associated with the differential expression of ANKRD35 in whole blood and that were in high linkage with variants previously associated with hypertension. By detecting differences in historic recombination, our method opens a way to assess the influence of recombination variation in phenotypic traits.

Relative influences of microhabitat incubation conditions and genetic parentage effects on lake sturgeon (Acipenser fulvescens) offspring traits during early ontogeny

Knowledge on factors influencing traits during critical early growth periods is essential for predicting population persistence. Genetic effects and microhabitat stream conditions at female selected oviposition sites influence larval phenotypes. However, limited work has examined contributions of both factors across sequential ontogenetic stages for larvae of wild origin. Using a wild population of lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan (USA), fertilized eggs were collected from stream substrate just prior to hatch at one-meter intervals along seven transect lines at an adult-selected spawning area. Microhabitat variables (depth, discharge, substrate size) were recorded at egg collection points. Body length, body area, and yolk-sac area were quantified for yolk-sac larvae (N = 359) at the time of hatch. Following the onset of exogenous feeding, larval growth was measured weekly for four weeks. Parentage was assigned using genetic-based analysis. Inter-individual variation in phenotypic traits quantified at hatch were attributed to stream microhabitat variables; mean depth had the largest influence. No additive genetic effects were detected at hatch. Post-emergence larval growth significantly varied within and among half-sibling groups with the greatest range in body size observed at 33 days post-hatch. Additive genetic variance and heritability increased with age. Results demonstrate that female-selected incubation habitats influenced traits at hatch for wild-origin fish, but effects do not persist to a sequential ontogenetic stage. Alternatively, growth after the onset of exogenous feeding was largely influenced by intrinsic (genetic) factors which must be considered when designing and implementing rehabilitation strategies for lake sturgeon and potentially other threatened riverine fishes.

Epigenetics of Animal Personality: DNA Methylation Cannot Explain the Heritability of Exploratory Behavior in a Songbird.

SynopsisThe search for the hereditary mechanisms underlying quantitative traits traditionally focused on the identification of underlying genomic polymorphisms such as single-nucleotide polymorphisms. It has now become clear that epigenetic mechanisms, such as DNA methylation, can consistently alter gene expression over multiple generations. It is unclear, however, if and how DNA methylation can stably be transferred from one generation to the next and can thereby be a component of the heritable variation of a trait. In this study, we explore whether DNA methylation responds to phenotypic selection using whole-genome and genome-wide bisulfite approaches. We assessed differential erythrocyte DNA methylation patterns between extreme personality types in the Great Tit (Parus major). For this, we used individuals from a four-generation artificial bi-directional selection experiment and siblings from eight F2 inter-cross families. We find no differentially methylated sites when comparing the selected personality lines, providing no evidence for the so-called epialleles associated with exploratory behavior. Using a pair-wise sibling design in the F2 intercrosses, we show that the genome-wide DNA methylation profiles of individuals are mainly explained by family structure, indicating that the majority of variation in DNA methylation in CpG sites between individuals can be explained by genetic differences. Although we found some candidates explaining behavioral differences between F2 siblings, we could not confirm this with a whole-genome approach, thereby confirming the absence of epialleles in these F2 intercrosses. We conclude that while epigenetic variation may underlie phenotypic variation in behavioral traits, we were not able to find evidence that DNA methylation can explain heritable variation in personality traits in Great Tits.

Implications of emmer (Triticum dicoccon Schrank) introgression on bread wheat response to heat stress

Wheat is sensitive to heat stress, particularly during grain filling, and this reduces grain yield. Ancestral wheat species, such as emmer wheat (Triticum dicoccon Schrank), represent potential sources of new genetic diversity for traits that may impact wheat responses to heat stress. However, the diversity available in emmer wheat has only been explored superficially. Recently developed emmer derived hexaploid wheat genotypes were evaluated for physiological, phenological and agronomic traits in a multi-environment, multi-season strategy. The emmer-based hexaploid lines were developed from crosses and backcrosses to 9 hexaploid recurrent parents and these genotypes and 7 commercial cultivars were evaluated under two times of sowing (E1 and E2) in the field for three consecutive years (2014–2016). The materials were genotyped using a 90 K SNP platform and these data used to estimate the contribution of emmer wheat to the progeny. Significant phenotypic and genetic variation for traits were observed. Higher temperature during reproductive development and grain filling reduced trait expression. Emmer progeny with greater trait values than their recurrent parents and commercial cultivars in both environments were found. Derivatives with higher physiological trait values yielded well in both environments; as indicated by the clustering of genotypes. The emmer wheat parent contributed between 1 and 43 % of the genome of the emmer-based hexaploid progeny, and progeny with greater emmer contribution had superior trait values in both environments. These results showed a positive effect of direct emmer introgression on wheat performance under heat stress. Mitigation of high temperature stress through the introgression of favorable alleles from wheat close relatives into modern wheat cultivars is possible.

Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits.

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement.

Contributions of source population and incubation temperature to phenotypic variation of hatchling Chinese skinks

Abstract Phenotypic plasticity and local adaptation are viewed as the main factors that result in between-population variation in phenotypic traits, but contributions of these factors to phenotypic variation vary between traits and between species and have only been explored in a few species of reptiles. Here, we incubated eggs of the Chinese skink (Plestiodon chinensis) from 7 geographically separated populations in Southeast China at 3 constant temperatures (24, 28, and 32 °C) to evaluate the combined effects of clutch origin, source population, and incubation temperature on hatchling traits. The relative importance of these factors varied between traits. Nearly all examined hatchling traits, including body mass, snout–vent length (SVL), tail length, head size, limb length, tympanum diameter, and locomotor speed, varied among populations and were affected by incubation temperature. Measures for hatchling size (body mass and SVL) varied considerably among clutches. Source population explained much of the variation in hatchling body mass, whereas incubation temperature explained much of the variation in other examined traits. Our results indicate that between-population variation in hatchling traits of P. chinensis likely reflects the difference in natural incubation conditions and genetic divergence.

Genetic control of tracheid properties in Norway spruce wood

Through the use of genome-wide association studies (GWAS) mapping it is possible to establish the genetic basis of phenotypic trait variation. Our GWAS study presents the first such effort in Norway spruce (Picea abies (L). Karst.) for the traits related to wood tracheid characteristics. The study employed an exome capture genotyping approach that generated 178 101 Single Nucleotide Polymorphisms (SNPs) from 40 018 probes within a population of 517 Norway spruce mother trees. We applied a least absolute shrinkage and selection operator (LASSO) based association mapping method using a functional multi-locus mapping approach, with a stability selection probability method as the hypothesis testing approach to determine significant Quantitative Trait Loci (QTLs). The analysis has provided 30 significant associations, the majority of which show specific expression in wood-forming tissues or high ubiquitous expression, potentially controlling tracheids dimensions, their cell wall thickness and microfibril angle. Among the most promising candidates based on our results and prior information for other species are: Picea abies BIG GRAIN 2 (PabBG2) with a predicted function in auxin transport and sensitivity, and MA_373300g0010 encoding a protein similar to wall-associated receptor kinases, which were both associated with cell wall thickness. The results demonstrate feasibility of GWAS to identify novel candidate genes controlling industrially-relevant tracheid traits in Norway spruce.

Within-Clutch Repeatability of Egg Size Traits in Blue Tits Cyanistes caeruleus in a Long-Term View

Female birds are exceptionally consistent in laying rather uniform and individually specific eggs, so that variation in eggs of individual females is low, while variation among females is high. Repeatability is a population-level parameter used in quantitative genetics to quantify the level of intraindividual consistency in relation to interindividual variation in phenotypic traits, in this case, the egg traits. The statistical measure of repeatability is intraclass correlation of particular egg traits clustered in clutches. This study is based on a long-term dataset on repeatabilities of the length, breadth, volume and shape of eggs of Blue Tits Cyanistes caeruleus investigated in two ecologically varying sites (an urban parkland versus a mature deciduous forest) around the city of Łódź, central Poland in 1999–2013. Coefficients of repeatability of egg length, breadth, volume and shape in the study populations of Blue Tits showed some variation between years and study sites, but were generally very high, on average 0.7 or more, and did not significantly differ between the traits within years. The observed differences between repeatabilities do not seem to be strongly associated with year-specific weather indicators for the first half of April. Only coefficients of variation in mean daily temperature influenced repeatabilities of egg length and breadth, whereas effects of mean temperature were non-significant. Repeatability of egg length in the forest and breadth in both sites increased with increasing variation in daily temperature, whereas repeatability of egg length in the urban park site showed a reverse relation with variation in temperature. Year-site-specific mean laying dates, clutch sizes and egg volumes, considered as indicators of breeding conditions, tended to negatively affect the repeatabilities. However, in general, repeatabilities of different egg traits were not consistent in their variation between years and sites, which suggests an important role of stochastic factors in shaping this variation. External factors that are able to force females to diversify traits of eggs in a particular laying sequence do not seem to directly result from the environmental conditions prevailing during a spring period critical for laying eggs in a population in a given year (the first half of April), but seem to be linked to more subtle aspects of variation in the conditions for egg laying, as shown by links with the mean values of basic breeding parameters.

Genome-Wide Association Study for Plant Architecture and Bioenergy Traits in Diverse Sorghum and Sudangrass Germplasm

Sorghum is an important grain, forage, and bioenergy crop. The objective of this study was to identify genetic signals associated with plant architecture and bioenergy traits in sorghum and sudangrass germplasm through a genome-wide association study (GWAS). Plant height (HT), tiller number (TN), internode number (IN), stem diameter (SD), panicle length (PL), panicle weight (PW), reducing sugar (RS) content, Brix, and protein (PRO) content were assessed in 300 germplasm consisting of grain sorghum, sweet sorghum, sudangrass, sweet sorghum-sweet sorghum recombinant inbred lines (RILs) and sudangrass-sudangrass RILs grown in three different environments over two years. Large variations of phenotypic traits were observed in the population panel. The heritability of traits were all higher than 0.5, ranging from 0.52 (PRO) to 0.92 (HT) with an average of 0.76. The population exhibited three population structures (Q) and minor relative kinship (K), assessed by using 7982 single-nucleotide polymorphisms (SNPs). After controlling Q and K, GWAS identified 24 SNPs that were significantly associated with traits, including three SNPs with HT, four with TN, four with PL, three with Brix, and ten with RS. Of them, seven SNPs were novel signals that were not identified previously, including one for HT, one for TN, one for Brix, and four for RS. The putative candidate genes involved in brassinosteroid regulatory pathway, auxin biosynthesis, carbohydrate metabolism, and sugar transport were identified underlying the significant SNPs. Identification of SNP signals and related candidate genes would enrich the current genomic resource for further molecular breeding aimed at improvement of food, feed, and biofuel productions of sorghum.

Red Hair Color Is Associated with Elevated CRP Levels among US Women

Red Hair Color Is Associated with Elevated CRP Levels among US Women

Genetic control of adventitious rooting traits in bi-parental pedigree of Eucalyptus tereticornis × E. camaldulensis

In commercial plantations, mass propagation and deployment of identified and tested clones has potential economic benefits. However, the major challenge is the adventitious rooting ability of high yielding genotypes. In Eucalyptus, large-scale plantations of hybrid clones with enhanced productivity are well documented. However, the understanding of genetic architecture of adventitious rooting traits in this genus is limited. The present study was conducted to decipher the genetic control of this quantitative trait in a bi-parental pedigree of E. tereticornis × E. camaldulensis. The selected parental clones used for controlled hybridization were divergent for their adventitious rooting capacity from stem cuttings. The juvenile shoots of parents and hybrids were coppiced and two-node stem cuttings were harvested and treated with 4000 mg L−1 Indole-3-butyric acid. Phenotypic variation in adventitious rooting traits was documented after 40 days of root induction in parents and 68 hybrids across two settings (March 2015 and April 2015). Significant difference in rooting percentage and number of roots was recorded between the settings. The study revealed a positive correlation between root length and rooting percentage. Broad sense heritability coefficient was the highest for rooting percentage and the predicted genetic advance was maximum for root volume (60.77%). Transgressive inheritance pattern was recorded for all rooting traits and several hybrids registered higher rooting percentage, enhanced root area and volume when compared to parents. These out-performing hybrid clones with superior root system will have potential resource use efficiency and can be deployed in arid and semi-arid zones to enhance productivity.

Latitudinal variation in climate‐associated genes imperils range edge populations

The ecological impacts of increasing global temperatures are evident in most ecosystems on Earth, but our understanding of how climatic variation influences natural selection and adaptive resilience across latitudes remains largely unknown. Latitudinal gradients allow testing general ecosystem-level theories relevant to climatic adaptation. We assessed differences in adaptive diversity of populations along a latitudinal region spanning highly variable temperate to subtropical climates. We generated and integrated information from environmental mapping, phenotypic variation and genome-wide data from across the geographical range of the rainbowfish Melanotaenia duboulayi, an emerging aquatic system for studies of climate change. We detected, after controlling for spatial population structure, strong interactions between genotypes and environment associated with variation in stream flow and temperature. Some of these hydroclimate-associated genes were found to interact within functional protein networks that contain genes of adaptive significance for projected future climates in rainbowfish. Hydroclimatic selection was also associated with variation in phenotypic traits, including traits known to affect fitness of rainbowfish exposed to different flow environments. Consistent with predictions from the "climatic variability hypothesis," populations exposed to extremes of important environmental variables showed stronger adaptive divergence and less variation in climate-associated genes compared to populations at the centre of the environmental gradient. Our findings suggest that populations that evolved at environmental range margins and at geographical range edges may be more vulnerable to changing climates, a finding with implications for predicting adaptive resilience and managing biodiversity under climate change.