Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture events.Adaptation to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed genomes.Results Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White Cornish.Signals of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation analysis.Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds.In these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies.Amongst them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold adaptation.Epigenetic factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds.These include genes representing the sine qua non for adaptation to harsh environments.Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

An assessment of the genetic diversity of pear(Pyrus L.)germplasm resources based on the fruit phenotypic traits

Germplasm resources are an important basis for genetic breeding and analysis of complex traits,and research on genetic diversity is conducive to the exploration and creation of new types of germplasm.In this study,the distribution frequency,coefficient of variation,Shannon-Wiener index,and variance and cluster analyses were used to analyze the diversity and trait differences of 39 fruit phenotypic traits from 570 pear accessions,which included 456 pear accessions from 11 species and 114 interspecific hybrid cultivars that had been stored in the National Germplasm Repository of Apple and Pear(Xingcheng,China).The comprehensive evaluation indices were screened by correlation,principal component and regression analyses.A total of 132 variant types were detected in 28 categorical traits of pear germplasm fruit,which indicate a rich diversity.The diversity indices in decreasing order were:fruit shape(1.949),attitude of calyx(1.908),flesh texture type(1.700),persistency of calyx(1.681),russet location(1.658),relief of area around eye basin(1.644),flavor(1.610)and ground color(1.592).The coefficient of variation of titratable acidity in the 11 numerical traits of pear germplasm fruit was as high as 128.43%,which could more effectively reflect the differences between pear accessions.The phenotypic differentiation coefficient V_(st)(66.4%)among the five cultivated pear species,including Pyrus bretschneideri(White Pear),P.pyrifolia(Sand Pear),P.ussuriensis(Ussurian Pear),P.sinkiangensis(Xinjiang Pear),and P.communis(European Pear),was higher than the within population phenotypic differentiation coefficient V_(st)(33.6%).The variation among populations was the main source of variation in pear fruit traits.A hierarchical cluster analysis divided the 389 accessions of six cultivated pear species,including P.pashia(Himalayan Pear),into six categories.There were certain characteristics within the populations,and the differences between populations were not completely clustered by region.For example,Sand Pear cultivars from Japan and the Korean Peninsula clustered together with those from China.Most of the White Pear cultivars clustered with the Sand Pear,and a few clustered with the Ussurian Pear cultivars.The Ussurian Pear and European Pear cultivars clustered separately.The Xinjiang Pear and Himalayan Pear did not cluster together,and neither did the cultivars.Seventeen traits,three describing fruit weight and edible rate(fruit diameter,fruit length and fruit core size),five describing outer quality and morphological characteristics(over color,amount of russeting,dot obviousness,fruit shape,and stalk length),and nine describing inner quality(flesh color,juiciness of flesh,aroma,flavor,flesh texture,flesh texture type,soluble solid contents,titratable acidity,and eating quality)were selected from the 39 traits by principal component and stepwise regression analyses.These 17 traits could reflect 99.3%of the total variation and can be used as a comprehensive evaluation index for pear germplasm resources.

Metabolic profiles and morphological characteristics of leaf tips among different sweet potato(Ipomoea batatas Lam.)varieties

Sweet potato leaf tips have high nutritional value,and exploring the differences in the metabolic profiles of leaf tips among different sweet potato varieties can provide information to improve their qualities.In this study,a UPLC-Q-Exactive Orbitrap/MS-based untargeted metabolomics method was used to evaluate the metabolites in leaf tips of 32 sweet potato varieties.Three varieties with distinct overall metabolic profiles(A01,A02,and A03),two varieties with distinct profiles of phenolic acids(A20 and A18),and three varieties with distinct profiles of flavonoids(A05,A12,and A16)were identified.In addition,a total of 163 and 29 differentially expressed metabolites correlated with the color and leaf shape of sweet potato leaf tips,respectively,were identified through morphological characterization.Group comparison analysis of the phenotypic traits and a metabolite-phenotypic trait correlation analysis indicated that the color differences of sweet potato leaf tips were markedly associated with flavonoids.Also,the level of polyphenols was correlated with the leaf shape of sweet potato leaf tips,with lobed leaf types having higher levels of polyphenols than the entire leaf types.The findings on the metabolic profiles and differentially expressed metabolites associated with the morphology of sweet potato leaf tips can provide useful information for breeding sweet potato varieties with higher nutritional value.

Leaf phenotypic variation of endangered plant Tetracentron sinense Oliv.and influence of geographical and climatic factors

To analyze the degree and pattern of phenotypic variation in leaves of Tetracentron sinense Oliv from the perspective of genetic and environmental adaptation and thus contribute to effective evidence-based conservation and management strategies for germplasm resources,we measured 17 morphological and epidermal micromorphological leaf traits from 24 natural populations of T.sinense.Nested analysis of variance,multiple comparison,principal component analysis(PCA),cluster analysis,and correlation analysis were used to explore phenotypic leaf variation among and within populations and potential correlations with geographic and environmental factors.There were significant differences in 17 leaf phenotypic traits among and within populations.The mean phenotypic differentiation coefficient of the 17 traits was 56.34%,and the variation among populations(36.4%)was greater than that within populations(27.2%).The coefficient of variation(CV)of each trait ranged from 4.6 to 23.8%,and the mean was 11.8%.Phenotypic variation of leaves was related to environmental factors such as average annual sunshine hours,average July temperature,and average annual rainfall.The variation changed along gradients of longitude,latitude,and altitude.The PCA clustered the 24 natural populations into four groups.Our study suggests that phenotypic variation in T.sinense occurred primarily among populations,with moderate levels of phenotypic differentiation among populations and low levels of phenotypic variation within populations.The plant’s poor adaptability to the environment is likely an important contributor to its endangerment.Accordingly,conservation strategies are proposed to protect and manage the natural populations of T.sinense.

A Study on the Phenotypic Genetic Diversity of Camellia Germplasm Resources in Macheng City

The genetic diversity analysis was done on 11 phenotypic traits of 35 camellia germplasm materials. The results showed that there were varying degrees of variation in 11 traits concerning the flowers and leaves selected in this study,and petal number had the largest coefficient of variation,followed by ovary height,and leaf length had the smallest coefficient of variation. F test results showed that the differences in 11 phenotypic traits reached a significant level. Through the trait correlation analysis,it was found that there was a positive or negative significant correlation between the 11 phenotypic traits. Principal component analysis results showed that the cumulative contribution rate of the first three principal components was 71. 185%,the eigenvector which reflected flower pattern was largest,and flower pattern had a great impact on classification of camellia variety. Based on the genetic differences in traits between varieties,the 35 test materials were divided into three categories: Group I was characterized by large flower pattern; Group II was characterized by large leaf pattern; Group Ⅲ was characterized by many petals. Flower diameter and flower height were important standards for classification of camellia variety.

Genetic Advances in Genome and Phenotypic Characters of Domestic Dog

Dogs represent such a rich potential resource to further understand diseases and genetic traits.Comparing the genomes of three species of canine,human,and rat in terms of genome analysis,it is found that dogs are highly conservative with humans and rats.The special population structure of dogs makes it a good model for studying the diversity of morphology and behavior,the genetic basis of mammalian evolution,and dis-eases.This article gives a brief review of recent advances in domestic dog origin and evolution,genomic structure,genetic variation in dog pheno-typic characteristics,and gene mapping.These research results are expected to provide a better theoretical basis for canine genetic breeding re-search and provide new ideas and methods for the prevention,diagnosis and treatment of human diseases.

Genome-wide scan for selection signatures based on whole-genome re-sequencing in Landrace and Yorkshire pigs

We performed a genome-wide scan to detect selection signatures that showed evidence of positive selection in the domestication process by re-sequencing the whole genomes of Landrace and Yorkshire pigs.Fifteen annotated elements with 13 associated genes were identified using the Z-transformed FST(Z(FST))method,and 208 annotated elements with 140 associated genes were identified using the Z-transformed heterozygosity(ZHp)method.The functional analysis and the results of previous studies showed that most of the candidate genes were associated with basic metabolism,disease resistance,cellular processes,and biochemical signals,and several were related to body morphology and organs.They included PPP3CA,which plays an essential role in the transduction of intracellular Ca2+-mediated signals,and WWTR1,which plays a pivotal role in organ size control and tumor suppression.These results suggest that genes associated with body morphology were subject to selection pressure during domestication,whereas genes involved in basic metabolism and disease resistance were subject to selection during artificial breeding.Our findings provide new insights into the potential genetic variation of phenotypic diversity in different pig breeds and will help to better understand the selection effects of modern breeding in Landrace and Yorkshire pigs.

Correlation and Path Coefficient Analyses of Yield in Cacao(Theobroma cacao L.)

Cacao(Theobroma cacao L.)is an important commodity tree crop which produces the cocoa bean,a major source of income for most West African countries and many smallholder farmers.Declining yield of cacao is a major limitation to cocoa production in Nigeria.This study aimed at determining the correlations of the phenotypic traits that were related in the yield of the cacao genotypes.Nine cacao hybrids produced from some high-yielding parents in the research farm of Cocoa Research Institute of Nigeria,Ibadan,Nigeria were evaluated from 2012 through 2017 in Owena(7°11’N,5°1’E),Ondo state,Nigeria.Character Correlations and Path Coefficient Analysis were used in the description of the performance of the genotypes.The study concluded that significant genotypic and phenotypic correlations existed among many of the pairs of the fruit and bean characters with one another and with pod index,suggesting a complex contribution of these characters either positively or negatively to growth and yield in cacao,and that fruit and bean traits are determinants of yield in cacao.

Environmental conditions and genetic differentiation:what drives the divergence of coexisting Leymus chinensis ecotypes in a large-scale longitudinal gradient?

Aims The two coexisting Leymus chinensis ecotypes exhibit remarkable divergences in adaptive strategies under drought and salinity in semi-humid meadows and semi-arid steppes.In order to detect the major genetic and environmental factors dominating the intraspecific phenotype variations and ecotype formation,the questions regarding the two distinct phenotypic forms(ecotypes)in L.chin-ensis were addressed:(i)did environments drive the L.chinensis ecotype formation?(ii)was there a molecular basis for the morphological divergence between the two ecotypes?(iii)which driving force dominated the intraspecies divergence,divergent natural selection,genetic drift or stabilizing selection?Methods We applied a series experiments on demographical,morphological and physiological traits of two Leymus chinensis ecotypes with gray green(GG)and yellow green(YG)leaf color in nine wild sites along a longitudinal gradient from 114°to 124°E in northeast China.The environmental data including mean annual precipitation,mean annual temperature,elevation and soil properties were collected.We compared the differences of morphological,physiological and genetic differentiations between the two ecotypes.Important FindingsThe GG type exhibited stronger fitness than YG type from the population densities,morphological traits(e.g.shoot height,leaf area,leaf and seed weights et al.),leaf mass per area(LMA)and physiological traits[relative water content(RWC),proline,soluble sugar contents].Most of above phenotypes(e.g.total shoot densities,spike length et al.)were significantly correlated with mean annual precipitation,mean annual temperature and soil water content(SWC),rarely a correlated with soil pH and soil nutrient.Transplanted populations showed convergence trend by their leaf chlorophyll contents and osmotic adjustments(proline and soluble sugar contents)in the greenhouse,but still exhibited their divergences between two ecotypes in the outdoor transplantation,suggesting that whether L.chinensis ecotype differentiated could be largely affected by the environmental conditions.Furthermore,by the comparison result of quantitative genetic variation(Q_(ST))values from phenotypes with theoretical neutral genetic differentiation(F_(ST)),differentiation in phenotypic traits greatly surpassed neutral predictions,implying that directional natural selection played a crucial role in L.chinen-sis ecotype differentiation.In addition,microsatellite analysis from Neighbor-joining tree and Bayesian assignment generated into two groups according to ecotypes,indicating molecular genetic differentiation also propelled the two ecotypes divergence.We conclude that L.chinensis population variations were driven by combing divergent natural selection(precipitation,temperature and SWCs)along the large-scale gradient and significantly intrinsic genetic differentiation.

AoATG5 plays pleiotropic roles in vegetative growth,cell nucleus development,conidiation,and virulence in the nematode-trapping fungus Arthrobotrys oligospora

Autophagy is an evolutionarily conserved process in eukaryotes,which is regulated by autophagy-related genes(ATGs).Arthrobotrys oligospora is a representative species of nematode-trapping(NT)fungi that can produce special traps for nematode predation.To elucidate the biological roles of autophagy in NT fungi,we characterized an orthologous Atg protein,AoAtg5,in A.oligospora.We found that AoATG5 deletion causes a significant reduction in vegetative growth and conidiation,and that the transcript levels of several sporulation-related genes were significantly downregulated during sporulation stage.In addition,the cell nuclei were significantly reduced in theΔAoATG5 mutant,and the transcripts of several genes involved in DNA bio-synthesis,repair,and ligation were significantly upregulated.InΔAoATG5 mutants,the autophagic process was significantly impaired,and trap formation and nematocidal activity were significantly decreased.Comparative transcriptome analysis results showed that AoAtg5 is involved in the regulation of multiple cellular processes,such as autophagy,nitrogen metabolism,DNA biosynthesis and repair,and vesicular transport.In summary,our results suggest that AoAtg5 is essential for autophagy and significantly contributes to vegetative growth,cell nucleus development,sporulation,trap formation,and pathogenicity in A.oligospora,thus providing a basis for future studies focusing on related mechanisms of autophagy in NT fungi.

Proximal and remote sensing in plant phenomics: 20 years of progress, challenges, and perspectives

Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.

Warming and elevated nitrogen deposition accelerate the invasion process of Solidago canadensis L.

Background:Invasive species can threaten native diversity and alter ecosystem processes while interacting with other components of global environmental change.Invasive plants are becoming increasingly problematic and this can be stimulated by changes in the environment.However,existing studies have primarily investigated the effects of environmental change on a specific stage of plant invasion rather than the continuous invasion process.Methods:A space-for-time substitution experiment was performed to investigate how warming and nitrogen deposition affects the invasion process of a plant.Specifically,different ratios of invasive Solidago canadensis L.to native Artemisia argyi Levl.et Van were employed as a proxy to represent successive levels of invasion.A total of seven treatments were applied in the experiment:ambient(CK),N addition(+5,+12 g m^(−2)year^(−1)),warming(+1.15,+1.86℃)and their interaction(5 g N m^(−2)year^(−1)+1.15℃,12 g N m^(−2)year^(−1)+1.86℃).The growth performance and competitiveness of S.canadensis were investigated.Results:The competitiveness of Solidago canadensis decreased linearly with its invasion degree(p<0.05).Non-linear regression showed that S.canadensis invasion levels of 53%,53%,68%,55%and 58%were the critical thresholds for shifting the direction or magnitude of chlorophyll,leaf nitrogen,leaf shape index,diameter,and root/shoot ratio,respectively.Compared with the ambient treatment(CK,no warming and no N addition),the diameter,height,bio-mass and relative competitiveness of S.canadensis were each limited by warming,to a certain extent,whereas these and the above parameters were significantly increased by nitrogen deposition.The interaction of increased temperature and nitrogen deposition led to significant increases in the growth and competitiveness of S.canadensis,and this effect was detected in every stage of the invasion,throughout the invasion process.Conclusions:Environmental change might have a continuous,progressive,and augmentative effect on the phenotypic traits of S.canadensis.This study provides fairly robust evidence that environmental change promotes the invasion process of S.canadensis in general,not simply in specific stages.In the future,rather than focusing on specific stages,experimental studies should consider examining invasion on a broader scale.