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.

Scanning for Genomic Regions Subject to Selective Sweeps Using SNP-MaP Strategy

Population genomic approaches, which take advantages of high-throughput genotyping, are powerful yet costly methods to scan for selective sweeps. DNA-pooling strategies have been widely used for association studies because it is a cost-effective alternative to large-scale individual genotyping. Here, we performed an SNP-MaP （single nucleotide polymorphism microarrays and pooling） analysis using samples from Eurasia to evaluate the efficiency of pooling strategy in genome-wide scans for selection. By conducting simulations of allelotype data, we first demonstrated that the boxplot with average heterozygosity （HET） is a promising method to detect strong selective sweeps with a moderate level of pooling error. Based on this, we used a sliding window analysis of HET to detect the large contiguous regions （LCRs） putatively under selective sweeps from Eurasia datasets. This survey identified 63 LCRs in a European population. These signals were further supported by the integrated haplotype score （iHS） test using HapMap II data. We also confirmed the European-specific signatures of positive selection from several previously identified genes （KEL, TRPV5, TRPV6, EPHB6）. In summary, our results not only revealed the high credibility of SNP-MaP strategy in scanning for selective sweeps, but also provided an insight into the population differentiation.

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wide association analyses combined with meta-analyses,Bayesian analyses,and selective sweep analyses were performed to screen single nucleotide polymorphisms(SNPs)and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines.Results:Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age,with heritability ranging from 0.034–0.258.Based on meta-analyses and selective sweep analyses,one region(10.81–13.05 Mb)on chromosome Z was associated with egg number in all lines.Further analyses using the W2 line was also associated with the same region,and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers.The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2.There are 36 genes in the region,with glial cell derived neurotrophic factor,DAB adaptor protein 2,protein kinase AMP-activated catalytic subunit alpha 1,NAD kinase 2,mitochondrial,WD repeat domain 70,leukemia inhibitory factor receptor alpha,complement C6,and complement C7 identified as being potentially affecting to egg number.In addition,three SNPs(rs318154184,rs13769886,and rs313325646)associated with egg number were located on or near the prolactin receptor gene.Conclusion:Our study used genomic information from different chicken lines and populations to identify a genomic region(spanning 2.24 Mb)associated with egg number.Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production.These results contribute to the identification of candidate genes and variants for egg traits in poultry.

Immunogenetic basis of chicken’s heterophil to lymphocyte ratio revealed by genome-wide indel variants analysis

Enhancing host immunity is an effective way to reduce morbidity in chickens.Heterophil to lymphocyte ratio(H/L)is associated with host disease resistance in birds.Chickens with different H/L levels show different disease resistances.However,the utility of the H/L as an indicator of immune function needs to be further analyzed.In this study,a H/L directional breeding chicken line(Jingxing yellow chicken)was constructed,which has been bred for 12 generations.We compared the function of heterophils,and combined statistical analysis to explore the candidate genes and pathways related to H/L.The oxidative burst function of the heterophils isolated from the H/L selection line(G12)was increased(P=0.044)compared to the non-selection line(NS).The 22.44 Mb genomic regions which annotated 300 protein-coding genes were selected in the genome of G9(n=92)compared to NS(n=92)based on a genome-wide selective sweep.Several selective regions were identified containing genes like interferon induced with helicase C domain 1(IFIH1)and moesin(MSN)associated with the intracellular receptor signaling pathway,C–C motif chemokine receptor 6(CCR6),dipeptidyl peptidase 4(DPP4)and hemolytic complement(HC)associated with the negative regulation of leukocyte chemotaxis and tight junction protein 1(TJP1)associated with actin cytoskeleton organization.In addition,45 genome-wide significant indels containing 29 protein-coding genes were also identified as associated with the H/L based on genome-wide association study(GWAS).The expression of protein tyrosine phosphatase non-receptor type 5(PTPN5)(r=0.75,P=0.033)and oxysterol binding protein like 5(OSBPL5)(r=0.89,P=0.0027)were positively correlated with H/L.Compared to the high H/L group,the expressions of PTPN5 and OSBPL5 were decreased(P<0.05)in the low H/L group of Beijing you chicken.The A/A allelic frequency of indel 5_13108985(P=3.85E–06)within OSBPL5 gradually increased from the NS to G5 and G9,and the individuals with A/A exhibited lower H/L than individuals with heterozygote A/ATCT(P=4.28E–04)and homozygous ATCT/ATCT(P=3.40E–05).Above results indicated oxidative burst function of heterophils were enhanced,and 22.44 Mb genomic regions were selected with the directional selection of H/L.In addition,PTPN5 and OSBPL5 genes were identified as H/L-related candidate genes.These findings revealed the complex genetic mechanism of H/L related to immunity and will allow selection for improving chicken immunity based on the H/L.

Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis

Background Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China.Three-dimensional genome structure is confirmed to be an important layer of transcription regulation.Although genome-wide interaction data of several livestock species have already been produced,the genome structure states and its regulatory rules in cattle muscle are still limited.Results Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle(Bos taurus).We showed that compartments,topologically associating domains(TADs),and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development.Furthermore,we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps.We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.Conclusions Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology,which will benefit the progress of genetic improvement of beef cattle.

Advances in Genomic,Transcriptomic,and Metabolomic Analyses of Fruit Quality in Fruit Crops

Fruit quality is the main factor determining market competitiveness;it represents the combination of fruit flavor,color,size,and the contents of aromatic and bioactive substances.Research on the genetic basis of fruit quality can provide new information about fruit biology,promote genomic-assisted breeding,and provide technological support for the regulation of fruit quality via habitat selection and/or the control of environmental conditions.High-throughput sequencing is a powerful research method for studying fruit quality traits,and reference genome sequences for many important fruit crops have provided vast amounts of genomic data.To study fruit quality,it is important to select appropriate omics strategies and to analyze omics data meaningfully.Here,we summarize genomic mechanisms of fruit quality formation:gene duplication,transposable element insertion,structural variations and genome methylation in functional genes.We review the genomic,transcriptomic,and metabolomic strategies that have been used to study the genetic basis of fruit quality traits.We also describe some of the genes associated with fruit traits;these genes are a valuable resource for genomics-assisted breeding and are useful models for deciphering the mechanisms of agronomic traits,such as fruit color,size,hardness,aroma components,sugar and acid content.Finally,to maximize the application of omics information,we propose some further directions for research using omics strategies.

Transcriptome analysis of the spleen of heterophils to lymphocytes ratio-selected chickens revealed their mechanism of differential resistance to Salmonella

Salmonella is one of the most common food-borne pathogens and its resistance in chicken can be improved through genetic selection.The heterophils/lymphocytes(H/L)ratio in the blood reflects the immune system status of chicken.We compared the genome data and spleen transcriptomes between the H/L ratio-selected and non-selected chickens,after Salmonella infection,aiming to identify the key genes participating in the antibacterial activity in the spleen.The results revealed that,the selected population had stronger(P<0.05)liver resistance to Salmonella typhimurium(ST)than the non-selected population.In the selected and non-selected lines,the identified differentiation genes encode proteins involved in biological processes or metabolic pathways that included the TGF-beta signaling pathway,FoxO signaling pathway,and Salmonella infection pathway.The results of the analysis of all identified differentially expressed genes(DEGs)of spleen revealed that the G protein-coupled receptor(GPCR)and insulin-like growth factor(IGF-I)signaling pathways were involved in the Salmonella infection pathway.Integrated analysis of DEGs and FST(fixation index),identified candidate genes involved in Salmonella infection pathway,such as GPR39,NTRK2,and ANXA1.The extensive genomic changes highlight the polygenic genetic of the immune response in these chicken populations.Numerous genes related to the immune performance are differentially expressed in the selected and non-selected lines and the selected lines has a higher resistance to Salmonella.

Urbanization drives adaptive evolution in a Neotropical bird

Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations.Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments,but few studies have investigated the genetic mechanisms of this process.Such investigations could provide insights into questions about both evolutionary theory and management of urban populations.In this study,we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species,Coereba flaveola,specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection.To answer this question,we sampled 24 individuals in urban and rural environments,and searched for selected loci through a genome-scan approach based on RADseq genomic data,generated and assembled using a reference genome for the species.We recovered 46 loci as putative selection outliers,and 30 of them were identified as associated with biological processes possibly related to urban adaptation,such as the regulation of energetic metabolism,regulation of genetic expression,and changes in the immunological system.Moreover,genes involved in the development of the nervous system showed signatures of selection,suggesting a link between behavioral and genetic adaptations.Our findings,in conjunction with similar results in previous studies,support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.

Whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics of wheat.Here,we investigated the population genomics of T.urartu by genome-wide sequencing of 59 representative accessions collected around the world.A total of 42.2 million highquality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome.The ancient T.urartu population experienced a significant reduction in effective population size(Ne)from3000000 to140000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period.A map of allelic drift paths displayed splits and mixtures between different geographic groups,and a strong genetic drift towards hexaploid wheat was also observed,indicating that the direct donor of the A subgenome originated from northwestern Syria.Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses.A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T.urartu ecotype groups.Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomicsenabled improvements in wheat breeding.

The ties of brotherhood between japonica and indica rice for regional adaptation

Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication,but the underlying genomic basis remains largely unexplored.Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms(SNPs)fixed in at least one subspecies.We classified these SNPs into three groups,jiS(japonica-and indica-selected),jS(japonica-selected only),and iS(indica-selected only),and documented evidence for selection acting on these groups,their relation to yield-related traits,such as heading date,and their practical value in cropping area prediction.We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability.Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving,cost-reducing selection strategy of genomic breeding,sweep-SNP-guided selection,for developing regionally-adapted heterosis.

Revisiting the false positive rate in detecting recent positive selection

There is increasing interest in studying the molecular mechanisms of recent adaptations caused by positive selection in the genomics era. Such endeavors to detect recent positive selection, however, have been severely handicapped by false positives due to the confounding impact of demography and the population structure. To reduce false positives, it is critical to conduct a functional analysis to identify the true candidate genes/mutations from those that are filtered through neutrality tests. However, the extremely high cost of such functional analysis may restrict studies within a small number of model species. In particular, when the false positive rate of neutrality tests is high, the efficiency of the functional analysis will also be very low. Therefore, although the recent improvements have been made in the （joint） inference of demography and selection, our ultimate goal, which is to understand the mechanism of adaptation generally in a wide variety of natural populations, may not be achieved using the currently available approaches. More attention should thus be spent on the development of more reliable tests that could not only free themselves from the confounding impact of demography and the population structure but also have reasonable power to detect selection.

Detection of genomic signatures for pig hairlessness using high-density SNP data

Hair provides thermal regulation for mammals and protects the skin from wounds,bites and ultraviolet(UV)radiation,and is important in adaptation to volatile environments.Pigs in nature are divided into hairy and hairless,which provide a good model for deciphering the molecular mechanisms of hairlessness.We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data,with the aim to better understand the genetic basis for the hairless phenotype in pigs.A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population(FST)values.Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes(SSC)1,3,7,8,10,11 and 16,and the biological functions of two notable genes,RGS17 and RB1,were revealed.When Mexican hairless pigs were contrasted with hairypigs,strong signatures were detected on SSC1 and SSC10,which harbor two functionally plausible genes,REV3L and BAMBI.KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway,MAPK signaling pathway and the tight junction pathways.All of these pathways may be important in local adaptability of hairless pigs.The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time.RB1 and BAMBI are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs,respectively.RGS17,REV3L,ICOS and RASGRP1 as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs.These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.