Comparative Study Of Gene Expression,Gene Regulatory Elements,and Artificial Selection In Poaceae Crops:Maize,Sorghum,and Setaria

Understanding the genetic differences across closely related species originated and diverged from common ancestor is an important way to uncover many biological problems.Along with the abundance of the genetic data resources,the genetic divergences and their influences to phenotypic and functional variance existed among close related species had taken more attentions by researchers.Although superficial phenotypic differences can be easily observed,it remains unclear how the genetic variances in the process of evolution affected the species divergence and their functions.This study used Gramineae crops,which is valuable and abundant in genetic sequences information,as the study system and analyzed the gene expression patterns and regulations in different tissues and development stages between two closed related species maize and sorghum.And then,the gene expression patterns and regularions of circadian genes in a series of timepoints were compared which sampled from the same age leaves across three close related species maize,sorghum and setaria,initially having an insight into the conservation and differentiation of gene expression and regulation across species.Moreover,the comparative studies of the parallel domesticated genes in different domestication stage uncovered the largely unlinked gene sets targeted by artificial selection during domestication.Lastly,this study conducted comparative analysis between populations and developed a new method to efficiently identify and compare the insertion polymorphisms of the non-reference TE(NRTE)and conserved non-coding sequences respectively,demonstrating the impact of these regulationary elements to gene expressions.Comparison among the species original from the common ancestor on the gene expression and regulation and domesticated selection offers the convenience to retroactive ancestral species,investigate the species evolution process,and understand their environmental adaptation mechanism.Combined with phenotypic data,these will provide important information for molecular breeding and high-quality agricultural traits materials cultivation.The details are as follows.(1)Comparative analysis of gene expression patterns of tissues between maize and sorgum.Integrated with 60 maize and 40 sorghum tissues including flower,seed and leaf,this study compared the gene expression patterns and regulated mechanism in transcriptomic level first across different tissues/cell types and development stages between species.Through constructing the co-expression network,we identified multiple gene clusters with correlations in gene expression and significantly biological functional enrichment among different tissues.Furthermore,using data on sytenic orthology,we compared gene co-expression networks across two closely related species and genes co-expressed at one species were subdivided into smaller sub-networks with higher resolution based on syntenic gene co-expression network from another species,which contributes to a more precise gene functional prediction and regulation mechanism analyzing.This study demonstrated that gene expressions in both maize and sorghum had tissue specificity and genes of 30%between species had similar expression patterns.Moreover,multiple conserved gene expression clusters and regulatory relationship were identified in comparison of co-expression networks between maize and sorghum.We further characterized the expression patterns of maize retained duplicate genes from the ancient maize polyploidy.48.5\%of the maize duplicate genes were observed common expression patterns in both subgenomes and enriched into the same gene clusters non-randomly.Our work analyzes the gene expression patterns in orthologous genes between maize and sorghum and paralogous genes between subgenomes of maize,provides a new insight in accessing the traditional gene functional enrichment studies and further identifies the gene functions with conserved expressed patterns and tissue specificities.(2)Comparative analysis of diurnal expression patterns of genes among maize,sorghum,and setaria.Circadian clock is the core mechanism that drives circadian rhythms allowing organisms optimally adapt to its external cues,such as day and night and four seasons.In this study,we sampled leaves under equivalent conditions in three close related grasses--maize,sorghum,and setaria--every three hours last for a period of 72 hours and sequenced their gene expression data,compared the expression patterns of circadian genes across three species and discussed whether circadian rhythms have similar performance in related species and circadian genes regulated by the common transcription factor potential.In this study,we found 1/3 genes have consistent diurnal expression patterns among sorghum,maize and setaria,and the numbers of expressed genes were higher at night than that in daytime,the orthologs showed strong rhythmic expression that peaks at dawn and dusk.A total of 16 gene co-expression clusters was identified to represent all the expression patterns of circadian genes around 24 hours using a co-expression network of k-means cluster.The majority of diurnal expression genes related to sugars and starch metabolism peak expressed at night,while a small number of genes with functions related to photosynthesis peak expressed at daytime.Combining the three grass-species,a set of well learned and novel conserved motifs and DNA binding sites of trans-regulated factors in promoters were identified using CMH testing.Two well learned motif CBS and EE related to the regulation of evening genes were enriched in gene clusters with peak phase at dusk.This study offers an overview of the expression pattern of circadian genes in grass species,which suggested the conserved gene expression and regulation patterns,establishing the foundation for analyzing the circadian regulation mechanism of important traits related gene in crops.(3)Comparative analysis of the molecular mechanisms behind the parallel selection on phenotypes between maize and sorghum.Besides genetic variations in gene expression and regulation,the divergence of structure and function between species are affected with genetic drift and stable selections,especially the high qualities in modern crops are correlated with artificial selections during long-term domestications.The domestication of diverse grain crops from wild grasses are resulted from artificial selection for a suite of overlapping traits producing changes,which adapt to the human requirement for living and production.It is for this reason that the domesticated traits in different species had parallel phenotypic changes,which can be accomplished by either selection on orthologous genes,or selection on non-orthologous genes with parallel phenotypic effects.To determine how often artificial selection for domestication traits in the grasses targeted orthologous genes,we employed resequencing data from wild and domesticated accessions of maize and sorghum.Many "classic" domestication genes identified through QTL mapping in populations resulting from wild/domesticated crosses indeed show signatures of parallel selection in both maize and sorghum.However,the overall number of genes showing signatures of parallel selection in both species is not significantly different from that expected by chance.Furthermore,the orthologous genes between two species are more likely to be the target of artificial selections than that of non-orthologous genes,and the bias in the signals of gene selections were also identified between two subgenomes in maize.This study suggests that,while a small number of genes will extremely large phenotypic effects have been targeted repeatedly by artificial selection during domestication,the optimization portion of domestication targeted small and largely non-overlapping subsets of all possible genes which could produce equivalent phenotypic alterations.(4)Identification of elements in gene expression and regulation.The conserved noncoding sequences(CNS)have attracted extensive attention because of their specifically temporal and spatial patterns in transcriptional regulation and important regulationary roles in gene expression.To circumvent the constraint in which the identified CNS in most current methods had relatively larger minimum sequence lengths than the average length of known transcription factor binding sites,we developed a new method named STAG-CNS which can simultaneously integrate the data from the promoters of conserved orthologous genes in three or more species was developed.Using the data from up to six grass species made it possible to identify conserved sequences as short as 9 bp with false discovery rate ?0.05.STAG-CNS was further employed to characterize loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy.Genes with fewer retained CNSs show lower overall expression,although this bias is more apparent in samples of complex organ systems containing many cell types,suggesting that CNS loss may correspond to a reduced number of expression contexts rather than lower expression levels across the entire ancestral expression domain.To give ingight into how TE insertion polymorphisms regulated the gene expression and their roles in crop environment adaptation,we identified 274,408 non-redundant TEs were identified using resequencing data generated from 83 maize inbred lines.Association mapping demonstrated that the presence/absence of 48 NRTEs were associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent.Therefore,NRTE-induced variation in gene transcriptional regulation may have been an important factor in the adaptation of maize to different environments.This study identified CNS between different species and NRTE between different populations,analyzing the structure and function of elements in gene expression and regulation and being of great significance in studies of phenotypic differentiation and environment adaptation.