Comparison Of The Population Genetic Structure Between Cultivated And Wild Barley And Identification Of Its MAPK Cascade-related Gene Families

As one of the most important cereal crops,Barley(Hordeum vulgare L.)has the fourth rank among the cereals in global production.It has both food,forage and brewing value and is of great significance for ensuring food security as well as social and economic development.At the same time,barley is one of the oldest and earliest domesticated crops.Evidence of archeology and molecular biology showed that the domesticated barley can be traced back to10,000 BC at Fertile Crescent.It is also considered to the origin of its ancestral wild barley(Hordeum spontaneum),which showed strong environmental plasticity due to its varied types and rich genetic diversity.Therefore,barley has become an ideal model system for studying the evolution of crop origin,artificial selection,and even the history of agricultural cultivation as well as the development of human civilization.The rise of next-generation sequencing and bioinformatics tools,together with the high-quality fine map of barley genome,will usher the opportunities in population genetics and genome study of barley.In this study,the wild barleys with different origins and cultivated barleys all over the world were employed to explore the genetic diversity and population structure of barley with the help of ISJ and SSR molecular markers,genome-wide re-sequencing,transcriptome sequencing and chloroplast genome sequencing.The genetic variation and haplotype of different geographical origins of wild barley were compared.We evaluated the artificial selective regions and related genes that barley suffered during the domestication events at various levels.Finally,by taking the MAPK cascade pathway gene family as an example,we analyzed the genomic composition,distribution and expression characteristics of barley domestication related gene families,which laid the foundation for further researches on its biological functions.The main findings are as follows:(1).Barley genetic diversity analysis based on ISJ and SSR molecular markers.Molecular markers are powerful tools for genetic diversity analysis.We evaluated the genetic diversity,population structure and phylogenetic relationships using 55 cultivated and89 wild barleys based on ISJ and SSR molecular markers.A total of 162 ISJ and 196 SSR polymorphic bands were detected.Population structure and phylogenetic analysis revealed that wild and cultivated barleys can be clustered into distinct branches,of which the wild accessions can be assigned into different groups in accordance with its geographic origin.The genetic diversity analysis showed that the wild population of Mount Gilboa possessed the highest genetic diversity(Na=3.944).In comparison with their ancestors,the cultivated barleys(Na=3.861)suffered a severe genetic bottleneck during artificial selection,which led the absent of alleles and the decline of genetic diversity.(2).Barley genetic diversity,population structure and artificial selection analysis based on whole genome re-sequencingArtificial selection is the driving force for the transition from wild barleys to cultivated barleys.In order to explore the domestication traces and artificial selection effects between cultivated and wild barley,we employed the whole genome re-sequencing to assess the genetic diversity and population structure of 40 wild and 22 cultivated barleys.A total of107.12×10~6 SNPs and 6.65×10~6 InDels were obtained,of which were randomly distributed in seven chromosomes.Population structure and phylogenetic analysis found a divergence between wild and cultivated barleys,of which the wild accessions can be further divided into subgroups according to ecological or geographical origins.Compared with wild barley,the genetic diversity of cultivated barleys declined obviously,with a reduction of 38%lost.The artificial selection also shaped the different demographic history patterns between wild and cultivated barleys.Selective sweep regions with a total of 2,470 genes were mainly focused on plant growth and development,hormone response,biotic and abiotic response,circadian clock and carbohydrate metabolism.This study provided important clues for understanding the biological function of barley domestication related genes,which will provide valuable resources for further origin,evolution,and selection analysis of barley genomes.(3).Comparative genomics analysis of chloroplasts between wild and cultivated barleyThe chloroplast sequence is an important tool for systematic evolution and genetic diversity analysis.In this study,we sequenced the chloroplast genome of 38 wild and 18cultivated barleys.A total of 188 SNPs and 108 InDels were detected,with an average of 1.38SNP/KB and 0.41 InDel/KB.Results showed that the wild barleys possessed a higher genetic diversity,which was consistent with the results of whole genome re-sequencing data.Besides,we identified 17 variants that exhibited a clear dimorphism between the wild and domesticated subgroups,including seven intergenic and two intron variations with moderate impact,as well as eight synonymous mutations with low impact.Population structure,phylogenetic and principal component analysis revealed that wild and cultivated accessions can be clustered into two branches,and the wild barley can be further divided into different subgroups according to its geographical distribution.The topology structure between genome re-sequencing and transcriptome was not consistent with each other,suggesting the different mutation rates between the two sets of genomes.The correlation analysis showed that the genetic distance increased by 0.1 for each additional 798.85km of geographical distance.The study explored the genetic diversity and population structure of barley with the help of chloroplast genome,which also laid the foundation for further barley chloroplast genome evolution studies.(4).Population transcriptome sequencing of cultivated and wild barleyPopulation transcriptome sequencing has become a kind of useful tool for genetic differentiation and comparative analysis.In this study,we investigated the expression profile of 26 cultivated and 29 wild barleys by employing the RNA-seq data.As a result,a total of12.6×10~6 SNPs was identified.Compared with the identified SNPs of the whole genome re-sequencing data,we observed a relative high consistency between them.The population structure and phylogenetic analysis showed that the wild and cultivated barleys can be assigned into different groups.The expression profile analysis showed that a total of 395differential expressed genes.GO enrichment analysis showed that the identified genes were enriched in ncRNA metabolic process,tRNA metabolic process,tRNA aminoacylation for protein translation,ligase activity,aminoacyl-tRNA ligase activity,ligase activity,forming aminoacyl-tRNA and related compounds,cytoplasm composition,chloroplast composition,plastid composition and so on.This study shed a light on further researches on biological researches of barley domestication.(5).Identification,expression profile and co-expression network analysis of the MAPK cascade gene familyThe protein kinase genes were considered to be domestication related genes based on the genome and transcriptome analysis.We here took the mitogen-activated protein kinase(MAPK)cascade gene family as an example to explored the biological function of domesticated genes by genome-wide identification,phylogenetic and expression profile analysis.In the present study,a genome-wide analysis resulted in the presentation of 20MAPKs,6 MAPKKs and 156 MAPKKKs using the latest published genomic data from barley.Phylogenetic tree assigned all the MAPK cascade genes into three groups in accordance to MAPK,MAPKK and MAPKKK,respectively.Remarkably,the MAPKKK genes were further classified into MEKK,RAF and ZIK subfamilies.The analysis of the genomic evolution revealed that both the segmental and tandem duplication events contributed to the expansion of MAPK cascade gene families.Regarding to the ratios of non-synonymous substitution rates(Ka)and synonymous substitution rates(Ks),the duplicated gene pairs have undergone strong purifying selection.Furthermore,the expression patterns of MAPK cascade genes during plant growth and development as well as under diverse biotic and abiotic stresses were investigated using the available RNA-seq data.And a total of 63 plant tissue-and stage-specific genes as well as differential expressed genes in response to different stresses.Finally,the regulatory network between MAPK cascade genes together with miRNAs was constructed using target prediction tools together with WGCNA methods,a total of 72 branches composed of 46 MAPK cascade genes and 11 mi RNAs were found to be involved in the regulatory network.Taken together,our first time systematic and comprehensive characteristics of the MAPK,MAPKK and MAPKKK families in barley will provide invaluable information to elucidate their biological roles in plant and also contribute to better understand function and regulatory network of other domesticated genes in this model species.