Genome-wide Identification Of BHLH And Dof Transcription Factors In Persian Walnut(juglans Regia L.)

Common walnut(Juglans regia L.)is a hardwood tree that is economically important and produces edible nuts and quality wood,distributed,primarily across temperate and sub tropical regions of the northern hemisphere.In addition to the natural influence of geomorphological barriers and climate,humans have significantly changed their genetic structure.It is commonly believed that J.regia endures and developed in entirely confined stands in Asia after the last glaciation.Antiquated people distributed walnuts into current territories through social extension and trade.The world production from the time when 2012,provided frequently by China,the USA,and Iran exceeds three million tons.The breeding began in the 20 th century in spite of the very early culture of walnut species(Juglans spp.).In the past 30 years,several genetic studies of walnut were conducted using various methods,from SSRs markers to latest improvements in genome analysis,including diversity examinations,phylogenetic relationships,and origin elucidation,and genetic map construct(TF)family and has an important role in the development of different tissues.In J.regia,the basic helix-loop-helix(bHLH)and Dof(DNA binding with one finger)are plant-specific transcription factors play a key role in diverse biological processes.Genome-wide comprehensive and systematic analyses of bHLH and Dof proteins have been well conducted in Arabidopsis,rice,tomato,and other plant species.However,there is no report of bHLH and Dof gene family genes that have been functionally characterized in Persian walnut Juglans regia.The important outputs are as follows:(i)As a therapeutic plant,Juglans regia has many health benefits which can be used as a antioxidant,antihistaminic,analgesic,bronchodilator,antiulcer,immunomodulatory,antidiabetic,hepatoprotective,antifertility,anti-inflammatory,antimicrobial,antihypertensive,neuroprotective,anticancer,lipolytic,wound healing,insecticidal and several other therapeutic properties.The current evaluation leads toward the chemical composition,nutritional value,ethnobotanical uses,and historical overview of molecular marker development and its importance toward the evolutionary history and genetic diversity ie,molecular markers,like SSRS,AFLPs + RAPDs,AFLPs,RFLPs,Isozymes and SNPs,for the study of genetic diversity/relationships determination of walnut.(ii)We identified a total of 189 bHLsH genes in J.regia,which are clustering into 18 subfamilies.All JrbHLH contained the conserved domains HLH.A total of 69 JrbHLH genes were expanded as whole genome duplications(WGD).The syntenic analysis was conducted for Persian walnut(J.regia)with other two woody plants(P.trichocarpa and O.europaea)to infer the bHLH genes' evolutionary relationship between these species.We identified a total of 42 pairs of orthologous bHLH genes between J.regia and P.trichocarpa,while only 29 orthologous gene pairs between J.regia and O.europaea,and 25 collinear gene pairs were found in three species J.regia,O.europaea and P.trichocarpa.Furthermore,JrbHLHs had different expressed patterns between reproduction and vegetative tissues based on the transcriptome expression profiles of female flowers,male flowers,leaves,and hulls,respectively.Moreover,both transcript data and quantitative polymerase chain response(qRT-PCR)assessment showed that two JrbHLH genes(Jrb HLH3-5 and JrbHLH13-13)remained highly represented in female and male flowers,while one JrbHLH gene(JrbHLH13-4)was highly expressed in leaves.Genome-wide identification,gene structure,phylogeny and expression analysis of the JrbHLH gene in J.regia,supplied a theoretical basis for the functional study of the JrbHLH gene family,and provide an understanding of the further facilitated molecular studies of Persian walnuts.(ii)We identified 39 JrDof genes in the genome of J.regia.Dof family genes clustered into 06 groups based on the phylogenetic tree and contain a highly conserved motif.The motif composition and conserved domain analysis showed that the common walnut Dof gene family contains one conserved motif and one conserved domain Zf-Dof.Most of the Dof genes contain 1 and 2 exons,as revealed by structural analysis.All Jr Dof genes distributed unevenly on 16 chromosomes with the maximum member(4 genes)found on chromosome 3,4,6,7,and 12.High expression of JrDof12-1,JrDof15-3,JrDof6-4,JrDof5-2,and JrDof13-2,(female flowers),JrDof10-1,JrDof3-3,and JrDof14-1,(male flowers),JrDof15-3 and JrDof13-2,(embryo),JrDof4-2,JrDof19-1,JrDof15-2,and JrDof12-4,(leaves,fruit and roots)were identified.RNA-Seq data also confirm that Dof genes may play a key role in the enlargement of J.regia male and female flowers.