Comparative Transcriptomic Analysis Of MADS-box Genes In Fruit-type Differentiations Of Pome And Drupe In Rosaceae

Pome and drupe are two important fruit types in Rosaceae,which have important economic and scientific value.Current research suggests that both pome and drupe fruit types are derived from the ancestral fruit type of follicetum,and they have produced today’s significant differences through two different evolutionary routes.MADS-box genes are a class of key genes that regulate the development of plant floral organs,and play an important role in plant reproductive growth and vegetative growth.Current studies have shown that after the genome-wide doubling event of Maleae,the gene doubling of AP1,FUL,AG and other genes in the MADS-box gene family may play a role in the formation of pome fruit.At present,the mechanism of MADS-box genes in the differentiation of pome fruit and drupe fruit types has not yet been clarified.In this study,the duplication type and phylogenetic relationship of MADS-box gene family members in genomes of seven species of Rosaceae(Malus domestica,Malus baccata,Pyrus bretschneideri,Prunus persica,Gillenia trifoliata,Fragaria ananassa and Dryas drummondii)are first analyzed.The evolutionary relationship and tissue-specific expression of type-II MADS-box genes related to the development of floral organs and fruit development of pome and drupe are mainly analyzed.Then,this study further used the transcriptome data of hypanthium,ovary wall and ovule at different developmental stages to select candidate genes affecting fruit type differentiation through differential expression analysis,co-expression trend analysis and weighted gene co-expression network.The results of this study will help to further determine the mechanism of differentiation of fleshy fruit types.The main results are as follows:(1)There is a correlation in the total number of MADS-box gene family members in Rosaceae plants with different fruit types.116,109,107,83,62,84 and 69 members of the MADS-box gene family identified in the Rosaceae species of Malus domestica,Malus baccata,Pyrus bretschneideri,Prunus persica,Gillenia trifoliata,Fragaria ananassa and Dryas drummondii,respectively.The amino acid length of most MADS-box proteins is between 200 and 300,the relative molecular weight is between 20 k Da and 30 k Da,the isoelectric point value distribution is between 8 and 10,and most of MADS-box proteins are basic proteins.The subcellular localization of all MADS-box proteins is in the nucleus,and they have transcriptional regulation functions.There are 5 and 2 hydrophobic proteins in cultivated apple(Golden Delicious)and Malus baccata respectively,and the remaining five species are all hydrophilic proteins.(2)There is specific replication of different subfamilies of MADS-box in Rosaceae species.In this study,a phylogenetic tree of MADS-box genes in seven Rosaceae species is constructed.According to the phylogenetic evolutionary tree,the MADS-box genes can be divided into two categories: Type-Ⅰ and Type-Ⅱ.Type-Ⅰ can be further divided into four subfamilies: Mα,Mβ,Mγ and Mδ.Type-Ⅱ can be further divided into twelve subfamilies: SVP,SEP,AGL16,AP1,FLC,AG,SOC1,AGL17,AP3,TT16,AGL12 and AGL15.Among these ABCDE floral organ identity genes of Type-Ⅱ MADS-box,class B gene AP3 maintains a single copy in Rosaceae,and class B gene PI has tandem duplication in strawberry,and maintains a single copy in the other six Rosaceae species.The class B gene TM6 and other ACDE floral organ identity genes have undergone whole-genome doubling events in the Maleae,and gene duplications have occurred in the Maleae.The six species of Rosaceae other than Gillenia trifoliata all have tandem duplication genes in the SVP paralog gene clade,and the tandem duplication of the SVP subfamily may have occurred before the differentiation of Rosaceae species.(3)There are specific translocations of MADS-box subfamily genes in phylogenetic clades of different species of Rosaceae plant.According to the synteny network,it is found that the Type-Ⅰ MADS-box gene subfamily Mα and Mβ have gene translocation before the differentiation of Rosaceae Amygdaloideae,Type-Ⅱ MADS-box gene FLC translocation occurred in Maleae of Rosaceae,and the class A gene FUL and the class E gene FBP9 have ancient tandem duplication.(4)Orthologous genes with significant differential expression trends are clustered in the hypanthium of pome and drupe,and these genes are significantly enriched in the auxin pathway.In this study,the cluster analysis of co-expression trends of orthologous genes is performed on the same tissues of pome(Malus domestica,Malus baccata and Pyrus bretschneideri)and drupe(Prunus persica),and found one cluster group containing 801 orthologous groups in hypanthium.In this cluster group,there are similar expression trends in the three pomes,while the expression trend in drupe is significantly different from the expression trend in pome.GO enrichment analysis results showed that this cluster group significantly enriched the enrich items related to auxin metabolism,auxin transport,auxin efflux and auxin homeostasis.(5)In this study,the transcriptome analysis of different tissues(hypanthium,ovary wall and ovule)is performed in three periods from post-anthesis to young fruit formation in pome(Malus domestical,Malus baccata and Pyrus bretschneideri)and drupe(Prunus persica)materials,and the number of differentially expressed genes in the three fruit tissues is found to be significantly different in pome type and drupe type.The total number of differentially expressed genes in the hypanthium of the four materials(Malus domestical,Malus baccata,Pyrus bretschneideri and Prunus persica)are: 9918,3478,1509,6765,respectively;the total number of differentially expressed genes in the ovary wall are: 8442,3837,1294,785,respectively;the total number of differentially expressed genes in ovule are: 5917,3739,1490,925,respectively.GO enrichment analysis showed that the differentially expressed genes of pome and drupe are significantly enriched to a large number of enrich items related to cell wall substance metabolism,cell wall substance synthesis,cell population proliferation and cell cycle transition,indicating that the young fruit of pome and drupe are growing rapidly.However,auxin-responsive and gibberellin-responsive genes are significantly enriched in the hypanthium of pome material,but not in the hypanthium of drupe.It indicated that the hypanthium of pome fruit has significantly higher hormone response ability than the hypanthium of drupe,and the difference in response to hormones may be one of the reasons that determine whether the hypanthium of pome and drupe can develop into fruit.(6)In this study,a combination of transcriptome differential gene analysis,gene coexpression trend analysis and weighted gene co-expression network(WGCNA)analysis selected 22 candidate genes associated with the formation of differential fruit types of pome and drupe,including: ZIP1,ZIP5,GLP3,GL5,NRT1.5,NIA1,RD22,GA2OX1,GID1 C,FIL,ILR1,PID,AUX1,PIN1,PIN6,ABCB19,AP1,SEP4,SOC1,AG,SHP and AGL79.Among them,MADS-box genes included AP1,SEP4,SOC1,AG,SHP,and AGL79.Based on gene expression changes and co-expression network,it is hypothesized that AP1 has an important role in fruit formation and fruit development of pome,AG and SHP play an important role in fruit formation of drupe,as well as SEP4,SOC1 and AGL79 also play important regulatory functions in pear and drupe fruit development.