A Transcriptome Study Of Seed Size And Seed Number In Lotus(Nelumbo Nucifera)

Lotus?Nelumbo nucifera Gaertn.?is a very important aquatic economic crop,which can be used as vegitables,ornamental and medicinal plant.Lotus seed is consumed as a favorite fruit.Lotus seed yield is one of the important economic traits of lotus.Seed size and number affect yield immediately.It will lay a good theoretical support of breeding for high seed yield to explore the molecular mechanism of lotus seed size and number during seed development.With lotus genome information,a large number of studies were conducted for lotus.Studies focused on economic traits such color,flowering and rhziome provide the foundation for our study on seed yield.Based on our goal,we focused on the period of rapid increase,substance accumulation in seed and carpel differentiation and performed comparative transcriptomic analyses between two lotus cultivars with contrasting seed yields,namely China Antique?CA,wild lotus?and Jianxuan-17?JX,seed lotus?in this study,which contributed to explore the molecular mechanism and regulatory network of seed yield at the transcriptional level.The main results are as follows.Hundred-grain weight of CA with thin seed is 92.6 g and the average number of lotus seed is 16,however,hundred-grain weight of JX with chubby seed is 194.5 g and the average number of lotus seed is 36.The significant difference in the seed size and number between two cultivars results in yield difference at the same time,which matches our goal for materials.The width of lotus seeds appeared to be a more important factor affecting lotus seed size than seed length.The period from 9 to 15 DAP was the key stage that determines seed size in both cultivars.During 9DAP to 15 DAP,lotus seed went through rapid accumulation phase of starch.Considering the decisive role to seed and the function for nutrient storage,cotyledons at 9,12,and 15 DAP were selected for RNA-seq analysis: the samples were designated as CA9,CA12,CA15,JX9,JX12,and JX15,respectively.In the study,we totally identified 22,549 genes including 2414 novel genes.721 and 624 genes were specifically expressed in CA and JX,respectively.DEGs were filtered according to the criteria of FDR?0.05 and fold change?2 in each pairwise comparison and assigned to six clusters by hierarchical clustering analysis based on expression pattern.2895 DEGs were identified both in CA and JX from 9DAP to 15 DAP.GO terms associated with cell proliferation and gene expression were highly enriched in both cultivars during seed development in biological process for those DEGs and the enriched KEGG pathways included photosynthesis,carbon fixation in photosynthetic organisms,and nitrogen metabolism.Oxidation reduction was enriched for DEGs?1521 genes?identified only in CA.Whereas photosynthesis and chloroplast stroma were enriched for DEGs?4021?identified only in JX and Carbon metabolism was the only enriched KEGG pathway for those genes.Candidate genes involved in brassinosteroids?BRs?biosynthesis and signal pathway were identified.Those genes showed different expression pattern and might be participate in different function.Nine genes controlling seed size by cell number and size were identified.There were AP2?APETALA2?,ARF2?AUXIN RESPONSE FACTOR 2?,ANT,GS5.In total,thirty-one DEGs involved in starch biosynthesis were identified in the study.The expression patterns of most of these DEGs were positively correlated with starch accumulation,emphasizing their roles in starch biosynthesis.Finally,the expression levels of most starch biosynthesis genes,particularly genes with high transcript levels,were higher in JX than in CA.This finding suggests that JX might be better able to synthesize starch than CA,ultimately contributing to the higher starch levels,therefore yields,in this cultivar.There are seven candidate genes encoding AGPase,which catalyzes the rate-limiting step in starch biosynthesis.We deduced that NNU₀5331,NNU₂0629 were the most important candidate genes in starch biosynthesis according to transcriptome and expression level for different lotus tissues and seed development stages.Bud size for carpel differentiation of CA and JX is 0.20 to 0.26 and 0.22 0.30,respectively.20651 genes were identified in bud transcriptome.We found 472 upregulated DEGs and 445 downregulated DEGs.Biological process and metabolism occupied the most DEGs.In addition,five candidate genes involved in carpel differentiation were identified,two encoding protein with MADS box domain and three encoding proteins with homeobox domain.This study explored the regulatory network of lotus seed size and number from transcriptional level.We screened some candidate genes.Those results not only provide cues for further study about lotus yield but also useful tool for cultivar breeding.