An Integrated Omics Analysis For The Differences Of Seed Oil And Starch Contents Between Glycine Max And Cicer Arietinum

The seed storage substance contents vary greatly across various leguminous crops.For example,average seed oil content is～20%in soybean and～6%in chickpea,while average seed starch content is～2%in soybean and～44%in chickpea.Most substrates required for seed oil and starch biosynthesis are derived from glycolysis-based carbon metabolites.Deeply digging into the possible molecular mechanisms of the differences of seed oil and starch contents in soybean and chickpea has important economic value for improving seed oil and starch contents and their compositions in soybean and chickpea.At present,the knowledge on biosynthesis-related genes and their regulatory mechanisms for seed oil and starch contents in soybean and chickpea are limited,especially,microRNA（miRNA）,transcription factors（TF）,and regulatory networks of storage-substance-synthesis-related genes.Thus,in this study omics-datasets in Arabidopsis,soybean,and chickpea were analyzed to obtain unique and common genes in soybean and chickpea,and investigate expression patterns of oil and starch biosynthesis-related genes based on acyl-lipid and starch metabolism-related genes in Arabidopsis,copy number variations of these genes across species,and the regulatory networks of TFs and miRNAs.Our purpose is to obtain candidate genes,TFs,and miRNAs,which may be responsible for the differences of seed oil and starch contents between soybean and chickpea,especially,phylogeny,conserved domains,expression patterns and co-expression network analyses for WRI1 gene family.The main results are as follow:1.The collinearity analysis identified 31,519 duplicated genes in soybean genome and 1443 duplicated genes in chickpea genome.The expression analysis of common genes at different seed development stages in the two crops clustered 37387 soybean genes and 20259 chickpea genes into six groups.The genes in the 3rd and 4th groups were up-regulated during the rapid accumulation of storage substances,and enriched in metabolic pathways related to substance synthesis,such as starch synthesis,glycolysis,and fatty acid synthesis and extension.This indicates that the two species can synthesize fatty acids and starch.The weighted gene co-expression network analysis（WGCNA）identified 7 co-expression modules of 18,657 soybean-specific genes and 9 co-expression modules of 8010 chickpea-specific genes.The genes in four soybean modules are highly expressed at oil accumulation stages,and these genes are significantly enriched in fatty acid synthesis and metabolism,carbon metabolism,glycolysis and photosynthesis pathways,while the genes in chickpea modules are significantly enriched in a relatively small number of metabolic pathways,such as cell-replication-related pathways.2.Based on oil-and starch-synthesis-related genes in Arabidopsis,87 gene families with copy number differences and expression pattern differences of common genes in the third and fourth groups between soybean and chickpea were mined,including 182soybean and 132 chickpea genes.During the rapid accumulation of soybean oil biosynthesis,the oil-synthesis-related genes are highly expressed.For example,high expression of Ru Bis CO fixes more CO₂at early seed development stages,high expression of ACCase allows more carbon metabolites to flow to fatty acid metabolism pathways,fatty acid synthesis-related genes LACS and triacylglycerol synthesis-related genes GPAT and LPCAT are highly expressed at later seed development stages to enable more fatty acids to be synthesized as TAGs,resulting in high soybean seed oil content.In chickpeas,AGPase is highly expressed during the rapid synthesis of storage substances and catalyzes more starch synthesis substrate Glc-1-P,while there were relatively low expression levels of ACCase and LACS and no expression of LPCAT,resulting in low seed oil content and high starch content in chickpea.3.In peanut and soybean of leguminous oil crops,transcription factor WRI1 was found to have a co-expression relationship with the genes such as ACCase,KAS,KAR,ACP and LACS,which are up-regulated during later seed development stages in soybean.In pea and chickpea of leguminous non-oil crops,WRI1 in pea was found to be co-expressed only with KAR,PDAT,and no lipid synthesis genes.It is speculated that there is a biosynthesis collaborative network of glycolysis and fatty acid biosynthesis centered on TF WRI1 in soybeans and peanuts.This network lets more carbon metabolites flow to lipid synthesis that strengthens lipid synthesis metabolic pathway.Meanwhile,there is no above-mentioned network in pea and chickpea.This may be another molecular mechanism for the difference of seed oil content between soybean and chickpea.This study identified a possible molecular mechanism for the difference in oil and starch content of soybean and chickpea seeds,which could partially explain the difference in storage material content between soybean and chickpea.If soybean seed starch content is to be increased and the oil,protein and starch contents of soybean seeds are to be balanced,the following genetic improvement options are suggested based on the results of this study:reducing soybean BAM5 enzyme activity through gene editing techniques orRNA interference to allow the early synthesis of starch in soybean seeds to be retained and seed starch content to be increased.Increasing the oil content of chickpea seeds will reduce the phytic acid content,improve digestibility and help make chickpea more digestible.Based on the results of this study,two genetic improvement options are suggested:the first way is to increase the oil content of chickpea seeds by gene editing the Ca WRI1 gene to regulate genes related to oil synthesis and increase the flow of carbon metabolites to oil synthesis;the second way is to increase the expression of miRNA159and miRNA319 to increase the expression of the transcription factor MYB33,which downregulates AGPase,and increase the flow of carbon metabolites to oil synthesis in chickpea seeds.The carbon metabolites flowed more towards fatty acid synthesis to increase the oil content of chickpea seeds.