Natural Variation Analysis And Candidate Gene Identification Of Oil Compositions In Soybean

Soybean(Glycine max L.Merr.)is one of the most important oilseed crops worldwide.Its major content of vegetable protein and oil made it widely used for human consumption and several food industries.High oil content is one of the most important goals of soybean breeding which is likely due to the rapidly increasing global demands for vegetable oil.Nevertheless,the complex pathway of oil metabolism has made the genetic improvement of soybean seed oil content difficult.In this study,the protein,oil and fatty acid(FA)compositions,including palmitic acid(PA),stearic acid(SA),oleic acid(OA),linoleic acid(LA),and linolenic acid(LNA),were evaluated in a large panel of 1551 diverse soybean accessions in multiple locations and years.A set of 1025 Chinese accessions derived from the total collection,1551 accessions,was evaluated to determine the effect of geographical origin on these seed compositions.Also,to investigate the variation in these seed compositions for a set of 633 soybean accessions originated from four diverse accession collections—including China,the United States of America(USA),Japan,and Russia.Furthermore,we conducted a BSA-seq approach to identify variations of candidate genes encoding key enzymes involved in oil biosynthesis pathways in soybean based on two bulk pools of soybeans accessions selected from a diverse panel.The main results were as follows:There were highly significant differences(P < 0.001)between accessions in protein,oil,PA,SA,OA,LA,and LNA contents.Growth year affected(P < 0.001)the abundance of protein,oil,and all FAs except PA.The mean protein,oil,PA,SA,OA,LA,and LNA contents were 44.8%,17%,12.2%,3.8%,21.5%,54.2%,and 8.3%,respectively.The geographical origin of the accession influenced all seed compositions,indicating that accessions originating in each ecoregion tend to have distinct protein,oil,and FA compositions.We observed significant positive correlations among the three locations and between the two years,suggesting the high heritability and stability of individual accessions across contrasting environments.We also observed a relatively high negative correlation between the contents of protein and oil(r = –0.90),OA and LA(r = –0.89),and OA and LNA(r = –0.56),each significant at P < 0.001).The results of correlation between these important FAs provide a potential entry point for developing lines producing oil with higher OA and lower LA and LNA levels.The results showed significant differences(P < 0.001)among the four accession origins for all protein,oil,and FA contents investigated.Higher levels,on average,of PA and LNA were observed in Russian accessions(12.31% and 8.15%,respectively),whereas higher levels of protein,SA,and OA were observed in Chinese accessions(43.93%,3.95%,and 21.95%,respectively).The highest levels of oil and LA were noticed in the USA accessions(20% and 56.34%,respectively).Among all seed compositions,the largest variation was found in LNA,while a large variation,among origins,was observed between Chinese and USA accessions for protein,oil,and LA levels.Maturity group(MG)significantly(P < 0.0001)affected all seed components and higher levels of oil,PA,SA,and OA were observed in early maturing accessions,while higher levels of protein,LA,and LNA were observed in late-maturing accessions.The trends of soybean seed compositions with different MG in this study further provide evidence of the importance of MG in breeding for such soybean seed components.Collectively,the unique accessions identified in this study can be used to strengthen the soybean breeding programs for meeting various human nutrition patterns around the globe.These would be appropriate for specialized use in the food industry.Our results will be useful in breeding soybean with improved quality to meet human nutritional and industrial needs.Using of BSA-seq approach,we identified 2030 genes with different variations between the two bulk pools of low oil pool(LO-pool)and high-oil pool(HO-pool).Among these candidate genes,ten candidate genes represent different genomic regions located at different chromosomes were identified to control FA and oil biosynthesis.The two candidate genes Glyma.11G088800 encoding DGAT2 and Glyma.04G047000 encoding LCAT1,were chosen for further analysis based on their annotations.The two genes LCAT1 and DGAT2 showed 1-and 17-bp frameshift insertions,respectively.Association analysis between PCR genotyping and oil phenotyping data revealed a significant association between the abundance of these InDel variants and reduced oil content.Also,the geographical distribution of such variants in DGAT2 and LCAT1 for Chinese accessions further indicated that these variants can be used as selective markers for differentiation between low-and high-oil varieties.We believed that the BSA-seq approach would be a rapid way to identify the genomic variation for key genes involved in oil biosynthesis in soybean seeds.