Nucleotide Variation Of Fatty Acid Metabolism-related Genes And Population Genetic Structure Of Wild Soybean,Glycine Soja

Wild soybean,Glycine soja,is wild progenitor of cultivated soybean G.max.It grows in a wide range of Eastern Asia,including Japan,Korea and the far eastern regions of Russia,and are centered in China.Wild soybean harbors abundant genetic resources before the artificial selection and domestication of cultivated soybean,making it unique gene reservoir for soybean breeding programs.The knowledge of genetic diversity and population structure of wild soybean is crucial to the conservation,effecient collection and utilization of this valuable genetic resource.Soybean oil is an important source of fatty acids for human nutrition.It is fatty acid biosynthesis pathway that determines the alteration of fatty acid profiles in soybean that are of significance in the improvement of the yield and quality of soybean oil.Given the importance of fatty acid metabolism pathway,genetic variation of genes ihvoloved in the pathway remains poorly known.The characterization of nucleotide variation of fatty acid metabolism-related genes of wild soybean germplasms is urgently needed to guide the utilization of wild soybean germpalsm resources to greatly enhance the improvement of the oil yield and quality of cultivated soybean.In this study,the levels of nucleotide variation and population genetic structure of wild soybean in China were examined in a total of 119 wild soybean accessions,including 59 individual plants and 60 individuals from four natural populations,using four fatty acid metabolism-related genes(ACCase-A,accB-1,GPAT,KAS1)as representatives.The lengths of sequenced gene fragments varied from 599 to 831 bp with a total length of 2,958 bp.A total of 50 polymorphic nucleotide sites,including four InDels and 46 substitutions were detected in these gene fragments for 59 individuals of G.soja,of which three SNPs are functional.In accB-1,the A to T substitution was observed,resulting in an amino acid substitution from asparagine to isoleucine;and C to T substitution resulted in the substitution from serine to phenylalanine.In KASI,C to A substitution caused the substitution from valine to phenylalanine.KASI and accB-1 possessed high levels of nucleotide diversity.No genes showed significant values of Tajima's D and Fu's Fs in G.soja suggesting that genetic drift may play a greater role than selection in shaping patterns of genetic variation for these genes before domestication.The construction of a neighbor-joining tree,principal component analysis and bayesian clustering indicated that all the accessions could be classified into three major groups,representing different eco-geographic regions,including northeastern china(NEC),southern China(SC)and Huang-Huai Valley(HHV),although there were admixtures among the three eco-geographical origins probably due to historical migration and/or gene flow among them.The higher level of genetic diversity was observed in NEC and SC groups,suggesting that there are multiple genetic diversity centers in northeastern china and southern China of Chinese wild soybean.The genetic differentiation was further investigated among three groups,and our results showed strong differentiation among three groups,probably resulting from climatic and geological changes in China.To understand the extent of genetic variation and differentiation of fatty acid biosynthesis-related genes within natural populations of wild soybean,by sequencing accB-1 and KASI gene fragments,we randomly sampled and surveyed 60 individuals of the four natural populations(WK,BJ,TJ and ZJ)of wild soybean from the three eco-geographic regions of cultivated soybean in China.A total of 16 haplotypes were identified in the four natural populations of wild soybean,and the aligned sequences of accB-1 and KASI were 1,352 bp that contained 22 variable sites(21 substitutions and 1 InDel).The assessment of genetic variation for the four populations showed that WK and ZJ harbored higher levels of genetic diversity than TJ and BJ.Therefore,both individual and population samples from eco-geographic regions of northeastern and southern China had the abundant genetic diversity measured by Hd and ?,high levels of diversity and the majority of private haplotypes were observed in both northeastern and southern China.The result suggest that the two genetic diversity centers of wild soybean exist in northeastern and southern China.The coefficient of differentiation for the four populations was FST 0.263(P<0.001),implying a low but strong phylogeographical structure of natural populations of G.soja.AMOVA of these populations suggested that 26.25%of variations could be attributed to the differentiation among populations,whereas 73.75%of genetic variation might account for the differentiation within populations.Such a finding suggest that we should collect more individuals within population to efficiently conserve enough representative genetic variations of wild soybean germplasms.Finally,we characterized the complete chloroplast genome sequences of wild and semi-wild soybean.The chloroplast genomes contains two inverted repeats blocks,separated by the large singlecopy block and small single-copy block.A total of111 unique genes were annotated,including 77 protein coding genes,30 tRNA genes and 4 rRNA genes.Phylogenetic analysis of the ten sequenced Glycine chloroplast genomes revealed that the semi-wild soybean G.gracilis is closer to cultivated soybean G.max than wild soybean G.soja.The newly characterized complete chloroplast genomes of G.gracilis and G.soja will provide useful resources for the further genetic characterization that would enhance the conservation of wild and semi-wild soybean.