Genome Comparison Of Foxtail Millet And Setaria Viridis And Identification And Analysis Of PT2

The yield of foxtail millet(Setaria italica)is low,and it is difficult to meet the growing demand of people.Therefore,it is the first choice for breeders to identify excellent genes and use them to cultivate high yield millet varieties with.Green foxtail(Setaria viridis)is the wild ancestor of foxtail millet.By comparing the differences between their genomes,we can find new important functional genes and lays the foundation for the functional analysis and breeding application of the important functional genes in foxtail millet.In this study,bioinformatics was used to compare the genome and transcriptome of Yugu 1 and green foxtail.The variation between the coding regions is analyzed.Finally,the predicted protein sequences were also tested for mutations.Grain shattering is an important agronomic trait in the process of plant domestication,and has a great impact on yield.To dissect the domestication of grain shattering related genes in the evolution process of green foxtail to foxtail millet,we have analyzed the difference of grain shattering related genes between green foxtail to foxtail millet on the basis of the whole genome comparing of them.And the PT2 gene was selected to study further.The results showed that:1)The whole genome size of foxtail millet is about 405.74 Mb,Scaffold N50 is about 47.25 Mb,Contig N50 is about 126.27 Kb.While the genome size of green foxtail is about 394.90 Mb,Scaffold N50 is about 46.08 Mb,and Contig N50 is about 51.66 Kb.2)MUMmer was used for comparison the genomes between foxtail millet(Yugul)and green foxtail genomes,and SNP,InDel and SV were also analyzed.The results showed that 441,231 SNPs were detected 2 Kb before the promoter region and 1 Kb after the terminator;420,574 SNPs were detected 2 Kb before the promoter of the millet gene and 1 Kb after the terminator.A total of 363,920 InDel and SV sites were detected.3)The transcript coding regions were aligned by MUMmer software.A total of 43,001 transcripts were obtained from the foxtail millet,of which 40,311 were similar to the green foxtail;48,594 transcripts were obtained from the green foxtail,including 44,416 sequences which were similar to foxtail millet.By the Blastn method,it was found that there were 38,695 sequences in the millet compared with 300 bp in length,and the consistency was over 90%.There were 42,837 sequences of green foxtail compared millet more than 300 bp and the consistency was more than 90%4)Blastp was used to compare the protein sequence of foxtail millet and green foxtail.The results showed that the consistency of 37,453 protein sequences in foxtail millet was more than 90%to green foxtail,and the consistency of 41,552 sequences in green foxtail was more than 90%to foxtail millet.5)The Panicle Traits 2(PT2)genes related to grain traits were screened out from the above analysis results and used for further analysis.It is found that the sequence of the PT2 gene is identical between foxtail millet and green foxtail,except one SNP locus causing amino acid change(T190A).Because of the high conservation of PT2 gene and its promoter in foxtail millet and green foxtail,it is suggested that there are other genes that determine the differences in grain related traits between these two species.