Analysis Of Full-Length Diploid Potato Transcript And The Construction Of Introgression Line

Potato(Solanum tuberosum L.)is the most important tuber crop and the food crop in the world,which is vital to the guarantee of food security.In China,the potato industry is faced with the problems of insufficient varieties and slow breeding progress.Most of the cultivar potatoes widely used were tetraploid,and propagated by tubers.Furthermore,the genome of tetraploid potato was complex,which greatly limited cultivar potato improvement.Additionally,the accuracy and completeness of the currently widely used double haploid potato DM reference annotation remains certain defects,the lacking of partial genes can lead to misinterpretation.Two diploid cultivars potato E4-63(S.tuberosum group Phureja)and A6-26(S.tuberosum group Stenotomum)were used as the basis of this study.We comprehensively analyzed their full-length transcriptomes by the third-generation transcriptome sequencing Iso-Seq(Isoform sequencing).The combined method of high-throughput sequencing technology and molecular marker-assisted selection was used to construct a diploid potato introgression line with E4-63 genetic background and A6-26 whole genome fragment.These results could provide fundamental resources for related research on diploid potato breeding improvement,gene location and functional gene mining.The main research contents are as follows:1.Diploid cultivar potato full-length transcriptome sequencing and analysisWe combined the Next generation sequencing technology to comprehensively reconstruct more accurate full-length transcript annotation of two diploid potato line E4-63 and A6-26 from two different cultivars.19,670 gene locus and 61,198 transcripts were annotated in A6-26 while 18,987 gene locus and 52,557 transcripts were annotated in E4-63.Besides,we also identified new gene,long non-coding RNA(lnc RNA)alternative polyadenylation(APA)event alternative splicing(AS)events and expression difference was analyzed.These results reveal the complexity of the diploid potato transcriptome,enhance our understanding of alternative splicing in potato,enrich the diploid potato transcriptome resources,and improve the annotation results in the existing reference genome.2.Construction of diploid potato introgression lineWe used the parental E4-63 and A6-26 genome sequencing data to identify the parental differential single nucleotide polymorphism(SNPs)locus datasets and combined with the progeny resequencing data to phase the genotype of each individual of progeny.Based on the phasing results,the backcross population of each generation was selected,which ensured that introgressed fragments of A6-26 could uniform and entirely cover in each generation.Finally,the BC3 population was obtained by one cross-breeding and three backcrosses with E4-63 as recurrent parent.Importantly,The constructing introgression line will boost the diploid potato breeding and facilitate to identify and verify genes related important agronomic trait.