The Genetic Basis Of Inbreeding Depression In Potato

Potato(Solanum tuberosum L.)is the most important tuber crop,and is vital to food security worldwide.However,two obstacles limit the process of potato breeding and improvement.First,cultivated potato is autotetraploid,highly heterozygous,increasing the difficulty of genetic analysis,which limits the process of genetic improvement.Second,potato is propagated from tubers,which comes with the challenges of high cost of seed potatoes and susceptible to diseases.To speed up the breeding process,substituting tetraploid by diversified diploid,and substituting seed potatoes by seeds,lead to a reformation of potato re-domestication.However,self-incompatibility and inbreeding depression severely hamper the development of inbred lines.In previous study,via genome editing technology and pollination in bud stage,we successfully obtained self-incompatible potato materials.However,the genetic mechanism of inbreeding depression is largely unknown.Decoding the genetic basis of inbreeding depression is of great significance for hybrid potato breeding.In this study,combined with high-throughput sequencing technologies,bioinformatic methods,we constructed three inbred lines and sequenced diploid landraces,tetraploid landraces and tetraploid cultivars.We obtained the following findings which are beneficial for potato breeding improvement:1.Deleterious mutations are the main factor causing inbreeding depression.2.Deleterious mutations scatter in whole genome,but abundant in pericentromeric regions,thus recombination can hardly eliminate the deleterious mutations.However,the mutation burden in potato is line-specific,by well-designed cross combinations can maintain deleterious mutations in heterozygous alleles to mask the harmful effects.3.By developing a parent-independent genotyping by sequencing method in potato,we analyzed three selfing populations and identified 15 genomic regions showing strong segregation distortions.4.Combining genotypes and phenotypes of three selfing populations,we identified nine large-effect deleterious mutations,causing lethality or obvious phenotypic defects.Genetic mapping showed that most of them are located in the genomic regions with high recombination,suggesting it is possible to effectively purge them by sexual propagation.5.The increase in deleterious mutations,during polyploidization,resulted from the rapid accumulation of heterozygous mutations,the harmful effects of which were masked by the wild-type alleles;thus,tetraploid potatoes had advantages in growth vigor and yield.6.The polyploidization events resulted in more deleterious mutations than improvement in potato.Continuous artificial selection in the improvement process can hardly effectively purge the deleterious mutations in potato.