| Elite parents refer to some Germplasm resources that can be directly used to breed several widely cultivated varieties.In general,the elite parents not only have excellecne agronomic traits,but also have high level of combining ability,which means,easy to cross with other materials to breed excellent varieties.But knowledge about potato elite parents and especially their genetic backgrounds is limited.In this research,we investigated the pedigree relationships of potato varieties bred worldwide and China.Then 2b-RAD,a reduced-representation sequencing method,was used to to genotype the elite parent Mira and its offspring which span 5 generations.The tetraploid SNPs called by FreeBayes and pedigree relationships were used to trace the conserved and frequently variance segments of the Mira genome.These regions,which have been formation across generations of highly selective breeding,may potentially be helpful for further breeding and performing genome-wide breeding by design.The The main founds are summarized as follows:1.4,397 cultivars listed in online potato pedigree database bred between 1841 to 2013 and 523 Chinese bred cultivars with clear pedigree information were investigated.A large large proportion cultivars were by few genotypes.The parents preferred in breeding changed over time.The pedigree relationships of elite parents were further investigated,and results indicated that excellent parents appeared in different periods;some of the offspring of elite parents were also excellent parents,and some of elite parents shared the same ancestors,implying that some genes were inherited during artificial selection.2.The genomes of Mira and its progenies from different generations were sequenced by 2b-RAD,a reduced-representation genotyping method.The average depth was 124 X of the 120,460 unique tags.50,448 tetraploid SNPs were identified using FreeBayes(an average of 37.1 SNPs per 1M genome,σ=12.46),and validated by Sanger sequencing.3.The conserved and frequently variance chromosome segments were traced by calculating the inheritance rates which were investigated based on information about SNP sites and pedigree relationships between Mira and its progenies.The inheritance rates have a distribution close to normal,but the tails of both ends in QQ plot are highly skewed from expected value of normal distribution and suggested these parts are under selection.4.The conserved segments are marked with identical or similar allele-specific SNPs among the analyzed genotypes.The conserved segments with inheritance rates>0.9 accounted for 20.8%of the Mira genome and included 4,037 chromosome segments with sizes>10,000 bp.Some genes in conserved segments were predicted to be involved in crucial biological processes,such as sugar metabolic process,photosynthesis,transport and signal transduction.Some of these genes are highly expressed in tuber transition and in biotic and abiotic stress.Furthermore,we found some characterized functional genes in these regions that are of interest to breeders.5.The polymorphic sites in variance chromosomal segments are frequently changes in Mira family genome,which means in Mira genome these regions may contained the alleles of genes that the resulting traits do not meet the breeders’ needs,and that parts of segments in the genome of elite parent-Mira need to be improved.5%of chromosome segments which the inherit rates<0.306 are defined as variance chromosome segments.A total of 1,328 genes with annotated functions and genes with crucial biological functions were found in the variance chromosomal segments.6.According to the planting area of Mira’ offspring bred,the variance chromosomal segments based on the changes of Mira genome in order to adapt to different planting area are chosen.1%of highly variance chromosomal segments in each of the 4 planting areas are analyzed for the predicted gene function,and found that some of the genes are highly expressed during the tuber transition and in biotic and abiotic stress. |
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