The Study Of Mutation Rate And Recombination Rate Via "Parent-progeny" Sequencing Of The Perennial Peach

Mutation and homologous recombination are the main sources of genetic diversity of the organism genome and are important in the process of biological evolution.At present,scientists have reported the mutation rates and recombination rates in many species(yeast,Drosophila,mouse,human,Arabidopsis,rice,etc.),but the systematic study focused only on few model organisms,for perennial woody plants,for the limitation of certain parts of the genome data,limited Marker sites,susceptible to the genetic background differences and other factors,lack systematic,accurate and reliable evaluation.In addition,many studies have shown that different species or different individuals within the same species,the mutation rate and recombination rate are related with generation cycle,the efficiency and accuracy of the DNA repair system,hybridization methods,and genome heterozygosity.And the results of these studies in different species among the universal also need more data to support and prove.In this study,the meiotic mutation rate and recombination rate of the parent-progeny of perennial woody peach were assessed with the genome-wide data by the next-generation sequencing method and also were compared with the annual plant Arabidopsis to explore the main factors of plant mutation and recombination.Three intraspecific and interspecific groups of peach were constructed in this study,and the F1 hybrids and F2 progeny individuals were sequenced with next-generation sequencing.Through bioinformatics analysis,240 mutations and 46 short indels were detected from the 63 F2 progeny.The results showed that the mutation rate of interspecific hybrid group Ⅲ with the highest heterozygosity was about 1.8 times higher than that of the intraspecific group I with lower heterozygosity(BM test,p = 2.22 x 10-5 base mutation and p = 0.0064 indel mutation).The ratios of point mutations to indels in different groups were no significant difference.Secondly,in a generation cycle,the mutation rate of meiosis in the intraspecific group of peach is almost the same as that of the annual plant Arabidopsis.This is in sharp contrast to the peach has an approximately 10～20 times longer generation than Arabidopsis,which equates to an approximately order of magnitude difference in the mutation rate per unit time,thus directly validates the contribution of the generation cycle to the evolution rate of species.In the evaluation of recombination rates in peach,286 crossovers were detected in the 24 F2 samples of intraspecific group I,corresponding to an average of 11.92 crossovers or 2.64 cM/Mbp per meiosis per sample,which was surprisingly similar to the previous evaluation.As a comparison,we used tetrad analysis,evaluated about 11.11 crossovers per meiosis,with a recombination rate of approximately 4.66 cM/Mbp in Arabidopsis.Clearly we can see that the recombination rate of each intraspecific sample per meiosis was significantly lower than that of annual Arabidopsis(4.0 cM/Mbp),and also rice(4.53cM/Mbp).This result is consistent with the previously reported lower recombination rate of other perennial woody plants(eg.apple,pear,grape,oak and walnut,0.63-2.5cM/Mbp).The innovation of this study is that the meiotic mutation rate and recombination rate of the perennial woody peach were first directly estimated by whole genome sequencing,filled the gap of accurate genome-wide assessment of mutation rate and recombination rate in perennial woody plants.Via the comparison with Arabidopsis mutation and recombination rate,the relationships between mutation,recombination and generation time were systematic examined.Thus the effect of hybridization method or heterozygosity on mutation rate was also tested,which providing new materials for the study of species evolution and laying the foundation for further exploration of mutation and recombination mechanism.