Distribution Of InDels And Their Genetic Linkage Maps In Populus Deltoides And Populus Simonii

There are significant differences in growth traits and stress resistance between Populus deltoides and P.simonii,and the progeny obtained from the hybridization of the two species had good heterosis.Therefore,these two species can provide valuable materials for studying genetic variations in the poplar genomes.Insertion or deletion polymorphism(InDel)is one of the main genetic variations in plant genomes.InDel variants is widely distributed in plant genomes and has the advantages of codominance and genetic stability.However,there are relatively few studies on InDel variants in Populus.With advances in next-generation sequencing(NGS)technology,researchers can obtain large amounts of DNA sequence data at a consistently low cost,making it possible to identify genetic variations in genomes with these data.However,it remains challenging to accurately infer InDel genotypes from short sequencing data.In this study,we first presented an integrated pipeline called InDelGT for extracting InDel genotypes in a hybrid population with sequencing data to construct InDel genetic linkage maps.Secondly,we analyzed the distribution of InDel variation in the genomes of P.deltoides and P.simonii.Finally,we constructed two parental InDel genetic linkage maps using restriction-site associated DNA sequencing(RAD-seq)data in an F1 hybrid population of P.deltoides and P.simonii.The detailed results of this study are as follows:1.The newly developed software InDelGT was written in Perl language for extracting InDel genotype data in a genetic mapping population with NGS data,which can be obtained for free at https://github.com/tongchf/InDelGT.The algorithms of InDelGT were implemented in three steps:(1)generating an InDel catalog of the two parents;(2)calling individual InDel genotypes in a mapping population such as the F1 hybrid population in forest trees and the traditional backcross and F2 population in inbred lines;and(3)filtering of InDel sites meet with Mendelian segregation for genetic mapping.InDelGT can complete the entire genotyping process by simply entering a command line,and it can perform multicore or multithreaded parallel computing,which greatly improves the efficiency of InDel genotyping.2.We investigated the distribution characteristics of InDel variants in the whole genomes of P.deltoides and P.simonii with RAD-seq data.A total of 119,066 InDels were identified in P.deltoides and P.simonii according to the reference genome of P.trichocarpa,including 58,532 unique InDels in P.deltoides,54,469 unique InDels in P.simonii,and 6,065 common InDels in both.Meanwhile,the distribution of these InDels was analyzed along chromosomes,indicating that the distribution patterns for both species were largely similar,but the average InDel density was slightly higher in P.deltoides than in P.simonii.GO annotation analysis of those genes harboring InDels showed the same patterns between the two poplar species.It is interesting to find that the ratio(~46%)of the common InDels within genes was higher than that of the specific InDels within genes in P.deltoides(~34%)or in P.simonii(~33%),possibly indicating that those InDels are more conservative between poplar species.3.We used InDelGT to extract the InDel genotypes of the two partents and their 140 progeny in the F1 hybrid population of P.deltoides and P.simonii and constructed the InDel genetic linkage maps of the two parents.Considering factors such as allele coverage and genotype quality,we obtained 889 InDel sites to construct InDel genetic map of the female parent P.deltoides,which are heterozygous in the female and homozygous in the male and follow the Mendelian segregation ratio.The maternal map contained 777 InDel markers and 19 linkage groups with a total distance of 2,867.76 c M and an average distance of 3.83 c M.Meanwhile,we obtained 731 InDel sites to construct the genetic map of the male P.simonii,which are homozygous in the female and heterozygous in the male and follow the Mendelian segregation ratio.The paternal map contained 669 InDel markers and 19 linkage groups with a total distance of 3,423.56 c M and an average distance of 5.61 c M.In summary,we investigated the distributions of InDel variation in P.deltoides and P.simonii with RAD-seq data,providing valuable genomic variation information for genetic and evolutionary studies in Populus.We also provided a powerful computing tool for extracting InDel genotypes for constructing InDel genetic maps with NGS data in forst trees.Moreover,we successfully constructed the InDel genetic maps of P.deltoides and P.simonii,which provide an indispensable genetic resource for studying economically and ecologically important traits of poplar.