Genome-wide Pattern Of Presence And Absence Variants(PAVs) In Elite Parents Of Excellent Hybrid Cotton

The presence/absence variants?PAVs?are an important genome structure variations,and they could cause greater phenotypic variation than SNP and InDels due to their impact of genome size which can range from a few Kb to several Mb.PAVs can be applied to cotton heterosis research as the lower polymorphism of SSR and other markers.In this study,based on genetic effects of back bone parents using 10×10 diallel crosses in our previous study,seven elite cotton genomes with 12-fold coverage will be selected be resequenced,and the origin and classification of PAVs in genome and their impact on related genes and genetic diversity will be analyzed.Furthermore,the possibility existences in genome and genetic characteristics of key LsPAVs which are longer than 30 Kb will be verified using combination of three recombinant inbred lines?F₆?.Finally,the correlation analysis will be performed between verified LsPAVs and agronomic traits in 204 natural populations,and the key LsPAVs which control genetic variation of elite partents will be explored.In this study,we found 241,733 PAVs with different sizes from the 7 elite cotton varieties,each 30×coverage,using the high-throughput genomic re-sequencing method by comparative genomics analysis.Here we discovered 20,580LsPAVs whose sizes larger than 30 Kb.These LsPAVs afftected almost 50%of the cotton genome.Futhermore,we uncovered 2,782 LsPAVs with 80 genes annotated to encode to cellular component and molecular function existing in 26 chromosomes among 7 cotton genomes.The PAVs were clustered to PPR protein family,the ABC2-membrane protein family and so on,mostly located in intergenic regions.These results were consistent with reports from other species.Moreover,the distribution of PAVs showed that the number of PAVs in A subgenome is more than that in D subgenome indicating that PAVs are not evenly distributed in each chromosome.This research will give a new clue to study how the genome structure variation to influence agronomic traits,and will greatly contribute to the correlation construction between gene and agronomic traits and cotton molecular breeding.