Genome-wide Patterns Of Large-size Presence/Absence Variants And Their Associations With Agronomic Traits In Sorghum (Sorghum Bicolour)

BackgroundThe presence/absence variants (PAVs) are a major source of genome structurevariation and have profound effects on human diseases as well as on genome sizesand phenotypic variation in animals. Little is understood about PAVs in plantgenomes. Sorghum (Sorghum bicolour) is a multi-functional C4crop providing food,feed, fibre and fuel, particularly in low-input water-limiting agriculture systems.Here we report our effort to dissect PAVs’ occurrence, diversity and associationswith biofuel-associated traits in sorghum.ResultsThree sorghum genomes were resequenced to12×coverage each and5364PAVswere uncovered, only including96lsPAVs (large-size PAVs)(larger than30kilobases) which affected5.2Mb genomic sequences. The lsPAVs were studied andthe occurrence of51large-size PAVs was confirmed as simple insertion and deletionevents. These lsPAVs affected a total size of2.92Mb of the sorghum genomecontaining202known and predicted genes, of which38were annotated to encodecell death and stress response genes. Detailed analysis of the genomic sequenceswithin and surrounding the lsPAVs demonstrated that there existed56expressedtransposon proteins and high numbers of repeats sequences of various retroelements,DNA transposons, simple repeats and low complexity sequences, suggesting that thelsPAVs resulted from transposable activities and non-homologous recombination.The frequency and distribution of these PAVs varied substantially in a panel of96sorghum inbred lines, and the low-and high-frequency lsPAVs differed in their gene categories. Our further association analysis demonstrated that21lsPAVs weresignificantly associated with the variation in15agronomic traits,10of the lsPAVsaffected more than one traits and more than half of the identified loci localised inprevious mapped QTLs intervals.ConclusionsThis report, for the first time, shed new lights on the occurrence, diversity andfunctions of lsPAVs in sorghum genomes, and established lsPAVs-trait associations.Our research exemplifies a new perspective to explore genome structure variation forgenetic improvement in plant breeding.