Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Prunus species include many important perennial fruit crops,such as peach,plum,apricot,and related wild species.Here,we report de novo genome assemblies for five species,including the cultivated species peach(Prunus persica),plum(Prunus salicina),and apricot(Prunus armeniaca),and the wild peach species Tibetan peach(Prunus mira)and Chinese wild peach(Prunus davidiana).The genomes ranged from 240 to 276 Mb in size,with contig N50 values of 2.27−8.30Mb and 25,333−27,826 protein-coding gene models.As the phylogenetic tree shows,plum diverged from its common ancestor with peach,wild peach species,and apricot~7 million years ago(MYA).We analyzed whole-genome resequencing data of 417 peach accessions,called 3,749,618 high-quality SNPs,577,154 small indels,31,800 deletions,duplications,and inversions,and 32,338 insertions,and performed a structural variant-based genome-wide association study(GWAS)of key agricultural traits.From our GWAS data,we identified a locus associated with a fruit shape corresponding to the OVATE transcription factor,where a large inversion event correlates with higher OVATE expression in flat-shaped accessions.Furthermore,a GWAS revealed a NAC transcription factor associated with fruit developmental timing that is linked to a tandem repeat variant and elevated NAC expression in early-ripening accessions.We also identified a locus encoding microRNA172d,where insertion of a transposable element into its promoter was found in double-flower accessions.Thus,our efforts have suggested roles for OVATE,a NAC transcription factor,and microRNA172d in fruit shape,fruit development period,and floral morphology,respectively,that can be connected to traits in other crops,thereby demonstrating the importance of parallel evolution in the diversification of several commercially important domesticated species.In general,these genomic resources will facilitate functional genomics,evolutionary research,and agronomic improvement of these five and other Prunus species.We believe that structural variant-based GWASs can also be used in other plants,animal species,and humans and be combined with deep sequencing GWASs to precisely identify candidate genes and genetic architecture components.

The NAC transcription factor MdNAC4 positively regulates nitrogen deficiency‑induced leaf senescence by enhancing ABA biosynthesis in apple

Although it is well established that nitrogen(N)deficiency induces leaf senescence,the molecular mechanism of N deficiency-induced leaf senescence remains largely unknown.Here,we show that an abscisic acid(ABA)-responsive NAC transcription factor(TF)is involved in N deficiency-induced leaf senescence.The overexpression of MdNAC4 led to increased ABA levels in apple calli by directly activating the transcription of the ABA biosynthesis gene MdNCED2.In addition,MdNAC4 overexpression promoted N deficiency-induced leaf senescence.Further investigation showed that MdNAC4 directly bound the promoter of the senescence-associated gene(SAG)MdSAG39 and upregulated its expression.Interestingly,the function of MdNAC4 in promoting N deficiency-induced leaf senescence was enhanced in the presence of ABA.Furthermore,we identified an interaction between the ABA receptor protein MdPYL4 and the MdNAC4 protein.Moreover,MdPYL4 showed a function similar to that of MdNAC4 in ABA-mediated N deficiencyinduced leaf senescence.These findings suggest that ABA plays a central role in N deficiency-induced leaf senescence and that MdPYL4 interacts with MdNAC4 to enhance the response of the latter to N deficiency,thus promoting N deficiency-induced leaf senescence.In conclusion,our results provide new insight into how MdNAC4 regulates N deficiency-induced leaf senescence.