The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we d...The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.展开更多
The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we ge...The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we generated two high-quality,gap-free genome assemblies for‘Dangshansu’(DS;503.92 Mb)and‘Lianglizaosu’(ZS;509.01 Mb),each anchored to 17 chromosomes,achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%.Our genome-wide association studies explored the associations between genetic variations and stone cell traits,revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene,designated PbdsZF.Through genetic transformation,we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation,as it transcriptionally activates multiple genes involved in these processes.By binding to the CT-rich motifs CT1(CTTTTTTCT)and CT2(CTCTTTTT),PbdsZF significantly influences the transcription of genes essential for lignin production,underscoring its regulatory importance in plant lignin metabolism.Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation,thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.32102364)the General Program of Shandong Natural Science Foundation(Grant No.ZR2022MC064)+3 种基金the Shanxi Province Postdoctoral Research Activity Fund(Grant No.K462101001)the Doctoral Research Initiation Fund of Shanxi Datong University(Grant No.2023-B-15)the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.2023CYJSTX07)the Shanxi Province Excellent Doctoral Work Award Project(Grant No.606-02010609)。
文摘The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.
基金supported by the National Natural Science Foundation of China(Grant Nos.32201602,32101486,32102364)the Natural Science Fund of Hubei Province(Grant No.2023AFB1036)+2 种基金the Funding of China Tobacco Genome Project(Grant No.110202201012[JY-12])the Beijing Life Science Academy Project(Grant No.2023200CC0270)the Shanxi Provincial Higher Education Youth Academic Leader Project(Grant No.2024Q031)。
文摘The Chinese white pear(Pyrus bretschneideri)is an economically significant fruit crop worldwide.Previous versions of the P.bretschneideri genome assembly contain numerous gaps and unanchored genetic regions.Here,we generated two high-quality,gap-free genome assemblies for‘Dangshansu’(DS;503.92 Mb)and‘Lianglizaosu’(ZS;509.01 Mb),each anchored to 17 chromosomes,achieving a benchmarking universal single-copy ortholog completeness score of nearly 99.0%.Our genome-wide association studies explored the associations between genetic variations and stone cell traits,revealing a significant association peak on DS chromosome 3 and identifying a novel non-tandem CCCH-type zinc finger gene,designated PbdsZF.Through genetic transformation,we verified the pivotal role of PbdsZF in regulation of both lignin biosynthesis and stone cell formation,as it transcriptionally activates multiple genes involved in these processes.By binding to the CT-rich motifs CT1(CTTTTTTCT)and CT2(CTCTTTTT),PbdsZF significantly influences the transcription of genes essential for lignin production,underscoring its regulatory importance in plant lignin metabolism.Our study illuminates the complex biology of fruit development and delineates the gene regulatory networks that influence stone cell and lignocellulose formation,thereby enriching genetic resources and laying the groundwork for the molecular breeding of perennial trees.
