Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cu...Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cultivation.However,genome variation,population structure and genetic architecture of garlic agronomic traits were still not well elucidated.Here,1100258 single nucleotide polymorphisms(SNPs)were identified using genotyping-by-sequencing in 606 garlic accessions collected from43 countries.Population structure,principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations.Twenty agronomic traits,including above-ground growth traits,bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study.In total,542 SNPs were associated with these agronomic traits,among which 188 SNPs were repeatedly associated with more than two traits.One SNP(chr6:1896135972)was repeatedly associated with ten traits.These associated SNPs were located within or near 858 genes,56 of which were transcription factors.Interestingly,one non-synonymous SNP(Chr4:166524085)in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits.Additionally,gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in‘vegetative to reproductive phase transition of meristem’,‘shoot system development’,‘reproductive process’,etc.These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.展开更多
The propagation of cultivated garlic relies on vegetative cloves,thus flowers become non-essential for reproduction in this species,driving the evolution of reproductive feature-derived traits.To obtain insights into ...The propagation of cultivated garlic relies on vegetative cloves,thus flowers become non-essential for reproduction in this species,driving the evolution of reproductive feature-derived traits.To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic,the evolutionary histories of two main reproduction-related traits,bolting and flower differentiation,were explored by genome analyses using 134 accessions displaying wide diversity in these two traits.Resequencing identified 272.8 million variations in the garlic genome,198.0million of which represent novel variants.Population analysis identified five garlic groups that have evolved into two clades.Gene expression,single-cell transcriptome sequencing,and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development,some of which display distinct selection signatures.Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1,the global transcription factor group E protein-encoding Asa5G01527.1,and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting.Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic.Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.展开更多
基金supported by the Natural Science Foundation of China(31872946,32172566,and 32272731)National Key R&D Program of China(2021YFD1200201),China Agriculture Research System of MOF and MARA(CARS-24-A-01)+4 种基金Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences(CAAS-XTCX2018021)Youth Innovation Special Task of Chinese Academy of Agricultural Sciences(Y2023QC06)Agricultural Basic Long-Term Scientific and TechnologicalWork(NAES-GR-005)Safe Preservation Project of Crop Germplasm Resources of MOF(2022NWB037)National Hoticultural Gerplasm Centre Project(NHGRC2022-NH01).
文摘Garlic,an asexually propagated crop,is the second important bulb crop after the onion and is used as a vegetable and medicinal plant.Abundant and diverse garlic resources have been formed over thousands of years of cultivation.However,genome variation,population structure and genetic architecture of garlic agronomic traits were still not well elucidated.Here,1100258 single nucleotide polymorphisms(SNPs)were identified using genotyping-by-sequencing in 606 garlic accessions collected from43 countries.Population structure,principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations.Twenty agronomic traits,including above-ground growth traits,bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study.In total,542 SNPs were associated with these agronomic traits,among which 188 SNPs were repeatedly associated with more than two traits.One SNP(chr6:1896135972)was repeatedly associated with ten traits.These associated SNPs were located within or near 858 genes,56 of which were transcription factors.Interestingly,one non-synonymous SNP(Chr4:166524085)in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits.Additionally,gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in‘vegetative to reproductive phase transition of meristem’,‘shoot system development’,‘reproductive process’,etc.These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.
基金supported by grants from the National Natural Science Foundation of China(31872946,32172566 to H.W.,32372689 to T.L.)the Scientific Research Foundation of Yangzhou University(5018/137012867 to T.L.)+1 种基金the Shandong Provincial Key Research and Development Program(2023CXPT045 to T.L.)the China Agriculture Research System of MOF and MARA(CARS-24-01 to H.W.).
文摘The propagation of cultivated garlic relies on vegetative cloves,thus flowers become non-essential for reproduction in this species,driving the evolution of reproductive feature-derived traits.To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic,the evolutionary histories of two main reproduction-related traits,bolting and flower differentiation,were explored by genome analyses using 134 accessions displaying wide diversity in these two traits.Resequencing identified 272.8 million variations in the garlic genome,198.0million of which represent novel variants.Population analysis identified five garlic groups that have evolved into two clades.Gene expression,single-cell transcriptome sequencing,and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development,some of which display distinct selection signatures.Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1,the global transcription factor group E protein-encoding Asa5G01527.1,and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting.Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic.Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.
