As access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant...As access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant(Solanum melongena) introgression lines(ILs) covering altogether 71.6% of the genome of the donor wildrelative parent S. incanum were evaluated for drought tolerance under water stress conditions. Plants at the five true leaves stage were irrigated at either 100%(control) or 30%(water stress) field capacity for 14 days, and growth and biochemical traits were measured. Reduced irrigation resulted in decreased growth and increased stress markers such as proline and malondialdehyde. Most ILs had lower growth and biomass production thanthe cultivated parent under both conditions. However, the wild alleles for two genomic regions related to stem and root dry weight conferred improved tolerance to water stress. In addition, several S. incanum alleles had a positive effect on important traits that may improve yield under drought conditions, such as leaf water content water use efficiency, and chlorophyll content. Fine-mapping the genomic regions for tolerance and reducinglinkage drag with regions affecting growth will be crucial for significantly improving eggplant drought tolerance through introgression breeding.展开更多
The main cultivated varieties in the world belong to the species of upland cotton(Gossypium hirsutum L.),and their genetic background is very narrow.However,the wild species and races in
One hundred and fifty-eight microsatellite markers showing polymorphism among parents were used to survey the introgressed segments in the 50 near-isogenic lines of F_1 pollen sterility. Two hundred and sixty introgre...One hundred and fifty-eight microsatellite markers showing polymorphism among parents were used to survey the introgressed segments in the 50 near-isogenic lines of F_1 pollen sterility. Two hundred and sixty introgressed segments were detected in 50 near-isogenic lines, each carrying 5.2 introgressed segments on an average. Among the 260 segments, one hundred carrying F_1 pollen sterility loci concentrated on the region of F_1 pollen sterility genes, and the remaining one hundred and sixty without F_1 pollen sterility loci distributed randomly over 12 chromosomes. Both the average number and length of the introgressed segments decreased along with the increase of backcross generations. The number of introgressed segments was less than four and the length was less than 20 cM in the near-isogenic lines after backcrossing for four or more times.展开更多
The wild cotton cultivars and species have abundant genetic polymorphisms,and they possess lots of excellent genes,such as drought resistance,insect resistance,fine and strong fiber,and so on.
Wild relatives and un-adapted germplasm of crop species harbors several adaptive traits.Introgression of genes for economic and adaptive traits brings in novel genetic variation into the gene
The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance...The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance （DT）. 52 selected DT ILs, derived from BC2Fz population developed by crossing and backcrossing the susceptible recurrent parent （RP） IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield （GY）, heading date （HD）, panicle numbers per plant （PN）, and plant height （PH） were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances （ANOVA） were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation （PV） for GY and 28% PV for PH, respectively. The other three QTLs linked with RM 163, RM 18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs （one for GY and one for PH） under irrigation condition and three QTLs （one for HD and two for PH） under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.展开更多
Emerging new races of wheat stem rust(Puccinia graminis f.sp.tritici)are threatening global wheat(Triticum aestivum L.)production.Host resistance is the most effective and environmentally friendly method of controllin...Emerging new races of wheat stem rust(Puccinia graminis f.sp.tritici)are threatening global wheat(Triticum aestivum L.)production.Host resistance is the most effective and environmentally friendly method of controlling stem rust.The stem rust resistance gene Sr59 was previously identified within a T2DS 2RL wheat-rye whole arm translocation,providing broad-spectrum resistance to various stem rust races.Seedling evaluation,molecular marker analysis,and cytogenetic studies identified wheat-rye introgression line#284 containing a new translocation chromosome T2BL 2BS-2RL.This line has demonstrated broad-spectrum resistance to stem rust at the seedling stage.Seedling evaluation and cytogenetic analysis of three backcross populations between the line#284 and the adapted cultivars SLU-Elite,Navruz,and Linkert confirmed that Sr59 is located within the short distal 2RL translocation.This study aimed physical mapping of Sr59 in the 2RL introgression segment and develop a robust molecular marker for marker-assisted selection.Using genotyping-by-sequencing(GBS),GBS-derived SNPs were aligned with full-length annotated rye nucleotide-binding leucine-rich repeat(NLR)genes in the parental lines CS ph1b,SLU238,SLU-Elite,Navruz,and Linkert,as well as in 33 BC4F5progeny.Four NLR genes were identified on the 2R chromosome,with Chr2R_NLR_60 being tightly linked to the Sr59resistance gene.In-silico functional enrichment analysis of the translocated 2RL region(25,681,915 bp)identified 223 genes,with seven candidate genes associated with plant disease resistance and three linked to agronomic performance,contributing to oxidative stress response,protein kinase activity,and cellular homeostasis.These findings facilitate a better understanding of the genetic basis of stem rust resistance provided by Sr59.展开更多
Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables...Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables and oilseeds,is a key model system for studying how polyploidy affects plant diversification and domestication.This review summarizes the current understanding of how multiple rounds of ancient and more recent polyploidization events laid the foundation for the wide diversity seen in Brassica.We discuss the key outcomes through which polyploidy facilitates the accumulation of genetic variation,including genomic buffering that enables mutation retention.Furthermore,we explore the significant roles of interspecies and interploidy introgression in introducing external genetic novelty.We highlight homoeologous exchange(HE)as a critical mechanism unique to allopolyploids,driving substantial genomic rearrangements including presence-absence variations and gene dosage alterations that directly contribute to significant phenotypic innovation and adaptation in Brassica.Together,these polyploidy-associated processes have led to the extensive range of genomic variations that shaped great morphological diversification in the domestication of Brassica.By integrating insights from genomics,genetics,and evolutionary biology,this review shows how polyploidy has been central to Brassica's success and agricultural value.We also suggest future research areas to better understand polyploid evolution and improve crop breeding.展开更多
As climate change triggers unprecedented ecological shifts,it becomes imperative to understand the genetic underpinnings of species’adaptability.Adaptive introgression significantly contributes to organismal adaptati...As climate change triggers unprecedented ecological shifts,it becomes imperative to understand the genetic underpinnings of species’adaptability.Adaptive introgression significantly contributes to organismal adaptation to new environments by introducing genetic variation across species boundaries.However,despite growing recognition of its importance,the extent to which adaptive introgression has shaped the evolutionary history of closely related species remains poorly understood.Here we employed population genetic analyses of high-throughput sequencing data to investigate the interplay between genetic introgression and local adaptation in three species of spruce trees in the genus Picea(P.asperata,P.crassifolia,and P.meyeri).We find distinct genetic differentiation among these species,despite a substantial gene flow.Crucially,we find bidirectional adaptive introgression between allopatrically distributed species pairs and unearthed dozens of genes linked to stress resilience and flowering time.These candidate genes most likely have promoted adaptability of these spruces to historical environmental changes and may enhance their survival and resilience to future climate changes.Our findings highlight that adaptive introgression could be prevalent and bidirectional in a topographically complex area,and this could have contributed to rich genetic variation and diverse habitat usage by tree species.展开更多
Pentaploid hybrids produced from crosses between hexaploid and tetraploid wheats combine the genetic variation of both parents.Crossing a synthetic hexaploid wheat LM/AT23 with its AB-genome donor,the durum wheat LM,a...Pentaploid hybrids produced from crosses between hexaploid and tetraploid wheats combine the genetic variation of both parents.Crossing a synthetic hexaploid wheat LM/AT23 with its AB-genome donor,the durum wheat LM,and selfing the pentaploid hybrids to the F7 generation yielded mostly euploid tetraploids and a few hexaploids.Two special derivatives of tetraploid were isolated,including a 4D(4B)substitution line with large panicles and high resistance to stripe rust and a 2DS.2AL translocation line with non-waxy epidermis.The discovery of small D-genome introgressions in the A and B genomes suggested that pentaploidization can be used to induce homoeologous recombination.The introgression of D genome from Aegilops tauschii to the AB genomes might promote the development of super tetraploid wheat with hexaploid biological characteristics(especially stress resistance)and quality functions and the functional study of the introduced chromosomes or fragments.展开更多
Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studyin...Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.展开更多
Gossypium raimondii(2n=2x=26,D_(5)),an untapped wild species,is the putative progenitor of the D-subgenome of G.hirsutum(2n=4x=52,AD_(1)),an extensively cultivated species.Here,we developed a G.hirsutum(recipient)–G....Gossypium raimondii(2n=2x=26,D_(5)),an untapped wild species,is the putative progenitor of the D-subgenome of G.hirsutum(2n=4x=52,AD_(1)),an extensively cultivated species.Here,we developed a G.hirsutum(recipient)–G.raimondii(donor)introgression population to exploit the favorable QTLs/genes and mapped potential quantitative trait loci(QTLs)from wild cotton species.The introgression population consisted of 256 lines with an introgression rate of 52.33%for the G.raimondii genome.The introgression segment length range was 0.03–19.12 Mb,with an average of 1.22 Mb.The coverage of total introgression fragments from G.raimondii was 386.98 Mb.Further genome-wide association analysis(Q+K+MLM)and QTL mapping(RSTEP-LRT)identified 59 common QTLs,including 14 stable QTLs and six common QTL(co-QTL)clusters,and one hotspot of micronaire(MIC).The common QTLs for seed index all showed positive additive effects,while the common QTLs for boll weight all had negative additive effects,indicating that the linkage between seed index and boll weight could be broken.QTLs for lint percentage showed positive effects and could be beneficial for improving cotton yield.Most QTLs for fiber quality had negative additive effects,implying these QTLs were domesticated/improved in G.hirsutum.A few fiber quality QTLs showed positive additive effects,so they could be used to improve cotton fiber quality.The introgression lines developed could be useful for molecular marker-assisted breeding and mapping QTLs precisely for mining desirable genes from the wild species G.raimondii.Such genes can improve cultivated cotton in the future through a designbreeding approach.展开更多
Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from souther...Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.展开更多
Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions.Less well understood is how genome organization and gene flow i...Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions.Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation.Here we conducted genomic footprint analyses to determine how three species of Pterocarya(P.stenoptera,P.hupehensis,and P.macroptera),which are sympatric but occupy different elevational niches,adapted to the heterogeneous environment of the Qinling-Daba Mountains,China.We identified candidate genes for environmental adaptation(i.e.,PIEZO1,WRKY39,VDAC3,CBL1,and RAF),and also identified regions of gene introgression between P.hupehensis and P.macroptera that show lower genetic load and higher genetic diversity than the rest of their genomes.The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates.We also identified candidate genes within these introgressed regions related to environmental adaptation(TPLC2,CYCH;1,LUH,bHLH112,GLX1,TLP-3,and ABC1).Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression.Together,these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.展开更多
Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, lowcopy, and potentially activ...Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, lowcopy, and potentially active long terminal repeat （LTR） retrotransposons occurred in one or more of three rice lines studied that were introgressed by wild rice （Zizania latifolia Griseb.）. For nine retrotransposons in which both the reverse-transcriptase （RT） region and the LTR region were available, largely concordant rearrangements occurred at both regions in five elements and at the RT region only in the remaining four elements. A marked proportion of the genomic changes was shared by two or all three introgression lines that were derived from a single F~ plant. This indicates that most of the genomic changes occurred at early developmental stages of the F~ somatic cells, which then gave rise to germline cells, and, hence, ensured inheritance of the changes to later generations. Possible causes and potential implications of the introgression-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant genome evolution and breeding.展开更多
基金supported by the grants CIPROM/2021/020 from Conselleria d’Educació, Universitats i Ocupació (Generalitat Valenciana, Spain)PID2021-128148OB-I00 funded by MCIN/AEI/10.13039/501100011033/ and by “ERDF A way of making Europ”, as well as by the initiative “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” supported by the Government of Norway+1 种基金Conselleria d’Educació, Universitats i Ocupació de la Generalitat Valenciana for a pre-doctoral grant within the Santiago Grisolía programme (GRISOLIAP/2021/151)Spanish Ministerio de Ciencia e Innovación for a postdoctoral grant (RYC2021-031999-I) funded by MCIN/ AEI/10.13039/501100011033 and the European Union through NextG enerationE U/PRTR。
文摘As access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant(Solanum melongena) introgression lines(ILs) covering altogether 71.6% of the genome of the donor wildrelative parent S. incanum were evaluated for drought tolerance under water stress conditions. Plants at the five true leaves stage were irrigated at either 100%(control) or 30%(water stress) field capacity for 14 days, and growth and biochemical traits were measured. Reduced irrigation resulted in decreased growth and increased stress markers such as proline and malondialdehyde. Most ILs had lower growth and biomass production thanthe cultivated parent under both conditions. However, the wild alleles for two genomic regions related to stem and root dry weight conferred improved tolerance to water stress. In addition, several S. incanum alleles had a positive effect on important traits that may improve yield under drought conditions, such as leaf water content water use efficiency, and chlorophyll content. Fine-mapping the genomic regions for tolerance and reducinglinkage drag with regions affecting growth will be crucial for significantly improving eggplant drought tolerance through introgression breeding.
文摘The main cultivated varieties in the world belong to the species of upland cotton(Gossypium hirsutum L.),and their genetic background is very narrow.However,the wild species and races in
文摘One hundred and fifty-eight microsatellite markers showing polymorphism among parents were used to survey the introgressed segments in the 50 near-isogenic lines of F_1 pollen sterility. Two hundred and sixty introgressed segments were detected in 50 near-isogenic lines, each carrying 5.2 introgressed segments on an average. Among the 260 segments, one hundred carrying F_1 pollen sterility loci concentrated on the region of F_1 pollen sterility genes, and the remaining one hundred and sixty without F_1 pollen sterility loci distributed randomly over 12 chromosomes. Both the average number and length of the introgressed segments decreased along with the increase of backcross generations. The number of introgressed segments was less than four and the length was less than 20 cM in the near-isogenic lines after backcrossing for four or more times.
文摘The wild cotton cultivars and species have abundant genetic polymorphisms,and they possess lots of excellent genes,such as drought resistance,insect resistance,fine and strong fiber,and so on.
文摘Wild relatives and un-adapted germplasm of crop species harbors several adaptive traits.Introgression of genes for economic and adaptive traits brings in novel genetic variation into the gene
基金funded by the National Basic Research Program of China (973 Program, 2004CB117204)the Program for Introduction of International Advanced Ag-ricultural Sciences & Technologies from the Ministry of Agriculture of China [948 Progam, 2006-G1(A)]the Project of Rockefeller Foundation, USA (RF2000)
文摘The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance （DT）. 52 selected DT ILs, derived from BC2Fz population developed by crossing and backcrossing the susceptible recurrent parent （RP） IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield （GY）, heading date （HD）, panicle numbers per plant （PN）, and plant height （PH） were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances （ANOVA） were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation （PV） for GY and 28% PV for PH, respectively. The other three QTLs linked with RM 163, RM 18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs （one for GY and one for PH） under irrigation condition and three QTLs （one for HD and two for PH） under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.
基金the financial support from FORMAS(2018-01029)the Swedish Institute(01132-2022)for supporting Ivan Motsnyi’s visit and research at Swedish University of Agricultural Sciences。
文摘Emerging new races of wheat stem rust(Puccinia graminis f.sp.tritici)are threatening global wheat(Triticum aestivum L.)production.Host resistance is the most effective and environmentally friendly method of controlling stem rust.The stem rust resistance gene Sr59 was previously identified within a T2DS 2RL wheat-rye whole arm translocation,providing broad-spectrum resistance to various stem rust races.Seedling evaluation,molecular marker analysis,and cytogenetic studies identified wheat-rye introgression line#284 containing a new translocation chromosome T2BL 2BS-2RL.This line has demonstrated broad-spectrum resistance to stem rust at the seedling stage.Seedling evaluation and cytogenetic analysis of three backcross populations between the line#284 and the adapted cultivars SLU-Elite,Navruz,and Linkert confirmed that Sr59 is located within the short distal 2RL translocation.This study aimed physical mapping of Sr59 in the 2RL introgression segment and develop a robust molecular marker for marker-assisted selection.Using genotyping-by-sequencing(GBS),GBS-derived SNPs were aligned with full-length annotated rye nucleotide-binding leucine-rich repeat(NLR)genes in the parental lines CS ph1b,SLU238,SLU-Elite,Navruz,and Linkert,as well as in 33 BC4F5progeny.Four NLR genes were identified on the 2R chromosome,with Chr2R_NLR_60 being tightly linked to the Sr59resistance gene.In-silico functional enrichment analysis of the translocated 2RL region(25,681,915 bp)identified 223 genes,with seven candidate genes associated with plant disease resistance and three linked to agronomic performance,contributing to oxidative stress response,protein kinase activity,and cellular homeostasis.These findings facilitate a better understanding of the genetic basis of stem rust resistance provided by Sr59.
基金supported by the National Key Research and Development Program of China(Grant No.2021YFF1000104)the Agricultural Science and Technology Innovation Program(ASTIP),Beijing Municipal Science and Technology Project(Grant No.Z231100003723009)+4 种基金the Central Public-interest Scientific Institution Basal Research Fund(Grant No.Y2023PT16)TKI project(Grant No.KV1605-004)support from the China Scholarship Councilthe NPO bursary funding from Wageningen universitythe scholarship from Institute of vegetables and flowers,CAAS.
文摘Polyploidy,or whole-genome duplication,is an important evolutionary process that has shaped the genomes and traits of many plants,including numerous important crops.The Brassica genus,which includes diverse vegetables and oilseeds,is a key model system for studying how polyploidy affects plant diversification and domestication.This review summarizes the current understanding of how multiple rounds of ancient and more recent polyploidization events laid the foundation for the wide diversity seen in Brassica.We discuss the key outcomes through which polyploidy facilitates the accumulation of genetic variation,including genomic buffering that enables mutation retention.Furthermore,we explore the significant roles of interspecies and interploidy introgression in introducing external genetic novelty.We highlight homoeologous exchange(HE)as a critical mechanism unique to allopolyploids,driving substantial genomic rearrangements including presence-absence variations and gene dosage alterations that directly contribute to significant phenotypic innovation and adaptation in Brassica.Together,these polyploidy-associated processes have led to the extensive range of genomic variations that shaped great morphological diversification in the domestication of Brassica.By integrating insights from genomics,genetics,and evolutionary biology,this review shows how polyploidy has been central to Brassica's success and agricultural value.We also suggest future research areas to better understand polyploid evolution and improve crop breeding.
基金the Project of Qinghai provincial central government guides local funds for science and technology development(2024ZY005).
文摘As climate change triggers unprecedented ecological shifts,it becomes imperative to understand the genetic underpinnings of species’adaptability.Adaptive introgression significantly contributes to organismal adaptation to new environments by introducing genetic variation across species boundaries.However,despite growing recognition of its importance,the extent to which adaptive introgression has shaped the evolutionary history of closely related species remains poorly understood.Here we employed population genetic analyses of high-throughput sequencing data to investigate the interplay between genetic introgression and local adaptation in three species of spruce trees in the genus Picea(P.asperata,P.crassifolia,and P.meyeri).We find distinct genetic differentiation among these species,despite a substantial gene flow.Crucially,we find bidirectional adaptive introgression between allopatrically distributed species pairs and unearthed dozens of genes linked to stress resilience and flowering time.These candidate genes most likely have promoted adaptability of these spruces to historical environmental changes and may enhance their survival and resilience to future climate changes.Our findings highlight that adaptive introgression could be prevalent and bidirectional in a topographically complex area,and this could have contributed to rich genetic variation and diverse habitat usage by tree species.
基金funded by the Natural Science Foundation of Sichuan Province for Young Scholars(2024NSFSC1218)the HighLevel Talent Introduction Project of Sichuan Academy of Agricultural Sciences(NKYRCZX2024022)+1 种基金the Accurate Identification Project of Crop Germplasm from Sichuan Provincial Finance Department(1+3 ZYGG001)the Strategic Scientist Studio of Sichuan Academy of Agricultural Sciences.
文摘Pentaploid hybrids produced from crosses between hexaploid and tetraploid wheats combine the genetic variation of both parents.Crossing a synthetic hexaploid wheat LM/AT23 with its AB-genome donor,the durum wheat LM,and selfing the pentaploid hybrids to the F7 generation yielded mostly euploid tetraploids and a few hexaploids.Two special derivatives of tetraploid were isolated,including a 4D(4B)substitution line with large panicles and high resistance to stripe rust and a 2DS.2AL translocation line with non-waxy epidermis.The discovery of small D-genome introgressions in the A and B genomes suggested that pentaploidization can be used to induce homoeologous recombination.The introgression of D genome from Aegilops tauschii to the AB genomes might promote the development of super tetraploid wheat with hexaploid biological characteristics(especially stress resistance)and quality functions and the functional study of the introduced chromosomes or fragments.
基金supported by the National Key Research and Development Program of China(2024YFF1001400)the Open Project of State Key Laboratory of Animal Biotech Breeding(2024SKLAB6-106)Fundamental Research Funds for Central University(7110100870).
文摘Background As an important genetic resource of chickens,gamecock has unique morphological and behavioral characteristics such as large size,muscular development and strong aggression,making it a good model for studying muscle development and behavior patterns,as well as an excellent breeding material.Gamecocks are distributed worldwide,forming different breeds and strains.However,the single or multiple origin of global gamecocks has not been fully established and much remains unknown about genetic introgression events between gamecocks and other chickens.Therefore,in this study,based on whole genome data of gamecocks,Chinese indigenous chickens,commercial chickens and wild jungle fowls,we performed population structure analysis,selection signal analysis,and genomic introgression analysis of gamecocks.Results The population structure analysis revealed that gamecocks have multiple origins.In addition,we used Fst,π-Ratio and XP-EHH methods to explore the candidate signatures of positive selection in gamecocks.A total number of fifteen shared candidate genes were identified using the three different detection strategies.Among these candidate genes,ETV1,DGKB,AGMO,MEOX2,ISPD and PLCB4 are related to the growth and muscle development,fighting performance and neurodevelopment of gamecocks.Furthermore,we detected the introgression event at the MYBPHL region from the Gallus sonneratii into Euramerican gamecocks and at the CPZ gene region from the Gallus gallus gallus into multiple gamecock populations,respectively,indicating the introgression from the wild junglefowl may impact the skeletal and muscle development as well as aggressive behavior of gamecocks.Conclusions In summary,we conducted a genome-wide exploration of gamecocks from multiple regions worldwide.Our analysis confirmed multiple origins of gamecocks and detected several candidate genes that are possibly related to important traits and characteristics in gamecocks.More importantly,this is the first study that has detected introgression events and genes from wild jungle fowls to gamecocks,which provides evidence of the wild jungle fowls contributing to the genetic diversity of gamecocks.Our findings offer new perspectives on the impact of introgression on gamecocks,and provide a basis for further resource conservation and utilization of gamecock,as well as provide excellent material for the genetic improvement of domestic chickens.
基金funded by the National Key Research and Development Program of China(2016YFD0100203 and 2016YFD0102000)the Key Scientific and Technological Projects of the Eighth Division of the Xinjiang Production and Construction Corps(XPCC),China(2024NY01,2023 NY09,2023 NY10)+2 种基金the Key Scientific and Technological Project of XPCC,China(2021AB010)the Postgraduate Research&Practice Innovation Program of Jiangsu Province,China(KYCX22_0748)supported by the High-performance Computing Platform of the Bioinformatics Center,Nanjing Agricultural University,China。
文摘Gossypium raimondii(2n=2x=26,D_(5)),an untapped wild species,is the putative progenitor of the D-subgenome of G.hirsutum(2n=4x=52,AD_(1)),an extensively cultivated species.Here,we developed a G.hirsutum(recipient)–G.raimondii(donor)introgression population to exploit the favorable QTLs/genes and mapped potential quantitative trait loci(QTLs)from wild cotton species.The introgression population consisted of 256 lines with an introgression rate of 52.33%for the G.raimondii genome.The introgression segment length range was 0.03–19.12 Mb,with an average of 1.22 Mb.The coverage of total introgression fragments from G.raimondii was 386.98 Mb.Further genome-wide association analysis(Q+K+MLM)and QTL mapping(RSTEP-LRT)identified 59 common QTLs,including 14 stable QTLs and six common QTL(co-QTL)clusters,and one hotspot of micronaire(MIC).The common QTLs for seed index all showed positive additive effects,while the common QTLs for boll weight all had negative additive effects,indicating that the linkage between seed index and boll weight could be broken.QTLs for lint percentage showed positive effects and could be beneficial for improving cotton yield.Most QTLs for fiber quality had negative additive effects,implying these QTLs were domesticated/improved in G.hirsutum.A few fiber quality QTLs showed positive additive effects,so they could be used to improve cotton fiber quality.The introgression lines developed could be useful for molecular marker-assisted breeding and mapping QTLs precisely for mining desirable genes from the wild species G.raimondii.Such genes can improve cultivated cotton in the future through a designbreeding approach.
基金supported by the National Key R&D Program of China(2022YFF1000100)Shaanxi Innovation Team Project(2022TD-10)+1 种基金Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project(2022GD-TSLD-46-0401)Postdoctoral Research Funding of Hainan Province。
文摘Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.
基金supported by the National Natural Science Foundation of China(32370386,32070372,and 32200295)Science Foundation for Distinguished Young Scholars of Shaanxi Province(2023-JC-JQ-22)+4 种基金Basic Research Project of Shaanxi Academy of Fundamental Science(22JHZ005)Shaanxi Key Research and Development Program(2024NC-YBXM-064)Science and Technology Program of Shaanxi Academy of Science(2023K-49,2023K-26,and 2019K-06)Shaanxi Forestry Science and Technology Innovation Key Project(SXLK2023-02-20)Qinling Hundred Talents Project of Shaanxi Academy of Science(Y23Z619F17).
文摘Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions.Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation.Here we conducted genomic footprint analyses to determine how three species of Pterocarya(P.stenoptera,P.hupehensis,and P.macroptera),which are sympatric but occupy different elevational niches,adapted to the heterogeneous environment of the Qinling-Daba Mountains,China.We identified candidate genes for environmental adaptation(i.e.,PIEZO1,WRKY39,VDAC3,CBL1,and RAF),and also identified regions of gene introgression between P.hupehensis and P.macroptera that show lower genetic load and higher genetic diversity than the rest of their genomes.The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates.We also identified candidate genes within these introgressed regions related to environmental adaptation(TPLC2,CYCH;1,LUH,bHLH112,GLX1,TLP-3,and ABC1).Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression.Together,these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.
文摘Stochastic introgression of alien DNA may impose a genomic stress to the recipient genome. Herein, we report that apparent de novo genomic rearrangements in 10 of 13 selected endogenous, lowcopy, and potentially active long terminal repeat （LTR） retrotransposons occurred in one or more of three rice lines studied that were introgressed by wild rice （Zizania latifolia Griseb.）. For nine retrotransposons in which both the reverse-transcriptase （RT） region and the LTR region were available, largely concordant rearrangements occurred at both regions in five elements and at the RT region only in the remaining four elements. A marked proportion of the genomic changes was shared by two or all three introgression lines that were derived from a single F~ plant. This indicates that most of the genomic changes occurred at early developmental stages of the F~ somatic cells, which then gave rise to germline cells, and, hence, ensured inheritance of the changes to later generations. Possible causes and potential implications of the introgression-induced genomic rearrangements in LTR retrotransposons are discussed in the context of plant genome evolution and breeding.
