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
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
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
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
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
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
Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable spe...Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.展开更多
Background Chicken is one of the most numerous and widely distributed species around the world,and many studies support the multiple ancestral origins of domestic chickens.The research regarding the yellow skin phenot...Background Chicken is one of the most numerous and widely distributed species around the world,and many studies support the multiple ancestral origins of domestic chickens.The research regarding the yellow skin phenotype in domestic chickens(regulated by BCO2)likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens.However,beyond the BCO2 gene region,much remains unknown about the introgression from the grey junglefowl into domestic chickens.Therefore,in this study,based on wholegenome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds,we explored the introgression events from the grey junglefowl to domestic chickens.Results We successfully detected introgression regions besides BCO2,including two associated with growth trait(IGFBP2 and TKT),one associated with angiogenesis(TIMP3)and two members of the heat shock protein family(HSPB2 and CRYAB).Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens.Furthermore,we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds,indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained.Additionally,our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens,possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.Conclusions In summary,our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens,laying the foundation for a deeper understanding of the genetic composition within domestic chickens,and offering new perspectives on the impact of introgression on domestic chickens.展开更多
A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A^r subgenome of B. rapa （A^rA^r） and C^c of B. carinata （B^cB^cC^cC^c） into natural B. napus （AnAncncn）. The...A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A^r subgenome of B. rapa （A^rA^r） and C^c of B. carinata （B^cB^cC^cC^c） into natural B. napus （AnAncncn）. The progenies with 38 chromosomes that were derived from the self-pollinated seeds of pentaploid hybrids （A^rA^nB^cC^cC^n） were used for further research. Some of the partial new-typed B. napus showed normal meiotic behavior, high portion of germinated pollen and normal embryological development. This indicates that the selected new-typed B. napus had a balanced genetic base. Molecular analysis showed that about 50% of the genome in the new-typed B. napus was replaced by A^r and C^c subgenome from B. rapa and B. carinata. Considering the genetic diversity among different lines of new-typed B. napus, it was deduced that the introgression of the genomic components from B, rapa and B. carinata could widen the genetic diversity of rapeseed.展开更多
Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design(BBD)built on massive information from functional and population genomic...Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design(BBD)built on massive information from functional and population genomics research.A novel strategy of breeding by selective introgression(BBSI)has been proposed and practiced for simultaneous improvement,genetic dissection and allele mining of complex traits to realize BBD.BBSI has three phases:a)developing large numbers of trait-specific introgression lines(ILs)using backcross breeding in elite genetic backgrounds as the material platform of BBD;b)efficiently identifying genes or quantitative trait loci(QTL)and mining desirable alleles affecting different target traits from diverse donors as the information platform of BBD;and c)developing superior cultivars by BBD using designed QTL pyramiding or marker-assisted recurrent selection.Phase(a)has been implemented massively in rice by many Chinese research institutions and IRRI,resulting in the development of many new green super rice cultivars plus large numbers of ILs in 30+elite genetic backgrounds.Phase(b)has been demonstrated in a series of proof-of-concept studies of high-efficiency genetic dissection of rice yield and tolerance to abiotic stresses using ILs and DNA markers.Phase(c)has also been implemented by designed QTL pyramiding,resulting in a prototype of BBD in several successful cases.The BBSI strategy can be easily extended for simultaneous trait improvement,efficient gene and QTL discovery and allele mining of complex traits using advanced breeding lines from crosses between a common"backbone"parent and a set of elite parents in conventional pedigree breeding programs.BBSI can be relatively easily adopted by breeding programs with small budgets,but the BBSI-based BBD strategy can be fully and more efficiently implemented by large seed companies with sufficient capacity.展开更多
Phosphorous （P） deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines （ILs） were used to ...Phosphorous （P） deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines （ILs） were used to characterize the responses of seedlings to low P availability and to identify QTLs for root traits, biomass, and plant height under P-deficiency and P-sufficiency conditions. Plant height, total dry weight, shoot dry weight, and root number were inhibited under P-deficiency, whereas maximum root length （MRL） and root-shoot ratio （RS） were induced by P-deficiency stress. Relative MRL （RMRL, the ratio of MRL under P-deficiency to MRL under P-sufficiency con- dition） and relative RS （RRS） were used to evaluate P-deficiency tolerance at the seedling stage. A total of 24 additive QTLs and 29 pairs of epistatic QTLs were detected, but only qRN4 was detected in both conditions. This suggested that different mechanisms may exist in both P supply levels. QTLs for adaptive traits （RMRL, RRS, RRV, and RRDW） and qRN4 consistently expressed to increase trait stability may contribute to P-deficiency tolerance. Twelve intervals were cluster regions of QTLs for P-deficiency tolerance, and one QTL （qRRSS） showed pleiotropic effects on P-deficiency tolerance and drought tolerance. These interesting QTLs can be used in marker-assisted breeding through the target ILs.展开更多
The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage.A total of 791 BC1F8 backcross recombinant lines,derived from the...The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage.A total of 791 BC1F8 backcross recombinant lines,derived from the cross of Xieqingzao B /N22 //Xieqingzao B,were used as materials.Each rice line was separated evenly into two groups,and the heat tolerance of all rice lines were evaluated at natural high temperature in fields.The rice lines with heat tolerant index higher than 90% or lower than 40% were selected to compare the phenotypic characters and further identify heat tolerance at the early milky stage in a phytotron.Rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were analyzed by 887 simple sequence repeat markers that were evenly distributed on the 12 rice chromosomes.In the result,12(6 pairs) rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were obtained.Molecular marker analysis indicated that the genomic polymorphism between 703T and 704S was the smallest in the 6 pairs of rice lines,with only 16 polymorphic sites,including 22 different alleles.The application of these two backcross introgression rice lines for future study on the mechanisms of heat tolerance in rice at the milky stage will be theoretically beneficial in reducing the interference caused by genetic differences from experimental materials.展开更多
[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. ...[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% （amplified by primer RM131） and the lowest was 60.25% （RM171）. The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% （RM171） and the lowest was 2.93% （RM1095）. There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%（RM401）. Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% （RM311） and the lowest was 0 （RM401）. The average rate of new bands was 1%. The average of Nei＇s gene di- versity （He） and Shannon＇s Information index （I） were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.展开更多
The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice(Oryza sativa L.).In this study,we focus on two types of genomic footprints,introgression and differ...The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice(Oryza sativa L.).In this study,we focus on two types of genomic footprints,introgression and differentiation,in a population of more than 1200 Chinese rice accessions.We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments,of which many contained functional sequence variants,quantitative trait loci,or genes controlling flowering,grain,and resistance traits.Notably,we found most introgressions,including the known heterotic loci Hd3 a and TAC1,were distributed differentially between the female and male parents of three-line indica hybrid rice,indicating their potential contribution to heterosis.We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci,such as DTH7,Hd1 for heading date,and qCT7 for cold tolerance,providing new candidates for studying local adaptation or heterosis.Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars.These findings also provide potential targets for rice genetic research and breeding.展开更多
Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple co...Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines（ILs）,which derived from an accession of Oryza minuta（accession No.101133） with BBCC genome,as the donor,and an elite indica cultivar IR24（O.sativa）,as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat（SSR） markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64% of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5% 25.2%,with an average of 8.3%.Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.展开更多
Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can s...Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.展开更多
Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar geneti...Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar genetic signatures.Previous studies have suggested that 2 closely related duck species,the Chinese spot-billed duck Anas zonorhyncha and the mallard A.platyrhynchosvjere polyphyletically intermixed.Here,we utilized a wide geographical sampling,multilocus data and a coalescent-based model to revisit this system.Our study confirms the finding that Chinese spot-billed ducks and Mallards are not monophyletic.There was no apparent interspecific differentiation across loci except those at the mitochondrial DNA(mtDNA)control region and the Z chromosome(CHD1Z).Based on an isolation-with-migration model and the geographical distribution of lineages,we suggest that both introgression and incomplete lineage sorting might contribute to the observed non-monophyly of the 2 closely related duck species.The mtDNA introgression was asymmetric,with high gene flow from Chinese spot-billed ducks to Mallards and negligible gene flow in the opposite direction.Given that the 2 duck species are phenotypically distinctive but weakly genetically differentiated,future work based on genomescale data is necessary to uncover genomic regions that are involved in divergence,and this work may provide further insights into the evolutionary histories of the 2 species and other waterfowls.展开更多
Background Geese are among the most important poultry species in the world.The current generally accepted hypothesis is that the European domestic geese originated from greylag geese(Anser anser),and Chinese domestic ...Background Geese are among the most important poultry species in the world.The current generally accepted hypothesis is that the European domestic geese originated from greylag geese(Anser anser),and Chinese domestic geese have two origins,most of which originated from swan geese(Anser cygnoides),and the Yili goose originated from greylag geese.To explain the origin and demographic history of geese,we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese,and whole genome sequencing data were obtained for 74 samples.Results Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese,except for Yili,is the swan geese,and the wild ancestor of Chinese Yili and European domestic geese is greylag geese.Analysis of the demographic history suggests that the domestication of Chinese geese occurred~3499 years ago and that of the European geese occurred~7552 years ago.Furthermore,gene flow was observed between domestic geese and their wild ancestors.Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese,and the body size of Yili geese may be influenced by introgression events of some growthrelated genes,including IGF-1.Conclusions Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.展开更多
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.
基金supported by the China Agriculture Research System(Grant No.CARS-23-A13)Hubei Agrotechnical Major Project(Grant No.2021-620-000-001-01)+1 种基金Wuhan Major Project of Key Technologies in Biological Breeding and New Variety Cultivation(Grant No.2022021302024852)HZAU-AGIS Cooperation Fund(Grant No.SZYJY2023022).
文摘Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.
基金supported by the earmarked fund for the Beijing Agriculture Innovation Consortium(BAIC06-2023-G01)open project of Xinjiang Production&Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin(BRZD2104)Fuyang Normal University Provincial and Ministerial Open Platform Fund(FSKFKT026D).
文摘Background Chicken is one of the most numerous and widely distributed species around the world,and many studies support the multiple ancestral origins of domestic chickens.The research regarding the yellow skin phenotype in domestic chickens(regulated by BCO2)likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens.However,beyond the BCO2 gene region,much remains unknown about the introgression from the grey junglefowl into domestic chickens.Therefore,in this study,based on wholegenome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds,we explored the introgression events from the grey junglefowl to domestic chickens.Results We successfully detected introgression regions besides BCO2,including two associated with growth trait(IGFBP2 and TKT),one associated with angiogenesis(TIMP3)and two members of the heat shock protein family(HSPB2 and CRYAB).Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens.Furthermore,we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds,indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained.Additionally,our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens,possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens.Conclusions In summary,our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens,laying the foundation for a deeper understanding of the genetic composition within domestic chickens,and offering new perspectives on the impact of introgression on domestic chickens.
基金This study was supported by High Project of Science and Technology in China (No. 2001AA21110103)Doctoral Foundation of Education Department in China (No. 20020504009).
文摘A breeding strategy for widening the germplasm of Brassica napus was proposed by introgression of the A^r subgenome of B. rapa （A^rA^r） and C^c of B. carinata （B^cB^cC^cC^c） into natural B. napus （AnAncncn）. The progenies with 38 chromosomes that were derived from the self-pollinated seeds of pentaploid hybrids （A^rA^nB^cC^cC^n） were used for further research. Some of the partial new-typed B. napus showed normal meiotic behavior, high portion of germinated pollen and normal embryological development. This indicates that the selected new-typed B. napus had a balanced genetic base. Molecular analysis showed that about 50% of the genome in the new-typed B. napus was replaced by A^r and C^c subgenome from B. rapa and B. carinata. Considering the genetic diversity among different lines of new-typed B. napus, it was deduced that the introgression of the genomic components from B, rapa and B. carinata could widen the genetic diversity of rapeseed.
基金funded by the National Key Research&Development Program of China(2017YFD0100100)Key-Area Research&Development Program of Guangdong Province(2020B020219004)+2 种基金Shenzhen Basic Research Special Project(2020231601)Agricultural Science and Technology Innovation Programthe Cooperation and Innovation Mission(CAAS2021-01)。
文摘Future demands for increased productivity and resilience to abiotic/biotic stresses of major crops require new technologies of breeding by design(BBD)built on massive information from functional and population genomics research.A novel strategy of breeding by selective introgression(BBSI)has been proposed and practiced for simultaneous improvement,genetic dissection and allele mining of complex traits to realize BBD.BBSI has three phases:a)developing large numbers of trait-specific introgression lines(ILs)using backcross breeding in elite genetic backgrounds as the material platform of BBD;b)efficiently identifying genes or quantitative trait loci(QTL)and mining desirable alleles affecting different target traits from diverse donors as the information platform of BBD;and c)developing superior cultivars by BBD using designed QTL pyramiding or marker-assisted recurrent selection.Phase(a)has been implemented massively in rice by many Chinese research institutions and IRRI,resulting in the development of many new green super rice cultivars plus large numbers of ILs in 30+elite genetic backgrounds.Phase(b)has been demonstrated in a series of proof-of-concept studies of high-efficiency genetic dissection of rice yield and tolerance to abiotic stresses using ILs and DNA markers.Phase(c)has also been implemented by designed QTL pyramiding,resulting in a prototype of BBD in several successful cases.The BBSI strategy can be easily extended for simultaneous trait improvement,efficient gene and QTL discovery and allele mining of complex traits using advanced breeding lines from crosses between a common"backbone"parent and a set of elite parents in conventional pedigree breeding programs.BBSI can be relatively easily adopted by breeding programs with small budgets,but the BBSI-based BBD strategy can be fully and more efficiently implemented by large seed companies with sufficient capacity.
基金supported by the Hi-Tech Research and Development Program of China (No. 2006AA10Z158 and No. 2006AA100101)the "948" Project (No. 2006-G1)+1 种基金China National Key Technologies R & D Program (No. 2006BAD13B01-6)the Program for Chang Jiang Scholars and Innovative Research Team in University, Program of Introducing Talents of Discipline to Universi-ties in China (111-2-03).
文摘Phosphorous （P） deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines （ILs） were used to characterize the responses of seedlings to low P availability and to identify QTLs for root traits, biomass, and plant height under P-deficiency and P-sufficiency conditions. Plant height, total dry weight, shoot dry weight, and root number were inhibited under P-deficiency, whereas maximum root length （MRL） and root-shoot ratio （RS） were induced by P-deficiency stress. Relative MRL （RMRL, the ratio of MRL under P-deficiency to MRL under P-sufficiency con- dition） and relative RS （RRS） were used to evaluate P-deficiency tolerance at the seedling stage. A total of 24 additive QTLs and 29 pairs of epistatic QTLs were detected, but only qRN4 was detected in both conditions. This suggested that different mechanisms may exist in both P supply levels. QTLs for adaptive traits （RMRL, RRS, RRV, and RRDW） and qRN4 consistently expressed to increase trait stability may contribute to P-deficiency tolerance. Twelve intervals were cluster regions of QTLs for P-deficiency tolerance, and one QTL （qRRSS） showed pleiotropic effects on P-deficiency tolerance and drought tolerance. These interesting QTLs can be used in marker-assisted breeding through the target ILs.
基金supported by the National Natural Science Foundation of China(Grant No.30671230)the Natural Science Foundation of Jiangxi Province,China(Grant No.2007GZN0253)
文摘The present study aimed at breeding new rice germplasms with similar genome but significantly differed in heat tolerance during the grain filling stage.A total of 791 BC1F8 backcross recombinant lines,derived from the cross of Xieqingzao B /N22 //Xieqingzao B,were used as materials.Each rice line was separated evenly into two groups,and the heat tolerance of all rice lines were evaluated at natural high temperature in fields.The rice lines with heat tolerant index higher than 90% or lower than 40% were selected to compare the phenotypic characters and further identify heat tolerance at the early milky stage in a phytotron.Rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were analyzed by 887 simple sequence repeat markers that were evenly distributed on the 12 rice chromosomes.In the result,12(6 pairs) rice lines with similar phenotypic characters but significantly differed in heat tolerance at the milky stage were obtained.Molecular marker analysis indicated that the genomic polymorphism between 703T and 704S was the smallest in the 6 pairs of rice lines,with only 16 polymorphic sites,including 22 different alleles.The application of these two backcross introgression rice lines for future study on the mechanisms of heat tolerance in rice at the milky stage will be theoretically beneficial in reducing the interference caused by genetic differences from experimental materials.
基金partially supported by National Natural Science Foundation of China(30860120,30900781)Science and Technology Projects of Jiangxi Education Department(GJJ09464)Natural Science Foundation of Jiangxi(2008GQN0059)~~
文摘[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% （amplified by primer RM131） and the lowest was 60.25% （RM171）. The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% （RM171） and the lowest was 2.93% （RM1095）. There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%（RM401）. Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% （RM311） and the lowest was 0 （RM401）. The average rate of new bands was 1%. The average of Nei＇s gene di- versity （He） and Shannon＇s Information index （I） were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.
基金partially supported by the National Key Research and Development Program(2020YFE0202300)grants from State Key Laboratory of Plant Genomics
文摘The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice(Oryza sativa L.).In this study,we focus on two types of genomic footprints,introgression and differentiation,in a population of more than 1200 Chinese rice accessions.We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments,of which many contained functional sequence variants,quantitative trait loci,or genes controlling flowering,grain,and resistance traits.Notably,we found most introgressions,including the known heterotic loci Hd3 a and TAC1,were distributed differentially between the female and male parents of three-line indica hybrid rice,indicating their potential contribution to heterosis.We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci,such as DTH7,Hd1 for heading date,and qCT7 for cold tolerance,providing new candidates for studying local adaptation or heterosis.Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars.These findings also provide potential targets for rice genetic research and breeding.
基金supported by grants from the National Natural Science Foundation of China (Grant No.31160277)the Ministry of Science and Technology of China (Grant No. 2010AA101803)+2 种基金the Ministry of Agriculture of China (Grant No. 2011ZX08001-001)the Guangxi Science and Technology Department,China (Grant No. 10100005-8,2012GXNSFAA053056)the Guangxi Academy of Agricultural Sciences,China (Grant No. 2011JZ02 2011JM02,12-071-09)
文摘Introgression line population is effectively used in mapping quantitative trait loci（QTLs）,identifying favorable genes,discovering hidden genetic variation,evaluating the action or interaction of QTLs in multiple conditions and providing the favorable experimental materials for plant breeding and genetic research.In this study,an advanced backcross and consecutive selfing strategy was used to develop introgression lines（ILs）,which derived from an accession of Oryza minuta（accession No.101133） with BBCC genome,as the donor,and an elite indica cultivar IR24（O.sativa）,as the recipient.Introgression segments from O.minuta were screened using 164 polymorphic simple sequence repeat（SSR） markers in the genome of each IL.Introgressed segments carried by 131 ILs covered the whole O.sativa genome.The average number of homozygous O.minuta segments per introgression line was about 9.99.The average length of introgressed segments was approximate 14.78 cM,and about 79.64% of these segments had sizes less than 20 cM.In the genome of each introgression line,the O.minuta chromosomal segments harbored chromosomal fragments of O.sativa ranging from 1.15% to 27.6%,with an overall average of 8.57%.At each locus,the ratio of substitution of O.minuta alleles had a range of 1.5% 25.2%,with an average of 8.3%.Based on the evaluation of the phenotype of these ILs,a wide range of alterations in morphological and yield-related traits were found.After inoculation,ILs 41,11 and 7 showed high resistance to bacterial blight,brown planthopper and whitebacked planthopper,respectively.These O.minuta-O.sativa ILs will serve as genetic materials for identifying and using favorable genes from O.minuta.
基金supported by the National Natural Science Foundation of China (NSFC-DFG, 31861133016NSFC, 31970564)。
文摘Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.
基金the National Natural Science Foundation of China(No.31401969,31772480)the Natural Science Foundation of Jiangxi Province(No.20161BAB214158).
文摘Incomplete lineage sorting and introgression are 2 major and nonexclusive causes of specieslevel non-monophyly.Distinguishing between these 2 processes is notoriously difficult because they can generate similar genetic signatures.Previous studies have suggested that 2 closely related duck species,the Chinese spot-billed duck Anas zonorhyncha and the mallard A.platyrhynchosvjere polyphyletically intermixed.Here,we utilized a wide geographical sampling,multilocus data and a coalescent-based model to revisit this system.Our study confirms the finding that Chinese spot-billed ducks and Mallards are not monophyletic.There was no apparent interspecific differentiation across loci except those at the mitochondrial DNA(mtDNA)control region and the Z chromosome(CHD1Z).Based on an isolation-with-migration model and the geographical distribution of lineages,we suggest that both introgression and incomplete lineage sorting might contribute to the observed non-monophyly of the 2 closely related duck species.The mtDNA introgression was asymmetric,with high gene flow from Chinese spot-billed ducks to Mallards and negligible gene flow in the opposite direction.Given that the 2 duck species are phenotypically distinctive but weakly genetically differentiated,future work based on genomescale data is necessary to uncover genomic regions that are involved in divergence,and this work may provide further insights into the evolutionary histories of the 2 species and other waterfowls.
基金funded by the Open Project of Xinjiang Production&Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basinthe National Nature Science Foundation of China (grant numbers:BRZD2104 and 31960648)the Joint Plan of Liaoning Province in the field of Livelihood Science and Technology (Rural Revitalization Science and Technology Support)。
文摘Background Geese are among the most important poultry species in the world.The current generally accepted hypothesis is that the European domestic geese originated from greylag geese(Anser anser),and Chinese domestic geese have two origins,most of which originated from swan geese(Anser cygnoides),and the Yili goose originated from greylag geese.To explain the origin and demographic history of geese,we selected 14 goose breeds from Europe and China and wild populations of swan and greylag geese,and whole genome sequencing data were obtained for 74 samples.Results Population structure analysis and phylogenetic trees showed that the wild ancestor of Chinese domestic geese,except for Yili,is the swan geese,and the wild ancestor of Chinese Yili and European domestic geese is greylag geese.Analysis of the demographic history suggests that the domestication of Chinese geese occurred~3499 years ago and that of the European geese occurred~7552 years ago.Furthermore,gene flow was observed between domestic geese and their wild ancestors.Analysis of introgression showed that Yili geese had been introgressed by Chinese domestic geese,and the body size of Yili geese may be influenced by introgression events of some growthrelated genes,including IGF-1.Conclusions Our study provides evidence for the origin of geese at the genome-wide level and advances the understanding of the history of goose domestication and the traits affected by introgression events.
