Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry...Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.展开更多
Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary traj...Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T.sinensis genome, we found evidence of a tetraploidization event(T. sinensis special tetraploidization, TST) that occurred approximately 15-17 million years ago(MYA) after the core eudicot-common hexaploidization(ECH or gamma) event. We characterized the synonymous nucleotide substitution rates(Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase(TPS) genes;conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.展开更多
Drought-resistant plants exhibit strong water retention capability.In this regard,the autotetraploid sour jujube leaves exhibit better water retention than diploid leaves.Morphological comparisons and physiological co...Drought-resistant plants exhibit strong water retention capability.In this regard,the autotetraploid sour jujube leaves exhibit better water retention than diploid leaves.Morphological comparisons and physiological comparisons of diploid and autotetraploid leaves showed that the autotetraploid leaves had thicker leaf cuticles and more leaf wax accumulation than the diploid leaves,which could reduce cuticle permeability and improve the drought tolerance of leaves.In this study,the cuticular wax crystalloids on the adaxial and abaxial sides of young and mature jujube leaves were observed in the two ploidy types,and unique cuticular wax crystalloids covering a large area of the cuticle on autotetraploid sour jujube leaves may provide an advantage in reducing leaf non-stomata transpiration and improving plant drought tolerance.Based on the transcriptome,115 differentially expressed genes between diploids and autotetraploids were further analyzed and found to be involved in the accumulation of cuticular wax components,including terpenoids,fatty acids,and lipids,as well as ABC transporter and wax biosynthetic process.Finally,14 genes differentially expressed between glossy autotetraploid leaves and nonglossy diploid leaves,such as LOC107414787,LOC107411574 and LOC107413721,were screened as candidate genes by qRT-PCR analysis.This findings provided insights into how polyploidization improved drought tolerance.展开更多
By using the laser scanning confocal microscope and plastic （Leica 7022 historesin embedding kit） semi-thin sectioning technique, comparative studies on the development of endosperm were carried out between autotetr...By using the laser scanning confocal microscope and plastic （Leica 7022 historesin embedding kit） semi-thin sectioning technique, comparative studies on the development of endosperm were carried out between autotetraploid and diploid rices. About one third of the ovaries in the autotetraploid showed normal endosperm development as those in the diploid. In these ovaries, one of the polar nuclei would fuse with the sperm nucleus, and the primary endosperm nucleus formed and underwent the first division in 4 hours after pollination; the anticlinal wall began to grow centripetally between the free nuclei starting from the wall ingrowths of the embryo sac near the micropylar end, and some of the phragmoplasts formed transformed into periclinal walls. In addition, some of the cell wall situated in the middle of the endosperm appeared to originate from phragmoplasts, whereas others seemed to develop randomly without the obvious formation of phragmoplasts. Cellulose began to accumulate in the wall of aleurone cell layer at 6 days after pollination. The cellulose wall of the cells of the aleurone cell layer appeared to have completely formed within 7 to 8 days after pollination. On the other hand, about two thirds of the ovaries in the autotetraploid showed abnormality in endosperm development with various types, such as non-fertilization, abnormal fertilization, endosperm development-delay and non-synchronization in the development of cellulose wall of cells of the aleurone layer. These abnormalities usually resulted in decreased seed setting in autotetraploid rice.展开更多
The structures of mature embryo sacs in 13 genetic stock lines of autotetraploid rice （Oryza sativa L.）, including indica, japonica and javanica, were studied by using the whole-mount stain-clearing laser scanning c...The structures of mature embryo sacs in 13 genetic stock lines of autotetraploid rice （Oryza sativa L.）, including indica, japonica and javanica, were studied by using the whole-mount stain-clearing laser scanning confocal microscopy （WCLSM）. Among the 13 autotetraploid rice, the majority of ovaries possess normal polygonum-type embryo sacs, while a few ovaries were characterized by abnormal embryo sacs. The abnormalities of embryo sacs could be classified into six categories, i. e. no female germ unit, abnormal polar nuclei, embryo sac degeneration, no egg apparatus, small embryo sac and ＇double set＇ of embryo sacs. The frequency of abnormal embryo sac in japonica （26.6%） was higher than that in indica （19.34%）. In addition, the major abnormalities in each autotetraploid line varied, suggesting that the abnormalities may be related to the genotypes of the varieties.展开更多
The process of double fertilization and the characters of embryo and endosperm development in an autotetraploid polyembryonic mutant rice IR36-Shuang were studied with a laser scanning confocal microscopy. Some abnorm...The process of double fertilization and the characters of embryo and endosperm development in an autotetraploid polyembryonic mutant rice IR36-Shuang were studied with a laser scanning confocal microscopy. Some abnormalities including degenerated ovary, abortive embryo sac, single fertilization, double-ovule and double-embryo and so on. were found dudng double fertilization and embryo development in IR36-Shuang. The rate of the abnormalities was 46.67% in IR36-Shuang, significantly higher than that in the control, an autotetraploid rice line IR36-4X （33.00%）. Cytological and embryonic evidences were provided for seed setting decline and the initiation of additional embryo in IR36-Shuang.展开更多
As maternal parents, diploid （L202-2x） and autotetraploid （L202-4x） of Oryza sativa cv. L2O2 were crossed with O. officinalis. Embryo development and fertilization in these two crosses were comparatively studied. ...As maternal parents, diploid （L202-2x） and autotetraploid （L202-4x） of Oryza sativa cv. L2O2 were crossed with O. officinalis. Embryo development and fertilization in these two crosses were comparatively studied. There were no mature hybrid seeds obtained because all the hybridized spikelets died 30 days after pollination. The main reasons for no seed set were abnormal fertilization and development of the embryos and endosperms in the interspecific hybrids. There were doublefertilization, egg cell single-fertilization and non-fertilization in these crosses. Although 59.45% and 54.87% of hybrid embryos produced in the crosses of L202-2x/O. officinalis and L202-4x/O. officinalis, respectively, hybrid embryos ceased to develop or degenerated and plenty of free endosperm nuclei were in disaggregating state without developing cellular endosperms three days after pollination. Besides, some embryological differences in these two crosses were found, that is, the rate of double-fertilization and total rate of doubleand single-fertilization in L202-2x/O. officinalis were higher than those in L202-4x/O. officinalis. The embryo and endosperm of hybrids developed more slowly, and embryos and free endosperm nuclei were more severely degenerated in L202-4x/O. officinalis than in L202-2x/O. officinalis. Five days after pollination, a few of embryos in L202-2x/O. officinalis developed into pear-shaped ones, however, embryos in L202-4x/O. officinalis were all degenerated. Therefore, it is more difficult to obtain interspecific hybrids by wide crosses between autotetraploid of O. sativa and O. officinalis.展开更多
The effect of Ar^＋ beam implantation and maize genome DNA on autotetraploid rice is studied. Better mutation types and higher mutation rates were discovered in M2 of T3 with ion implantation and immersion in maize ge...The effect of Ar^＋ beam implantation and maize genome DNA on autotetraploid rice is studied. Better mutation types and higher mutation rates were discovered in M2 of T3 with ion implantation and immersion in maize genome DNA. In the five agronomic categories investigated, the mutation rate of the seed setting rate was 9.1%, and the total mutation rate was 14.8% in the T3. However, the total mutation rate was 2.1% with the treatment of only ion implantation and 1.3% with the treatment of only immersion in maize genome DNA. Mutant FA36（4） was discovered in M1 with ion beam implantation and immersion in maize genome DNA. Its RuBPCase activity, PEPCase activity and seed setting rate were 32%, 153%, and 36.79%, respectively, higher than its parent IR36（4）. Rapid analysis of polymorphicDNA （RAPD） analysis of three M2 plants of FA36（4） （FMI, FM2, FM3） and two controls （purple maize and IR36（4）） were also conducted with 40 random primers. S5-3 was RAPD fragment amplified with a template of purple maize, FM2 and FM3 genome DNA using primer S5. There was no S5-3 in the RAPD pattern of IR36（4） or FMI.展开更多
OBJECTIVE： To establish and optimize the propaga- tion of Nianmaohuangqin （Radix Scutellariae Viscid- ulae） and induce and characterize polyploidy of Nianmaohuangqin （Radix Scutellariae Viscidulae）. METHODS： Bud...OBJECTIVE： To establish and optimize the propaga- tion of Nianmaohuangqin （Radix Scutellariae Viscid- ulae） and induce and characterize polyploidy of Nianmaohuangqin （Radix Scutellariae Viscidulae）. METHODS： Buds from germinating seed-derived explants were induced by tissue culture. With an or- thogonal test, different concentrations of 6-benzyl- aminopurine （BAP）, indole-3-acetic acid （IAA） and kinetin （KT） were used to determine the optimal concentrations for the propagation of Nianmaohuangqin （Radix Scutellariae Viscidulae）. The differ- ent concentrations of IAA and rooting powder （ABT） were used to induce rooting. A 0.3% w/v col- chicine solution was used to induce polyploidy and the induced buds was identified by root-tip chromosome determination and stomatal apparatus ob- servation. RESULTS： A large number of buds could be in- duced directly from epicotyl and hypocotyl ex- plants on Murashige and Skoog （MS） （Murashige and Skoog 1962） medium supplemented with 1.1-1.3 mg/L BAP and 0.2 mg/L IAA. Root induction and development could be observed within 20 days of inoculation on 1/2 MS medium supplemented with 0.2 mg/L IAA and 0.1 mg/L ABTo Furthermore, 27 lines of autotetraploid individuals were ob- tained with a plantlet chromosome number of 2n= 4x=36. CONCLUSION： Autotetraploid lines could be ob- tained through induction with colchicine in vitro, proving that this method might be used for plant selection and breeding.展开更多
Calluses of two autotetraploid rice （DPR （4） and Zijing （4）） were implanted with 30 KeV N＋beams at doses ranging from 1.0×1015 to 9.0×1015 ions cm-2. The differentiation rates of calluses, the concent...Calluses of two autotetraploid rice （DPR （4） and Zijing （4）） were implanted with 30 KeV N＋beams at doses ranging from 1.0×1015 to 9.0×1015 ions cm-2. The differentiation rates of calluses, the concentration of malondialdehyde （MDA）, the activities of superoxide dismutase （SOD）, catalase （CAT） and peroxidase （POD）, and the change of esterase （EST） spectrum were measured and analyzed on the calluses stage. The results showed that differentiation rates of calluses under 3.0×1015 ions cm-2 （（46.12±2.01）%） were higher than the other treatment groups in DPR （4）, and those of Zijing （4） were similar under the doses of 1.0×1015, 3.0×1015 and 5.0×1015 ions cm-2 （（40.55±2.74）, （37.77±3.04） and （34.56±2.65）%） and were higher than that of 7.0×1015 and 9.0×1015 ions cm-2. When the doses were 3.0×1015 and 5.0×1015 ions cm-2, the activities of SOD, POD and CAT were notably enhanced, and the accumulation of MDA content was markedly alleviated in the implanted calluses of two materials, as well as the activity of EST was increased by the additional isforms DPR （4）. Whereas the anti-oxidative systems and enzymes spectrum of EST were destroyed seriously, the accumulation of MDA was signiifcantly aggravated, also the differentiation rate of calluses reduced sharply and almost closed to zero when the implantation doses were 7.0×1015 and 9.0×1015 ions cm-2. It suggested that the proper dose of ion implantation effectively maintained the normal membrane structure and metabolism, and it would be also a feasible approach for autotetraploid rice to improve its genetic characteristics at calluses stage. Additionally, the differences of the radiation resistance between DPR （4） and Zijing （4） could be related to the different genotypes.展开更多
Autotetraploid indic, a/japonica rice hybrid combines both the advantages of polyploidy and the heterosis between indica and japonica rice. Embryo sac abortion is an important factor influencing spikelet fertility in ...Autotetraploid indic, a/japonica rice hybrid combines both the advantages of polyploidy and the heterosis between indica and japonica rice. Embryo sac abortion is an important factor influencing spikelet fertility in autotetraploid dce hybrid. To clarify the cytological mechanism of embryo sac abortion, the megasporogenesis and megagametogenesis in an autotetraploid japonicaAndica hybrid were examined by the whole-mount eosin B-staining confocal laser scanning microscopy （WE-CLSM） technique. Abnormalities were observed from the megasporocyte stage to the mature embryo sac stage. The degeneration of the tetrad cells and the functional megaspore was the characteristic of abnormalities during megasporogenesis. Abnormal small embryo sacs and disordered number of nuclei were frequently observed during embryo sac development. Some interesting phenomena, such as two functional megaspores, the diplospory-like megasporocyte, and five-nucleate embryo sac were found. The abnormalities that occurred during female gametophyte development resulted in more than five types of abnormal embryo sacs （i.e. embryo sac degeneration, embryo sac without female germ unit, embryo sac without egg apparatus, embryo sac with abnormal polar nuclei and abnormal small embryo sac） in autotetraploid japonica/ndica hybdd. Embryo sac fertility was lower in diploid japonica/ndica hybdd than in autotetraploid japonicaAndica hybrid although many abnormal phenomena were observed in autotetraploid hybrid.展开更多
Genetic diversity in peanut (Arachishypogaea L.) is narrow due to its evolution and domestication processes. Amphidiploids and autotetraploids (newly synthesized tetraploids) were created to broaden its genetic base. ...Genetic diversity in peanut (Arachishypogaea L.) is narrow due to its evolution and domestication processes. Amphidiploids and autotetraploids (newly synthesized tetraploids) were created to broaden its genetic base. Molecular analysis has shown that the newly synthesized tetraploids had broader genetic base;and were genetically divergent when compared to cultivated peanut. Nutritional composition relative to oil, fatty acid composition, O/L ratio, protein, iodine value and presence of plant proteinase inhibitors such as trypsin and chymotrypsin inhibitors were studied in the synthesized tetraploids. Some of the newly synthesized tetraploids had higher amounts of proteinase inhibitors. Evaluation of newly synthesized tetraploids revealed several lines resistant to late leaf spot (LLS) and peanut bud necrosis disease (PBND).展开更多
In the present study autotetraploid rice IR36-4X was treated by an ion implantation technique with nitrogen ion beams. A polyembryonic mutant （named IR36-Shuang） was identified in the M2 generation. The mutant line ...In the present study autotetraploid rice IR36-4X was treated by an ion implantation technique with nitrogen ion beams. A polyembryonic mutant （named IR36-Shuang） was identified in the M2 generation. The mutant line and its offspring were systematically investigated in regard to their major agronomic properties and the rate of polyembryonic seedling in the M3-M6 generation. The abnormal phenomena in the embryo sac development and the cytological mechanism of the initiation of additional embryo in IR36-Shuang were observed by Laser Scanning Confocal Microscopy. The results were as follows. 1） The plant height, the panicle length and 1000 grain weight of IRB6-Shuang were lower than that of its control by 35.41%, 5.08% and 15.72% respectively, Moreover, the setting percentage decreased 12.39% compared with that in normal IRB6-4X plants. 2） The polyembryonic trait of IRB6-Shuang was genetically stable and the frequency of the polyembryonic seedlings in the IR36-Shuang line was also relatively stable. 3） The rate of abnormal embryo sacs in IR36-Shuang was significantly higher than that in the control IR36-4X. 4） The additional embryo in IR36-Shuang might arise from the double Jet of embryo sacs in a single owry, antipodal cells or endosperm cells. These results suggest that IRB6-Shuang is a polyembryonic mutant and a new apomixis rice line induced by low energy ion implantation. The prospects for the application in production of the IR36-Shuang line are also discussed. The present study may provide a basis for future investigations of apomixis rice breeding via the ion implantation biotechnology.展开更多
Autotetraploid Carassius auratus is a stable hereditary autotetraploid fish resulting from the hybridization of Carassius auratus red var.(RCC,♀)×Megalobrama amblycephala(BSB,♂),containing four sets of RCC chro...Autotetraploid Carassius auratus is a stable hereditary autotetraploid fish resulting from the hybridization of Carassius auratus red var.(RCC,♀)×Megalobrama amblycephala(BSB,♂),containing four sets of RCC chromosomes.However,the molecular mechanism underlying the determination of sex in this species remains largely unknown.Currently,there lacks a full understanding of the molecular mechanisms governing sex determination and specific molecular markers to differentiate sex in this species.In this study,25,801,677 SNPs(Singlenucleotide polymorphism)and 6,210,306 Indels(insertion-deletion)were obtained from whole-genome resequencing of 100 individuals(including 50 female and 50 male).Further identification confirmed the candidate chromosomes as Chr46B,with the sex-determining region located at Chr46B:22,500,000‒22,800,000 bp.Based on the male-specific insertion(26 bp)within the candidate sex-determining region,a pair of sex-specific molecular markers has been identified.In addition,based on the screening of candidate sex-determining region genes and RT-qPCR validation analysis,ADAM10,AQP9 and tc1a were identified as candidate sex-determining genes.These findings provide a robust foundation for investigating sex determination mechanisms in fish,the evolution of sex chromosomes,and the development of monosex populations.展开更多
Polyploids have elevated stress tolerance,but the underlying mechanisms remain largely elusive.In this study,we showed that naturally occurring tetraploid plants of trifoliate orange(Poncirus trifoliata(L.) Raf.) exhi...Polyploids have elevated stress tolerance,but the underlying mechanisms remain largely elusive.In this study,we showed that naturally occurring tetraploid plants of trifoliate orange(Poncirus trifoliata(L.) Raf.) exhibited enhanced cold tolerance relative to their diploid progenitors.Transcriptome analysis revealed that whole-genome duplication was associated with higher expression levels of a range of well-characterized cold stress-responsive genes.Global DNA methylation profiling demonstrated that the tetraploids underwent more extensive DNA demethylation in comparison with the diploids under cold stress.CHH methylation in the promoters was associated with up-regulation of related genes,whereas CG,CHG,and CHH methylation in the 3’-regions was relevant to gene down-regulation.Of note,genes involved in unsaturated fatty acids(UFAs) and jasmonate(JA)biosynthesis in the tetraploids displayed different CHH methylation in the gene flanking regions and were prominently up-regulated,consistent with greater accumulation of UFAs and JA when exposed to the cold stress.Collectively,our findings explored the difference in cold stress response between diploids and tetraploids at both transcriptional and epigenetic levels,and gained new insight into the molecular mechanisms underlying enhanced cold tolerance of the tetraploid.These results contribute to uncovering a novel regulatory role of DNA methylation in better cold tolerance of polyploids.展开更多
Alfalfa(Medicago sativa L.)is the most important legume forage crop worldwide with high nutritional value and yield.For a long time,the breeding of alfalfa was hampered by lacking reliable information on the autotetra...Alfalfa(Medicago sativa L.)is the most important legume forage crop worldwide with high nutritional value and yield.For a long time,the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits.We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4,a cultivar widely cultivated in China,and a comprehensive database of genomic variations based on resequencing of 220 germplasms.Approximate 2.74 Gb contigs(N50 of 2.06 Mb),accounting for 88.39%of the estimated genome,were assembled,and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes.A total of 34,922 allelic genes were identified from the allele-aware genome.We observed the expansion of gene families,especially those related to the nitrogen metabolism,and the increase of repetitive elements including transposable elements,which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula.Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe,suggesting that geography may influence alfalfa genetic divergence during local adaption.Genome-wide association studies identified 101 single nucleotide polymorphisms(SNPs)associated with 27 agronomic traits.Two candidate genes were predicted to be correlated with fall dormancy and salt response.We believe that the alleleaware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.展开更多
Potato is the fourth most important food crop in the world.Although with a long history for breeding approaches,genomic information and association between genes and agronomic traits remain largely unknown particularl...Potato is the fourth most important food crop in the world.Although with a long history for breeding approaches,genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars,which limit the molecular breeding progression.By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center,with approximate 20-fold coverage,we revealed more than 27 million Single Nucleotide Polymorphisms and~3 million Insertion and Deletions with high quality and accuracy.Domestication analysis and genome-wide association studies(GWAS)identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance,providing informative insights into the selection and domestication of cultivar potato.In addition,GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals,especially those related to tuber size,small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis.Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32170236,31501333,and 32000405)Natural Science Foundation of Hebei Province(Grant No.C2020209064)the Innovation and Entrepreneurship Training Program for College Students of North China University of Science and Technology(Grant No.X2019252)。
文摘Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.
基金supported by the National Natural Science Foundation of China(Grant No.32170236 and 31501333)the Natural Science Foundation of Hebei Province(Grant No.C2020209064)+2 种基金the Project of Youth Fund for National Natural Science Foundation of China(Grant No.32001791)the Tangshan Science and Technology Planning Project(Grant No.20150209C)the innovation and entrepreneurship training program for college students of North China University of Science and Technology(Grant No.X2019256).
文摘Chinese mahogany(Toona sinensis) is of considerable medical and economic importance, and its genome has been deciphered. However, the process underlying its polyploidy is unclear, and the chromosomal evolutionary trajectory is poorly understood. Here, by reanalysing the T.sinensis genome, we found evidence of a tetraploidization event(T. sinensis special tetraploidization, TST) that occurred approximately 15-17 million years ago(MYA) after the core eudicot-common hexaploidization(ECH or gamma) event. We characterized the synonymous nucleotide substitution rates(Ks values) of collinear genes and found that T. sinensis genes affected by the TST evolve at a slower rate than Acer yangbiense genes. Furthermore, we identified homologous genes related to polyploidization and speciation and constructed multiple alignments with different reference genomes. Notably, the significant balance of gene retention and loss characterized in the two TST-derived subgenomes suggests an autopolyploid nature of the TST. Moreover, we deduced the chromosomal karyotypes of the two subgenomes and identified 7chromosomal fusions that have shaped the T. sinensis genome;more information is available on a newly constructed karyotype platform(http://www.cgrpoee.top/Toona_sinensis/index.html). The T. sinensis genome preserves the ancestral chromosome structure of dicotyledons well and could serve as a good reference for understanding genomic changes in other Meliaceae and Sapindales plants. In addition, we verified that tandem duplication and the ECH have promoted the expansion of terpene synthase(TPS) genes;conversely, the TST seems to have inhibited expansion of these genes. This present effort has clarified the polyploidy events of the T. sinensis genome, filled gaps in the history of karyotype evolution, and laid a solid foundation for further genomic studies in the Meliaceae research community and beyond.
基金supported by grants from the Fundamental Research Funds for the Central Universities(Grant No.2021JD02)the National Key Research and Development Program of China(Grant No.2018YFD1000607)。
文摘Drought-resistant plants exhibit strong water retention capability.In this regard,the autotetraploid sour jujube leaves exhibit better water retention than diploid leaves.Morphological comparisons and physiological comparisons of diploid and autotetraploid leaves showed that the autotetraploid leaves had thicker leaf cuticles and more leaf wax accumulation than the diploid leaves,which could reduce cuticle permeability and improve the drought tolerance of leaves.In this study,the cuticular wax crystalloids on the adaxial and abaxial sides of young and mature jujube leaves were observed in the two ploidy types,and unique cuticular wax crystalloids covering a large area of the cuticle on autotetraploid sour jujube leaves may provide an advantage in reducing leaf non-stomata transpiration and improving plant drought tolerance.Based on the transcriptome,115 differentially expressed genes between diploids and autotetraploids were further analyzed and found to be involved in the accumulation of cuticular wax components,including terpenoids,fatty acids,and lipids,as well as ABC transporter and wax biosynthetic process.Finally,14 genes differentially expressed between glossy autotetraploid leaves and nonglossy diploid leaves,such as LOC107414787,LOC107411574 and LOC107413721,were screened as candidate genes by qRT-PCR analysis.This findings provided insights into how polyploidization improved drought tolerance.
基金supported by the National Natural Science Foundation of China(30270814)the Teaching and Research Award Program for Outstanding Young Teachers in Higher Education Institutions of MOE,R R.Chinathe Group Project of Natural Science Foundation of Guangdong Province(200023).
文摘By using the laser scanning confocal microscope and plastic （Leica 7022 historesin embedding kit） semi-thin sectioning technique, comparative studies on the development of endosperm were carried out between autotetraploid and diploid rices. About one third of the ovaries in the autotetraploid showed normal endosperm development as those in the diploid. In these ovaries, one of the polar nuclei would fuse with the sperm nucleus, and the primary endosperm nucleus formed and underwent the first division in 4 hours after pollination; the anticlinal wall began to grow centripetally between the free nuclei starting from the wall ingrowths of the embryo sac near the micropylar end, and some of the phragmoplasts formed transformed into periclinal walls. In addition, some of the cell wall situated in the middle of the endosperm appeared to originate from phragmoplasts, whereas others seemed to develop randomly without the obvious formation of phragmoplasts. Cellulose began to accumulate in the wall of aleurone cell layer at 6 days after pollination. The cellulose wall of the cells of the aleurone cell layer appeared to have completely formed within 7 to 8 days after pollination. On the other hand, about two thirds of the ovaries in the autotetraploid showed abnormality in endosperm development with various types, such as non-fertilization, abnormal fertilization, endosperm development-delay and non-synchronization in the development of cellulose wall of cells of the aleurone layer. These abnormalities usually resulted in decreased seed setting in autotetraploid rice.
基金supported by the National Natural Science Foundations of China(Grant No.30270814)the Teaching and Research Award Program for 0utstanding Young Teachers in Higher Education Institutions of M0E,P.R.China.
文摘The structures of mature embryo sacs in 13 genetic stock lines of autotetraploid rice （Oryza sativa L.）, including indica, japonica and javanica, were studied by using the whole-mount stain-clearing laser scanning confocal microscopy （WCLSM）. Among the 13 autotetraploid rice, the majority of ovaries possess normal polygonum-type embryo sacs, while a few ovaries were characterized by abnormal embryo sacs. The abnormalities of embryo sacs could be classified into six categories, i. e. no female germ unit, abnormal polar nuclei, embryo sac degeneration, no egg apparatus, small embryo sac and ＇double set＇ of embryo sacs. The frequency of abnormal embryo sac in japonica （26.6%） was higher than that in indica （19.34%）. In addition, the major abnormalities in each autotetraploid line varied, suggesting that the abnormalities may be related to the genotypes of the varieties.
基金supported by the National Science & Technology Pillar Program of China in the Tenth Five-Year Plan Period(Grant No.2001BA302B)the Education Department of Henan Province, China(Grant No.2008A208019)
文摘The process of double fertilization and the characters of embryo and endosperm development in an autotetraploid polyembryonic mutant rice IR36-Shuang were studied with a laser scanning confocal microscopy. Some abnormalities including degenerated ovary, abortive embryo sac, single fertilization, double-ovule and double-embryo and so on. were found dudng double fertilization and embryo development in IR36-Shuang. The rate of the abnormalities was 46.67% in IR36-Shuang, significantly higher than that in the control, an autotetraploid rice line IR36-4X （33.00%）. Cytological and embryonic evidences were provided for seed setting decline and the initiation of additional embryo in IR36-Shuang.
基金supported by the Guangdong Provincial Key Project of Natural Science Foundation, China (Grant No. 021037)Guangdong Province Natural Science Foundation, China (Grant No. 7301008)+1 种基金South China Agricultural University President Foundation, China (Grant No. 2007K036)The Confocal Laser Scanning Microscope was provided by the Testing Center of South China Agricultural University, Guangzhou, China
文摘As maternal parents, diploid （L202-2x） and autotetraploid （L202-4x） of Oryza sativa cv. L2O2 were crossed with O. officinalis. Embryo development and fertilization in these two crosses were comparatively studied. There were no mature hybrid seeds obtained because all the hybridized spikelets died 30 days after pollination. The main reasons for no seed set were abnormal fertilization and development of the embryos and endosperms in the interspecific hybrids. There were doublefertilization, egg cell single-fertilization and non-fertilization in these crosses. Although 59.45% and 54.87% of hybrid embryos produced in the crosses of L202-2x/O. officinalis and L202-4x/O. officinalis, respectively, hybrid embryos ceased to develop or degenerated and plenty of free endosperm nuclei were in disaggregating state without developing cellular endosperms three days after pollination. Besides, some embryological differences in these two crosses were found, that is, the rate of double-fertilization and total rate of doubleand single-fertilization in L202-2x/O. officinalis were higher than those in L202-4x/O. officinalis. The embryo and endosperm of hybrids developed more slowly, and embryos and free endosperm nuclei were more severely degenerated in L202-4x/O. officinalis than in L202-2x/O. officinalis. Five days after pollination, a few of embryos in L202-2x/O. officinalis developed into pear-shaped ones, however, embryos in L202-4x/O. officinalis were all degenerated. Therefore, it is more difficult to obtain interspecific hybrids by wide crosses between autotetraploid of O. sativa and O. officinalis.
基金the National Key Program of China(2001BA302B03)Doctoral Startup Foundation of Huuan Science and Technology University of China(E54141)Educational Department Foundation of Hunan Province of China
文摘The effect of Ar^＋ beam implantation and maize genome DNA on autotetraploid rice is studied. Better mutation types and higher mutation rates were discovered in M2 of T3 with ion implantation and immersion in maize genome DNA. In the five agronomic categories investigated, the mutation rate of the seed setting rate was 9.1%, and the total mutation rate was 14.8% in the T3. However, the total mutation rate was 2.1% with the treatment of only ion implantation and 1.3% with the treatment of only immersion in maize genome DNA. Mutant FA36（4） was discovered in M1 with ion beam implantation and immersion in maize genome DNA. Its RuBPCase activity, PEPCase activity and seed setting rate were 32%, 153%, and 36.79%, respectively, higher than its parent IR36（4）. Rapid analysis of polymorphicDNA （RAPD） analysis of three M2 plants of FA36（4） （FMI, FM2, FM3） and two controls （purple maize and IR36（4）） were also conducted with 40 random primers. S5-3 was RAPD fragment amplified with a template of purple maize, FM2 and FM3 genome DNA using primer S5. There was no S5-3 in the RAPD pattern of IR36（4） or FMI.
基金Supported by the Natural Science Fund of Anhui University of Chinese Medicine (No.2010zr011B)the Natural Science Fund of Education Department of Anhui Province,China (No.KJ2011A191)
文摘OBJECTIVE： To establish and optimize the propaga- tion of Nianmaohuangqin （Radix Scutellariae Viscid- ulae） and induce and characterize polyploidy of Nianmaohuangqin （Radix Scutellariae Viscidulae）. METHODS： Buds from germinating seed-derived explants were induced by tissue culture. With an or- thogonal test, different concentrations of 6-benzyl- aminopurine （BAP）, indole-3-acetic acid （IAA） and kinetin （KT） were used to determine the optimal concentrations for the propagation of Nianmaohuangqin （Radix Scutellariae Viscidulae）. The differ- ent concentrations of IAA and rooting powder （ABT） were used to induce rooting. A 0.3% w/v col- chicine solution was used to induce polyploidy and the induced buds was identified by root-tip chromosome determination and stomatal apparatus ob- servation. RESULTS： A large number of buds could be in- duced directly from epicotyl and hypocotyl ex- plants on Murashige and Skoog （MS） （Murashige and Skoog 1962） medium supplemented with 1.1-1.3 mg/L BAP and 0.2 mg/L IAA. Root induction and development could be observed within 20 days of inoculation on 1/2 MS medium supplemented with 0.2 mg/L IAA and 0.1 mg/L ABTo Furthermore, 27 lines of autotetraploid individuals were ob- tained with a plantlet chromosome number of 2n= 4x=36. CONCLUSION： Autotetraploid lines could be ob- tained through induction with colchicine in vitro, proving that this method might be used for plant selection and breeding.
基金financially supported by the National Natural Science Foundation of China(10505018)the Natural Science Foundation of Henan ProvinceChina(091100110401)
文摘Calluses of two autotetraploid rice （DPR （4） and Zijing （4）） were implanted with 30 KeV N＋beams at doses ranging from 1.0×1015 to 9.0×1015 ions cm-2. The differentiation rates of calluses, the concentration of malondialdehyde （MDA）, the activities of superoxide dismutase （SOD）, catalase （CAT） and peroxidase （POD）, and the change of esterase （EST） spectrum were measured and analyzed on the calluses stage. The results showed that differentiation rates of calluses under 3.0×1015 ions cm-2 （（46.12±2.01）%） were higher than the other treatment groups in DPR （4）, and those of Zijing （4） were similar under the doses of 1.0×1015, 3.0×1015 and 5.0×1015 ions cm-2 （（40.55±2.74）, （37.77±3.04） and （34.56±2.65）%） and were higher than that of 7.0×1015 and 9.0×1015 ions cm-2. When the doses were 3.0×1015 and 5.0×1015 ions cm-2, the activities of SOD, POD and CAT were notably enhanced, and the accumulation of MDA content was markedly alleviated in the implanted calluses of two materials, as well as the activity of EST was increased by the additional isforms DPR （4）. Whereas the anti-oxidative systems and enzymes spectrum of EST were destroyed seriously, the accumulation of MDA was signiifcantly aggravated, also the differentiation rate of calluses reduced sharply and almost closed to zero when the implantation doses were 7.0×1015 and 9.0×1015 ions cm-2. It suggested that the proper dose of ion implantation effectively maintained the normal membrane structure and metabolism, and it would be also a feasible approach for autotetraploid rice to improve its genetic characteristics at calluses stage. Additionally, the differences of the radiation resistance between DPR （4） and Zijing （4） could be related to the different genotypes.
基金supported by the National Science Foundation of China(Grant No.30771328)the Teaching and Research Award Program for Outstanding Young Teachers in Higher Education Institutions of Ministry of Education,China
文摘Autotetraploid indic, a/japonica rice hybrid combines both the advantages of polyploidy and the heterosis between indica and japonica rice. Embryo sac abortion is an important factor influencing spikelet fertility in autotetraploid dce hybrid. To clarify the cytological mechanism of embryo sac abortion, the megasporogenesis and megagametogenesis in an autotetraploid japonicaAndica hybrid were examined by the whole-mount eosin B-staining confocal laser scanning microscopy （WE-CLSM） technique. Abnormalities were observed from the megasporocyte stage to the mature embryo sac stage. The degeneration of the tetrad cells and the functional megaspore was the characteristic of abnormalities during megasporogenesis. Abnormal small embryo sacs and disordered number of nuclei were frequently observed during embryo sac development. Some interesting phenomena, such as two functional megaspores, the diplospory-like megasporocyte, and five-nucleate embryo sac were found. The abnormalities that occurred during female gametophyte development resulted in more than five types of abnormal embryo sacs （i.e. embryo sac degeneration, embryo sac without female germ unit, embryo sac without egg apparatus, embryo sac with abnormal polar nuclei and abnormal small embryo sac） in autotetraploid japonica/ndica hybdd. Embryo sac fertility was lower in diploid japonica/ndica hybdd than in autotetraploid japonicaAndica hybrid although many abnormal phenomena were observed in autotetraploid hybrid.
文摘Genetic diversity in peanut (Arachishypogaea L.) is narrow due to its evolution and domestication processes. Amphidiploids and autotetraploids (newly synthesized tetraploids) were created to broaden its genetic base. Molecular analysis has shown that the newly synthesized tetraploids had broader genetic base;and were genetically divergent when compared to cultivated peanut. Nutritional composition relative to oil, fatty acid composition, O/L ratio, protein, iodine value and presence of plant proteinase inhibitors such as trypsin and chymotrypsin inhibitors were studied in the synthesized tetraploids. Some of the newly synthesized tetraploids had higher amounts of proteinase inhibitors. Evaluation of newly synthesized tetraploids revealed several lines resistant to late leaf spot (LLS) and peanut bud necrosis disease (PBND).
基金supported by National Key Projects of China(No.2001BA302B)
文摘In the present study autotetraploid rice IR36-4X was treated by an ion implantation technique with nitrogen ion beams. A polyembryonic mutant （named IR36-Shuang） was identified in the M2 generation. The mutant line and its offspring were systematically investigated in regard to their major agronomic properties and the rate of polyembryonic seedling in the M3-M6 generation. The abnormal phenomena in the embryo sac development and the cytological mechanism of the initiation of additional embryo in IR36-Shuang were observed by Laser Scanning Confocal Microscopy. The results were as follows. 1） The plant height, the panicle length and 1000 grain weight of IRB6-Shuang were lower than that of its control by 35.41%, 5.08% and 15.72% respectively, Moreover, the setting percentage decreased 12.39% compared with that in normal IRB6-4X plants. 2） The polyembryonic trait of IRB6-Shuang was genetically stable and the frequency of the polyembryonic seedlings in the IR36-Shuang line was also relatively stable. 3） The rate of abnormal embryo sacs in IR36-Shuang was significantly higher than that in the control IR36-4X. 4） The additional embryo in IR36-Shuang might arise from the double Jet of embryo sacs in a single owry, antipodal cells or endosperm cells. These results suggest that IRB6-Shuang is a polyembryonic mutant and a new apomixis rice line induced by low energy ion implantation. The prospects for the application in production of the IR36-Shuang line are also discussed. The present study may provide a basis for future investigations of apomixis rice breeding via the ion implantation biotechnology.
基金financially supported by the National Natural Science Foundation of China(32172972)the Science and Technology Innovation Program of Hunan Province(2021RC4028)+1 种基金the Special Funds for Construction of Innovative Provinces in Hunan Province(2021NK1010)Special Science Found of Nansha-South China Agricultural University Fishery Research Institute,Guangzhou,the Aid Program for Science and Technology Innovative Research Team in Higher Educational Institutions of Hunan Province,the earmarked fund for HARS(HARS-07)。
文摘Autotetraploid Carassius auratus is a stable hereditary autotetraploid fish resulting from the hybridization of Carassius auratus red var.(RCC,♀)×Megalobrama amblycephala(BSB,♂),containing four sets of RCC chromosomes.However,the molecular mechanism underlying the determination of sex in this species remains largely unknown.Currently,there lacks a full understanding of the molecular mechanisms governing sex determination and specific molecular markers to differentiate sex in this species.In this study,25,801,677 SNPs(Singlenucleotide polymorphism)and 6,210,306 Indels(insertion-deletion)were obtained from whole-genome resequencing of 100 individuals(including 50 female and 50 male).Further identification confirmed the candidate chromosomes as Chr46B,with the sex-determining region located at Chr46B:22,500,000‒22,800,000 bp.Based on the male-specific insertion(26 bp)within the candidate sex-determining region,a pair of sex-specific molecular markers has been identified.In addition,based on the screening of candidate sex-determining region genes and RT-qPCR validation analysis,ADAM10,AQP9 and tc1a were identified as candidate sex-determining genes.These findings provide a robust foundation for investigating sex determination mechanisms in fish,the evolution of sex chromosomes,and the development of monosex populations.
基金National Key Research and Development Program of China(2018YFD1000302)the National Natural Science Foundation of China(31972377)。
文摘Polyploids have elevated stress tolerance,but the underlying mechanisms remain largely elusive.In this study,we showed that naturally occurring tetraploid plants of trifoliate orange(Poncirus trifoliata(L.) Raf.) exhibited enhanced cold tolerance relative to their diploid progenitors.Transcriptome analysis revealed that whole-genome duplication was associated with higher expression levels of a range of well-characterized cold stress-responsive genes.Global DNA methylation profiling demonstrated that the tetraploids underwent more extensive DNA demethylation in comparison with the diploids under cold stress.CHH methylation in the promoters was associated with up-regulation of related genes,whereas CG,CHG,and CHH methylation in the 3’-regions was relevant to gene down-regulation.Of note,genes involved in unsaturated fatty acids(UFAs) and jasmonate(JA)biosynthesis in the tetraploids displayed different CHH methylation in the gene flanking regions and were prominently up-regulated,consistent with greater accumulation of UFAs and JA when exposed to the cold stress.Collectively,our findings explored the difference in cold stress response between diploids and tetraploids at both transcriptional and epigenetic levels,and gained new insight into the molecular mechanisms underlying enhanced cold tolerance of the tetraploid.These results contribute to uncovering a novel regulatory role of DNA methylation in better cold tolerance of polyploids.
基金supported by the National Natural Science Foundation of China(Grant Nos.31971758 to QY and 32071865 to RL)the Collaborative Research Key Project between China and EU(Grant No.2017YFE0111000)+2 种基金the China Agriculture Research System of MOF and MARA(Grant No.CARS-34)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(Grant No.ASTIP-IAS14)the Key Projects in Science and Technology of Inner Mongolia,China(Grant No.2021ZD0031)。
文摘Alfalfa(Medicago sativa L.)is the most important legume forage crop worldwide with high nutritional value and yield.For a long time,the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits.We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4,a cultivar widely cultivated in China,and a comprehensive database of genomic variations based on resequencing of 220 germplasms.Approximate 2.74 Gb contigs(N50 of 2.06 Mb),accounting for 88.39%of the estimated genome,were assembled,and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes.A total of 34,922 allelic genes were identified from the allele-aware genome.We observed the expansion of gene families,especially those related to the nitrogen metabolism,and the increase of repetitive elements including transposable elements,which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula.Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe,suggesting that geography may influence alfalfa genetic divergence during local adaption.Genome-wide association studies identified 101 single nucleotide polymorphisms(SNPs)associated with 27 agronomic traits.Two candidate genes were predicted to be correlated with fall dormancy and salt response.We believe that the alleleaware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.
文摘Potato is the fourth most important food crop in the world.Although with a long history for breeding approaches,genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars,which limit the molecular breeding progression.By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center,with approximate 20-fold coverage,we revealed more than 27 million Single Nucleotide Polymorphisms and~3 million Insertion and Deletions with high quality and accuracy.Domestication analysis and genome-wide association studies(GWAS)identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance,providing informative insights into the selection and domestication of cultivar potato.In addition,GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals,especially those related to tuber size,small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis.Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.
