Polyploidy plays a major role in genome evolution,which corresponds to environmental changes over millions of years.The mechanisms of genome evolution,particularly during the process of domestication,are of broad inte...Polyploidy plays a major role in genome evolution,which corresponds to environmental changes over millions of years.The mechanisms of genome evolution,particularly during the process of domestication,are of broad interest in the fields of plant science and crop breeding.Upland cotton is derived from the hybridization and polyploidization of its ancient A and D diploid ancestors.As a result,cotton is a model for polyploid genome evolution and crop domestication.To explore the genomic mysteries of allopolyploid cotton,we investigated asymmetric evolution and domestication in the A and D subgenomes.Interestingly,more structural rearrangements have been characterized in the A subgenome than in the D subgenome.Correspondingly,more transposable elements,a greater number of lost and disrupted genes,and faster evolution have been identified in the A subgenome.In contrast,the centromeric retroelement(RT-domain related) sequence of tetraploid cotton derived from the D subgenome progenitor was found to have invaded the A subgenome centromeres after allotetrapolyploid formation.Although there is no genome-wide expression bias between the subgenomes,as with expression-level alterations,gene expression bias of homoeologous gene pairs is widespread and varies from tissue to tissue.Further,there are more positively selected genes for fiber yield and quality in the A subgenome and more for stress tolerance in the D subgenome,indicating asymmetric domestication.This review highlights the asymmetric subgenomic evolution and domestication of allotetraploid cotton,providing valuable genomic resources for cotton research and enhancing our understanding of the basis of many other allopolyploids.展开更多
The cultivated Gossypium A genome diploid species G.arboreum and G.herbaceum and the allotetraploid species G.hirsutum and G.barbadense share common morphology for various floral traits,
Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkali...Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years ago.Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.展开更多
The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetrap...The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago （Mya）, respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.展开更多
Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and e...Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.展开更多
Thirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross be- tween Yiben No.4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. icha...Thirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross be- tween Yiben No.4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. χ2 (Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However, these progenies were clustered into three major groups using dendrogram constructed by UPGMA, skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribu- tion was predominant in progenies, respectively.展开更多
Cotton is not only an important source of textile fibre and edible oil but also a valuable source of high-quality protein and fodder, because 45％—50％ of the cotton seed powder is protein. However, the cotton seed o...Cotton is not only an important source of textile fibre and edible oil but also a valuable source of high-quality protein and fodder, because 45％—50％ of the cotton seed powder is protein. However, the cotton seed of cultivated cotton usually contains a special polyphenol compound called gossypol, which is poisonous and hinders the utilization of the seeds. Therefore breeding new cotton species with no展开更多
Ecological safety is a major consideration in the commercialization of transgenic fish. Development of sterile transgenic triploid fish through hybridization of transgenic tetraploid fish and transgenic diploid fish i...Ecological safety is a major consideration in the commercialization of transgenic fish. Development of sterile transgenic triploid fish through hybridization of transgenic tetraploid fish and transgenic diploid fish is a feasible way to solve this problem. The "all-fish" transgene, pbcAbcGHc, containing the black carp β-actin gene promoter and the open reading frame (ORF) of the black carp growth hormone (GH) gene was constructed and introduced into fertilized eggs of allotetraploid fish through microinjection. Contrast cultivation results showed that the growth rate of 150 day-old P 0 black carp GH gene transgenic allotetraploid fish was much higher than that of controls. Sixty 150 day-old transgenic allotetraploid fish were assayed by PCR for transgene integration and 90% of fish were positive for the transgene. The transgene was detected in 13 of 20 sperm samples from male transgenic allotetraploid fish. RT-PCR detected transcription of the exogenous black carp GH gene in the muscle, liver, kidney and ovaries of the largest transgenic allotetraploid fish. This study has developed P 0 black carp GH gene transgenic allotetraploid fish with a highly increased growth rate, which provides a solid foundation for the establishment of a pure line of transgenic allotetraploid fish and for the large scale production of sterile transgenic triploid fish.展开更多
The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate. Using ISSR and AFLP markers a...The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate. Using ISSR and AFLP markers and the cyclins genes, the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents. The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations. However, the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor. DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent's genome. Some non-parental bands were found in the allotetraploid hybrids. Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents, leading to non-parental amino acid loci. We speculate that the non-additivity in the allotetraploids, compared with their progenitors, could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.展开更多
基金supported by the National Natural Science Foundation of China(Nos.3133058,31290213)the Fundamental Research Funds for the Central Universities,the Priority Academic Program Development of Jiangsu Higher Education Institutionsthe 111 Project(B08025)
文摘Polyploidy plays a major role in genome evolution,which corresponds to environmental changes over millions of years.The mechanisms of genome evolution,particularly during the process of domestication,are of broad interest in the fields of plant science and crop breeding.Upland cotton is derived from the hybridization and polyploidization of its ancient A and D diploid ancestors.As a result,cotton is a model for polyploid genome evolution and crop domestication.To explore the genomic mysteries of allopolyploid cotton,we investigated asymmetric evolution and domestication in the A and D subgenomes.Interestingly,more structural rearrangements have been characterized in the A subgenome than in the D subgenome.Correspondingly,more transposable elements,a greater number of lost and disrupted genes,and faster evolution have been identified in the A subgenome.In contrast,the centromeric retroelement(RT-domain related) sequence of tetraploid cotton derived from the D subgenome progenitor was found to have invaded the A subgenome centromeres after allotetrapolyploid formation.Although there is no genome-wide expression bias between the subgenomes,as with expression-level alterations,gene expression bias of homoeologous gene pairs is widespread and varies from tissue to tissue.Further,there are more positively selected genes for fiber yield and quality in the A subgenome and more for stress tolerance in the D subgenome,indicating asymmetric domestication.This review highlights the asymmetric subgenomic evolution and domestication of allotetraploid cotton,providing valuable genomic resources for cotton research and enhancing our understanding of the basis of many other allopolyploids.
文摘The cultivated Gossypium A genome diploid species G.arboreum and G.herbaceum and the allotetraploid species G.hirsutum and G.barbadense share common morphology for various floral traits,
基金This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA28030000)the National Key Research and Development Program of China(2022YFD1500503,2022YFF1003401)+2 种基金Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta(2022SZX14)the earmarked fund for CARS-Green Manure(CARS-22)the Youth Innovation Promotion Association of CAS(Y2022039).
文摘Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal land.Here,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline soil.To understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of S.cannabina spanning~2,087 Mb.The assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric characteristics.Further genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years ago.Comparative genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A homoeolog.We further identified four specific alkali-induced phosphate transporter genes in S.cannabina;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline soil.Our work highlights the significance of S.cannabina as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.
文摘The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Here, we report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber, and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago （Mya）, respectively, and the allotetraploidization happened at some point between 26 Mya and 3 Mya, the estimated date when C. maxima and C. moschata diverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization has not been commonly observed in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in the C. maxima ×C. moschata interspecific F1 hybrid and their two parents indicates the predominance of trans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into polyploid genome evolution and valuable resources for genetic improvement of cucurbit crops.
基金?nancially supported, in part, by grants from NSFC (31330058)National Key R & D Program for Crop Breeding in China (2016YFD0100203)+1 种基金the Priority Academic Program Development of Jiangsu Higher Education Institutions, the 111 project (B08025)the JCIC-MCP project
文摘Whole genome duplication, a prevalent force of evolution in plants, results in massive genome restructuring in different organisms. Roles of the resultant duplicated genes are poorly understood both functionally and evolutionarily. In the present study, differentially expressed ethylene responsive factors(GhERF1 s), anchored on Chr-A07 and Chr-D07 were isolated from a high-yielding cotton hybrid(XZM2)and its parents. The GhERF1 was located in the B3 subgroup of the ethylene responsive factors subfamily involved in conferring tolerance to abiotic stress Nucleotide sequence analysis of 524 diverse accessions together with quantitative real-time polymerase chain reaction analysis, elucidated that de-functionalization of GhERF1-7 A occurred due to one base insertion following formation of the allotetraploid cotton. Our quantitative trait loci and association mapping analyses highlighted a role for GhERF1-7 A in conferring high boll number per plant in modern cotton cultivars. Overexpression of GhERF1-7 A in transgenic Arabidopsis resulted in a substantial increase in the number of siliques and total seed yield. Neo-functionalization of GhERF1-7 A was also observed in modern cultivars rather than in races and/or landraces, further supporting its role in the development of high-yielding cotton cultivars. Both de-and neofunctionalization occurred in one of the duplicate genes,thus providing new genomic insight into the evolution of allotetraploid cotton species.
基金the National Natural Science Foundation of China (Grant No. 30070079)the National Key Technologies R & D Program (Grant No. 2002BA515B)the Program for Innovative Research Team in University (Grant No. IRT0548)
文摘Thirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross be- tween Yiben No.4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. χ2 (Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However, these progenies were clustered into three major groups using dendrogram constructed by UPGMA, skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribu- tion was predominant in progenies, respectively.
文摘Cotton is not only an important source of textile fibre and edible oil but also a valuable source of high-quality protein and fodder, because 45％—50％ of the cotton seed powder is protein. However, the cotton seed of cultivated cotton usually contains a special polyphenol compound called gossypol, which is poisonous and hinders the utilization of the seeds. Therefore breeding new cotton species with no
基金supported by the National Special Fund for Scientific Research in Public Benefits (Grant No. 20090304608)the National Basic Research Program of China (Grant No. 2007CB109006)+1 种基金the National Natural Science Foundation of China (Grant No. 30500294)the Excellent Talent Program of Hunan Normal University (Grant No. ET31004)
文摘Ecological safety is a major consideration in the commercialization of transgenic fish. Development of sterile transgenic triploid fish through hybridization of transgenic tetraploid fish and transgenic diploid fish is a feasible way to solve this problem. The "all-fish" transgene, pbcAbcGHc, containing the black carp β-actin gene promoter and the open reading frame (ORF) of the black carp growth hormone (GH) gene was constructed and introduced into fertilized eggs of allotetraploid fish through microinjection. Contrast cultivation results showed that the growth rate of 150 day-old P 0 black carp GH gene transgenic allotetraploid fish was much higher than that of controls. Sixty 150 day-old transgenic allotetraploid fish were assayed by PCR for transgene integration and 90% of fish were positive for the transgene. The transgene was detected in 13 of 20 sperm samples from male transgenic allotetraploid fish. RT-PCR detected transcription of the exogenous black carp GH gene in the muscle, liver, kidney and ovaries of the largest transgenic allotetraploid fish. This study has developed P 0 black carp GH gene transgenic allotetraploid fish with a highly increased growth rate, which provides a solid foundation for the establishment of a pure line of transgenic allotetraploid fish and for the large scale production of sterile transgenic triploid fish.
基金Supported by the National Natural Science Fund for Distinguished Young Scholars (Grant No. 30725028)State Key Basic Research and Development Program of China (Grant No. 2007CB109206)Specially-appointed Professor for Lotus Scholars Program of Hunan Province
文摘The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate. Using ISSR and AFLP markers and the cyclins genes, the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents. The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations. However, the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor. DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent's genome. Some non-parental bands were found in the allotetraploid hybrids. Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents, leading to non-parental amino acid loci. We speculate that the non-additivity in the allotetraploids, compared with their progenitors, could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.
