The Chinese wheat landrace Kaixianluohanmai(KL)expresses the ph-like phenotype.A major QTL,QPh.sicau-3A(syn.phKL),responsible for this effect has been mapped to chromosome arm 3AL.This study presents some characterist...The Chinese wheat landrace Kaixianluohanmai(KL)expresses the ph-like phenotype.A major QTL,QPh.sicau-3A(syn.phKL),responsible for this effect has been mapped to chromosome arm 3AL.This study presents some characteristics of homoeologous pairing and recombination induced by phKL.In KL haploids,the level of homoeologous pairing was elevated relative to Ph1 Chinese Spring(CS)haploids.There was a clear preference for A–D pairing and less frequent for A–B and B–D,reflecting the higher levels of affinity between genomes A and D in wheat.The characteristics of pairing were affected by temperature and magnesium ion supplementation.The suitability of phKL for chromosome engineering was tested on three pairs of homoeologues:2Sv-2B,2Sv-2D,and 2RL-2BL.The recombination rates were 1.68%,0.17%,and 0%,respectively.The phKL locus in KL induced a moderate level of homoeologous chromosome pairing and recombination when the Ph1 locus of wheat was present,both in wheat haploids and hexaploids.The Ph1-imposed criteria for chromosome pairing and crossing over were relaxed to some degree,permitting homoeologous crossing over but only between closely related chromosomes;there was no crossing over between more differentiated chromosomes.Therefore,the phKL system(QPh.sicau-3A)can be a useful tool in chromosome engineering of wheat to transfer genes from closely related species with the benefit of reduced genomic chaos generated by the ph1b mutation.展开更多
The purpose of this study was to characterize Ta14 S homoeologs and assess their functions in wheat seed development.The genomic and c DNA sequences of three Ta14 S homoeologous genes encoding 14-3-3 proteins were iso...The purpose of this study was to characterize Ta14 S homoeologs and assess their functions in wheat seed development.The genomic and c DNA sequences of three Ta14 S homoeologous genes encoding 14-3-3 proteins were isolated.Sequence analysis revealed that the three homoeologs consisted of five exons and four introns and were very highly conserved in the coding regions and in exon/intron structure,whereas the c DNA sequences were variable in the 5′ and 3′-UTR.The three genes,designated as Ta14S-2A,Ta14S-2B and Ta14S-2D,were located in homoeologous group 2 chromosomes.The polypeptide chains of the three Ta14 S genes were highly similar.These genes were most homologous to Hv14 A from barley.Real-time quantitative PCR indicated that the three Ta14 S genes were differentially expressed in different organs at different developmental stages and all exhibited greater expression in primary roots of 1-day-old germlings than in other tissues.Comparison of the expression patterns of the three homoeologous genes at different times after pollination also revealed that their expression was developmentally regulated.The transcription of Ta14S-2B was clearly higher during seed germination,whereas expressions of Ta14S-2A and Ta14S-2D were up-regulated at the beginning of seed imbibition(0–12 h),but declined thereafter.The results suggested that the three Ta14 S homoeologous genes have regulatory roles in seed development and germination.展开更多
While Upland cotton(Gossypium hirsutum L.) represents 95% of the world production,its genetic improvement is hindered by the shortage of effective genomic tools and resources.The
Wheat 1BL/1RS translocations are widely planted in China as well as in most of the wheat producing area in the world for their good qualities of disease resistance and high yield. 1BL/1RS translocations are however po...Wheat 1BL/1RS translocations are widely planted in China as well as in most of the wheat producing area in the world for their good qualities of disease resistance and high yield. 1BL/1RS translocations are however poor in bread making, partially caused by a family of small monomeric proteins, ω-secalins, which are encoded by genes on 1RS. Based on published sequence of a rye ω-secalin gene we designed a pair of primers to cover the whole mature protein coding sequence. A major band could be amplified from 1BL/1RS translocations but not from euploid wheat. Using this primer set we conducted PCR amplification by using high fidelity Pfu polymerase on the genomic DNAs and cDNAs purified from a 1BL/1RS translocation Lankao 906. Sequencing analysis indicated that this gene family contains several mem- bers of 1150 bp, 1076 bp, 1075 bp, 1052 bp and 1004 bp genes, including two pseudogenes and three active genes. The gene transcripts were differentially expressed in developing seeds.展开更多
Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chin...Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring （CS）-H. californicum amphidiploid （2n = 6x = 56, AABBDDHH） was established. By genomic in situ hybridization （GISH） and multicolor fluorescent in situ hybridization （FISH） using repetitive DNA clones （pTa71, pTa794 and pSc119.2） as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat--alien chromosome lines, including four disomic addition lines （DAH1, DAH3, DAH5 and DAH6）, five telosomic addition lines （MtH7L, MtHIS, MtH1L, DtH6S and DtH6L）, one multiple addition line involving H. californicum chromosome H2, one disomic substitution line （DSH4） and one translocation line （TH7S/1BL）, were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST （expressed sequence tag） or SSR （simple sequence repeat） markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5Hc, 2He, 6Hc, 3Hc and 1Hc, respectively. The chromosomes H1 and H6 were designated as 7Hc and 4Hc, respectively, by referring to SSR markers located on rye chromosomes.展开更多
Homoeologous recombination(HR),the exchange of homoeologous chromosomes,contributes to subgenome adaptation to diverse environments by producing various phenotypes.However,the potential relevance of HR and innate immu...Homoeologous recombination(HR),the exchange of homoeologous chromosomes,contributes to subgenome adaptation to diverse environments by producing various phenotypes.However,the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species.In our study,two allotriploid genotypes(R_(2)C and RC_(2)),whose innate immunity was stronger than their inbred parents(Carassius auratus red var.and Cyprinus carpio L.),were obtained from backcrossing between male allotetraploids of C.auratus red var.×C.carpio L.and females of their two inbred parents,respectively.The work detected 140 HRs shared between the two triploids at the genomic level.Further,transcriptions of 54 homoeologous recombinant genes(HRGs)in R_(2)C and 65 HRGs in RC_(2) were detected using both Illumina and PacBio data.Finally,by comparing expressed recombinant reads to total expressed reads in each of the genes,a range of 0.1%-10% was observed in most of the 99-193 HRGs,of which six recombinant genes were classified as"response to stimulus".These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels,but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.展开更多
With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at ...With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at Zhejiang University,assembled an allopolyploid B.juncea genome and uncovered differential homoeolog gene expression influencing selection,which was published in Nature展开更多
WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previo...WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.展开更多
Barley yellow dwarf virus(BYDV),vectored by several aphid species,is the most significant viral pathogen of wheat and other grain cereals.Significant economic losses resulting from BYDV in wheat,barley and oats have b...Barley yellow dwarf virus(BYDV),vectored by several aphid species,is the most significant viral pathogen of wheat and other grain cereals.Significant economic losses resulting from BYDV in wheat,barley and oats have been reported in many countries.The most economic means of controlling BYDV is to develop wheat varieties with resistance to BYDV. So far no BYDV resistance has been described in wheat collections except one gene in some cultivars tolerant to BYDV. However, Thinopyrum intermedium ,two octoploids Zhong 4 awnless and TAF46,and the disomic addition lines,L1,Z1,Z2 and Z6 all showed resistance to BYDV. We developed several wheat Th.Intermedium translocation lines, Yw642, Yw443 and Yw243 etc., showing good BYDV resistance from L1 by inducing homologous pairing using CS Ph1 mutant. It was found that their BYDV resistance was controlled by a single dominant gene. Characterization of these wheat lines was carried out by GISH and RFLP analysis. The results of GISH showed that the lines, Yw642, Yw443 and Yw243 etc., were homozygous wheat Th.intermedium translocation lines containing 20 pairs of wheat chromosomes and 1 pair of wheat Th.intermedium translocation chromosomes,in which the chromosome segments of Th intermedium were transferred to the distal end of a pair of wheat chromosomes. RFLP analysis indicated that the translocation chromosome of the wheat lines was T7DS·7DL 7XL translocation. The breakpoint of translocation is located on the distal end of 7DL,between Xpsr965 and Xpsr680,about 90 99 cM from the centromere. The BYDV gene is located on the distal end of 7XL around Xpsr680,Xpsr687 and Xwg380.The RFLP markers of psr680,psr687 and wg380 co segregated with the BYDV resistance and could be used for marker assisted selection(MAS)in wheat breeding program for BYDV resistance.展开更多
基金supported by the National Natural Science Foundation of China(31971884,31601300,32172020)USDANIFA(#CA-R-BPS-5411-H)to AJL+1 种基金Natural Science Foundation of Sichuan Province(2022NSFSC1696,2019YJ0415)the National Key Research and Development Program of China(2016YFD0102000)。
文摘The Chinese wheat landrace Kaixianluohanmai(KL)expresses the ph-like phenotype.A major QTL,QPh.sicau-3A(syn.phKL),responsible for this effect has been mapped to chromosome arm 3AL.This study presents some characteristics of homoeologous pairing and recombination induced by phKL.In KL haploids,the level of homoeologous pairing was elevated relative to Ph1 Chinese Spring(CS)haploids.There was a clear preference for A–D pairing and less frequent for A–B and B–D,reflecting the higher levels of affinity between genomes A and D in wheat.The characteristics of pairing were affected by temperature and magnesium ion supplementation.The suitability of phKL for chromosome engineering was tested on three pairs of homoeologues:2Sv-2B,2Sv-2D,and 2RL-2BL.The recombination rates were 1.68%,0.17%,and 0%,respectively.The phKL locus in KL induced a moderate level of homoeologous chromosome pairing and recombination when the Ph1 locus of wheat was present,both in wheat haploids and hexaploids.The Ph1-imposed criteria for chromosome pairing and crossing over were relaxed to some degree,permitting homoeologous crossing over but only between closely related chromosomes;there was no crossing over between more differentiated chromosomes.Therefore,the phKL system(QPh.sicau-3A)can be a useful tool in chromosome engineering of wheat to transfer genes from closely related species with the benefit of reduced genomic chaos generated by the ph1b mutation.
基金financially supported by the Key Transgenic Breeding Program of the Ministry of Agriculture of China(No.2014ZX0800205B-003)the National Natural Science Foundation of China(No.30771332)
文摘The purpose of this study was to characterize Ta14 S homoeologs and assess their functions in wheat seed development.The genomic and c DNA sequences of three Ta14 S homoeologous genes encoding 14-3-3 proteins were isolated.Sequence analysis revealed that the three homoeologs consisted of five exons and four introns and were very highly conserved in the coding regions and in exon/intron structure,whereas the c DNA sequences were variable in the 5′ and 3′-UTR.The three genes,designated as Ta14S-2A,Ta14S-2B and Ta14S-2D,were located in homoeologous group 2 chromosomes.The polypeptide chains of the three Ta14 S genes were highly similar.These genes were most homologous to Hv14 A from barley.Real-time quantitative PCR indicated that the three Ta14 S genes were differentially expressed in different organs at different developmental stages and all exhibited greater expression in primary roots of 1-day-old germlings than in other tissues.Comparison of the expression patterns of the three homoeologous genes at different times after pollination also revealed that their expression was developmentally regulated.The transcription of Ta14S-2B was clearly higher during seed germination,whereas expressions of Ta14S-2A and Ta14S-2D were up-regulated at the beginning of seed imbibition(0–12 h),but declined thereafter.The results suggested that the three Ta14 S homoeologous genes have regulatory roles in seed development and germination.
文摘While Upland cotton(Gossypium hirsutum L.) represents 95% of the world production,its genetic improvement is hindered by the shortage of effective genomic tools and resources.The
基金supported by the National Basic Research Program of China(973)(No.2004CB117200).
文摘Wheat 1BL/1RS translocations are widely planted in China as well as in most of the wheat producing area in the world for their good qualities of disease resistance and high yield. 1BL/1RS translocations are however poor in bread making, partially caused by a family of small monomeric proteins, ω-secalins, which are encoded by genes on 1RS. Based on published sequence of a rye ω-secalin gene we designed a pair of primers to cover the whole mature protein coding sequence. A major band could be amplified from 1BL/1RS translocations but not from euploid wheat. Using this primer set we conducted PCR amplification by using high fidelity Pfu polymerase on the genomic DNAs and cDNAs purified from a 1BL/1RS translocation Lankao 906. Sequencing analysis indicated that this gene family contains several mem- bers of 1150 bp, 1076 bp, 1075 bp, 1052 bp and 1004 bp genes, including two pseudogenes and three active genes. The gene transcripts were differentially expressed in developing seeds.
基金supported by the Technology Support Program of Jiangsu Province (No. BE2012306)the Program of Introducing Talents of Discipline to Universities (No. B08025)+1 种基金the Project No.7 from Science and High-Tech Based Major Program of Agriculture Committee of Shanghai Municipal Administration (No.20127)the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)
文摘Hordeum californicum （2n = 2x = 14, HH） is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring （CS）-H. californicum amphidiploid （2n = 6x = 56, AABBDDHH） was established. By genomic in situ hybridization （GISH） and multicolor fluorescent in situ hybridization （FISH） using repetitive DNA clones （pTa71, pTa794 and pSc119.2） as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat--alien chromosome lines, including four disomic addition lines （DAH1, DAH3, DAH5 and DAH6）, five telosomic addition lines （MtH7L, MtHIS, MtH1L, DtH6S and DtH6L）, one multiple addition line involving H. californicum chromosome H2, one disomic substitution line （DSH4） and one translocation line （TH7S/1BL）, were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST （expressed sequence tag） or SSR （simple sequence repeat） markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5Hc, 2He, 6Hc, 3Hc and 1Hc, respectively. The chromosomes H1 and H6 were designated as 7Hc and 4Hc, respectively, by referring to SSR markers located on rye chromosomes.
基金supported by the National Natural Science Foundation of China(31702334,31730098,U19A2040 and31430088)the Key Research and Development Program of Hunan Province(2018NK2072 and 2017NK1031)+4 种基金the Earmarked Fund for China Agriculture Research System(CARS-45)111 Project(D20007)High-Level Talent Agglomeration Program of HunanChina(2019RS1044)the Cooperative Innovation Center of Engineering and New Products for Developmental Biology of Hunan Province(20134486)。
文摘Homoeologous recombination(HR),the exchange of homoeologous chromosomes,contributes to subgenome adaptation to diverse environments by producing various phenotypes.However,the potential relevance of HR and innate immunity is rarely described in triploid cyprinid fish species.In our study,two allotriploid genotypes(R_(2)C and RC_(2)),whose innate immunity was stronger than their inbred parents(Carassius auratus red var.and Cyprinus carpio L.),were obtained from backcrossing between male allotetraploids of C.auratus red var.×C.carpio L.and females of their two inbred parents,respectively.The work detected 140 HRs shared between the two triploids at the genomic level.Further,transcriptions of 54 homoeologous recombinant genes(HRGs)in R_(2)C and 65 HRGs in RC_(2) were detected using both Illumina and PacBio data.Finally,by comparing expressed recombinant reads to total expressed reads in each of the genes,a range of 0.1%-10% was observed in most of the 99-193 HRGs,of which six recombinant genes were classified as"response to stimulus".These results not only provide a novel way to predict HRs in allopolyploids based on cross prediction at both genomic and transcriptional levels,but also insight into the potential relationship between HRs related to innate immunity and adaptation of the triploids and allotetraploids.
文摘With the long-term support by the National Natural Science Foundation of China,Ministry of Agriculture,and Science and Technology Department of Zhejiang Province,the research team led by Prof.Zhang Mingfang(张明方)at Zhejiang University,assembled an allopolyploid B.juncea genome and uncovered differential homoeolog gene expression influencing selection,which was published in Nature
基金funded by the Start-up Foundation for High Talents of Qingdao Agricultural University(No.665/1120012)the Natural Science Foundation of Shandong Province,China(ZR2019QC017)+4 种基金the National Key Research and Development Program,China(2022YFD2300101-1)the Key Research and Development Program of Shandong Province,China(2021LZGC003 and 2021LZGC026-03)Peanut Seed Industry Project in Shandong Province,China(2022LZGC007)the Science&Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta,China(2022SZX18)the Graduate Student Innovation Program of Qingdao Agricultural University(QNYCX23001).
文摘WRKY transcription factors(TFs)have been identified as important core regulators in the responses of plants to biotic and abiotic stresses.Cultivated peanut(Arachis hypogaea)is an important oil and protein crop.Previous studies have identified hundreds of WRKY TFs in peanut.However,their functions and regulatory networks remain unclear.Simultaneously,the AdWRKY40 TF is involved in drought tolerance in Arachis duranensis and has an orthologous relationship with the AhTWRKY24 TF,which has a homoeologous relationship with AhTWRKY106 TF in A.hypogaea cv.Tifrunner.To reveal how the homoeologous AhTWRKY24 and AhTWRKY106 TFs regulate the downstream genes,DNA affinity purification sequencing(DAP-seq)was performed to detect the binding sites of TFs at the genome-wide level.A total of 3486 downstream genes were identified that were collectively regulated by the AhTWRKY24 and AhTWRKY106 TFs.The results revealed that W-box elements were the binding sites for regulation of the downstream genes by AhTWRKY24 and AhTWRKY106 TFs.A gene ontology enrichment analysis indicated that these downstream genes were enriched in protein modification and reproduction in the biological process.In addition,RNA-seq data showed that the AhTWRKY24 and AhTWRKY106 TFs regulate differentially expressed genes involved in the response to drought stress.The AhTWRKY24 and AhTWRKY106 TFs can specifically regulate downstream genes,and they nearly equal the numbers of downstream genes from the two A.hypogaea cv.Tifrunner subgenomes.These results provide a theoretical basis to study the functions and regulatory networks of AhTWRKY24 and AhTWRKY106 TFs.
文摘Barley yellow dwarf virus(BYDV),vectored by several aphid species,is the most significant viral pathogen of wheat and other grain cereals.Significant economic losses resulting from BYDV in wheat,barley and oats have been reported in many countries.The most economic means of controlling BYDV is to develop wheat varieties with resistance to BYDV. So far no BYDV resistance has been described in wheat collections except one gene in some cultivars tolerant to BYDV. However, Thinopyrum intermedium ,two octoploids Zhong 4 awnless and TAF46,and the disomic addition lines,L1,Z1,Z2 and Z6 all showed resistance to BYDV. We developed several wheat Th.Intermedium translocation lines, Yw642, Yw443 and Yw243 etc., showing good BYDV resistance from L1 by inducing homologous pairing using CS Ph1 mutant. It was found that their BYDV resistance was controlled by a single dominant gene. Characterization of these wheat lines was carried out by GISH and RFLP analysis. The results of GISH showed that the lines, Yw642, Yw443 and Yw243 etc., were homozygous wheat Th.intermedium translocation lines containing 20 pairs of wheat chromosomes and 1 pair of wheat Th.intermedium translocation chromosomes,in which the chromosome segments of Th intermedium were transferred to the distal end of a pair of wheat chromosomes. RFLP analysis indicated that the translocation chromosome of the wheat lines was T7DS·7DL 7XL translocation. The breakpoint of translocation is located on the distal end of 7DL,between Xpsr965 and Xpsr680,about 90 99 cM from the centromere. The BYDV gene is located on the distal end of 7XL around Xpsr680,Xpsr687 and Xwg380.The RFLP markers of psr680,psr687 and wg380 co segregated with the BYDV resistance and could be used for marker assisted selection(MAS)in wheat breeding program for BYDV resistance.
