Conserved domains e.g. nucleotide binding site (NBS) were found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogs (RGAs) have been isolated previously and were used as ...Conserved domains e.g. nucleotide binding site (NBS) were found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogs (RGAs) have been isolated previously and were used as probes to screen a soybean (Glycine max L. Merr.) cDNA library. A full-length cDNA, KR3, was obtained by screening the library and rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that the cDNA is 2 353 bp in length and the open reading frame (ORF) codes for a polypeptide of 636 amino acids with a Toll-Interleukin-1 receptor (TIR) and a NBS domain. Sequence alignment showed that it was similar to N gene of tobacco. The phylogenetic tree analysis of R proteins with NBS from higher plants was performed. The KR3 gene has low copies in soybean genome and its expression was induced by exogenous salicylic acid (SA).展开更多
A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b＇ a...A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b＇ and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region （SCAR） marker tightly linked with Stv-b＇ and a cleaved amplified polymorphic sequence （CAPS） marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.展开更多
Success in conventional breeding for resistance to mycotoxin-producing or other phytopathogenic fungi is dependent on the availability of resistance gene(s) in the germplasm.Even when it is available,breeding for dise...Success in conventional breeding for resistance to mycotoxin-producing or other phytopathogenic fungi is dependent on the availability of resistance gene(s) in the germplasm.Even when it is available,breeding for disease-resistant crops is very time consuming,especially in perennial crops such展开更多
Lesion mimic mutant（LMM） genes, stimulating lesion formation in the absence of pathogens, play significant roles in immune response. In this study, we characterized a rice lesion mimic mutant, lmm5,which displayed l...Lesion mimic mutant（LMM） genes, stimulating lesion formation in the absence of pathogens, play significant roles in immune response. In this study, we characterized a rice lesion mimic mutant, lmm5,which displayed light-dependent spontaneous lesions. Additionally, lmm5 plants exhibited enhanced resistance to all of the tested races of Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae（Xoo） by increasing the expression of defense-related genes and the accumulation of hydrogen peroxide. Genetic analysis showed that the lesion mimic phenotype of lmm5 was controlled by two genes, lmm5.1 and lmm5.4, which were isolated with a map-based cloning strategy. Remarkably, LMM5.1 and LMM5.4 share a 97.4% amino acid sequence identity, and they each encode a eukaryotic translation elongation factor 1A（e EF1A）-like protein. Besides, LMM5.1 and LMM5.4 were expressed in a tissue-specific and an indicaspecific manner, respectively. In addition, high-throughput m RNA sequencing analysis confirmed that the basal immunity was constitutively activated in the lmm5 mutant. Taken together, these results suggest that the homologous e EF1A-like genes, LMM5.1 and LMM5.4, negatively affect cell death and disease resistance in rice.展开更多
Resistance to rice blast of transgenic rice lines harboring rice blast resistance gene Pi-d2 transformed from three different expression vectors of pCB6.3kb, pCB5.3kb and pZH01-2.72kb were analyzed. Nine advanced-gene...Resistance to rice blast of transgenic rice lines harboring rice blast resistance gene Pi-d2 transformed from three different expression vectors of pCB6.3kb, pCB5.3kb and pZH01-2.72kb were analyzed. Nine advanced-generation transgenic rice lines with Pi-d2 gene displayed various resistance to 39 rice blast strains, and the highest disease-resistant frequency reached 91.7%. Four early-generation homozygous transgenic lines with Pi-d2 gene exhibited resistance to more than 81.5% of 58 rice blast strains, showing the characteristic of wide-spectrum resistance. The transgenic embryonic calli selected by the crude toxin of rice blast fungus showed that the callus induction rate of immature embryo from transgenic rice plants decreased as the concentration of crude toxin in the culture medium increased. When the concentration of crude toxin reached 40%, the callus induction rate of immature embryo from transgenic lines was 49.3%, and that of the receptor control was 5%. The disease incidence of neck blast of the transgenic rice lines in fields under induction was 0% to 50%, indicating that the rice blast resistance of transgenic rice lines is much higher than that of the receptor control.展开更多
Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs...Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs)and the development of related molecular markers are of great importance for the breeding of LLS-resistant peanut.In this study,173 individual lines of a recombinant inbred line(RIL)population and the 48K SNP array for genotyping were used to construct a high-density genetic map with 1,475 bin markers and 20 linkage groups.A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map.Among them,the stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments,with the phenotypic variation explained(PVE)ranging from 15.57 to 31.09%.QTL-seq technology was also employed for a QTL analysis of LLS resistance.As a result,14 QTL loci related to LLS resistance were identified using the G prime algorithm.Notably,the physical positions of qLLS02 and qLLS03 coincided with those of qLLS.LG02 and qLLS.LG03,respectively.Gene annotation analysis within the 14 QTL intervals from QTL-seq revealed a total of 163 nucleotide-binding site-leucine-rich repeat(NBS-LRR)disease resistance genes,accounting for 22.86%of all resistance(R)genes in the peanut genome and showing a 4.26-fold enrichment with a P-value of 5.19e-57.Within the QTL region qLLS02 of the resistant parent Mi-2,there was a 5 Mb structural variation(SV)interval containing 81 NBS-LRR genes.A PCR diagnostic marker was developed,and validation data suggested that this SV might lead to gene deletion or replacement with other genes.This SV has the potential to enhance peanut resistance to LLS.The results of this study have significant implications for improving peanut breeding for LLS resistance through the development of associated molecular markers.展开更多
Southern corn rust(SCR)caused by Puccinia polysora Underw and maize stalk rot caused by Pythium inflatum Matthews(MSR-2)are two destructive diseases of maize(Zea mays L.)in China.Our previous studies indicated that ma...Southern corn rust(SCR)caused by Puccinia polysora Underw and maize stalk rot caused by Pythium inflatum Matthews(MSR-2)are two destructive diseases of maize(Zea mays L.)in China.Our previous studies indicated that maize inbred line Qi319 is highly resistant to SCR but susceptible to MSR-2,while inbred line 1145 is highly resistant to MSR-2 but susceptible to SCR.The SCR resistant gene(RppQ)in Qi319 and MSR-2 resistant gene(Rpi1)in 1145 have been mapped on chromosome 10 and 4 respectively.In this research,through marker-assisted selection(MAS)with the molecular markers,bnlg1937 tightly linked to Rpi1 and phi041 tightly linked to RppQ,pyramid breeding of the two kinds of disease resistant genes were carried out from the year of 2003 to 2007.Two homozygotic inbred lines of F5 generation,DR94-1-1-1 and DR36-1-1-1 were identified.MAS result suggested DR94-1-1-1 and DR36-1-1-1 contained the two resistance genes RppQ and Rpi1.Field inoculation tests confirmed their high resistance to the two diseases.In addition,field investigation indicated that the two selected inbred lines,particularly DR94-1-1-1,had excellent agronomic traits such as plant height,ear height and yield-relating traits including ear length,ear diameter,ear weight,kernels per ear,kernels per row and kernel weight per ear.The two selected inbred lines DR94-1-1-1 and DR36-1-1-1 can either be directly developed into commercial variety or used as immediate donors of SCR and MSR resistance breeding programs in maize.展开更多
Powdery mildew is a serious disease of wheat in China. As part of ITEC (International Triteace EST cooperation), EST (expressed sequence tags) technique was used to explore the gene expression in leaf induced by Ery...Powdery mildew is a serious disease of wheat in China. As part of ITEC (International Triteace EST cooperation), EST (expressed sequence tags) technique was used to explore the gene expression in leaf induced by Erysiphe graminis DC. A conventional cDNA library was constructed, and a total of 1 500 clones picked randomly from the library were sequenced, three hundred and eighty_seven ESTs of them were unique, which got the Accession Number in GenBank. About 49.4% ESTs showed significant similarity to functions of known sequences in GenBank. There are 196 ESTs' with functions not able to be determined, and eighty_four ESTs were demonstrated to be novel sequences. High_density dot membranes from unique clones were produced, and several disease resistance related genes were screened by differential hybridization.展开更多
Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resist...Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resistance.But strategies for expanding NLR recognition spectra[[1],[2],[3],[4],[5]]are often limited by the rapid evolution of pathogens and pests.In our recent study,we developed an innovative strategy to engineer broad-spectrum,durable and complete disease resistance in plants by remodeling autoactive NLRs into protease-activated switches[6].展开更多
Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between ...Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between rye and wheat chromosomes,not only introduced Yr9into wheat but also incorporated Sr31,Lr26,and Pm8,thereby forming a robust arsenal of disease-resistance genes(Mago et al.,2005).In China,the 1RS-1BL cultivars like "Aimengniu", "Lovrin 10".展开更多
Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide.The genomic data of several kiwifruit species have been released,providing an unprecedented opportunity for pan-genome analys...Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide.The genomic data of several kiwifruit species have been released,providing an unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter-and intra-species genetic diversity and facilitate utilization for kiwifruit breeding.Here,we generated a kiwifruit super pan-genome using 15 high-quality assemblies of eight Actinidia species.For genebased pan-genome,a total of 61,465 gene families were identified,and the softcore and dispensable genes were enriched in biological processes like response to endogenous stimulus,response to hormone and cell wall organization or biogenesis.Then,structural variations(SVs)against A.chinensis‘Donghong’were identified and then used to construct a graph-based genome.Further population-scale SVs based on resequencing data from 112 individuals of 20 species revealed extensive SVs which probably contributed to the phenotypic diversity among the Actinidia species.SV hotspot regions were found contributed to environmental adaptation.Furthermore,we systematically identified resistance gene analogs(RGAs)in the 15 assemblies and generated a pan-RGA dataset to reveal the diversity of genes potentially involved in disease resistance in Actinidia.The pan-genomic data obtained here is useful for evolutionary and functional genomic studies in Actinidia,and facilitates breeding design.展开更多
Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at leas...Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.展开更多
文摘Conserved domains e.g. nucleotide binding site (NBS) were found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogs (RGAs) have been isolated previously and were used as probes to screen a soybean (Glycine max L. Merr.) cDNA library. A full-length cDNA, KR3, was obtained by screening the library and rapid amplification of cDNA ends (RACE) method. Sequence analysis revealed that the cDNA is 2 353 bp in length and the open reading frame (ORF) codes for a polypeptide of 636 amino acids with a Toll-Interleukin-1 receptor (TIR) and a NBS domain. Sequence alignment showed that it was similar to N gene of tobacco. The phylogenetic tree analysis of R proteins with NBS from higher plants was performed. The KR3 gene has low copies in soybean genome and its expression was induced by exogenous salicylic acid (SA).
基金supported by the Key Program of the Development of Variety of Genetically Modified Organisms(Grant Nos.2009ZX08001-019B and 2008ZX08001-006)the Special Program for Rice Scientific Research of Ministry of Agriculture(Grant No.nyhyzx 07-001-006)+1 种基金the Key Support Program of Science and Technology of Jiangsu Province(Grant No.BE2008354)the Self-directed Innovation Fund of Agricultural Science and Technology in Jiangsu Province,China(Grant No.CX[09]634)
文摘A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b＇ and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region （SCAR） marker tightly linked with Stv-b＇ and a cleaved amplified polymorphic sequence （CAPS） marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.
文摘Success in conventional breeding for resistance to mycotoxin-producing or other phytopathogenic fungi is dependent on the availability of resistance gene(s) in the germplasm.Even when it is available,breeding for disease-resistant crops is very time consuming,especially in perennial crops such
基金supported by the grants from the Ministry of Science and Technology of China(No.2016YFD0101801)the Ministry of Agriculture of China(No.2014ZX08001002)the National Natural Science Foundation of China(Nos.31371590 and 31571245)
文摘Lesion mimic mutant（LMM） genes, stimulating lesion formation in the absence of pathogens, play significant roles in immune response. In this study, we characterized a rice lesion mimic mutant, lmm5,which displayed light-dependent spontaneous lesions. Additionally, lmm5 plants exhibited enhanced resistance to all of the tested races of Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae（Xoo） by increasing the expression of defense-related genes and the accumulation of hydrogen peroxide. Genetic analysis showed that the lesion mimic phenotype of lmm5 was controlled by two genes, lmm5.1 and lmm5.4, which were isolated with a map-based cloning strategy. Remarkably, LMM5.1 and LMM5.4 share a 97.4% amino acid sequence identity, and they each encode a eukaryotic translation elongation factor 1A（e EF1A）-like protein. Besides, LMM5.1 and LMM5.4 were expressed in a tissue-specific and an indicaspecific manner, respectively. In addition, high-throughput m RNA sequencing analysis confirmed that the basal immunity was constitutively activated in the lmm5 mutant. Taken together, these results suggest that the homologous e EF1A-like genes, LMM5.1 and LMM5.4, negatively affect cell death and disease resistance in rice.
基金supported by the Program for Supporting New-century Excellent Talents of Ministry of Education, China (Grant No. NCET-04-0907)the Program for Supporting Development of Innovative Research Teams of Ministry of Education, China (Grant No. IRT0453)the Applied Basic Research Program of Sichuan Province, China (Grant No. 2008JY0023-1)
文摘Resistance to rice blast of transgenic rice lines harboring rice blast resistance gene Pi-d2 transformed from three different expression vectors of pCB6.3kb, pCB5.3kb and pZH01-2.72kb were analyzed. Nine advanced-generation transgenic rice lines with Pi-d2 gene displayed various resistance to 39 rice blast strains, and the highest disease-resistant frequency reached 91.7%. Four early-generation homozygous transgenic lines with Pi-d2 gene exhibited resistance to more than 81.5% of 58 rice blast strains, showing the characteristic of wide-spectrum resistance. The transgenic embryonic calli selected by the crude toxin of rice blast fungus showed that the callus induction rate of immature embryo from transgenic rice plants decreased as the concentration of crude toxin in the culture medium increased. When the concentration of crude toxin reached 40%, the callus induction rate of immature embryo from transgenic lines was 49.3%, and that of the receptor control was 5%. The disease incidence of neck blast of the transgenic rice lines in fields under induction was 0% to 50%, indicating that the rice blast resistance of transgenic rice lines is much higher than that of the receptor control.
基金funded by the Key Research and Development Program of Shandong Province,China(2022LZGC007 and 2018GNC110036)the Natural Science Foundation of Shandong Province,China(ZR2024MC038 and ZR2020QC121)+5 种基金the Taishan Scholar Project Funding,China(tsqn201812121)the Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences,China(CXGC2024G20,CXGC2023A06,CXGC2022A03,and CXGC2022F33)the Science and Technology for People’s Livelihood Project of Qingdao,China(20-3-4-26-nsh)the China Agriculture Research System(CARS-13)the National Natural Science Foundation of China(32072107)the Major Scientific and Technological Project in Xinjiang,China(2022A02008-3).
文摘Late leaf spot disease(LLS)is one of the most important diseases that cause severe yield losses in peanut.Peanut has various sources of resistance to LLS,so the identification of resistant quantitative trait loci(QTLs)and the development of related molecular markers are of great importance for the breeding of LLS-resistant peanut.In this study,173 individual lines of a recombinant inbred line(RIL)population and the 48K SNP array for genotyping were used to construct a high-density genetic map with 1,475 bin markers and 20 linkage groups.A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map.Among them,the stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments,with the phenotypic variation explained(PVE)ranging from 15.57 to 31.09%.QTL-seq technology was also employed for a QTL analysis of LLS resistance.As a result,14 QTL loci related to LLS resistance were identified using the G prime algorithm.Notably,the physical positions of qLLS02 and qLLS03 coincided with those of qLLS.LG02 and qLLS.LG03,respectively.Gene annotation analysis within the 14 QTL intervals from QTL-seq revealed a total of 163 nucleotide-binding site-leucine-rich repeat(NBS-LRR)disease resistance genes,accounting for 22.86%of all resistance(R)genes in the peanut genome and showing a 4.26-fold enrichment with a P-value of 5.19e-57.Within the QTL region qLLS02 of the resistant parent Mi-2,there was a 5 Mb structural variation(SV)interval containing 81 NBS-LRR genes.A PCR diagnostic marker was developed,and validation data suggested that this SV might lead to gene deletion or replacement with other genes.This SV has the potential to enhance peanut resistance to LLS.The results of this study have significant implications for improving peanut breeding for LLS resistance through the development of associated molecular markers.
文摘Southern corn rust(SCR)caused by Puccinia polysora Underw and maize stalk rot caused by Pythium inflatum Matthews(MSR-2)are two destructive diseases of maize(Zea mays L.)in China.Our previous studies indicated that maize inbred line Qi319 is highly resistant to SCR but susceptible to MSR-2,while inbred line 1145 is highly resistant to MSR-2 but susceptible to SCR.The SCR resistant gene(RppQ)in Qi319 and MSR-2 resistant gene(Rpi1)in 1145 have been mapped on chromosome 10 and 4 respectively.In this research,through marker-assisted selection(MAS)with the molecular markers,bnlg1937 tightly linked to Rpi1 and phi041 tightly linked to RppQ,pyramid breeding of the two kinds of disease resistant genes were carried out from the year of 2003 to 2007.Two homozygotic inbred lines of F5 generation,DR94-1-1-1 and DR36-1-1-1 were identified.MAS result suggested DR94-1-1-1 and DR36-1-1-1 contained the two resistance genes RppQ and Rpi1.Field inoculation tests confirmed their high resistance to the two diseases.In addition,field investigation indicated that the two selected inbred lines,particularly DR94-1-1-1,had excellent agronomic traits such as plant height,ear height and yield-relating traits including ear length,ear diameter,ear weight,kernels per ear,kernels per row and kernel weight per ear.The two selected inbred lines DR94-1-1-1 and DR36-1-1-1 can either be directly developed into commercial variety or used as immediate donors of SCR and MSR resistance breeding programs in maize.
文摘Powdery mildew is a serious disease of wheat in China. As part of ITEC (International Triteace EST cooperation), EST (expressed sequence tags) technique was used to explore the gene expression in leaf induced by Erysiphe graminis DC. A conventional cDNA library was constructed, and a total of 1 500 clones picked randomly from the library were sequenced, three hundred and eighty_seven ESTs of them were unique, which got the Accession Number in GenBank. About 49.4% ESTs showed significant similarity to functions of known sequences in GenBank. There are 196 ESTs' with functions not able to be determined, and eighty_four ESTs were demonstrated to be novel sequences. High_density dot membranes from unique clones were produced, and several disease resistance related genes were screened by differential hybridization.
基金supported by the Biological Breeding-National Science and Technology Major Project(2024ZD04077).
文摘Remodeling plant intracellular nucleotide-binding leucine-rich repeat immune receptors(NLRs)to engineer synthetic disease-resistance genes has emerged as a promising approach to achieving broad-spectrum disease resistance.But strategies for expanding NLR recognition spectra[[1],[2],[3],[4],[5]]are often limited by the rapid evolution of pathogens and pests.In our recent study,we developed an innovative strategy to engineer broad-spectrum,durable and complete disease resistance in plants by remodeling autoactive NLRs into protease-activated switches[6].
基金supported by the National Natural Science Foundation of China (NSFC31991212)the National Key Research and Development Program of China (2022YFF1003303)。
文摘Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between rye and wheat chromosomes,not only introduced Yr9into wheat but also incorporated Sr31,Lr26,and Pm8,thereby forming a robust arsenal of disease-resistance genes(Mago et al.,2005).In China,the 1RS-1BL cultivars like "Aimengniu", "Lovrin 10".
基金supported by grants from the Hubei Provincial Natural Science Foundation of China(2024AFA035)the National Natural Science Foundation of China(32170395 and 32070377)the Foundation of Hubei Hongshan Laboratory(2021hszd017).
文摘Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide.The genomic data of several kiwifruit species have been released,providing an unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter-and intra-species genetic diversity and facilitate utilization for kiwifruit breeding.Here,we generated a kiwifruit super pan-genome using 15 high-quality assemblies of eight Actinidia species.For genebased pan-genome,a total of 61,465 gene families were identified,and the softcore and dispensable genes were enriched in biological processes like response to endogenous stimulus,response to hormone and cell wall organization or biogenesis.Then,structural variations(SVs)against A.chinensis‘Donghong’were identified and then used to construct a graph-based genome.Further population-scale SVs based on resequencing data from 112 individuals of 20 species revealed extensive SVs which probably contributed to the phenotypic diversity among the Actinidia species.SV hotspot regions were found contributed to environmental adaptation.Furthermore,we systematically identified resistance gene analogs(RGAs)in the 15 assemblies and generated a pan-RGA dataset to reveal the diversity of genes potentially involved in disease resistance in Actinidia.The pan-genomic data obtained here is useful for evolutionary and functional genomic studies in Actinidia,and facilitates breeding design.
基金supported by the International Science and Technology Cooperation of China(2011DFA32730)
文摘Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs(76,336 unigenes), of which 100,648 contigs(66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes(DEGs) were upregulated(246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology(GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-Co A synthase(HMGS), mevalonate kinase(MVK), and squalene epoxidase(SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.
