Harmful cyanobacterial blooms, especially Microcystis blooms, occur worldwide and draw widespread attention. The dynamics of microcystin-producing Microcystis and competition between microcystin-producing Microcystis ...Harmful cyanobacterial blooms, especially Microcystis blooms, occur worldwide and draw widespread attention. The dynamics of microcystin-producing Microcystis and competition between microcystin-producing Microcystis and non-microcystin-producing Microcystis are key to predicting and treating Microcystis blooms. Multiplex qPCR is a useful tool to assess such issues. In this study, we developed multiplex qPCR methods with newly-designed probes and primers for the microcystin-synthesis related genes mcyA and mcyE. We used seven toxic Microcystis strains and four non-toxic Microcystis strains to compare the differences in the ratios of toxic and non-toxic Microcystis in mixed cultures, which were calculated using abundances of the genes mcyA, mcyB, mcyD, mcy E and phycocyanin( PC). We also compared traditional cell counting and multiplex qPCR. Hierarchical clustering and principal component analysis indicated that mcyD was the most suitable mcy gene for quantification in laboratory experiments. mcyB abundances were always higher; we suggest that the amount of toxic Microcystis measured using mcyB might overestimate the actual percentages.展开更多
In wheat breeding, it is a difficult task to select the most suitable parents for making crosses aimed at the improvement of both grain yield and grain quality. By quantitative genetics theory,the best cross should ha...In wheat breeding, it is a difficult task to select the most suitable parents for making crosses aimed at the improvement of both grain yield and grain quality. By quantitative genetics theory,the best cross should have high progeny mean and large genetic variance, and ideally yield and quality should be less negatively or positively correlated. Usefulness is built on population mean and genetic variance, which can be used to select the best crosses or populations to achieve the breeding objective. In this study, we first compared five models(RR-BLUP, Bayes A, Bayes B, Bayes ridge regression, and Bayes LASSO) for genomic selection(GS) with respect to prediction of usefulness of a biparental cross and two criteria for parental selection, using simulation. The two parental selection criteria were usefulness and midparent genomic estimated breeding value(GEBV). Marginal differences were observed among GS models. Parental selection with usefulness resulted in higher genetic gain than midparent GEBV. In a population of 57 wheat fixed lines genotyped with 7588 selected markers, usefulness of each biparental cross was calculated to evaluate the cross performance, a key target of breeding programs aimed at developing pure lines. It was observed that progeny mean was a major determinant of usefulness, but the usefulness ratings of quality traits were more influenced by their genetic variances in the progeny population. Near-zero or positive correlations between yield and major quality traits were found in some crosses, although they were negatively correlated in the population of parents. A selection index incorporating yield, extensibility, and maximum resistance was formed as a new trait and its usefulness for selecting the crosses with the best potential to improve yield and quality simultaneously was calculated. It was shown that applying the selection index improved both yield and quality while retaining more genetic variance in the selected progenies than the individual trait selection. It was concluded that combining genomic selection with simulation allows the prediction of cross performance in simulated progenies and thereby identifies candidate parents before crosses are made in the field for pure-line breeding programs.展开更多
Zero-tillage has become increasingly attractive in rice production in China.This study was conducted to determine the feasibility of two possible improved N management practices with fewer N applications in zero-tilla...Zero-tillage has become increasingly attractive in rice production in China.This study was conducted to determine the feasibility of two possible improved N management practices with fewer N applications in zero-tillage rice:(1)two split applications of urea at75 kg N ha^(-1)at mid-tillering and 45 kg N ha^(-1)at panicle initiation(U_(120–2)),and(2)a single application of cross-linked polyacrylamide-coated urea(a slow-release fertilizer)at midtillering at a rate of 150 kg N ha^(-1)(PCU_(150–1)).Three field experiments were conducted to compare grain yield and N-use efficiency among several N treatments:a zero-N control(CK),U_(120–2),PCU_(150–1),a single application of urea at mid-tillering at a rate of 150 kg N ha^(-1)(U_(150–1)),and a commonly recommended N management practice for conventional tillage rice(three split applications of urea with 75 kg N ha^(-1)as basal,30 kg N ha^(-1)at mid-tillering,and 45 kg N ha^(-1)at panicle initiation)(U_(150–3)).Treatments with N application(U_(120–2),PCU_(150–1),U_(150–1),and U_(150–3))produced 1.08–3.16 t ha^(-1)higher grain yields than CK.Grain yields under both U_(120–2)and PCU_(150–1)were comparable to that in U_(150–3).Recovery efficiency of N(RE_N),agronomic N-use efficiency(AE_N)and partial factor productivity of applied N(PFP_N)were increased under U_(120–2)and were similar under PCU_(150–1)to those under U_(150–3).U_(150–1)showed lower grain yield,RE_N,AE_N,and PFP_Nthan U_(150–3).These results suggest that U_(150–3)can be replaced with U_(120–2)to achieve both an increase in N-use efficiency and a reduction in number of N applications and or by PCU_(150–1)to achieve a maximum reduction in number of N applications in zero-tillage rice production in China.展开更多
Cyanobacterial blooms are a global problem, with their occurrence tightly tied to nutrient loading. We cultured Microcystis aeruginosa FACHB-905 in growth medium with either inorganic(orthophosphate) or organic(β-gly...Cyanobacterial blooms are a global problem, with their occurrence tightly tied to nutrient loading. We cultured Microcystis aeruginosa FACHB-905 in growth medium with either inorganic(orthophosphate) or organic(β-glycerophosphate or polyphosphate) phosphorus and at different N:P ratios with 50:1, 30:1, 16:1, 4:1 and 1:4, serving as the phosphorus source. Fluorescence parameters were measured to determine the response of cellular responses to nutrient stress. Scanning electron microscopy(SEM) and estimates of antioxidant activity were employed to examine potential mechanisms of physical change. The results demonstrate that inorganic phosphorus was more bioavailable to M. aeruginosa relative to organic phosphorus in culture. The highest cell concentration(2.21×10~6 cells/mL), chlorophyll-a(0.39 pg/cell) and phycocyanin(1.57 pg/cell) quotas and high levels of chlorophyll fluorescence parameters( rETR, E_k, α, φ_(PSⅡ) and F_v/F_m) were obtained when phosphorus was supplied as K_2 HPO_4 at a N:P ratio of 16–30. Organic sources of phosphorus(β-glycerophosphate and polyphosphate) were bioavailable to M. aeruginosa. In addition, too concentrated orthophosphate(N:P=1:4) resulted in the oxidative stress and lipid peroxidation of cell membrane(identified by the antioxidant system activity), and the photosynthetic activity declined consequently. This study has demonstrated the effects of different phosphorus chemistries and N:P ratios on the cyanobacterial growth, photosynthetic activity and cell physiology, which could be an effective tool for predicting cyanobacterial dominance or N-deficiency in natural lakes(due to the superior ability of cyanobacteria for dissolved N and fix atmospheric N in some cases).展开更多
A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN （duplex-specific nuclease） normalization method combined with the SMART （Switching Mechanism At 5＇ end ...A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN （duplex-specific nuclease） normalization method combined with the SMART （Switching Mechanism At 5＇ end of the RNA Transcript） technique. The titer of the original cDNA library was about 1.5 × 10^6 cfu·mL^-1 and the average insertion size was about 1 kb with a high recombination rate （97%）. The 5011 high-quality expressed sequence tags （ESTs） were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally anno- tated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 （50.1%） unigenes were associated with 4082 Gene Ontology （GO） terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups （COG） functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase （RLK） genes were screened. Furthermore, a total of 94 simple sequence repeats （SSRs） were discovered, of which 20 loci were successfully amplified in C debaoensis. This study is the first EST analysis for the coralloid roots of C debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C debaoensis and related cycad species.展开更多
Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in...Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton. Results： In this study, we identified 22, 31, 55 and 60 SWEETgenes from the sequenced genomes of Gossypium orboreum, G. rairnondii, G. hirsutum and G. borbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification. Conclusion： SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEETgenes and more candidates for specific genetic modification, which will be useful in future research.展开更多
基金Supported by the National Natural Science Foundation of China(Nos.31370418,41561144008)the Jiangxi Water Science and Technology Fund(No.KT201602)the State Key Laboratory of Freshwater Ecology and Biotechnology(No.2016FBZ07)
文摘Harmful cyanobacterial blooms, especially Microcystis blooms, occur worldwide and draw widespread attention. The dynamics of microcystin-producing Microcystis and competition between microcystin-producing Microcystis and non-microcystin-producing Microcystis are key to predicting and treating Microcystis blooms. Multiplex qPCR is a useful tool to assess such issues. In this study, we developed multiplex qPCR methods with newly-designed probes and primers for the microcystin-synthesis related genes mcyA and mcyE. We used seven toxic Microcystis strains and four non-toxic Microcystis strains to compare the differences in the ratios of toxic and non-toxic Microcystis in mixed cultures, which were calculated using abundances of the genes mcyA, mcyB, mcyD, mcy E and phycocyanin( PC). We also compared traditional cell counting and multiplex qPCR. Hierarchical clustering and principal component analysis indicated that mcyD was the most suitable mcy gene for quantification in laboratory experiments. mcyB abundances were always higher; we suggest that the amount of toxic Microcystis measured using mcyB might overestimate the actual percentages.
基金supported by the National Key Basic Research Program of China(2014CB138105)the National Natural Science Foundation of China(31371623)
文摘In wheat breeding, it is a difficult task to select the most suitable parents for making crosses aimed at the improvement of both grain yield and grain quality. By quantitative genetics theory,the best cross should have high progeny mean and large genetic variance, and ideally yield and quality should be less negatively or positively correlated. Usefulness is built on population mean and genetic variance, which can be used to select the best crosses or populations to achieve the breeding objective. In this study, we first compared five models(RR-BLUP, Bayes A, Bayes B, Bayes ridge regression, and Bayes LASSO) for genomic selection(GS) with respect to prediction of usefulness of a biparental cross and two criteria for parental selection, using simulation. The two parental selection criteria were usefulness and midparent genomic estimated breeding value(GEBV). Marginal differences were observed among GS models. Parental selection with usefulness resulted in higher genetic gain than midparent GEBV. In a population of 57 wheat fixed lines genotyped with 7588 selected markers, usefulness of each biparental cross was calculated to evaluate the cross performance, a key target of breeding programs aimed at developing pure lines. It was observed that progeny mean was a major determinant of usefulness, but the usefulness ratings of quality traits were more influenced by their genetic variances in the progeny population. Near-zero or positive correlations between yield and major quality traits were found in some crosses, although they were negatively correlated in the population of parents. A selection index incorporating yield, extensibility, and maximum resistance was formed as a new trait and its usefulness for selecting the crosses with the best potential to improve yield and quality simultaneously was calculated. It was shown that applying the selection index improved both yield and quality while retaining more genetic variance in the selected progenies than the individual trait selection. It was concluded that combining genomic selection with simulation allows the prediction of cross performance in simulated progenies and thereby identifies candidate parents before crosses are made in the field for pure-line breeding programs.
基金supported by the National Natural Science Foundation of China(31301267)the China Agriculture Research System(CARS-01)
文摘Zero-tillage has become increasingly attractive in rice production in China.This study was conducted to determine the feasibility of two possible improved N management practices with fewer N applications in zero-tillage rice:(1)two split applications of urea at75 kg N ha^(-1)at mid-tillering and 45 kg N ha^(-1)at panicle initiation(U_(120–2)),and(2)a single application of cross-linked polyacrylamide-coated urea(a slow-release fertilizer)at midtillering at a rate of 150 kg N ha^(-1)(PCU_(150–1)).Three field experiments were conducted to compare grain yield and N-use efficiency among several N treatments:a zero-N control(CK),U_(120–2),PCU_(150–1),a single application of urea at mid-tillering at a rate of 150 kg N ha^(-1)(U_(150–1)),and a commonly recommended N management practice for conventional tillage rice(three split applications of urea with 75 kg N ha^(-1)as basal,30 kg N ha^(-1)at mid-tillering,and 45 kg N ha^(-1)at panicle initiation)(U_(150–3)).Treatments with N application(U_(120–2),PCU_(150–1),U_(150–1),and U_(150–3))produced 1.08–3.16 t ha^(-1)higher grain yields than CK.Grain yields under both U_(120–2)and PCU_(150–1)were comparable to that in U_(150–3).Recovery efficiency of N(RE_N),agronomic N-use efficiency(AE_N)and partial factor productivity of applied N(PFP_N)were increased under U_(120–2)and were similar under PCU_(150–1)to those under U_(150–3).U_(150–1)showed lower grain yield,RE_N,AE_N,and PFP_Nthan U_(150–3).These results suggest that U_(150–3)can be replaced with U_(120–2)to achieve both an increase in N-use efficiency and a reduction in number of N applications and or by PCU_(150–1)to achieve a maximum reduction in number of N applications in zero-tillage rice production in China.
基金Supported by the National Key R&D Program of China(No.2016YFC0502700)the Major Program of National Social Science Foundation of China(No.14ZDB140)the National Science Foundation(USA)(Nos.IOS1451528,DEB1240870)
文摘Cyanobacterial blooms are a global problem, with their occurrence tightly tied to nutrient loading. We cultured Microcystis aeruginosa FACHB-905 in growth medium with either inorganic(orthophosphate) or organic(β-glycerophosphate or polyphosphate) phosphorus and at different N:P ratios with 50:1, 30:1, 16:1, 4:1 and 1:4, serving as the phosphorus source. Fluorescence parameters were measured to determine the response of cellular responses to nutrient stress. Scanning electron microscopy(SEM) and estimates of antioxidant activity were employed to examine potential mechanisms of physical change. The results demonstrate that inorganic phosphorus was more bioavailable to M. aeruginosa relative to organic phosphorus in culture. The highest cell concentration(2.21×10~6 cells/mL), chlorophyll-a(0.39 pg/cell) and phycocyanin(1.57 pg/cell) quotas and high levels of chlorophyll fluorescence parameters( rETR, E_k, α, φ_(PSⅡ) and F_v/F_m) were obtained when phosphorus was supplied as K_2 HPO_4 at a N:P ratio of 16–30. Organic sources of phosphorus(β-glycerophosphate and polyphosphate) were bioavailable to M. aeruginosa. In addition, too concentrated orthophosphate(N:P=1:4) resulted in the oxidative stress and lipid peroxidation of cell membrane(identified by the antioxidant system activity), and the photosynthetic activity declined consequently. This study has demonstrated the effects of different phosphorus chemistries and N:P ratios on the cyanobacterial growth, photosynthetic activity and cell physiology, which could be an effective tool for predicting cyanobacterial dominance or N-deficiency in natural lakes(due to the superior ability of cyanobacteria for dissolved N and fix atmospheric N in some cases).
基金supported by the Grant(201522)from Shenzhen Urban Management
文摘A normalized full-length cDNA library was constructed from the coralloid roots of Cycas debaoensis by the DSN （duplex-specific nuclease） normalization method combined with the SMART （Switching Mechanism At 5＇ end of the RNA Transcript） technique. The titer of the original cDNA library was about 1.5 × 10^6 cfu·mL^-1 and the average insertion size was about 1 kb with a high recombination rate （97%）. The 5011 high-quality expressed sequence tags （ESTs） were obtained from 5393 randomly picked cDNA clones. Clustering and assembly of ESTs resulted in 2984 unique sequences, consisting of 618 contigs and 2366 singlets. EST sequence annotation revealed that 2333 and 1901 unigenes were functionally anno- tated in the NCBI non-redundant database and Swiss-Prot protein database, respectively. Functional analysis demonstrated that 1495 （50.1%） unigenes were associated with 4082 Gene Ontology （GO） terms. A total of 847 unigenes were grouped into 22 Cluster of Orthologous Groups （COG） functional categories. Based on the EST dataset, 22 ESTs that encoded putative receptor-like protein kinase （RLK） genes were screened. Furthermore, a total of 94 simple sequence repeats （SSRs） were discovered, of which 20 loci were successfully amplified in C debaoensis. This study is the first EST analysis for the coralloid roots of C debaoensis and provides a valuable genomic resource for novel gene discovery, gene expression and comparative genomics, conservation and management studies as well as applications in C debaoensis and related cycad species.
基金supported by the The National Key ResearchDevelopment Program of China(2016YFD0101400,2017YFD0101600)
文摘Background： The SWEET （Sugars will eventually be exported transporters） gene family plays multiple roles in plant physiological activities and development process. It participates in reproductive development and in the process of sugar transport and absorption, plant senescence and stress responses and plant-pathogen interaction. However, thecomprehensive analysis of SWEET genes has not been reported in cotton. Results： In this study, we identified 22, 31, 55 and 60 SWEETgenes from the sequenced genomes of Gossypium orboreum, G. rairnondii, G. hirsutum and G. borbadense, respectively. Phylogenetic tree analysis showed that the SWEET genes could be divided into four groups, which were further classified into 14 sub-clades. Further analysis of chromosomal location, synteny analysis and gene duplication suggested that the orthologs showed a good collinearity and segmental duplication events played a crucial role in the expansion of the family in cotton. Specific MtN3_slv domains were highly conserved between Arabidopsis and cotton by exon-intron organization and motif analysis. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of SWEET genes showed that the different genes were induced by diverse stresses. The identification and functional analysis of SWEET genes in cotton may provide more candidate genes for genetic modification. Conclusion： SWEET genes were classified into four clades in cotton. The expression patterns suggested that the duplicated genes might have experienced a functional divergence. This work provides insights into the evolution of SWEETgenes and more candidates for specific genetic modification, which will be useful in future research.
