In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed t...In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat （Triticum aestivum L.）. GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 （PR2） plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.展开更多
The changes of chlorophyll and malondialde-hyde (MDA) contents, plasma membrane permeability confirmed that 0.1 and 1 mmol/L sodium nitroprusside (SNP), a donor of nitric oxide (NO) in vivo, could markedly alleviate t...The changes of chlorophyll and malondialde-hyde (MDA) contents, plasma membrane permeability confirmed that 0.1 and 1 mmol/L sodium nitroprusside (SNP), a donor of nitric oxide (NO) in vivo, could markedly alleviate the oxidative damage to wheat (Triticum aestivum L.) leaves induced by 150 and 300 mmol/L NaCl treatments, respectively. Further results proved that NO significantly enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), both of which separately contributed to the delay of O2- and H2O2 accumulation in wheat leaves under saltstress. Meanwhile, the accumulation of proline was apparently accelerated. Therefore, these results suggested that NO could strongly protect wheat leaves from oxidative damage caused by salt stress.展开更多
Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage ...Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai＇an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions （QEs）. Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rhtl and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection （MAS）.展开更多
Parameters of chlorophyll fluorescence kinetics （PCFKs） under drought stress condition are generally used to characterize instincts for dehydration tolerance in wheat （Triticum aestivum L.）. Therefore, it is impor...Parameters of chlorophyll fluorescence kinetics （PCFKs） under drought stress condition are generally used to characterize instincts for dehydration tolerance in wheat （Triticum aestivum L.）. Therefore, it is important to map quantitative trait loci （QTLs） for PCFKs in wheat genetic improvement for drought tolerance. A doubled haploid （DH） population with 150 lines, derived from a cross between two common wheat varieties, Hanxuan 10 and Lumai 14, was used to analyze the correlation between PCFKs and chlorophyll content （CHIC） and to map QTLs at the grainfilling stage under conditions of both rainfed （drought stress, DS） and well-watered （WW）, respectively. QTLs for these traits were detected by QTLMapper version 1.0 based on the composite Interval mapping method of the mixed-linear model. The results showed a very significant positive correlation between Fv, Fm, Fv/Fm and Fv/Fo. The correlation coefficients were generally higher under WW than under DS. Also, there was a significant or a highly significant positive correlation between Fv, Fm, Fv/Fm, Fv/Fo and CHIC. The correlation coefficients were higher in the DS group than the WW group. A total of 14 additive QTLs （nine QTLs detected under DS and five QTLs under WW） and 25 pairs of eplstatlc QTLs （15 pairs detected under DS and 10 pairs under WW） for PCFKs were mapped on chromosomes 6A, 7A, 1B, 3B, 4D and 7D. The contributions of additive QTLs for PCFKs to phenotype variation were from 8.40% to 72.72%. Four additive QTLs （two QTLs detected under DS and WW apiece） controlling Chic were mapped on chromosomes 1A, 5A and 7A. The contributions of these QTLs for ChIC to phenotype variation were from 7.27% to 11.68%. Several QTL clusters were detected on chromosomes 1B, 7A and 7D, but no shared chromosomal regions for them were identified under different water regimes, indicating that these QTLs performed different expression patterns under rainfed and well-watered conditions.展开更多
Winter wheat-maize rotations are dominant cropping systems on the North China Plain, where recently the use of organic manure with grain crops has almost disappeared. This could reduce soil fertility and crop producti...Winter wheat-maize rotations are dominant cropping systems on the North China Plain, where recently the use of organic manure with grain crops has almost disappeared. This could reduce soil fertility and crop productivity in the long run. A 20-year field experiment was conducted to 1) assess the effect of inorganic and organic nutrient sources on yield and yield trends of both winter wheat and maize, 2) monitor the changes in soil organic matter content under continuous wheat-maize cropping with different soil fertility management schemes, and 3) identify reasons for yield trends observed in Xuzhou City, Jiangsu Province, over a 20-year period. There were eight treatments applied to both wheat and maize seasons: a control treatment (C); three inorganic fertilizers, that is, nitrogen (N), nitrogen and phosphorus (NP), and nitrogen, phosphorus and potassium (NPK); and addition of farmyard manure (FYM) to these four treatments, that is, M, MN, MNP, and MNPK. At the end of the experiment the MN, MNP, and MNPK treatments had the highest yields, about 7 t wheat ha-1 and 7.5 t maize ha-1, with each about 1 t ha-1 more than the NPK treatments. Over 20 years with FYM soil organic matter increased by 80% compared to only 10% with NPK, which explained yield increases. However, from an environmental and agronomic perspective, manure application was not a superior strategy to NPK fertilizers. If manure was to be applied, though, it would be best applied to the wheat crop, which showed a better response than maize.展开更多
Wheat biomass can be estimated using appropriate spectral vegetation indices.However,the accuracy of estimation should be further improved for on-farm crop management.Previous studies focused on developing vegetation ...Wheat biomass can be estimated using appropriate spectral vegetation indices.However,the accuracy of estimation should be further improved for on-farm crop management.Previous studies focused on developing vegetation indices,however limited research exists on modeling algorithms.The emerging Random Forest(RF) machine-learning algorithm is regarded as one of the most precise prediction methods for regression modeling.The objectives of this study were to(1) investigate the applicability of the RF regression algorithm for remotely estimating wheat biomass,(2) test the performance of the RF regression model,and(3) compare the performance of the RF algorithm with support vector regression(SVR) and artificial neural network(ANN) machine-learning algorithms for wheat biomass estimation.Single HJ-CCD images of wheat from test sites in Jiangsu province were obtained during the jointing,booting,and anthesis stages of growth.Fifteen vegetation indices were calculated based on these images.In-situ wheat above-ground dry biomass was measured during the HJ-CCD data acquisition.The results showed that the RF model produced more accurate estimates of wheat biomass than the SVR and ANN models at each stage,and its robustness is as good as SVR but better than ANN.The RF algorithm provides a useful exploratory and predictive tool for estimating wheat biomass on a large scale in Southern China.展开更多
基金Supported by the Sate Key Basic Research and Development Plan of China （2003CB715904） and the National Science Foundation for 0verseas Distinguished Young Scholar （30428003）
文摘In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion, chloroplast and nuclear genes in common wheat （Triticum aestivum L.）. GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of mitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level. The Parity Rule 2 （PR2） plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.
文摘The changes of chlorophyll and malondialde-hyde (MDA) contents, plasma membrane permeability confirmed that 0.1 and 1 mmol/L sodium nitroprusside (SNP), a donor of nitric oxide (NO) in vivo, could markedly alleviate the oxidative damage to wheat (Triticum aestivum L.) leaves induced by 150 and 300 mmol/L NaCl treatments, respectively. Further results proved that NO significantly enhanced the activities of superoxide dismutase (SOD) and catalase (CAT), both of which separately contributed to the delay of O2- and H2O2 accumulation in wheat leaves under saltstress. Meanwhile, the accumulation of proline was apparently accelerated. Therefore, these results suggested that NO could strongly protect wheat leaves from oxidative damage caused by salt stress.
基金This work was supported by the National Natural Science Foundation of China(No.30471082)the Hi-Tech Research and Development(863)Program of China(No.2006AA100101 and 2006AA10Z1E9).
文摘Quantitative trait loci （QTLs） for plant height in wheat （Triticum aestivum L.） were studied using a set of 168 doubled haploid （DH） lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai＇an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions （QEs）. Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rhtl and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection （MAS）.
文摘Parameters of chlorophyll fluorescence kinetics （PCFKs） under drought stress condition are generally used to characterize instincts for dehydration tolerance in wheat （Triticum aestivum L.）. Therefore, it is important to map quantitative trait loci （QTLs） for PCFKs in wheat genetic improvement for drought tolerance. A doubled haploid （DH） population with 150 lines, derived from a cross between two common wheat varieties, Hanxuan 10 and Lumai 14, was used to analyze the correlation between PCFKs and chlorophyll content （CHIC） and to map QTLs at the grainfilling stage under conditions of both rainfed （drought stress, DS） and well-watered （WW）, respectively. QTLs for these traits were detected by QTLMapper version 1.0 based on the composite Interval mapping method of the mixed-linear model. The results showed a very significant positive correlation between Fv, Fm, Fv/Fm and Fv/Fo. The correlation coefficients were generally higher under WW than under DS. Also, there was a significant or a highly significant positive correlation between Fv, Fm, Fv/Fm, Fv/Fo and CHIC. The correlation coefficients were higher in the DS group than the WW group. A total of 14 additive QTLs （nine QTLs detected under DS and five QTLs under WW） and 25 pairs of eplstatlc QTLs （15 pairs detected under DS and 10 pairs under WW） for PCFKs were mapped on chromosomes 6A, 7A, 1B, 3B, 4D and 7D. The contributions of additive QTLs for PCFKs to phenotype variation were from 8.40% to 72.72%. Four additive QTLs （two QTLs detected under DS and WW apiece） controlling Chic were mapped on chromosomes 1A, 5A and 7A. The contributions of these QTLs for ChIC to phenotype variation were from 7.27% to 11.68%. Several QTL clusters were detected on chromosomes 1B, 7A and 7D, but no shared chromosomal regions for them were identified under different water regimes, indicating that these QTLs performed different expression patterns under rainfed and well-watered conditions.
基金Project supported by the National Natural Science Foundation of China (No. 30030090)the National High-Tech Research and Development Program of China (863 Program) (No. 2003AA209030).
文摘Winter wheat-maize rotations are dominant cropping systems on the North China Plain, where recently the use of organic manure with grain crops has almost disappeared. This could reduce soil fertility and crop productivity in the long run. A 20-year field experiment was conducted to 1) assess the effect of inorganic and organic nutrient sources on yield and yield trends of both winter wheat and maize, 2) monitor the changes in soil organic matter content under continuous wheat-maize cropping with different soil fertility management schemes, and 3) identify reasons for yield trends observed in Xuzhou City, Jiangsu Province, over a 20-year period. There were eight treatments applied to both wheat and maize seasons: a control treatment (C); three inorganic fertilizers, that is, nitrogen (N), nitrogen and phosphorus (NP), and nitrogen, phosphorus and potassium (NPK); and addition of farmyard manure (FYM) to these four treatments, that is, M, MN, MNP, and MNPK. At the end of the experiment the MN, MNP, and MNPK treatments had the highest yields, about 7 t wheat ha-1 and 7.5 t maize ha-1, with each about 1 t ha-1 more than the NPK treatments. Over 20 years with FYM soil organic matter increased by 80% compared to only 10% with NPK, which explained yield increases. However, from an environmental and agronomic perspective, manure application was not a superior strategy to NPK fertilizers. If manure was to be applied, though, it would be best applied to the wheat crop, which showed a better response than maize.
基金supported by the National Natural Science Foundation of China(No.31271642)the Natural Science Foundation of Education Department of Jiangsu Province(No.09KJB20013,No.12KJB520018)+1 种基金the Six Talent Summit Project of Jiangsu Province(No.2011-NY039)the Science and Technology Innovation Development Foundation of Yangzhou University(No.2015CXJ022)
文摘Wheat biomass can be estimated using appropriate spectral vegetation indices.However,the accuracy of estimation should be further improved for on-farm crop management.Previous studies focused on developing vegetation indices,however limited research exists on modeling algorithms.The emerging Random Forest(RF) machine-learning algorithm is regarded as one of the most precise prediction methods for regression modeling.The objectives of this study were to(1) investigate the applicability of the RF regression algorithm for remotely estimating wheat biomass,(2) test the performance of the RF regression model,and(3) compare the performance of the RF algorithm with support vector regression(SVR) and artificial neural network(ANN) machine-learning algorithms for wheat biomass estimation.Single HJ-CCD images of wheat from test sites in Jiangsu province were obtained during the jointing,booting,and anthesis stages of growth.Fifteen vegetation indices were calculated based on these images.In-situ wheat above-ground dry biomass was measured during the HJ-CCD data acquisition.The results showed that the RF model produced more accurate estimates of wheat biomass than the SVR and ANN models at each stage,and its robustness is as good as SVR but better than ANN.The RF algorithm provides a useful exploratory and predictive tool for estimating wheat biomass on a large scale in Southern China.
