Development of partial inter-specific hybrid (PIH) rice is a promising approach for exploiting inter-specific heterosis between Oryza glaberrima and Oryza sativa. In the present study, the relationship between genetic distance (GD) of parental lines and yield performance of the PIHs was assessed using partial diallel crosses between three indica male sterile lines and 14 introgression lines (ILs) with different fragments of O. glaberrima genes. Twenty two out of the 42 PIHs expressed positive heterobeltiosis (i.e., the Fl hybrid showed superiority over the better parent in the target trait) for panicle number, spikelet number, thousand grain weight and grain yield/plant. The proportion of O. glaberrima genome in the ILs ranged from 0·03 to 0·41, as revealed by 16 informative simple sequence repeat markers. Significant positive correlations were found between the proportion of O. glaberrima genome of the ILs and the GD between the ILs and the three different female parents. Heterosis of spikelet number per panicle in the hybrids was positively proportional with the O. glaberrima genome content of the parental ILs, while that of fertile grain percentage was negatively proportional to the O. glaberrima genome proportion. On average, the PIHs with higher grain yield and highest heterobeltiosis were obtained from the ILs carrying between 0·15 and 0·30 of O. glaberrima genome. The results indicated that a small proportion (<0·15) of the O. glaberrima genome in the ILs might limit heterosis expression of spikelet number per panicle, while a very large proportion (>0·30) of the O. glaberrima genome decreased the grain filling percentage in the PIHs, thus an intermediate range of O. glaberrima genome proportion should be more suitable for breeding heterotic PIHs. The exploitation of inter-specific heterosis between O. glaberrima and O. sativa has potential value for heterotic breeding in rice.

Safety evaluation of a genetically modified (GM) crop is accomplished by establishing its substantial equivalence to non-GM reference crops with a history of safe use. Testing hypotheses of equivalence rather than difference is the appropriate statistical approach. A necessary first step in this regard is to specify a reasonable equivalence criterion that includes a measure for discrepancy between the GM and reference crops as well as a regulatory threshold. The present work explored several equivalence criteria and discussed their pros and cons. Each criterion addresses one of three ordered classes of equivalence: super, conditional and marginal equivalence. Their implications were investigated over an array of parameter values estimated from a real-world dataset. Marginal equivalence was identified as adhering most closely to the concept of substantial equivalence. Because conditional equivalence logically implies marginal equivalence and is practically quantifiable from current field designs, the present work recommends conditional equivalence criteria while encouraging producers to improve their design to enable testing marginal equivalence in the future. Contrary to concerns of the ag-biotech industry, empirical evidence from recent publications indicates that a linear mixed model currently implemented by the European Food Safety Authority is adequate for assessing equivalence despite its lack of genotype-by-environment interaction terms.

Dairy farms are under pressure to increase productivity while reducing environmental impacts. Effective fertilizer management practices are critical to achieve this. In the present study the effect of timing and rate of nitrogen (N) fertilizer application on pasture production and N losses, either via direct leaching of fertilizer N or indirectly through consumption of N in pasture and subsequent excretion via dairy cow grazing, was modelled. The Agricultural Production Systems Simulator (APSIM) was first tested with experimental data from N fertilizer response experiments conducted on a well-drained soil in the Waikato region of New Zealand. The model was then used in a 20-year simulation to investigate the effect of fertilizer management on the impacts on potential N leaching losses. Year-to-year variability was assessed by incorporating 20 years of climate data into the model. Modelling indicated that N fertilization at rates of 140 and 220 kg N/ha/year, applied in four split applications and avoiding application in winter months, could increase pasture yield on average by 2·2–3·0 t dry matter (DM)/ha (25–38%). There were some significant amounts of direct leaching in some years, related to environmental conditions. The maximum loss was as high as 61 kg N/ha at an N application rate of 220 kg N/ha/year, in a year with low pasture production and high rainfall following fertilizer application. In general, however, the risk of direct N leaching from applied fertilizer was low. It seems the main effect of N fertilization is to increase the risk of indirect N leaching, due to increased N intake and excretion. The modelling indicated that the major contribution to increased indirect N leaching risk was from the extra DM grown (more urine deposited per ha). Increased N concentration in the pasture due to fertilization and the resultant extra partitioning of excretal N to urine had only a minor effect on indirect leaching losses. The exception was N fertilizer applied in late winter/early spring (July), where fertilizer N (55 kg/ha) increased pasture N concentration by c. 25%, suggesting that the N concentration in urine patch areas could increase from c. 550 to 840 kg N/ha. Further measurements are required to test the hypothesis developed from the modelling that the main effect of N fertilizer on urinary N leaching is by increasing DM production rather than increasing pasture N concentration.

Estimating crop nutrient requirements for winter oilseed rape (Brassica napus L.) is a crucial step in optimizing fertilization to enhance seed yield and improve fertilizer use efficiency. In the present paper, a database composed of 1035 on-farm observations collected from 2005 to 2010 across the major winter oilseed rape production regions in China was used to evaluate internal nutrient efficiencies (kg seed per kg nutrient in plant dry matter); then the Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS) model for winter oilseed rape was developed to describe the nutrient uptake-yield relationship of oilseed rape over a wide range of environmental conditions and predict the nutrient requirements for a target yield. After excluding observations with low harvest index values, <0·20, and excluding 0·025 of the highest and lowest internal nutrient efficiencies, the minimum and maximum internal nutrient efficiencies were estimated as 13·1 and 31·6 kg seed/kg nitrogen (N), 68·9 and 200·3 kg seed/kg phosphorus (P) and 8·9 and 31·1 kg seed/kg potassium (K), respectively. On the basis of the data settings, the balanced N, P and K uptake at different yield potential levels was calculated using a linear–parabolic–plateau curve with the QUEFTS model. Crop nutrient requirements increased linearly until the yield reached approximately 0·60–0·70 of the potential yield, and 46·0 kg N, 8·0 kg P and 57·1 kg K were found to be needed to produce 1000 kg of seed. The corresponding internal nutrient efficiencies were 21·8, 125·1 and 17·5 kg seed/kg N, P and K, respectively. However, when the target yields approached the yield potential, a decrease in internal nutrient efficiencies was detected in the model. The predicted nutrient requirement values simulated by the QUEFTS model compared well with observed values across a range of conditions. To conclude, the QUEFTS model was shown to be a practical and robust tool for assessing the crop nutrient requirements of winter oilseed rape.

Canola (Brassica napus L.) meal is widely used in animal feed as a protein source, and its quality relies on protein and amino acid content. However, little information is available regarding amino acid regulation in canola seed with nitrogen (N) application. The present study is aimed to evaluate the effect of N rate and genotype on canola seed amino acid concentrations under field conditions. A split-plot design comprising four N rates (0, 120, 240 and 360 kg N/ha) and three genotypes differing in seed protein content were used in 2010/11 and 2011/12. The results showed that increasing N rate decreased seed oil content linearly but increased seed protein content in all of the genotypes. The total amino acid concentration and absolute concentrations of individual amino acids in canola seed also improved significantly with the N rates in all of the genotypes. Regarding the proportions of amino acids, a group that included glutamic acid (Glu), proline (Pro) and arginine (Arg) dominated and occupied > 0·30 compared with other amino acids. The ratio of amino acids in this group increased by 8·3% with 360 kg N/ha compared with the control. However, the proportions of the other amino acids showed negative responses to the N rates. The results of regression analysis of the responses of individual amino acids to N rate indicated that Glu, Pro and Arg had a greater improvement potential with application of N fertilizer, as revealed by higher slopes in the linear equations compared with the other amino acids. Additionally, the concentrations of sulphur-containing amino acids, methionine and cysteine, were also a potential target for improving with N application because these are always deficient in major crops. In conclusion, N application cannot only improve seed protein content but also enhance deposition of amino acids such as Glu, Pro and Arg.

Perennial ryegrass (Lolium perenne L.) cultivars are out-breeding populations of differing phenotypes, potentially allowing for directional selection to occur after sowing. To investigate this, the morphology of individual space plants (i.e. isolated plants sown at 0·75 m row spaces) grown from tillers extracted from single-cultivar swards subjected to frequent cutting (FC) or infrequent cutting (IC) for 5 years (aged accessions) were compared with plants grown from seed (seed accessions). The study examined 12 cultivars, creating 36 ‘accessions’ of 80 plants in each. These plants were examined for 23 morphological measurements to test for and classify directional selection in perennial ryegrass swards. A high degree of separation was achieved between the 12 seed accessions, validating the discriminating power of the experiment. Changes in morphological expression of plants taken from swards indicated selection in favour of particular morphological ideotypes. This directional selection was identified in 10 of the accessions subjected to FC and eight subjected to IC management. Emergence natural height (plant undisturbed height at inflorescence emergence) and plant volume (emergence width × emergence natural height) were the characters modified most between seed and aged accessions. The magnitude of these morphological changes varied between cultivars. Glencar had the greatest number of morphological characters exhibiting directional selection under frequent cutting, whereas Greengold had the greatest number exhibiting directional selection under infrequent cutting. The plants grown from aged swards were also smaller than the seed accessions in all characters, raising the possibility that they may also be less productive. The present study showed that sward management can cause and influence directional selection of plants from within the morphological range of expression within perennial ryegrass cultivars.

The extent and severity of wheat take-all (caused by Gaeumannomyces graminis var. tritici (Ggt)) can vary considerably between growing seasons. The current study aimed to identify climatic factors associated with differing concentrations of Ggt DNA in soil and take-all disease at different stages of a sequence of wheat crops. Pre-sowing soil Ggt DNA concentrations and subsequent take-all disease in consecutive wheat crop sequences were compared across six seasons in 90 commercial cropping fields in Canterbury and Southland, New Zealand, between 2003 and 2009. Disease progress was assessed in additional fields in 2004/05 and 2005/06. While a general pattern in inoculum and disease fluctuations was evident, there were exceptions among wheat crop sequences that commenced in different years, especially for first wheat crops. In three consecutive growing seasons, there was very low inoculum increase in the first wheat crop, while increases in first wheat crops during the following three seasons was much greater. Low spring–summer rainfall was associated with low build-up of inoculum in first wheat crops. The inoculum derived from the first wheat then determined the amount of primary inoculum for the subsequent second wheat, thereby influencing the severity of take-all in that crop. Differing combinations of weather conditions during one wheat crop in a sequence and the conditions experienced by the next crop provided explanations of the severity of take-all at grain fill and the resulting post-harvest soil Ggt DNA concentrations in second wheat crops. Examples of contrasting combinations were: (a) a moderate take-all epidemic and high post-harvest inoculum that followed high rainfall during grain fill, despite low pre-sowing soil Ggt DNA concentrations; (b) severe take-all and moderate to high inoculum build-up following high pre-sowing soil Ggt DNA concentrations and non-limiting rainfall; and (c) low spring and early summer rainfall slowing epidemic development in second wheat crops, even where there were high pre-sowing soil Ggt DNA concentrations. The importance of the environmental conditions experienced during a particular growing season was also illustrated by differences between growing seasons in take-all progress in fields in the same take-all risk categories based on pre-sowing soil Ggt DNA concentrations.

Deploying resistant cultivars is an economical and essential management method in controlling viral diseases, and there are several mutational resources for tobacco. In the present study, the inoculation of tobacco plants with tobacco viruses was performed in a greenhouse from 2011 to 2014 to identify mutants resistant to tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). The high-throughput screening included seeding uniformly, transplanting in seedbeds, inoculating by cloth brushes and reporting symptoms based on disease indices. A total of 4000 second generation segregating (M2) mutants of tobacco cultivar Zhongyan100 were screened. Seeds from highly resistant mutant M2 plants were selected and planted separately. The M3 were grown and mutational stability was measured. For TMV, ten highly resistant plants were selected in the M2 generation and the mutation rate was 0·012%. In the M3 generation, there were seven mutants with hereditary high resistance and, according to the results of real-time polymerase chain reaction, the N gene was detected in all seven M3. Two hereditary immune M4 mutants, one of which was a male sterile line, were identified and evaluated in the glasshouse and in the field. For CMV, seven highly resistant plants were selected from the M2 generation and the mutation rate was 0·009%. In the M3 generation, there was one mutant with hereditary high resistance. The results indicate that hereditary mutants may be identified in the M4 generation and back-crossed to wild-type Zhongyan100 to identify anti-viral genes.

Trifoliate orange (Poncirus trifoliata (L.) Raf.) is a very useful taxon for the citrus industry since this rootstock is immune to the Citrus Tristeza virus and confers cold tolerance. Numerous trifoliate orange varieties exist but little is known regarding their behavioural variability when subjected to abiotic constraints. The diversity of 74 P. trifoliata accessions maintained in the INRA-CIRAD Citrus Germplasm Collection was investigated using simple sequence repeat markers. Two major genetic groups were clearly identified as a few homonyms, intergroup or intra-group hybrids and doubled-chromosome tetraploid forms. The Group 1 phenotype was characterized by larger flowers and leaves and smaller seeds than Group 2. Tetraploid accessions showed larger leaves and heavier seeds than all other diploid accessions, regardless of genetic classification. Eight genotypes belonging to both genetic groups, as well as two hybrids between the two groups, were selected to investigate their water deficit tolerance. Stress was applied by withdrawing irrigation for 4 weeks. Physiological parameters such as leaf stomatal conductance, quantum yield of photosystem II electron transport, soil water potential, leaf osmotic potential and transpiration rate were estimated. Some varieties, such as Rubidoux 0101033, were clearly more tolerant to water deficit than others, such as Pomeroy 0101040 and Pomeroy 0110081. Interestingly, accessions that had the highest soil water potential and were the least affected by stress belonged to genetic Group 2. Conversely, trifoliate oranges of genetic Group 1 were the least tolerant.

Relationships between milk fatty acids (MFA) and methane (CH4) emissions from dairy cattle were explored. Data from a total of 12 studies including 39 treatments were gathered in the database. Methane was expressed as daily emissions (g/d), relative to dry matter intake (g/kg), milk production (g/kg milk) and body weight (g/kg). The univariate correlations between MFA and CH4 were based on absolute means and on relative changes of each treatment compared with its corresponding control. Saturated fatty acids, odd- and branched-chain FA and long-chain poly-unsaturated FA were positively related to CH4, while cis- and trans-isomers of mono-unsaturated FA were negatively related to CH4. However, most of the coefficients of determination (R2) of these univariate regressions ranged from 0·2 to 0·7, indicating that individual MFA only explain a limited part of the variation in CH4. Significant relationships between MFA and CH4 varied depending on the unit in which emissions were expressed. Similarly, some MFA seemed more suited to predict relative changes in CH4 emissions rather than absolute amounts. The present findings contribute to the exploration of the potential of MFA as biomarkers for CH4 emissions from dairy cattle, although differences between studies in the detail of MFA analysis and hence the number of MFA reported in the current study, complicates this kind of literature survey.

An experiment was performed to determine the effect of triterpenoid saponins from powdered root of Saponaria officinalis L. (SO) on some blood metabolic parameters and hormone concentrations in dairy cows. Three dairy Polish Holstein-Friesian cows were used in the experiment in a 3 × 3 Latin Square arrangement. Animals were fed twice a day with a control diet and two experimental diets – a diet supplemented with either 440 or 660 g/d of the powdered S. officinalis root (SO1 and SO2, respectively). Each of the three experimental cycles lasted for 26 days, including a 23-day adaptation period and a 3-day sample collection period. Blood samples were collected from the jugular vein from 24th to 26th day of the experiment. Total high-density lipoproteins cholesterol (HDL) and low-density lipoproteins cholesterol (LDL), as well as triglycerides, free fatty acids (FFA) and glucose, were assayed in serum. Fatty acid composition in the blood was also analysed. Moreover, concentrations of insulin, glucagon, leptin, triiodothyronine (T3) and thyroxine (T4) were measured. It was demonstrated that total and HDL-cholesterol concentrations were significantly elevated in the blood of cows treated with experimental diets; however, LDL-cholesterol remained unchanged. No concentrations of triglycerides, FFA or glucose were influenced by saponins. Two fatty acids (C16 : 0 and C16 : 1c9) were markedly reduced when SO was used, while C18 : 1t11 decreased with increasing levels of SO. The significant increase of C20 : 4n-6 in animals treated with SO was observed. Both saponin diets resulted in a slight increase in insulin concentration and the SO2 diet evoked an emphatic rise of glucagon concentration. The concentration of T3 also increased after consumption of the experimental diet. The current study shows for the first time that triterpenoid saponins from S. officinalis can alter blood parameters in ruminants. These effects seem to result from saponin-induced changes in the rumen.

Thirty-two lambs (n = 8 per treatment) were fed a total mixed ration (TMR) formulated either with palm oil (CTRL; 34 g palm oil/kg TMR) or flaxseed (FS) (85 g FS/kg TMR) alone or enriched with quercetin (QCT, 34 g palm oil plus 2 g QCT/kg TMR; FS-QCT, 85 g FS plus 2 g QCT/kg TMR). The animals were slaughtered after being fed for at least 5 weeks with the experimental diets and samples of ruminal contents and ruminal liquid were collected for quantitative real-time polymerase chain reaction analyses of ruminal microbial species and fatty acid profile or in vitro fermentation, respectively. Results demonstrated that Butyrivibrio vaccenic acid (VA) and Butyrivibrio stearic acid (SA) producing bacteria copy numbers were decreased when FS was added to the diet of fattening lambs, which seemed to be in agreement with numerically (but not significantly) lower values for gas production, methane production and butyric acid during in vitro incubation. Ciliate protozoa were significantly enhanced by QCT, which was in accordance with numerically (but not significantly) higher values for in vitro methane production. Moreover, the modifications observed in ruminal microbial populations (Butyrivibrio and ciliate protozoa) when FS and QCT were included together (but not separately) in the diet of fattening lambs were probably related to a trend towards significantly higher values of rumenic acid (RA) in ruminal content. In conclusion, when FS and QCT were administered together in the diet of fattening lambs quantitative changes in the ruminal microbiota were observed, which might have promoted an increment of RA concentration in ruminal contents.

Although forage lipid is generally rich in polyunsaturated fatty acids (PUFA), recovery of these fatty acids (FA) in milk and meat of ruminant origin is generally low, due to microbial biohydrogenation (BH) taking place in the rumen. Since lipolysis is a prerequisite for BH, the latter process is expected to be enhanced when (conserved) forages contain lower levels of esterified FA (particularly polar lipids; PL). However, this was not observed in former studies with red clover (Trifolium pratense L.). Furthermore, red clover inclusion in the herbivore's diet was associated with decreased rumen BH as compared with other forages. Differences in plant lipase activity during wilting and ensiling has been attributed to changes in disappearance from the PL fraction, but a potential role of microbial lipases in silo has not yet been elucidated. Therefore, the aims of the present study were to assess whether BH of red clover FA is linked with PL levels of the (conserved) starting material and to clarify the possible role of in silo microbial activity on PL disappearance. In order to obtain sufficient variation in forage PL and microbial activity, laboratory-scale silages were made by wilting and ensiling damaged or undamaged red clover using molasses or formic acid as ensiling additive, while perennial ryegrass (Lolium perenne L.) was used as a control. Distribution of lipids within three lipid fractions (PL, free FA and neutral lipids) in forages was determined and BH calculated after 24 h in vitro rumen incubation. Results indicated microbial lipases in silages did not enhance FA disappearance from the PL fraction. A gradual decrease of FA in the PL fraction upon conservation was found, both in red clover and ryegrass, irrespective of the degree of damage. In red clover PL losses started from the wilting phase, while substantial PL disappearance from ryegrass only started upon ensiling. Proportions of PUFA remaining in the PL fraction after wilting and ensiling of red clover were positively correlated with PUFA BH, while this effect was not observed for ryegrass. Red clover PUFA seemed to be partially protected against ruminal BH, while disappearance of FA from the PL fraction did not seem to be hampered. Results indicated the encapsulation mechanism as a consequence of protein-bound phenol formation induced by polyphenol oxidase is still the most probable hypothesis to explain red clover's increased flow of PUFA across the rumen.