Association mapping based on linkage disequilibrium (LD) is a promising tool to identify genes responsible for quantitative variations underlying complex traits. The present paper presents an association mapping panel consisting of 172 upland cotton (Gossypium hirsutum L.) accessions. The panel was phenotyped for five cotton plant architecture traits across multiple environments and genotyped using 386 simple sequence repeat (SSR) markers. Of these markers, 101 polymorphic SSR markers were used in the final analysis. There were abundant phenotypic variations within this germplasm panel and a total of 267 alleles ranging from two to seven per locus were identified in all collections. The threshold of LD decay was set to r2 = 0·1 and 0·2, and the genome-wide LD extended up to about 13–14 and 6–7 cM, respectively, providing the potential for association mapping of agronomically important traits in upland cotton. A total of 66 marker–trait associations were detected based on a mixed linear model, of which 35 were found in more than one environment. The favourable alleles from 35 marker loci can be used in marker-assisted selection of target traits. Both the synergistic alleles and the negative alleles for some traits, especially plant height and fruit branch angle, can be utilized in plant architecture breeding programmes according to specific breeding objectives.

Rice (Oryza sativa L.) is one of the most important cereal crops in the world and a potentially important source of zinc (Zn) in the diet. The improvement of Zn content of rice is a global challenge with implications for both rice production and human health. The objective of the present study was to identify the effects of nitrogen (N) fertilizer rates and Zn application methods on Zn content of rice by evaluating rice production on native soils with different Zn availabilities in 2010/11. The results indicated that Zn application increased rice grain yield and Zn content in grains compared with the control; however, this effect was also affected by the native soil Zn availability, N fertilizer rate and Zn fertilizer application method. The native soil Zn status was the dominant factor influencing grain yield and grain Zn content in response to Zn fertilizer application. Grain Zn content ranged from 19·74 to 26·93 mg/kg under the different Zn statuses. The results also indicated that Zn application method has a significant influence on grain yield. Application of Zn fertilizer to the soil was more effective than the foliar spray on rice grain yield; however, the foliar spray resulted in a greater increase in grain Zn content when compared with soil application. Grain Zn content was affected by application method and displayed the following general trend: soil application + foliar spray > foliar spray > soil application. The experiments investigating the effect of N fertilizer rate combined with Zn application method showed a clear increase in both grain yield and Zn content as the N fertilizer level increased from 200 to 300 kg/ha. In addition, the results also indicated that N content and accumulation increased in all plant tissues, which suggests that Zn application might influence the uptake and translocation of N in rice plants. These results suggest that soil application in addition to a foliar spray of Zn should be considered as an important strategy to increase grain yield and grain Zn content of rice grown in soils with low background levels of Zn-associated diethylene triamine pentaacetate acid. Moreover, this process could be further strengthened by a high N application rate. In conclusion, these results demonstrate the potential of optimizing nutrient management using Zn fertilizer to obtain higher grain yields and higher grain Zn content in fields with low native Zn status.

Crop canopy characteristics and management factors that affect the canopy structure can influence crop competitive ability against weeds. The goal of the current study was to understand the interaction between nitrogen (N) fertilizer rate and redroot pigweed (Amaranthus retroflexus) density on common bean (Phaseolus vulgaris L.) canopy characteristics and N assimilation. Experiments were conducted to determine the growth responses of two bean genotypes with contrasting growth habits to different N fertilizer rates under no, low and high redroot pigweed pressure. Nitrogen was applied at rates of 0, 50, 100 and 200 kg/ha for a semi-erect variety and 0, 35, 70 and 140 kg/ha for an erect bean variety. Leaf area index (LAI), leaf area duration (LAD), leaf chlorophyll, N assimilation and N assimilation rate for both bean growth habits increased with N application rate at no and low weed density. The negative effect of redroot pigweed competition on LAI, LAD, N assimilation and N assimilation rate increased with redroot pigweed density, and with N application rate for the high weed density. Stepwise multiple regression analysis showed that N assimilation and chlorophyll concentration accounted for 0·73–0·87, overall, of the variation in yield loss due to weed competition. It is concluded that greater N assimilation in the semi-erect growth habit compared with the erect growth habit is the cause of its higher competitive ability against the weed, as it improves the effective canopy traits that confer potential for resource pre-emption.

Understanding the effect of genetic factors controlling flowering time is essential to fine-tune crop development to each target environment and to maximize yield. A set of 35 durum wheat genotypes of spring growth-habit involving different allelic combinations at Ppd-A1 and Ppd-B1 genes was grown for 2 years at four sites at latitudes ranging from 19°N to 41°N. The emergence-flowering period was reduced from north to south. The frequency in the collection of the insensitive allele GS-105 at Ppd-A1 was greater (34%) than that of allele GS-100 (20%). Genotypes that flowered earlier due to the presence of alleles causing photoperiod insensitivity extended their grain-filling period, but less than the shortening in flowering time. The effect of the allele conferring photoperiod sensitivity at Ppd-A1 was stronger than that at Ppd-B1 (Ppd-A1b > Ppd-B1b). The effect of photoperiod insensitivity alleles was classified as GS-100 > GS-105 > Ppd-B1a. The phenotypic expression of alleles conferring photoperiod insensitivity at Ppd-A1 increased at sites with average day length from emergence to flowering lower than 12 h. An interaction effect was found between Ppd-A1 and Ppd-B1. Differences between allelic combinations in flowering time accounted for c. 66% of the variability induced by the genotype effect, with the remaining 34% being explained by genes controlling earliness per se. The shortest flowering time across sites corresponded to the allelic combination GS-100/Ppd-B1a, which reduced flowering time by 11 days irrespective of the Ppd-A1b/Ppd-B1b combination. The current study marks a further step towards elucidation of the phenotypic expression of genes regulating photoperiod sensitivity and their interaction with the environment.

Saline-sodic soils are widely distributed in the western Songnen Plain of Northeast China and planting rice has been found to be an effective and feasible approach for improving saline-sodic soil and increasing food production. Assessment of the effectiveness and sustainability of this method requires monitoring of the changes in soil salinity and nutrient content. The objective of the current study was to investigate the changes of soil salinity and nitrogen (N) contents over 1, 3, 6 and 9 years of cultivation, four application rates of N (N0: no N, N1: 100 kg N/ha, N2: 200 kg N/ha and N3: 300 kg N/ha) and two irrigation water types: ground water irrigation (GWI) and river water irrigation (RWI). Salinity and N contents of soil and water samples were analysed before planting and after harvest throughout the experiments. Soil pH and electrical conductivity (EC), especially in the surface layer of 0–40 cm depth, decreased with years of cultivation with both GWI and RWI, while soil inorganic N and total N contents increased. Moreover, with increasing N application rates, soil inorganic N and total N contents increased significantly in the 0–20 cm soil layer. Increasing N application had little effect on soil pH and EC. Reclaiming and planting rice promoted desalination of the surface and formation of a fertile tillage layer in saline-sodic paddy fields. In terms of irrigation and drainage in saline-sodic paddy fields, both soil salinity and N contents increased. Soil total salinity increased annually by 34 and 12·8 kg/ha, and inorganic N contents increased annually by 9 and 13·5 kg/ha with GWI and RWI, respectively. Therefore, comprehensive agricultural practices should be adopted for improving and cropping rice in saline-sodic paddy fields.

Breeding for resistance to Striga hermonthica Del. (Benth) and tolerance to drought has been a major strategy to improve maize (Zea mays L.) production and productivity in West and Central Africa during the last three decades. The three decades consisted of three breeding periods or eras based on the germplasm and methodologies used; that is, 1988–2000, 2001–06 and 2007–11. A total of 50 early maturing cultivars, combining Striga resistance with drought tolerance were developed, including 15, 16 and 19 cultivars for the three periods, respectively. Although the cultivars were not selected intentionally for low-nitrogen (N) tolerance, it was hypothesized that tolerance to low-N had been significantly improved while selecting for drought tolerance and Striga resistance. This hypothesis was tested by evaluating the 50 cultivars in 2010 and 2011 in Nigeria at Mokwa and Ile-Ife under both low-N (30 kg N/ha) and high-N (90 kg N/ha) levels. Under low-N conditions, grain yield improved from 2280 kg/ha during the first period to 2610 kg/ha during the third period, an increase of 165 kg/ha per period with r2 of 0·99. Under high-N, yield increased from 3200 to 3650 kg/ha, an increase of 225 kg/ha and r2 of 0·93. Relative gain per period was 30 kg/ha for the two N rates with r2 values of 0·99 and 0·94 respectively. Grain yield performance of the 50 cultivars under low-N conditions adequately predicted their performance under high-N. Selection for Striga resistance and drought tolerance in early maturing maize populations enhanced low-N tolerance in the maize cultivars derived from the populations. The improvement was higher in later than earlier breeding periods.

The aim of the current research was to analyse the effect of four water irrigation treatments (1·20, 1·00, 0·80 and 0·60 of the crop water requirement) on the relationships among leaf area index (LAI), radiation use efficiency (RUE) and green canopy cover in a potato crop (Solanum tuberosum L.) cv. Agria. The crop was established in a commercial plot irrigated with a centre pivot system in Southeast Spain during the 2011 and 2012 seasons. In both seasons, the highest light absorption efficiency values occurred at the LAI value of 3 that corresponded to maximum ground cover. With regard to the irrigation treatment, a significant linear response was indicated for RUE. The results indicate that the 1·00 irrigation treatment produced the best result, improving water resources management without reducing crop yield.

In agricultural production systems, nitrogen (N) losses to the environment can occur through nitrous oxide (N2O) emissions and nitrate (NO3−) leaching. The objectives of the present study were to evaluate: (1) if urine excreted by non-lactating dairy cows pulse-dosed with dicyandiamide (DCD) and applied to lysimeters reduced N2O-N emissions and NO3−-N leaching on two soil types; and (2) if urine + DCD would increase herbage production over winter. Lysimeters were used to measure N2O emissions and NO3-N leaching. The soils used were a free-draining acid brown earth of sandy loam to loam texture (termed free-draining) and a poorly drained silt loam gley (termed poorly drained). Grass plots were established on the free-draining soil to measure herbage production. The N loading rate of the urine + DCD was 508 kg N/ha and the urine without DCD (urine only) was 451 kg N/ha. Total NO3−-N leaching losses from the free-draining and poorly draining soils were reduced from 100 and 81 kg NO3−-N/ha on the urine-only treatment, respectively, to 9 and 11·6 kg NO3−-N/ha on the urine + DCD treatment, respectively. Total N2O-N emissions from the free-draining and poorly drained soils were reduced significantly from 13·6 and 12·1 kg N2O-N/ha on the urine-only treatment, respectively, to 2·23 and 5·24 kg N2O-N/ha on the urine + DCD treatment, respectively. Applying urine with DCD to pastures inhibited the nitrification process for up to 56 days after treatment application. In the current experiment, there was no significant effect on spring herbage production when urine + DCD was applied to grass plots. Therefore, feeding DCD to dairy cows to apply DCD directly in urine patches was shown to be an effective mitigation strategy to reduce NO3−-N leaching and N2O-N emissions but did not appear to increase spring herbage production.

To support tropical maize (Zea mays L.) breeding efforts, the current work aimed to assess harvest index (HI) in modern hybrids and determine the effect of different planting densities on grain yield and HI under well-fertilized (HN) and nitrogen (N) deficient conditions. Harvest index and grain yield of 34 hybrids on average reached 0·42 and 7·06 t/ha (five environments), indicating a large potential for improvement in HI relative to temperate hybrids. Ear weight (r = 0·88), HI (r = 0·78) and shoot dry weight (r = 0·68) were strongly associated with grain yield. In the second experiment, seven hybrids were evaluated at planting densities of 5, 7, 9 and 11 plants/m2 under HN (six environments) and N deficient (LN) conditions (four environments) to assess the effect of planting density on grain yield and HI. Grain yield increased by 40·4 and 21·8% under HN and LN conditions when planting density was increased relative to the lowest planting density. Harvest index increased from 0·42 at 5 plants/m2 to 0·45 at 11 plants/m2 under HN conditions and decreased from 0·44 at 5 plants/m2 to 0·42 at 9 plants/m2 under LN conditions. Harvest index was maximized at planting densities of 8·33 plants/m2 and 5·30 plants/m2 under HN and LN conditions, respectively, while grain yield was maximized at 9·93 plants/m2 and 7·89/m2. Optimal planting density maximizing both HI and grain yield were higher than planting densities currently used in tropical germplasm. It can be concluded that productivity in tropical maize could be increased both under intensive (+40·4%) and lower-input management (+21·8%) by increasing planting densities above those currently used in smallholder agriculture in Latin America and Sub-Saharan Africa, in environments targeted by the International Maize and Wheat Improvement Center.

Identifying and applying the optimum fertilizer nitrogen (N) rate is a permanent challenge for farmers. Prediction of fertilizer N requirement, based on crop chlorophyll measurements (CMs), relies on a strong relationship between fertilizer N supply and leaf chlorophyll concentration at a given crop growth stage. A methodological approach is described, aiming to develop an algorithm that uses CM inputs to derive the economically optimum fertilizer N rate for top-dressing, without using a reference plot for data normalization. The method was tested on maize (Zea mays L. cvar Jabali) at experimental and farmer sites in the central (‘Bajío’) region of Mexico over 3 years (2010–12). Increasing fertilizer N supply at planting significantly influenced chlorophyll concentration at the seventh unfolded maize leaf stage (GS 17 on the Zadoks scale). Maize grain yields increased with increasing total fertilizer N supply and fitted quadratic models, which allowed economically optimum fertilizer N rates (Nopt) to be calculated. The Nopt ranged from 160 to 300 kg N/ha and corresponding grain yields ranged from 7·7 to 14 t/ha. Grouped data analysis (sites–years) confirmed a highly significant relationship between the Nopt and the chlorophyll concentration at GS 17, which could be described by a linear model: Nopt = 513·3–0·58 × CM. This model predicted the top-dressing Nopt within a fertilizer N management regime adapted to local maize cropping systems and led to similar grain yields across test sites compared with the same parameters calculated based on grain yield response trials. The current approach is variety-specific, so development of so-called correction factors accounting for variety-related differences in chlorophyll concentration is described. The results demonstrated the feasibility of the proposed algorithms to support decision-making on the optimum fertilizer N rate to apply in maize production systems with one top-dressing application.

The control of Campylobacter in poultry is considered a public health priority and some intervention strategies have been implemented in Denmark. Nonetheless, Campylobacter infection in poultry can still be considerable particularly during the summer when the most promising Campylobacter control strategy seems to be the use of fly screens. The use of cost-effective vaccines against Campylobacter is also desirable. In order to control Campylobacter, poultry producers need to make crucial decisions under conditions of uncertainty. With the aim of assisting poultry producers in decision making regarding Campylobacter control strategies, the objective of the present study was to produce a decision support system that integrated knowledge and used a Bayesian approach to handle uncertainty. This decision support system integrated epidemiological data, microbiological considerations, financial information and potential control strategies (the use of fly screens and hypothetical vaccines). In conclusion, results from model and sensitivity analyses indicated that the financial variables (cost–benefit functions) and the effectiveness of the different control strategies drove the results.

The mixing of pigs unacquainted with each other in commercial pig production is a standard procedure which leads to agonistic interactions with a wide range of individual pig behaviour. Hence, the aims of the present study were to assess the heritabilities of agonistic behaviour and to estimate correlations between three different age groups (weaned pigs n = 1111, growing pigs n = 446 and breeding gilts n = 279). The behavioural observation analysis included a period of 17 h directly after mixing as weaned pigs, growing pigs and breeding gilts (220 days of age) whereby the following agonistic traits were observed: number of fights (NF), duration of fights (DF), initiated fights (IF), received fights (RF), fights won (FW) and fights lost (FL). The behaviour of the weaned and growing pigs was significantly influenced by cross-fostering, their weight at mixing and litter attributes. Cross-fostered animals showed fewer agonistic interactions as weaned pigs and as growing pigs than non-cross-fostered animals. The influence of weight revealed that heavier pigs had a higher NF score at weaning and as growing pigs. The random litter effect explained up to 0·08 of the total variance in weaned and 0·04 in growing pigs, whereby this could partly be explained by litter size. Pigs from larger litters tended to have more agonistic interactions. The heritabilities of the recorded traits were at a low to medium level but similar between the age groups. There were high correlations between NF and all other traits in weaned pigs. The trait IF showed that the more fights a pig initiated, the more it won. This was also found for growing pigs and breeding gilts. The relationships between the age groups provided no uniform trend. The phenotypic correlations were low and the genetic correlations varied widely, partly due to the small sample size.

The B-biotype of Bemisia tabaci (Homoptera: Aleyrodidae) has become extremely resistant to commonly used insecticides in China. To further explore the mechanisms of resistance to diafenthiuron, the diafenthiuron induction profiles of carboxylesterase (COE1), glutathione S-transferase (GST) and seven cytochrome P450 genes in both resistant (R-DfWf) and susceptible (S-Lab) strains were characterized. The detoxification genes GST, CYP6CX4, CYP6DW3, CYP6DZ6 and CYP9F, which are known to be constitutively over-expressed in the R-DfWf strain, were significantly upregulated in R-DfWf and S-Lab strains exposed to diafenthiuron at LC50 compared with their levels in strains treated with distilled water (controls); however, CYP6CX1, another detoxification gene, was not upregulated. The upregulation was more pronounced in the R-DfWf strain than in the S-Lab strain exposed to different concentrations of diafenthiuron (LC10 or LC50). Interestingly, COE1, CYP6CM1 and CYP6A, which are not constitutively over-expressed in the R-DfWf strain, were all significantly upregulated after exposure to diafenthiuron. Similarly, significant differences in the expression of these detoxification genes, with the exception of CYP6CM1 in the S-Lab strain, were also observed after exposure to diafenthiuron. However, the induction of CYP6A and COE1 was more pronounced in the S-Lab strain than in the R-DfWf strain after treatment with diafenthiuron at both concentrations, indicating that diafenthiuron induction of CYP6CM1 is specific to the R-DfWf strain, while diafenthiuron induction of the other genes is common to both the R-DfWf and S-Lab strains. These results demonstrate that multiple detoxification genes are co-upregulated in the R-DfWf strain through both constitutive over-expression and induction mechanisms. This knowledge will be useful for rational selection of insecticides for use in resistance management and control of this species.