Genetic analysis of potassium use efficiency in Brassica oleracea

Potassium (K) fertilizers are used in intensive and extensive agricultural systems to maximize production. However, there are both financial and environmental costs to K-fertilization. It is therefore important to optimize the efficiency with which K-fertilizers are used. Cultivating crops that acquire and/or utilize K more effectively can reduce the use of K-fertilizers. The aim of the present study was to determine the genetic factors affecting K utilization efficiency (KUtE), defined as the reciprocal of shoot K concentration (1/K(shoot)), and K acquisition efficiency (KUpE), defined as shoot K content, in Brassica oleracea. Genetic variation in K(shoot) was estimated using a structured diversity foundation set (DFS) of 376 accessions and in 74 commercial genotypes grown in glasshouse and field experiments that included phosphorus (P) supply as a treatment factor. Chromosomal quantitative trait loci (QTL) associated with K(shoot) and KUpE were identified using a genetic mapping population grown in the glasshouse and field. Putative QTL were tested using recurrent backcross substitution lines in the glasshouse. More than two-fold variation in K(shoot) was observed among DFS accessions grown in the glasshouse, a significant proportion of which could be attributed to genetic factors. Several QTL associated with K(shoot) were identified, which, despite a significant correlation in K(shoot) among genotypes grown in the glasshouse and field, differed between these two environments. A QTL associated with K(shoot) in glasshouse-grown plants (chromosome C7 at 62 center dot 2 cM) was confirmed using substitution lines. This QTL corresponds to a segment of arabidopsis chromosome 4 containing genes encoding the K(+) transporters AtKUP9, AtAKT2, AtKAT2 and AtTPK3. There is sufficient genetic variation in B. oleracea to breed for both KUtE and KUpE. However, as QTL associated with these traits differ between glasshouse and field environments, marker-assisted breeding programmes must consider carefully the conditions under which the crop will be grown.

Relationships between yield and mineral concentrations in potato tubers

There is concern that modern cultivars and/or agronomic practices have resulted in reduced concentrations of mineral elements essential to human nutrition in edible crops. Increased yields are often associated with reduced concentrations of mineral elements in produce, and a number of recent studies have indicated that, when grown under identical conditions, the concentrations of several mineral elements are lower in genotypes yielding more grain or shoot biomass than in older, lower-yielding genotypes. Potato is a significant crop, grown worldwide, yet few studies have investigated whether increasing yields, through agronomy or breeding, affects the concentrations of mineral elements in tubers. This article examines the hypothesis that increasing yields, either by the application of mineral fertilizers and/or by growing higher-yielding varieties, leads to decreased concentrations of mineral elements in tubers. It reports that the application of fertilizers influences tuber elemental composition in a complex manner, presumably as a consequence of soil chemistry and interactions between mineral elements within the plant, that considerable variation exists between potato genotypes in the concentrations of mineral elements in their tubers, and that, like in other crops, higher-yielding genotypes occasionally have lower concentrations of some mineral elements in their edible tissues than lower-yielding genotypes.

Bio-fortification of potato tubers using foliar zinc-fertiliser

Worldwide, many people are zinc (Zn)-deficient. Dietary Zn intake can be increased by producing crops with higher concentrations of Zn in their edible portions. This can be achieved by applying Zn-fertilisers to varieties with an increased ability to acquire Zn and to accumulate Zn in their edible portions. Potato (Solanum tuberosum L.) is an important food crop and is, therefore, a target for bio-fortification with Zn. Field trials incorporating a core collection of 23 potato genotypes, performed over 4 years (2006 – 2009), indicated significant genotypic effects on tuber Zn concentration and suggested that tuber Zn concentration was influenced by environmental effects, but also found that genotype environment (G E) interactions were not significant. Tuber Zn concentrations averaged 10.8 mg kg–1 dry matter (DM), and the ratio between the lowest and the highest varietal tuber Zn-concentration averaged 1.76. Tuber Zn concentrations could be increased by foliar Zn-fertilisation. Tuber yields of ‘Maris Piper’ were unaffected by foliar applications of < 1.08 g Zn plant–1. The relationship between tuber Zn concentration and foliar Zn application followed a saturation curve, reaching a maximum at approx. 30 mg Zn kg–1 DM at a foliar Zn application rate of 1.08 g plant–1. Despite a 40-fold increase in shoot Zn concentration compared to the unfertilised controls following foliar Zn fertilisation with 2.16 g Zn plant–1, only a doubling in tuber Zn concentration was observed. This suggests that the biofortification of tubers with Zn was restricted by the limited mobility of Zn in the phloem. A significant positive linear relationship between tuber Zn concentration and tuber N concentration supported the hypothesis of co-transport of Zn and N-compounds in the phloem.

Evidence for a genetic interaction in allergy-related responsiveness to vitamin D deficiency

Our study on white European adults was consistent with a previous study on children from largely non-white ethnic groups, suggesting that IL4 and MS4A2 genotypes modify the association between VDD and allergy risk. The risk allele in IL4 is present in nearly 90% of white Europeans, while less than a quarter are carriers in some other populations, highlighting the need to consider possible ethnic differences in allergy-related responsiveness to VDD.

Association of the PPARGC1A gene polymorphism with diabetic nephropathy in an Asian Indian population (CURES-41)

BACKGROUND: The aim of this study was to evaluate the association of polymorphisms of the peroxisome proliferator-activated receptor gamma (PPARG) gene and peroxisome proliferators-activated receptor gamma co-activator 1 alpha (PPARGC1A) gene with diabetic nephropathy (DN) in Asian Indians. METHODS: Six common polymorphisms, 3 of the PPARG gene [-1279G/A, Pro12Ala, and His478His (C/T)] and 3 of the PPARGC1A gene (Thr394Thr, Gly482Ser, and +A2962G) were studied in 571 normal glucose-tolerant (NGT) subjects, 255 type 2 diabetic (T2D) subjects without nephropathy, and 141 DN subjects. Genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing. Logistic regression analysis was performed to assess the covariables associated with DN. RESULTS: Among the 6 polymorphisms examined, only the Gly482Ser of the PPARGC1A gene was significantly associated with DN. The genotype frequency of Ser/Ser genotype of the PPARGC1A gene was 8.8% (50/571) in NGT subjects, 7.8% (20/255) in T2D subjects, and 29.8% (42/141) in DN subjects. The odds ratios (ORs) for DN for the susceptible Gly/Ser and Ser/Ser genotype after adjusting for age, sex, body mass index, and duration of diabetes were 2.14 [95% confidence interval (CI), 1.23-3.72; P = 0.007] and 8.01 (95% CI, 3.89-16.47; P < 0.001), respectively. The unadjusted OR for DN for the XA genotype of the Thr394Thr polymorphism was 1.87 (95% CI, 1.20-2.92; P = 0.006) compared to T2D subjects. However, the significance was lost (P = 0.061) when adjusted for age, sex, BMI, and duration of diabetes. The +A2962G of PPARGC1A and the 3 polymorphisms of PPARG were not associated with DN. CONCLUSION: The Gly482Ser polymorphism of the PPARGC1A gene is associated with DN in Asian Indians.

A novel association of a polymorphism in the first intron of adiponectin gene with type 2 diabetes, obesity and hypoadiponectinemia in Asian Indians

Adiponectin is an adipose tissue specific protein that is decreased in subjects with obesity and type 2 diabetes. The objective of the present study was to examine whether variants in the regulatory regions of the adiponectin gene contribute to type 2 diabetes in Asian Indians. The study comprised of 2,000 normal glucose tolerant (NGT) and 2,000 type 2 diabetic, unrelated subjects randomly selected from the Chennai Urban Rural Epidemiology Study (CURES), in southern India. Fasting serum adiponectin levels were measured by radioimmunoassay. We identified two proximal promoter SNPs (-11377C-->G and -11282T-->C), one intronic SNP (+10211T-->G) and one exonic SNP (+45T-->G) by SSCP and direct sequencing in a pilot study (n = 500). The +10211T-->G SNP alone was genotyped using PCR-RFLP in 4,000 study subjects. Logistic regression analysis revealed that subjects with TG genotype of +10211T-->G had significantly higher risk for diabetes compared to TT genotype [Odds ratio 1.28; 95% Confidence Interval (CI) 1.07-1.54; P = 0.008]. However, no association with diabetes was observed with GG genotype (P = 0.22). Stratification of the study subjects based on BMI showed that the odds ratio for obesity for the TG genotype was 1.53 (95%CI 1.3-1.8; P < 10(-7)) and that for GG genotype, 2.10 (95% CI 1.3-3.3; P = 0.002). Among NGT subjects, the mean serum adiponectin levels were significantly lower among the GG (P = 0.007) and TG (P = 0.001) genotypes compared to TT genotype. Among Asian Indians there is an association of +10211T-->G polymorphism in the first intron of the adiponectin gene with type 2 diabetes, obesity and hypoadiponectinemia.

Lack of association between serum adiponectin levels and the Pro12Ala polymorphism in Asian Indians

AIMS: The aim of the study was to investigate the association of serum adiponectin levels with the Pro12Ala polymorphism of the peroxisome proliferator activated receptor-gamma (PPARG) gene in Asian Indians. METHODS: We selected 400 diabetic subjects, 200 with the Pro12Pro genotype (100 male and 100 female) and 200 with the Pro12Ala genotype (100 male and 100 female) and 400 age- and sex-matched normal glucose tolerance subjects with similar genotype profiles from the Chennai Urban Rural Epidemiology Study. Fasting serum adiponection levels were measured using radioimmunoassay. The Pro12Ala polymorphism was genotyped by PCR-restriction fragment length polymorphism using BstUI. RESULTS: All clinical and biochemical parameters were similar in the subjects with the Pro12Pro and Pro12Ala genotypes. There was no significant difference in serum adiponectin values between subjects with the Pro12Pro and Pro12Ala genotypes (males 5.4 vs. 5.8 microg/ml, P = 0.546; females 6.9 vs. 7.2 microg/ml, P = 0.748). Adiponectin values did not differ among these two genotypes even when categorized based on their diabetes status (normal glucose tolerance Pro12Pro 7.9 vs. Pro12Ala 7.7 microg/ml, P = 0.994; diabetes Pro12Pro 4.7 vs. Pro12Ala 5.4 microg/ml, P = 0.622). CONCLUSION: The Pro12Ala polymorphism of the PPARG gene is not associated with serum adiponectin levels in Asian Indians.

Thr54 allele carriers of the Ala54Thr variant of FABP2 gene have associations with metabolic syndrome and hypertriglyceridemia in urban South Indians

The intestinal fatty acid-binding protein gene is proposed as a candidate gene for diabetes because the protein it codes is involved in fatty acid absorption and metabolism. This study investigates the association of the Ala54Thr variant of the intestinal fatty acid-binding protein gene on type 2 diabetes mellitus and other related metabolic traits in Asian Indians. Ala54Thr polymorphism was genotyped by using polymerase chain reaction-restriction fragment length polymorphism in unrelated 773 type 2 diabetic and 899 normal glucose-tolerant (NGT) subjects, randomly chosen from the Chennai Urban Rural Epidemiology Study, an ongoing population-based study in South India. The Ala54Thr polymorphism was not associated with type 2 diabetes mellitus or obesity. However, genotype-phenotype study revealed that the NGT subjects carrying the Thr54 allele had significantly higher 2-hour plasma glucose (P = .007), glycated hemoglobin (P = .004), 2-hour insulin (P = .027), and fasting low-density lipoprotein cholesterol (P = .032) levels compared with those with the Ala54 allele. Normal glucose-tolerant subjects with Ala54Thr and Thr54Thr genotypes had significantly higher fasting serum triglyceride levels (P = .003) compared with those with Ala54Ala. The subjects were stratified into those with hypertriglyceridemia (serum triglyceride levels >or=150 mg/dL) and those without. The odds ratio for hypertriglyceridemia for the individuals carrying the Ala54Thr genotype was 1.491 (95% confidence interval [CI], 1.22-1.83, P < .0001), and for those carrying the Thr54Thr genotype, it was 1.888 (95% CI, 1.34-2.67; P < .0001). Subjects were also stratified into those with metabolic syndrome (MS) and those without, according to modified Adult Treatment Panel III guidelines. The odds ratio (adjusted for age and sex) for MS for the individuals carrying the Ala54Thr genotype was 1.240 (95% CI, 1.02-1.51; P = .03), whereas for those carrying the Thr54Thr genotype, it was 1.812 (95% CI, 1.28-2.57; P = .001). Carriers of the Thr54 allele have associations with MS and hypertriglyceridemia in this urban South Indian population.

Sensory and instrumental analysis of medium and long shelf-life Charentais cantaloupe melons (Cucumis melo L.) harvested at different maturities

The flavour profiles of two genotypes of Charentais cantaloupe melons (medium shelf-life and long shelf-life), harvested at two distinct maturities (immature and mature fruit), were investigated. Dynamic headspace extraction (DHE), solid-phase extraction (SPE), gas chromatography–mass spectrometry (GC-MS) and gas chromatography–olfactometry/mass spectrometry (GC-O/MS) were used to determine volatile and semi-volatile compounds. Qualitative descriptive analysis (QDA) was used to assess the organoleptic impact of the different melons and the sensory data were correlated with the chemical analysis. There were significant, consistent and substantial differences between the mature and immature fruit for the medium shelf-life genotype, the less mature giving a green, cucumber character and lacking the sweet, fruity character of the mature fruit. However, maturity at harvest had a much smaller impact on the long shelf-life melons and fewer differences were detected. These long shelf-life melons tasted sweet, but lacked fruity flavours, instead exhibiting a musty, earthy character.

Host selection and performance of the giant willow aphid, Tuberolachnus salignus (Gmelin) - Implications for pest management

1 The recent increase in planting of selected willow clones as energy crops for biomass production has resulted in a need to understand the relationship between commonly grown, clonally propagated genotypes and their pests. 2 For the first time, we present a study of the interactions of six willow clones and a previously unconsidered pest, the giant willow aphid Tuberolachnus salignus. 3 Tuberolachnus salignus alatae displayed no preference between the clones, but there was genetic variation in resistance between the clones; Q83 was the most resistant and led to the lowest reproductive performance in the aphid 4 Maternal effects buffered changes in aphid performance. On four tested willow clones fecundity of first generation aphids on the new host clone was intermediate to that of the second generation and that of the clone used to maintain the aphids in culture. 5 In the field, patterns of aphid infestation were highly variable between years, with the duration of attack being up to four times longer in 1999. In both years there was a significant effect of willow clone on the intensity of infestation. However, whereas Orm had the lowest intensity of infestation in the first year, Dasyclados supported a lower population level than other monitored clones in the second year.

An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.

Competition and dispersal in Pseudomonas aeruginosa

Dispersal plays a crucial role in a range of evolutionary and ecological processes; hence there is strong motivation to understand its evolution. One key prediction is that the relative benefits of dispersal should be greater when dispersing away from close relatives, because in this case dispersal has the additional benefit of alleviating competition with individuals who share the same dispersal alleles. We tested this prediction for the first time using experimental populations of the opportunistic pathogen Pseudomonas aeruginosa. We measured the fitness of isogenic genotypes that differed only in their dispersal behaviors in both clonal and mixed populations. Consistent with theory, the benefit of dispersal was much higher in clonal populations, and this benefit decreased with increasing growth rate costs associated with dispersal.

Effects of water availability on free amino acids, sugars, and acrylamide-forming potential in potato

Irrigation is used frequently in potato cultivation to maximize yield, but water availability may also affect the composition of the crop, with implications for processing properties and food safety. Five varieties of potatoes, including drought-tolerant and -sensitive types, which had been grown with and without irrigation, were analyzed to show the effect of water supply on concentrations of free asparagine, other free amino acids, and sugars and on the acrylamide-forming potential of the tubers. Two varieties were also analyzed under more severe drought stress in a glasshouse. Water availability had profound effects on tuber free amino acid and sugar concentrations, and it was concluded that potato farmers should irrigate only if necessary to maintain the health and yield of the crop, because irrigation may increase the acrylamide-forming potential of potatoes. Even mild drought stress caused significant changes in composition, but these differed from those caused by more extreme drought stress. Free proline concentration, for example, increased in the field-grown potatoes of one variety from 7.02 mmol/kg with irrigation to 104.58 mmol/kg without irrigation, whereas free asparagine concentration was not affected significantly in the field but almost doubled from 132.03 to 242.26 mmol/kg in response to more severe drought stress in the glasshouse. Furthermore, the different genotypes were affected in dissimilar fashion by the same treatment, indicating that there is no single, unifying potato tuber drought stress response.

The current status of anticoagulant resistance in rats and mice in the UK

Introduction: Resistance to anticoagulants in Norway rats (Rattus norvegicus) and house mice (Mus domesticus) has been studied in the UK since the early 1960s. In no other country in the world is our understanding of resistance phenomena so extensive and profound. Almost every aspect of resistance in the key rodent target species has been examined in laboratory and field trials and results obtained by independent researchers have been published. It is the principal purpose of this document to present a short synopsis of this information. More recently, however, the development of genetical techniques has provided a definitive means of detection of resistant genotypes among pest rodent populations. Preliminary information from a number of such surveys will also be presented. Resistance in Norway rats: A total of nine different anticoagulant resistance mutations (single nucleotide polymorphisms or SNPs) are found among Norway rats in the UK. In no other country worldwide are present so many different forms of Norway rat resistance. Among these nine SNPs, five are known to confer on rats that carry them a significant degree of resistance to anticoagulant rodenticides. These mutations are: L128Q, Y139S, L120Q, Y139C and Y139F. The latter three mutations confer, to varying degrees, practical resistance to bromadiolone and difenacoum, the two second-generation anticoagulants in predominant use in the UK. It is the recommendation of RRAG that bromadiolone and difenacoum should not be used against rats carrying the L120Q, Y139C and Y139F mutations because this will promote the spread of resistance and jeopardise the long-term efficacy of anticoagulants. Brodifacoum, flocoumafen and difethialone are effective against these three genotypes but cannot presently be used because of the regulatory restriction that they can only be applied against rats that are living and feeding predominantly indoors. Our understanding of the geographical distribution of Norway rat resistance in incomplete but is rapidly increasing. In particular, the mapping of the focus of L120Q Norway rat resistance in central-southern England by DNA sequencing is well advanced. We now know that rats carrying this resistance mutation are present across a large part of the counties of Hampshire, Berkshire and Wiltshire, and the resistance spreads into Avon, Oxfordshire and Surrey. It is also found, perhaps as outlier foci, in south-west Scotland and East Sussex. L120Q is currently the most severe form of anticoagulant resistance found in Norway rats and is prevalent over a considerable part of central-southern England. A second form of advanced Norway rat resistance is conferred by the Y139C mutation. This is noteworthy because it occurs in at least four different foci that are widely geographically dispersed, namely in Dumfries and Galloway, Gloucestershire, Yorkshire and Norfolk. Once again, bromadiolone and difenacoum are not recommended for use against rats carrying this genotype and a concern of RRAG is that continued applications of resisted active substances may result in Y139C becoming more or less ubiquitous across much of the UK. Another type of advanced resistance, the Y139F mutation, is present in Kent and Sussex. This means that Norway rats, carrying some degree of resistance to bromadiolone and difenacoum, are now found from the south coast of Kent, west into the city of Bristol, to Yorkshire in the north-east and to the south-west of Scotland. This difficult situation can only deteriorate further where these three genotypes exist and resisted anticoagulants are predominantly used against them. Resistance in house mice: House mouse is not so well understood but the presence in the UK of two resistant genotypes, L128S and Y139C, is confirmed. House mice are naturally tolerant to anticoagulants and such is the nature of this tolerance, and the presence of genetical resistance, that house mice resistant to the first-generation anticoagulants are considered to be widespread in the UK. Consequently, baits containing warfarin, sodium warfarin, chlorophacinone and coumatetralyl are not approved for use against mice. This regulatory position is endorsed by RRAG. Baits containing brodifacoum, flocoumafen and difethialone are effective against house mice and may be applied in practice because house mouse infestations are predominantly indoors. There are some reports of resistance among mice in some areas to the second-generation anticoagulant bromadiolone, while difenacoum remains largely efficacious. Alternatives to anticoagulants: The use of habitat manipulation, that is the removal of harbourage, denial of the availability of food and the prevention of ingress to structures, is an essential component of sustainable rodent pest management. All are of importance in the management of resistant rodents and have the advantage of not selecting for resistant genotypes. The use of these techniques may be particularly valuable in preventing the build-up of rat infestations. However, none can be used to remove any sizeable extant rat infestation and for practical reasons their use against house mice is problematic. Few alternative chemical interventions are available in the European Union because of the removal from the market of zinc phosphide, calciferol and bromethalin. Our virtual complete reliance on the use of anticoagulants for the chemical control of rodents in the UK, and more widely in the EU, calls for improved schemes for resistance management. Of course, these might involve the use of alternatives to anticoagulant rodenticides. Also important is an increasing knowledge of the distribution of resistance mutations in rats and mice and the use of only fully effective anticoagulants against them.

Effect of high temperature and water stress on groundnuts under field conditions

Groundnuts cultivated in the semiarid tropics are often exposed to water stress (mid-season and end season) and high temperature (> 34 °C) during the critical stages of flowering and pod development. This study evaluated the effects of both water stress and high temperature under field conditions at ICRISAT, India. Treatments included two irrigations (full irrigation, 100 % of crop evapotranspiration; and water stress, 40 % of crop evapotranspiration), four temperature treatments from a combination of two sowing dates and heat tunnels with mean temperatures from sowing to maturity of 26.3° (T1), 27.3° (T2), 29.0° (T3) and 29.7 °C (T4) and two genotypes TMV2 and ICGS 11. The heat tunnels were capable of raising the day temperature by > 10 °C compared to ambient. During the 20-day high-temperature treatment at flowering, mean temperatures were 33.8° (T1), 41.6° (T2), 38.7° (T3) and 43.5°C (T4). The effects of water stress and high temperature were additive and temporary for both vegetative and pod yield, and disappeared as soon as high-temperature stress was removed. Water use efficiency was significantly affected by the main effects of temperature and cultivar and not by water stress treatments. Genotypic differences for tolerance to high temperature can be attributed to differences in flowering pattern, flower number, peg-set and harvest index. It can be inferred from this study that genotypes that are tolerant to water stress are also tolerant to high temperature under field conditions. In addition, genotypes with an ability to establish greater biomass and with a significantly greater partitioning of biomass to pod yield would be suitable for sustaining higher yields in semiarid tropics with high temperature and water stress.