Puroindolines: the molecular genetic basis of wheat grain hardness

The variation in grain hardness is the single most important trait that determines end-use quality of wheat. Grain texture classification is based primarily on either the resistance of kernels to crushing or the particle size distribution of ground grain or flour. Recently, the molecular genetic basis of grain hardness has become known, and it is the focus of this review. The puroindoline proteins a and b form the molecular basis of wheat grain hardness or texture. When both puroindolines are in their `functional' wild state, grain texture is soft. When either one of the puroindolines is absent or altered by mutation, then the result is hard texture. In the case of durum wheat which lacks puroindolines, the texture is very hard. Puroindolines represent the molecular-genetic basis of the Hardness locus on chromosome 5DS and the soft (Ha) and hard (ha) alleles present in hexaploid bread wheat varieties. To date, seven discrete hardness alleles have been described for wheat. All involve puroindoline a or b and have been designated Pina-D1b and Pinb-D1b through Pinb-D1g. A direct role of a related protein, grain softness protein (as currently defined), in wheat grain texture has yet to be demonstrated.     

Time trends, environmental factors and genetic basis of semen traits collected in Holstein bulls under commercial conditions

The fact that results of artificial insemination (AI) are declining in highly selected dairy cattle populations has added a renewed interest to the evaluation of male fertility. Data from 42,348 ejaculates collected from 1990 to 2007 on 502 Holstein bulls were analysed in a Bayesian framework to provide estimates of the evolution of semen traits routinely collected in AI centres throughout the last decades of intense selection for production traits and estimate genetic parameters. The traits under consideration were volume (VOL), concentration (CONC), number of spermatozoa per ejaculate (NESPZ), mass motility score (MM), individual motility (IM), and post-thawing motility (PTM). The environmental factors studied were year-season and week of collection, which account for changes in environmental and technical conditions along time, age at collection, ejaculate order, time from previous collection (TPC) and time between collection and freezing (TCF) (only for PTM). Bull's inbreeding coefficient (Fi), bull's permanent environmental and additive genetic effects were also considered. The use of reduced models was evaluated using the Bayes factor. For all the systematic effects tested, strong or very strong evidence in favour of including the effect in the model was obtained, except for Fi for motility traits and TCF for PTM. No systematic time trends for environment or bull effects were observed, except for PTM, which showed an increasing environmental trend, associated with improvements in freezing-thawing protocols. Heritability estimates were moderate (0.16-0.22), except for IM, which presented a low value (0.07). Genetic correlations among motilities and between motilities and CONC were large and positive [0.38-0.87], VOL showed a negative correlation with CONC (-0.13) but with ample HPD 95%. The magnitude of heritabilities would allow an efficient selection if required and grants the use of these traits as indicators of the sperm viability component of bulls breeding soundness.     

The genetic control of milling yield, dough rheology and baking quality of wheat

Improving the end-use quality of wheat is a key target for many breeding programmes. With the exception of the relationship between glutenin alleles and some dough rheological characters, knowledge concerning the genetic control of wheat quality traits is somewhat limited. A doubled haploid population produced from a cross between two Australian cultivars ‘Trident’ and ‘Molineux’ has been used to construct a linkage map based largely on microsatellite molecular makers. ‘Molineux’ is superior to ‘Trident’ for a number of milling, dough rheology and baking quality characteristics, although by international standards ‘Trident’ would still be regarded as possessing moderately good end-use quality. This population was therefore deemed useful for investigation of wheat end-use quality. A number of significant QTL identified for dough rheological traits mapped to HMW and LMW glutenin loci on chromosomes 1A and 1B. However, QTL associated with dough strength and loaf volume were also identified on chromosome 2A and a significant QTL associated with loaf volume and crumb quality was identified on chromosome 3A. A QTL for flour protein content and milling yield was identified on chromosome 6A and a QTL associated with flour colour reported previously on chromosome 7B was confirmed in this population. The detection of loci affecting dough strength, loaf volume and flour protein content may provide fresh opportunities for the application of marker-assisted selection to improve bread-making quality.     

Comparative genetic analyses of metric traits using diallel and factorial mating designs in bread wheat

Summary For studying the inheritance of metric traits, diallel cross and factorial mating designs are commonly used. Since factorial mating design is less restrictive in crossing plans, the genetic information drawn from it was compared with that from a diallel cross. The comparison was made using graphical, genetic components and combining ability analyses for grain yield, grain weight and spike length in a field experiment of bread wheat (Triticum aestivum L.). Analyses were made on a nine parent diallel cross and a 4 × 5 factorial mating design which was sampled from the diallel cross. In general, there was a high degree of agreement between the results obtained from factorial mating design and diallel cross analyses showing thereby that the former provides almost equivalent genetic information to the latter.     

Bread matters: a national initiative to profile the genetic diversity of Australian wheat

The large and complex genome of wheat makes genetic and genomic analysis in this important species both expensive and resource intensive. The application of next-generation sequencing technologies is particularly resource intensive, with at least 17?Gbp of sequence data required to obtain minimal (1×) coverage of the genome. A similar volume of data would represent almost 40× coverage of the rice genome. Progress can be made through the establishment of consortia to produce shared genomic resources. Australian wheat genome researchers, working with Bioplatforms Australia, have collaborated in a national initiative to establish a genetic diversity dataset representing Australian wheat germplasm based on whole genome next-generation sequencing data. Here, we describe the establishment and validation of this resource which can provide a model for broader international initiatives for the analysis of large and complex genomes.     

Leaf shape: genetic controls and environmental factors

In recent years, many genes have been identified that are involved in the developmental processes of leaf morphogenesis. Here, I review the mechanisms of leaf shape control in a model plant, Arabidopsis thaliana, focusing on genes that fulfill special roles in leaf development. The lateral, two-dimensional expansion of leaf blades is highly dependent on the determination of the dorsoventrality of the primordia, a defining characteristic of leaves. Having a determinate fate is also a characteristic feature of leaves and is controlled by many factors. Lateral expansion is not only controlled by general regulators of cell cycling, but also by the multi-level regulation of meristematic activities, e.g., specific control of cell proliferation in the leaf-length direction, in leaf margins and in parenchymatous cells. In collaboration with the polarized control of leaf cell elongation, these redundant and specialized regulating systems for cell cycling in leaf lamina may realize the elegantly smooth, flat structure of leaves. The unified, flat shape of leaves is also dependent on the fine integration of cell proliferation and cell enlargement. Interestingly, while a decrease in the number of cells in leaf primordia can trigger a cell volume increase, an increase in the number of cells does not trigger a cell volume decrease. This phenomenon is termed compensation and suggests the existence of some systems for integration between cell cycling and cell enlargement in leaf primordia via cell-cell communication. The environmental adjustment of leaf expansion to light conditions and gravity is also summarized.     

Covariation in life-history traits: differential effects of diet on condition, hormones, behavior, and reproduction in genetic finch morphs

The relative contribution of genetic and environmental factors in determining variation in life-history traits is of central interest to evolutionary biologists, but the physiological mechanisms underlying these traits are still poorly understood. Here we experimentally demonstrate opposing effects of nutritional stress on immune function, endocrine physiology, parental care, and reproduction between red and black head-color morphs of the Gouldian finch (Erythrura gouldiae). Although the body condition of black morphs was largely unaffected by diet manipulation, red birds were highly sensitive to dietary changes, exhibiting considerable within-individual changes in condition and immune function. Consequently, nutritionally stressed red birds delayed breeding, produced smaller broods, and reared fewer and lower-quality foster offspring than black morphs. Differences in offspring quality were largely due to morph-specific differences in parental effort: red morphs reduced parental provisioning, whereas black morphs adaptively elevated their provisioning effort to meet the increased nutritional demands of their foster brood. Nutritionally stressed genetic morphs also exhibited divergent glucocorticoid responses. Black morphs showed reduced corticosterone-binding globulin (CBG) concentrations and increased levels of free corticosterone, whereas red morphs exhibited reduced free corticosterone levels and elevated CBG concentrations. These opposing glucocorticoid responses highlight intrinsic differences in endocrine sensitivities and plasticity between genetic morphs, which may underlie the morph-specific differences in condition, behavior, and reproduction and thus ultimately contribute to the evolution and maintenance of color polymorphism.     

Genetic control of grain yield and its related traits in bread wheat

Summary Genetic control of tiller number, grain number, grain weight, harvest index and grain yield in six generations, along with the biparentals, F₃s, F₂xparental progeny, and F₂xF₁ progeny were investigated in an intervarietal cross of bread wheat involving two highly competitive varieties, WL711 and HD 2009. The performance of F₁, B₁, B₂, F₂, × p₁, F₂ × P₂ and F₂ × F₁ progeny was midway between the parents involved with respect to all the evaluated characters. The biparental progeny excelled the mean performance of their corresponding F₂ and F₃ progeny in tiller number, seed weight and grain yield. The estimates of variance components obtained from the two models deployed were almost similar. Considerable additive genetic variance was observed for grains per spike, seed weight and grain yield while dominance variance was more pronounced for harvest index. The additive-dominance model was adequate for grains per spike and harvest index. Epistatic effects of additive × additive and additive × dominance type for tiller number and grain yield, and of additive × dominance type for seed weight were observed. The digenic epistatic model was inadequate for explaining the nature of gene action for tiller number, seed weight and grain yield. The studies indicated that non-allelic interactions should not be ignored in formulating wheat breeding programmes and that a biparental approach could be adopted as an extremely useful tool for enhancing genetic variability and the creation of transgressive segregants. The usefulness of breeding methodologies utilising a biparental approach is discussed.     

Quantifying effects of environmental and geographical factors on patterns of genetic differentiation

Elucidating the factors influencing genetic differentiation is an important task in biology, and the relative contribution from natural selection and genetic drift has long been debated. In this study, we used a regression-based approach to simultaneously estimate the quantitative contributions of environmental adaptation and isolation by distance on genetic variation in Boechera stricta, a wild relative of Arabidopsis. Patterns of discrete and continuous genetic differentiation coexist within this species. For the discrete differentiation between two major genetic groups, environment has larger contribution than geography, and we also identified a significant environment-by-geography interaction effect. Elsewhere in the species range, we found a latitudinal cline of genetic variation reflecting only isolation by distance. To further confirm the effect of environmental selection on genetic divergence, we identified the specific environmental variables predicting local genotypes in allopatric and sympatric regions. Water availability was identified as the possible cause of differential local adaptation in both geographical regions, confirming the role of environmental adaptation in driving and maintaining genetic differentiation between the two major genetic groups. In addition, the environment-by-geography interaction is further confirmed by the finding that water availability is represented by different environmental factors in the allopatric and sympatric regions. In conclusion, this study shows that geographical and environmental factors together created stronger and more discrete genetic differentiation than isolation by distance alone, which only produced a gradual, clinal pattern of genetic variation. These findings emphasize the importance of environmental selection in shaping patterns of species-wide genetic variation in the natural environment.     

Allergic asthma: influence of genetic and environmental factors

Allergic asthma is a chronic airway inflammatory disease in which exposure to allergens causes intermittent attacks of breathlessness, airway hyper-reactivity, wheezing, and coughing. Allergic asthma has been called a "syndrome" resulting from a complex interplay between genetic and environmental factors. Worldwide, >300 million individuals are affected by this disease, and in the United States alone, it is estimated that >35 million people, mostly children, suffer from asthma. Although animal models, linkage analyses, and genome-wide association studies have identified numerous candidate genes, a solid definition of allergic asthma has not yet emerged; however, such studies have contributed to our understanding of the multiple pathways to this syndrome. In contrast with animal models, in which T-helper 2 (T(H)2) cell response is the dominant feature, in human asthma, an initial exposure to allergen results in T(H)2 cell-dependent stimulation of the immune response that mediates the production of IgE and cytokines. Re-exposure to allergen then activates mast cells, which release mediators such as histamines and leukotrienes that recruit other cells, including T(H)2 cells, which mediate the inflammatory response in the lungs. In this minireview, we discuss the current understanding of how associated genetic and environmental factors increase the complexity of allergic asthma and the challenges allergic asthma poses for the development of novel approaches to effective treatment and prevention.     

The genetic analysis of age-dependent traits: modeling the character process

The extension of classical quantitative genetics to deal with function-valued characters (also called infinite-dimensional characters) such as growth curves, mortality curves, and reaction norms, was begun by Kirkpatrick and co-workers. In this theory, the analogs of variance components for single traits are covariance functions for function-valued traits. In the approach presented here, we employ a variety of parametric models for covariance functions that have a number of desirable properties: the functions (1) are positive definite, (2) can be estimated using procedures like those currently used for single traits, (3) have a small number of parameters, and (4) allow simple hypotheses to be easily tested. The methods are illustrated using data from a large experiment that examined the effects of spontaneous mutations on age-specific mortality rates in Drosophila melanogaster. Our methods are shown to work better than a standard multivariate analysis, which assumes the character value at each age is a distinct character. Advantages over existing methods that model covariance functions as a series of orthogonal polynomials are discussed.     

Molecular genetic analysis of grain protein content and flour whiteness degree using RILs in common wheat

Grain protein content (GPC) and flour whiteness degree (FWD) are important qualitative traits in common wheat. Quantitative trait locus (QTL) mapping for GPC and FWD was conducted using a set of 131 recombinant-inbred lines derived from the cross ‘Chuan 35050 × Shannong 483’ in six environmental conditions. A total of 22 putative QTLs (nine GPC and 13 FWD) were identified on 12 chromosomes with individual QTL explaining 4.5–34.0% phenotypic variation. Nine QTLs (40.9%) were detected in two or more environments. The colocated QTLs were on chromosomes 1B and 4B. Among the QTLs identified for GPC, QGpc.sdau-4A from the parent Shannong 483 represented some important favourable QTL alleles. QGpc.sdau-2A.1 and QFwd.sdau-2A.1 had a significant association with both GPC and FWD. The markers detected on top of QTL regions could be potential targets for marker-assisted selection.     

Common genetic and environmental factors among craniofacial traits in Belgian nuclear families: Comparing skeletal and soft-tissue related phenotypes

The major objective of this study was to determine the possible effects of common genetic and environmental factors among 18 craniofacial anthropometric traits, with special attention to the differences between skeletal and soft-tissue related phenotypes. The studied sample consisted of 122 nuclear families living in Brussels and included 251 males and 258 females aged from 13 to 72 years. Univariate and bivariate quantitative genetic analyses were performed using a variance components procedure implemented in SOLAR software.All phenotypes were significantly influenced by additive genetic factors with heritability estimates ranging from 0.46 (nose height) to 0.72 (external biocular breadth). Sex, age and their interactions explained 7-46% of the total phenotypic variance of the traits. Bivariate analysis revealed that several traits share a common genetic and/or environmental basis while other traits show genetic and environmental independence from one another. More and greater genetic and environmental correlations were observed among skeletal phenotypes, than among soft-tissue traits and between both categories. Apart from the tissue composition, other characteristics of the craniofacial morphology such as the orientation (e.g. heights, breadths) have shown to be important factors in determining pleiotropy and common environmental effects between some pairs of traits. In conclusion, the results confirm that overall head configuration is largely determined by additive genetic effects, and that common genetic and environmental factors affecting craniofacial size and shape are stronger for the skeletal traits than for the soft-tissue traits.     

Tocopherol biosynthesis: chemistry, regulation and effects of environmental factors

Tocopherols are lipophilic antioxidants and together with tocotrienols belong to the vitamin-E family. The four forms of tocopherols (??-, ??-, ??- and ??-tocopherols) consist of a polar chromanol ring and lipophilic prenyl chain with differences in the position and number of methyl groups. The biosynthesis of tocopherols takes place mainly in plastids of higher plants from precursors derived from two metabolic pathways: homogentisic acid, an intermediate of degradation of aromatic amino acids, and phytyldiphosphate, which arises from methylerythritol phosphate pathway. The regulation of tocopherol biosynthesis in photosynthetic organisms occurs, at least partially, at the level of key enzymes as such including p-hydroxyphenylpyruvate dioxygenase (HPPD, EC 1.13.11.27), homogentisate phytyltransferase (HPT, EC 2.5.1.-), tocopherol cyclase (TC, EC 5.4.99.-), and two methyltransferases. Tocopherol biosynthesis changes during plant development and in response toward different stresses induced by high-intensity light, drought, high salinity, heavy metals, and chilling. It is supposed that scavenging of lipid peroxy radicals and quenching of singlet oxygen are the main functions of tocopherols in photosynthetic organisms. The antioxidant action of tocopherols is related to the formation of tocopherol quinone and its following recycling or degradation. However, until now, the mechanisms of tocopherol degradation in plants have not been established in detail. This review focuses on mechanisms of tocopherols biosynthesis and its regulation in photosynthetic organisms. In addition, available information on tocopherol degradation is summarized.     

Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations

Key message

A novel high-density consensus wheat genetic map was obtained based on three related RIL populations, and the important chromosomal regions affecting yield and related traits were specified.

Abstract

A prerequisite for mapping quantitative trait locus (QTL) is to build a genetic linkage map. In this study, three recombinant inbred line populations (represented by WL, WY, and WJ) sharing one common parental line were used for map construction and subsequently for QTL detection of yield-related traits. PCR-based and diversity arrays technology markers were screened in the three populations. The integrated genetic map contains 1,127 marker loci, which span 2,976.75 cM for the whole genome, 985.93 cM for the A genome, 922.16 cM for the B genome, and 1,068.65 cM for the D genome. Phenotypic values were evaluated in four environments for populations WY and WJ, but three environments for population WL. Individual and combined phenotypic values across environments were used for QTL detection. A total of 165 putative additive QTL were identified, 22 of which showed significant additive-by-environment interaction effects. A total of 65 QTL (51.5 %) were stable across environments, and 23 of these (35.4 %) were common stable QTL that were identified in at least two populations. Notably, QTkw-5B.1, QTkw-6A.2, and QTkw-7B.1 were common major stable QTL in at least two populations, exhibiting 11.28–16.06, 5.64–18.69, and 6.76–21.16 % of the phenotypic variance, respectively. Genetic relationships between kernel dimensions and kernel weight and between yield components and yield were evaluated. Moreover, QTL or regions that commonly interact across genetic backgrounds were discussed by comparing the results of the present study with those of previous similar studies. The present study provides useful information for marker-assisted selection in breeding wheat varieties with high yield.     

Characterization of the main effects,epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice

Main effects, epistatic effects and their environmental interactions of QTLs are all important genetic components of quantitative traits. In this study, we analyzed the main effects, epistatic effects of the QTLs, and QTL by environment interactions (QEs) underlying four yield traits, using a population of 240 recombinant inbred lines from a cross between two rice varieties tested in replicated field trials. A genetic linkage map with 220 DNA marker loci was constructed. A mixed linear model approach was used to detect QTLs with main effects, QTLs involved in digenic interactions and QEs. In total, 29 QTLs of main effects, and 35 digenic interactions involving 58 loci were detected for the four traits. Thirteen QTLs with main effects showed QEs; no QE was detected for the QTLs involved in epistatic interactions. The amount of variations explained by the QTLs of main effect were larger than the QTLs involved in epistatic interactions, which in turn were larger than QEs for all four traits. This study illustrates the ability of the analysis to assess the genetic components underlying the quantitative traits, and demonstrates the relative importance of the various components as the genetic basis of yield traits in this population.     

Age-related macular degeneration: genetic and environmental factors of disease

Age-related macular degeneration (AMD) is the most common cause of visual impairment among the elderly in developed countries, and its prevalence is thus increasing as the population ages; however, treatment options remain limited because the etiology and pathogenesis of AMD are incompletely defined. Recently, much progress has been made in gene discovery and mechanistic studies, which clearly indicate that AMD involves the interaction of multiple genetic and environmental factors. The identification of genes that have a substantial impact on the risk for AMD is not only facilitating the diagnosis and screening of populations at risk but is also elucidating key molecular pathways of pathogenesis. Pharmacogenetic studies of treatment responsiveness among patients with the "wet" form of AMD are increasingly proving to be clinically relevant; pharmacogenetic approaches hold great promise for both identifying patients with the best chance for vision recovery as well as tailoring individualized therapies.     

Cardiovascular risk factors in a French-Canadian population: resolution of genetic and familial environmental effects on blood pressure by using extensive information on environmental correlates.

Genetic and environmental influences on systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial blood pressure (MBP) were examined in 371 French-Canadian families by using path analysis. Familial environment was estimated with environmental indices constructed from as many as 14 (of a pool of more than 100) correlates of blood pressure (BP). Approximately 20% of the variance in BP can be accounted for by the composite index, and the types of variables and the direction of their effects vary as a function of age and of the multivariate context. Path analysis of the family data suggests that genetic heritability is relatively high in children (from 0.49 for SBP to 0.56 for MBP) but much smaller in adults (from 0.08 for DBP to 0.18 for SBP). The proportion of variability explained by familial environment is estimated to be the same in children and adults and is much higher than reported to date (from 0.30 for SBP to 0.42 for DBP). In addition, sibships share significant nontransmitted environmental effects, and there is no evidence to suggest specific maternal effects in the aggregation of BP. Two unique findings emerge from this study. First, unlike in most earlier studies, we were able to arrive at the same parsimonious model for each of the BP variables. Second, the familial environment accounts for a substantial proportion of the variability in BP, which has been considerably underestimated in earlier studies.     

Sponge and dough bread making: genetic and phenotypic relationships with wheat quality traits

The genetic and phenotypic relationships among wheat quality predictors and sponge and dough bread making were evaluated in a population derived from a cross between an Australian cultivar ‘Chara’ and a Canadian cultivar ‘Glenlea’. The genetic correlation across sites for sponge and dough loaf volume was high; however, phenotypic correlations across sites for loaf volume were relatively low compared with rheological tests. The large difference between sites was most likely due to temperature differences during grain development reflected in a decrease in the percentage of unextractable polymeric protein and mixing time. Predictive tests (mixograph, extensograph, protein content and composition, micro-zeleny and flour viscosity) showed inconsistent and generally poor correlations with end-product performance (baking volume and slice area) at both sites, with no single parameter being effective as a predictor of end-product performance. The difference in the relationships between genetic and phenotypic correlations highlights the requirement to develop alternative methods of selection for breeders and bakers in order to maximise both genetic gain and predictive assessment of grain quality.