Arunas P. Verbyla

Sodium exclusion QTL associated with improved seedling growth in bread wheat under salinity stress

Worldwide, dryland salinity is a major limitation to crop production. Breeding for salinity tolerance could be an effective way of improving yield and yield stability on saline-sodic soils of dryland agriculture. However, this requires a good understanding of inheritance of this quantitative trait. In the present study, a doubled-haploid bread wheat population (Berkut/Krichauff) was grown in supported hydroponics to identify quantitative trait loci (QTL) associated with salinity tolerance traits commonly reported in the literature (leaf symptoms, tiller number, seedling biomass, chlorophyll content, and shoot Na+ and K+ concentrations), understand the relationships amongst these traits, and determine their genetic value for marker-assisted selection. There was considerable segregation within the population for all traits measured. With a genetic map of 527 SSR-, DArT- and gene-based markers, a total of 40 QTL were detected for all seven traits. For the first time in a cereal species, a QTL interval for Na+ exclusion (wPt-3114-wmc170) was associated with an increase (10%) in seedling biomass. Of the five QTL identified for Na+ exclusion, two were co-located with seedling biomass (2A and 6A). The 2A QTL appears to coincide with the previously reported Na+ exclusion locus in durum wheat that hosts one active HKT1;4 (Nax1) and one inactive HKT1;4 gene. Using these sequences as template for primer design enabled mapping of at least three HKT1;4 genes onto chromosome 2AL in bread wheat, suggesting that bread wheat carries more HKT1;4 gene family members than durum wheat. However, the combined effects of all Na+ exclusion loci only accounted for 18% of the variation in seedling biomass under salinity stress indicating that there were other mechanisms of salinity tolerance operative at the seedling stage in this population. Na+ and K+ accumulation appear under separate genetic control. The molecular markers wmc170 (2A) and cfd080 (6A) are expected to facilitate breeding for salinity tolerance in bread wheat, the latter being associated with seedling vigour.

MAGIC populations in crops: current status and future prospects

Key messageMAGIC populations present novel challenges and opportunities in crops due to their complex pedigree structure. They offer great potential both for dissecting genomic structure and for improving breeding populations.AbstractThe past decade has seen the rise of multiparental populations as a study design offering great advantages for genetic studies in plants. The genetic diversity of multiple parents, recombined over several generations, generates a genetic resource population with large phenotypic diversity suitable for high-resolution trait mapping. While there are many variations on the general design, this review focuses on populations where the parents have all been inter-mated, typically termed Multi-parent Advanced Generation Intercrosses (MAGIC). Such populations have already been created in model animals and plants, and are emerging in many crop species. However, there has been little consideration of the full range of factors which create novel challenges for design and analysis in these populations. We will present brief descriptions of large MAGIC crop studies currently in progress to motivate discussion of population construction, efficient experimental design, and genetic analysis in these populations. In addition, we will highlight some recent achievements and discuss the opportunities and advantages to exploit the unique structure of these resources post-QTL analysis for gene discovery.

Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL

BackgroundNext-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeline that analyses, by RNA-sequencing, multiple near-isogenic lines segregating for a targeted QTL.ResultsWe use this approach to characterize a major and widely utilized seed dormancy QTL located on chromosome 4AL. It exploits the power and mapping resolution afforded by large multi-parent mapping populations, whilst reducing complexity by using multi-allelic contrasts at the targeted QTL region. Our approach identifies two adjacent candidate genes within the QTL region belonging to the ABA-induced Wheat Plasma Membrane 19 family. One of them, PM19-A1, is highly expressed during grain maturation in dormant genotypes. The second, PM19-A2, shows changes in sequence causing several amino acid alterations between dormant and non-dormant genotypes. We confirm that PM19 genes are positive regulators of seed dormancy.ConclusionsThe efficient identification of these strong candidates demonstrates the utility of our transcriptomic pipeline for rapid QTL to gene mapping. By using this approach we are able to provide a comprehensive genetic analysis of the major source of grain dormancy in wheat. Further analysis across a diverse panel of bread and durum wheats indicates that this important dormancy QTL predates hexaploid wheat. The use of these genes by wheat breeders could assist in the elimination of pre-harvest sprouting in wheat.

Assessing the importance of subsoil constraints to yield of wheat and its implications for yield improvement

Abstract. Many of the soils in the Australian cereal belt have subsoils with chemical and physical properties that restrict root growth, which limits water use and yield. On alkaline sodic soils salinity, high pH, high available boron (B), deficiencies of zinc (Zn) and manganese (Mn) and high soil strength occur commonly and aluminium (Al) toxicity restricts root growth on acid soils. While the effects of individual subsoil constraints have been studied there is some debate about the relative importance to yield of the different soil stresses across the region. To address this issue yield variation among a set of 52 varieties of bread wheat was analysed using yield data from 233 trials conducted over 12 years. The trials were conducted in all mainland States but the majority were in South Australia and Western Australia. Each variety was characterised for its response to high B, high pH, Al toxicity, salinity, deficiencies in Zn and Mn and resistance to root lesion nematode (Pratylenchus neglectus), root growth through strong soil, seminal root angle, carbon isotope discrimination (CID) and maturity. This data was then used to examine the contribution of each trait to the genetic variation in yield at each of the 233 trials. The contribution of a specific trait to the genetic variation in yield at each site was used to infer the importance of a particular constraint to yield at that site. Of the traits linked to soil constraints, salinity tolerance, (measured by Na+ exclusion) was most often associated with genetic variation in grain yield (34% of all experiments), followed by tolerance to high Al (26%) and B tolerance (21%). Tolerance to low Zn and Mn were not consistently associated with yield variation. However, maturity was the trait that was most frequently associated with yield variation (51% of experiments), although the relative importance of early and late flowering varied among the States. Yield variation was largely associated with early flowering in Western Australia and the relative importance of late flowering increased as trials moved eastward into South Australia, Victoria and New South Wales. Narrow, rather than wide, seminal root angle was more commonly associated with high yield (25% of sites) and there was little evidence of any regional pattern in the importance of root angle. CID was important in 18% of trials with a low CID being most commonly associated with high yields. The yield advantage at sites where a trait contributed significantly to yield variation ranged from ∼15% for Na+ exclusion and B tolerance to 4% for tolerance to high pH. The analysis has provided an assessment of the relative importance of a range of traits associated with adaptation to environments where subsoil constraints are likely to affect yield and has indicated patterns in the importance and effects of these traits that may be linked to regional variation in rainfall and soils.

Use of a large multiparent wheat mapping population in genomic dissection of coleoptile and seedling growth

Identification of alleles towards the selection for improved seedling vigour is a key objective of many wheat breeding programmes. A multiparent advanced generation intercross (MAGIC) population developed from four commercial spring wheat cultivars (cvv. Baxter, Chara, Westonia and Yitpi) and containing ca. 1000 F(2) -derived, F(6:7) RILs was assessed at two contrasting soil temperatures (12 and 20 °C) for shoot length and coleoptile characteristics length and thickness. Narrow-sense heritabilities were high for coleoptile and shoot length (h(2) = 0.68-0.70), indicating a strong genetic basis for the differences among progeny. Genotypic variation was large, and distributions of genotype means were approximately Gaussian with evidence for transgressive segregation for all traits. A number of significant QTL were identified for all early growth traits, and these were commonly repeatable across the different soil temperatures. The largest negative effects on coleoptile lengths were associated with Rht-B1b (-8.2%) and Rht-D1b (-10.9%) dwarfing genes varying in the population. Reduction in coleoptile length with either gene was particularly large at the warmer soil temperature. Other large QTL for coleoptile length were identified on chromosomes 1A, 2B, 4A, 5A and 6B, but these were relatively smaller than allelic effects at the Rht-B1 and Rht-D1 loci. A large coleoptile length effect allele (a = 5.3 mm at 12 °C) was identified on chromosome 1AS despite the relatively shorter coleoptile length of the donor Yitpi. Strong, positive genetic correlations for coleoptile and shoot lengths (r(g) = 0.85-0.90) support the co-location of QTL for these traits and suggest a common physiological basis for both. The multiparent population has enabled the identification of promising shoot and coleoptile QTL despite the potential for the confounding of large effect dwarfing gene alleles present in the commercial parents. The incidence of these alleles in commercial wheat breeding programmes should facilitate their ready implementation in selection of varieties with improved establishment and early growth.

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.

The development of fire-induced damage functions for forest recreation activity in Alberta, Canada

This study develops an intertemporal fire damage function for forest recreation activity in the eastern slopes region of the Canadian Rocky Mountains. The methodology employed combined revealed-stated preference data in which the behavioral response variable was annual camping trip frequencies. Photographs were used to portray changes in stand ages and related changes in trip frequencies. The data were analysed using negative binomial count data models. Unlike previous studies employing similar methods, a random effects specification was used to develop trip demand parameters. The results suggest that fires initially decrease annual trips from ~2.56 to 1.0 after the burn. As the stand ages, the effect of the fire decreases until ~12 years after the fire when the trip frequencies recover to about their previous ‘old-growth’ levels. This function is different from others described in the literature for similar mountain ecosystems in North America.

Estimated breeding values and association mapping for persistency and total milk yield using natural cubic smoothing splines.

BackgroundFor dairy producers, a reliable description of lactation curves is a valuable tool for management and selection. From a breeding and production viewpoint, milk yield persistency and total milk yield are important traits. Understanding the genetic drivers for the phenotypic variation of both these traits could provide a means for improving these traits in commercial production.MethodsIt has been shown that Natural Cubic Smoothing Splines (NCSS) can model the features of lactation curves with greater flexibility than the traditional parametric methods. NCSS were used to model the sire effect on the lactation curves of cows. The sire solutions for persistency and total milk yield were derived using NCSS and a whole-genome approach based on a hierarchical model was developed for a large association study using single nucleotide polymorphisms (SNP).ResultsEstimated sire breeding values (EBV) for persistency and milk yield were calculated using NCSS. Persistency EBV were correlated with peak yield but not with total milk yield. Several SNP were found to be associated with both traits and these were used to identify candidate genes for further investigation.ConclusionNCSS can be used to estimate EBV for lactation persistency and total milk yield, which in turn can be used in whole-genome association studies.