Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes (Triticum aestivum L.) Under Limited Water Availability.

The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.

Increase in coleoptile length and establishment by Lcol-A1, a genetic locus with major effect in wheat.

BACKGROUND: Good establishment is important for rapid leaf area development in wheat crops. Poor establishment results in fewer, later-emerging plants, reduced leaf area and tiller number. In addition, poorly established crops suffer from increased soil moisture loss through evaporation and greater competition from weeds while fewer spikes are produced which can reduce grain yield. By protecting the emerging first leaf, the coleoptile is critical for achieving good establishment, and its length and interaction with soil physical properties determine the ability of a cultivar to emerge from depth. RESULTS: Here we characterise a locus on chromosome 1AS, that increases coleoptile length in wheat, which we designate as Lcol-A1. We identified Lcol-A1 by bulked-segregant analysis and used a Halberd-derived population to fine map the gene to a 2 cM region, equivalent to 7 Mb on the IWGSC genome reference sequence of Chinese Spring (RefSeqv1.0). By sowing recently released cultivars and near-isogenic lines in the field at both conventional and deep sowing depths, we confirmed that Locl-A1 was associated with increased emergence from depth in the presence and absence of conventional dwarfing genes. Flanking markers IWB58229 and IWA710 were developed to assist breeders to select for long coleoptile wheats. CONCLUSIONS: Increased coleoptile length is sought in many global wheat production areas to improve crop emergence. The identification of the gene Lcol-A1, together with tools to allow wheat breeders to track the gene, will enable improvements to be made for this important trait.

Rhizosheaths on wheat grown in acid soils: phosphorus acquisition efficiency and genetic control.

Rhizosheaths comprise soil bound to roots, and in wheat (Triticum aestivum L.) rhizosheath size correlates with root hair length. The aims of this study were to determine the effect that a large rhizosheath has on the phosphorus (P) acquisition by wheat and to investigate the genetic control of rhizosheath size in wheat grown on acid soil.Near-isogenic wheat lines differing in rhizosheath size were evaluated on two acid soils. The soils were fertilized with mineral nutrients and included treatments with either low or high P. The same soils were treated with CaCO3 to raise the pH and detoxify Al(3+) Genotypic differences in rhizosheath size were apparent only when soil pH was low and Al(3+) was present. On acid soils, a large rhizosheath increased shoot biomass compared with a small rhizosheath regardless of P supply. At low P supply, increased shoot biomass could be attributed to a greater uptake of soil P, but at high P supply the increased biomass was due to some other factor. Generation means analysis indicated that rhizosheath size on acid soil was controlled by multiple, additive loci. Subsequently, a quantitative trait loci (QTL) analysis of an F6 population of recombinant inbred lines identified five major loci contributing to the phenotype together accounting for over 60% of the total genetic variance. One locus on chromosome 1D accounted for 34% of the genotypic variation. Genetic control of rhizosheath size appears to be relatively simple and markers based on the QTL provide valuable tools for marker assisted breeding.

Early vigour improves phosphate uptake in wheat.

Quantitative trait loci (QTLs) for shoot biomass were identified in wheat grown on a soil high in total phosphorus (P) but low in plant-available P. The two populations screened included recombinant inbred lines (RILs) from Chuan-Mai 18/Vigour 18 and doubled-haploid lines from Kukri/Janz. Glasshouse-grown plants were harvested at the five-leaf stage. Seven QTLs for shoot biomass were identified in the RILs, with the largest on chromosome 7A accounting for 7.4% of the phenotypic variance. RILs from the upper tail had larger embryos than RILs from the lower tail. Tail lines were then grown in non-limiting P and the results indicated that early vigour and the capacity to access P contributed to the initial distribution. The influence of early vigour on P nutrition was examined further with advanced vigour lines (AVLs). The AVLs accumulated more shoot biomass, maintained lower shoot P concentrations, and showed greater P-acquisition efficiency than Vigour 18. Nine QTLs for shoot biomass were identified in the Kukri/Janz population. Two on chromosomes 4B and 4D accounted for 24.8% of the variance. Candidates underlying these QTLs are the Rht genes. We confirmed the influence of these genes using near-isogenic lines with different Rht alleles. The dwarf and semi-dwarf alleles affected shoot and root biomass at high and low P but not the efficiency of P acquisition. We conclude that early vigour contributed to the distributions in both populations. Early vigour can increase plant growth at suboptimal P and some sources can also improve the efficiency of P acquisition.

Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments.

Seedling roots enable plant establishment. Their small phenotypes are measured routinely. Adult root systems are relevant to yield and efficiency, but phenotyping is challenging. Root length exceeds the volume of most pots. Field studies measure partial adult root systems through coring or use seedling roots as adult surrogates. Here, we phenotyped 79 diverse lines of the small grass model Brachypodium distachyon to adults in 50-cm-long tubes of soil with irrigation; a subset of 16 lines was droughted. Variation was large (total biomass, ×8; total root length [TRL], ×10; and root mass ratio, ×6), repeatable, and attributable to genetic factors (heritabilities ranged from approximately 50% for root growth to 82% for partitioning phenotypes). Lines were dissected into seed-borne tissues (stem and primary seminal axile roots) and stem-borne tissues (tillers and coleoptile and leaf node axile roots) plus branch roots. All lines developed one seminal root that varied, with branch roots, from 31% to 90% of TRL in the well-watered condition. With drought, 100% of TRL was seminal, regardless of line because nodal roots were almost always inhibited in drying topsoil. Irrigation stimulated nodal roots depending on genotype. Shoot size and tillers correlated positively with roots with irrigation, but partitioning depended on genotype and was plastic with drought. Adult root systems of B. distachyon have genetic variation to exploit to increase cereal yields through genes associated with partitioning among roots and their responsiveness to irrigation. Whole-plant phenotypes could enhance gain for droughted environments because root and shoot traits are coselected.

The influence of shoot and root size on nitrogen uptake in wheat is affected by nitrate affinity in the roots during early growth.

Shoot and root system size influences N uptake in wheat (Triticum aestivum L.). Previously, we showed that four wheat genotypes with different biomass had similar N uptake at tillering. In the present study, we determined whether the similarity in N uptake in these genotypes was associated with genotypic differences in the affinity of the root system for NO3- uptake. Kinetic parameters of NO3- uptake were measured in hydroponic seedlings of vigorous and nonvigorous early growth wheat genotypes by exposing them to solutions with differing concentrations of K15NO3 for 15min. In the low concentration range, the high-affinity transport system of the nonvigorous cultivar Janz showed a higher maximum influx rate than the three vigorous lines and a higher affinity than two of the three vigorous lines. At high NO3- concentrations, where the low-affinity transport system was functional, the responsiveness of NO3- uptake to external concentrations was greater in Janz than in the vigorous lines. Both the high- and low-affinity transport systems were inducible. The genotypic variation in the kinetic parameters of NO3- uptake was large enough to offset differences in morphological traits and should be considered in efforts to improve N uptake. In a field trial, the growth and N uptake performance of the four wheat genotypes was investigated over the winter-spring growing season (June-November of 2010). The field trial showed that although early N uptake was disproportionately large relative to biomass accumulation, the differences in uptake at tillering can be changed by subsequent patterns of uptake.

Wheat genotypes with high early vigour accumulate more nitrogen and have higher photosynthetic nitrogen use efficiency during early growth.

Genotypic differences in early growth and nitrogen (N) uptake among 24 wheat (Triticum aestivum L.) genotypes were assessed in a field trial. At late tillering, large genetic variation was observed for shoot biomass (23-56gm-2 ground area) and N uptake (1.1-1.8gm-2 ground area). A strong correlation between aboveground biomass and N uptake was observed. Variation around this relationship was also found, with some genotypes having similar N uptake but large differences in aboveground biomass. A controlled environment experiment was conducted to investigate the underlying mechanisms for this variation in aboveground biomass using three vigorous genotypes (38-19, 92-11 and CV97) and a non-vigorous commercial cultivar (Janz). Vigorous genotypes had lower specific leaf N in the youngest fully expanded leaf than Janz. However, there was no difference in chlorophyll content, maximum Rubisco activity or the rate of electron transport per unit area. This suggests that Janz invested more N in non-photosynthetic components than the vigorous lines, which could explain the higher photosynthetic N use efficiency of the vigorous genotypes. The results suggest that the utilisation of wheat genotypes with high early vigour could improve the efficiency of N use for biomass production in addition to improving N uptake during early growth.

Genotypic variation in the accumulation of water soluble carbohydrates in wheat.

Water-soluble carbohydrates (WSC) stored in the stems and leaf sheaths of winter cereals provide an important source of assimilate for remobilisation during grain-filling. Consequently, WSC are a major contributor to wheat grain yield and grain size in all environments but especially where photosynthesis is compromised as occurs where water is limiting. Breeding programs targeting greater WSC should provide improved varieties with greater and more stable yields in stress environments. To facilitate selection for WSC, genetic and genomic approaches are being used to determine the genetic basis of - and define DNA probes for - marker-aided selection for this important drought-adaptive trait. Empirical studies have identified both WSC concentration and content to be under complex genetic control of many genes. Quantitative trait loci (QTL) for WSC have been identified in several wheat populations with individual QTL explaining small amounts of phenotypic variation, typically of less than 20%. Many of these QTL are common across multiple, genetically-unrelated wheat populations. Evaluation of gene expression in high and low WSC wheat progeny lines from a well characterised wheat population has identified significant differences in expression of genes from different gene categories. For example, high WSC progeny lines have higher levels of expression of genes involved in carbohydrate metabolism and lower levels of expression of genes involved in cell wall and amino acid metabolism than low WSC lines. Genetic mapping reveals several candidate genes co-locating with QTL for WSC. In addition, expression QTL (eQTL) for selected candidate genes co-locate with WSC QTL; co-location of the genes and eQTL with WSC QTL make these genes stronger candidate genes for the WSC trait.

A wheat genotype developed for rapid leaf growth copes well with the physical and biological constraints of unploughed soil.

Conventional wheat (Triticum aestivum L.) cultivars grow slowly in unploughed soil because of physical and biological constraints. Here a conventional cultivar (Janz) is compared with a novel experimental line (Vigour 18), bred for high leaf vigour, to explore the hypothesis that a vigorous wheat grows better in unploughed soil. Roots of both genotypes in unploughed soil were three times more distorted with 30% shorter apices and 60% shorter expansion zones than roots in ploughed soil, because of voids between blocky peds and packed sand particles that impeded root apices. More than half the root length contacted dead, remnant roots. Vigour 18 roots grew 39% faster, were thicker and distorted less than Janz roots in unploughed soil, but developed similarly in ploughed soil. Vigour 18 shoots grew 64% faster in unploughed soil, but 15% faster in ploughed soil. Fumigation of unploughed soil improved the growth of Janz only. We suggest that faster root growth, different exudates promoting a more beneficial rhizosphere microflora, or modified shoot responses are possible mechanisms to explain Vigour 18's superior growth. Vigorous genotypes may present a new opportunity for increased productivity with conservation farming.