Allan R. Rattey

Genomic regions for canopy temperature and their genetic association with stomatal conductance and grain yield in wheat

Stomata are the site of CO2 exchange for water in a leaf. Variation in stomatal control offers promise in genetic improvement of transpiration and photosynthetic rates to improve wheat performance. However, techniques for estimating stomatal conductance (SC) are slow, limiting potential for efficient measurement and genetic modification of this trait. Genotypic variation in canopy temperature (CT) and leaf porosity (LP), as surrogates for SC, were assessed in three wheat mapping populations grown under well-watered conditions. The range and resulting genetic variance were large but not always repeatable across days and years for CT and LP alike. Leaf-to-leaf variation was large for LP, reducing heritability to near zero on a single-leaf basis. Replication across dates and years increased line-mean heritability to ~75% for both CT and LP. Across sampling dates and populations, CT showed a large, additive genetic correlation with LP (rg=-0.67 to -0.83) as expected. Genetic increases in pre-flowering CT were associated with reduced final plant height and both increased harvest index and grain yield but were uncorrelated with aerial biomass. In contrast, post-flowering, cooler canopies were associated with greater aerial biomass and increased grain number and yield. A multi-environment QTL analysis identified up to 16 and 15 genomic regions for CT and LP, respectively, across all three populations. Several of the LP and CT QTL co-located with known QTL for plant height and phenological development and intervals for many of the CT and LP quantitative trait loci (QTL) overlapped, supporting a common genetic basis for the two traits. Notably, both Rht-B1b and Rht-D1b dwarfing alleles were paradoxically positive for LP and CT (i.e. semi-dwarfs had higher stomatal conductance but warmer canopies) highlighting the issue of translation from leaf to canopy in screening for greater transpiration. The strong requirement for repeated assessment of SC suggests the more rapid CT assessment may be of greater value for indirect screening of high or low SC among large numbers of early-generation breeding lines. However, account must be taken of variation in development and canopy architecture when interpreting performance and selecting breeding lines on the basis of CT.

A multisite managed environment facility for targeted trait and germplasm phenotyping

Field evaluation of germplasm for performance under water and heat stress is challenging. Field environments are variable and unpredictable, and genotype×environment interactions are difficult to interpret if environments are not well characterised. Numerous traits, genes and quantitative trait loci have been proposed for improving performance but few have been used in variety development. This reflects the limited capacity of commercial breeding companies to screen for these traits and the absence of validation in field environments relevant to breeding companies, and because little is known about the economic benefit of selecting one particular trait over another. The value of the proposed traits or genes is commonly not demonstrated in genetic backgrounds of value to breeding companies. To overcome this disconnection between physiological trait breeding and uptake by breeding companies, three field sites representing the main environment types encountered across the Australian wheatbelt were selected to form a set of managed environment facilities (MEFs). Each MEF manages soil moisture stress through irrigation, and the effects of heat stress through variable sowing dates. Field trials are monitored continuously for weather variables and changes in soil water and canopy temperature in selected probe genotypes, which aids in decisions guiding irrigation scheduling and sampling times. Protocols have been standardised for an essential core set of measurements so that phenotyping yield and other traits are consistent across sites and seasons. MEFs enable assessment of a large number of traits across multiple genetic backgrounds in relevant environments, determine relative trait value, and facilitate delivery of promising germplasm and high value traits into commercial breeding programs.

Variation for and relationships among biomass and grain yield component traits conferring improved yield and grain weight in an elite wheat population grown in variable yield environments

Grain yield and kernel size (grain weight) are important industry traits for wheat in the water-limited environments of the north-eastern wheatbelt of Australia. These, and underpinning morphological and physiological traits, were evaluated in a population of recombinant inbred lines from the elite CIMMYT cross Seri/Babax, segregating for the presence of the rye translocation (T1BL.1RS). The population was examined to determine the variation among lines, relationships among traits, the extent of line × environment interactions, potential efficiency of direct and indirect selection, and to identify trait combinations that are associated with higher grain yield and grain weight. Transgressive segregation was observed for all traits, and line × environment interaction effects were frequently larger than line main effects. Across six environments ranging in yield from 202 to 660 g/m2, the T1BL.1RS wheat-rye translocation had a positive effect on grain weight (+3.4%) but resulted in decreased grain number per m2 (–6.5%) and grain yield (–3.1%). Realised selection responses indicated that broad adaptation was best achieved by selection for mean performance across the range of target environments. However, specific adaptation for performance in high- or low-yielding environments was best detected by direct selection in those types of environments. A group of broadly adapted Seri/Babax lines exceeded the mean of five cultivars grown commercially in the north-eastern wheatbelt by 8% for grain yield and 17% for grain weight. These Seri/Babax lines with both high grain yield and grain weight were associated with a combination of several traits: earlier flowering, reduced tillering, a greater proportion of tillers that produce grain-bearing spikes at maturity, high water-soluble carbohydrate stem reserves at anthesis, a higher proportion of competent florets at anthesis to maximise grains per spikelet leading to a high harvest index, and possibly a greater capacity to extract soil water. These results suggest a suitable ideotype for breeding high-yielding wheat cultivars with high grain weight adapted to environments with hotter, drier conditions during the post-anthesis period.

Developmental and growth controls of tillering and water-soluble carbohydrate accumulation in contrasting wheat (Triticum aestivum L.) genotypes: can we dissect them?

In wheat, tillering and water-soluble carbohydrates (WSCs) in the stem are potential traits for adaptation to different environments and are of interest as targets for selective breeding. This study investigated the observation that a high stem WSC concentration (WSCc) is often related to low tillering. The proposition tested was that stem WSC accumulation is plant density dependent and could be an emergent property of tillering, whether driven by genotype or by environment. A small subset of recombinant inbred lines (RILs) contrasting for tillering was grown at different plant densities or on different sowing dates in multiple field experiments. Both tillering and WSCc were highly influenced by the environment, with a smaller, distinct genotypic component; the genotype×environment range covered 350–750 stems m–2 and 25–210mg g–1 WSCc. Stem WSCc was inversely related to stem number m–2, but genotypic rankings for stem WSCc persisted when RILs were compared at similar stem density. Low tillering–high WSCc RILs had similar leaf area index, larger individual leaves, and stems with larger internode cross-section and wall area when compared with high tillering–low WSCc RILs. The maximum number of stems per plant was positively associated with growth and relative growth rate per plant, tillering rate and duration, and also, in some treatments, with leaf appearance rate and final leaf number. A common threshold of the red:far red ratio (0.39–0.44; standard error of the difference=0.055) coincided with the maximum stem number per plant across genotypes and plant densities, and could be effectively used in crop simulation modelling as a ‘cut-off’ rule for tillering. The relationship between tillering, WSCc, and their component traits, as well as the possible implications for crop simulation and breeding, is discussed.

Can citrate efflux from roots improve phosphorus uptake by plants? Testing the hypothesis with near‐isogenic lines of wheat

Phosphorus (P) deficiency in some plant species triggers the release of organic anions such as citrate and malate from roots. These anions are widely suggested to enhance the availability of phosphate for plant uptake by mobilizing sparingly-soluble forms in the soil. Carazinho is an old wheat (Triticum aestivum) cultivar from Brazil, which secretes citrate constitutively from its root apices, and here we show that it also produces relatively more biomass on soils with low P availability than two recent Australian cultivars that lack citrate efflux. To test whether citrate efflux explains this phenotype, we generated two sets of near-isogenic lines that differ in citrate efflux and compared their biomass production in different soil types and with different P treatments in glasshouse experiments and field trials. Citrate efflux improved relative biomass production in two of six glasshouse trials but only at the lowest P treatments where growth was most severely limited by P availability. Furthermore, citrate efflux provided no consistent advantage for biomass production or yield in multiple field trials. Theoretical modeling indicates that the effectiveness of citrate efflux in mobilizing soil P is greater as the volume of soil into which it diffuses increases. As efflux from these wheat plants is restricted to the root apices, the potential for citrate to mobilize sufficient P to increase shoot biomass may be limited. We conclude that Carazinho has other attributes that contribute to its comparatively good performance in low-P soils.

Plot size matters: interference from intergenotypic competition in plant phenotyping studies

Genetic and physiological studies often comprise genotypes diverse in vigour, size and flowering time. This can make the phenotyping of complex traits challenging, particularly those associated with canopy development, biomass and yield, as the environment of one genotype can be influenced by a neighbouring genotype. Limited seed and space may encourage field assessment in single, spaced rows or in small, unbordered plots, whereas the convenience of a controlled environment or greenhouse makes pot studies tempting. However, the relevance of such growing conditions to commercial field-grown crops is unclear and often doubtful. Competition for water, light and nutrients necessary for canopy growth will be variable where immediate neighbours are genetically different, particularly under stress conditions, where competition for resources and influence on productivity is greatest. Small hills and rod-rows maximise the potential for intergenotypic competition that is not relevant to a crops performance in monocultures. Response to resource availability will typically vary among diverse genotypes to alter genotype ranking and reduce heritability for all growth-related traits, with the possible exception of harvest index. Validation of pot experiments to performance in canopies in the field is essential, whereas the planting of multirow plots and the simple exclusion of plot borders at harvest will increase experimental precision and confidence in genotype performance in target environments.

Use of dry matter content as a rapid and low-cost estimate for ranking genotypic differences in water-soluble carbohydrate concentrations in the stem and leaf sheath of Triticum aestivum

Stem water-soluble carbohydrates (WSC) are an important source of temporary carbohydrate reserve in cool-season cereals. Genotypic variation in stem WSC concentration in wheat at anthesis is often positively associated with grain weight and yield in water-limited environments. In this study we have examined the relationship between dry matter content (DMC, dry weight per unit of fresh weight) and WSC concentration in field-grown bread wheat. Strong correlations (r = 0.92–0.95) were observed between DMC and WSC concentration in the stem and leaf sheath from the top two or three internodes of recombinant inbred lines from a cross between Seri M82 and Babax, at anthesis or 1 week after anthesis, in several field experiments. This strong correlation was also observed in diverse genotypes grown under rainfed or irrigated conditions. DMC and WSC concentration were also positively correlated in the whole above-ground biomass of wheat at anthesis (r = 0.74–0.91). Measurement of stem and leaf sheath DMC and WSC concentration in a small number of samples would allow the rapid prediction of WSC concentrations in a large number of field samples with reasonable accuracy, as demonstrated in a small dataset in this study. These data indicate that DMC can serve cereal breeding as a rapid and low-cost selection tool for genotypic ranking of WSC concentrations in breeding populations.

Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems

High levels of water-soluble carbohydrates (WSC) provide an important source of stored assimilate for grain filling in wheat. To better understand the interaction between carbohydrate metabolism and other metabolic processes associated with the WSC trait, a genome-wide expression analysis was performed using eight field-grown lines from the high and low phenotypic tails of a wheat population segregating for WSC and the Affymetrix wheat genome array. The 259 differentially expressed probe sets could be assigned to 26 functional category bins, as defined using MapMan software. There were major differences in the categories to which the differentially expressed probe sets were assigned; for example, probe sets upregulated in high relative to low WSC lines were assigned to category bins such as amino acid metabolism, protein degradation and transport and to be involved in starch synthesis-related processes (carbohydrate metabolism bin), whereas downregulated probe sets were assigned to cell wall-related bins, amino acid synthesis and stress and were involved in sucrose breakdown. Using the set of differentially expressed genes as input, chemical–protein network analyses demonstrated a linkage between starch and N metabolism via pyridoxal phosphate. Twelve C and N metabolism-related genes were selected for analysis of their expression response to varying N and water treatments in the field in the four high and four low WSC progeny lines; the two nitrogen/amino acid metabolism genes demonstrated a consistent negative association between their level of expression and level of WSC. Our results suggest that the assimilation of nitrogen into amino acids is an important factor that influences the levels of WSC in the stems of field-grown wheat.

Preferential retention of chromosome regions in derived synthetic wheat lines: a source of novel alleles for wheat improvement

Abstract. Synthetic hexaploid wheats (SHWs) and their synthetic derivative lines (SDLs) are being used as a means of introducing novel genetic variation into bread wheat (BW). Phenotypic information for days to flowering, height, grain weight and grain yield was collected from multiple environments for three SDL families, each with ∼50 lines, and their elite BW parents. In general, the SDLs were earlier flowering and taller with larger grain size, but similar grain yield to the BWs. The three SDL families and their SHW and BW parents were genotyped using mapped DArT (diversity arrays technology) markers. Within each SDL family, SHW-specific DArT markers were used to identify SHW-derived chromosomal regions that appeared to be preferentially retained in the SDL families, as determined by retention at frequencies >0.25, the expected frequency for Mendelian segregation. Regions on chromosomes 2BS and 7BL appeared to be preferentially retained in all three SDL families, while regions on chromosomes 1AL, 1BS, 3BS, 5AS, 5BL, and 7AS were preferentially retained in two of the three SDL families. Other regions were preferentially retained in single families only, including some regions located on the D genome. Single-marker regression analysis was performed using the preferentially retained markers and identified markers and regions that were significantly associated with one or more of the four traits measured. Comparative mapping also indicates that these preferentially retained markers and chromosome regions may co-locate with previously identified QTLs for anthesis, height, grain weight and/or grain yield. Therefore, SHWs may contain novel alleles at these loci in these regions for these traits, which may provide a selective advantage to the SDLs. This approach could provide a useful method for identifying chromosomal regions of interest with potentially novel alleles for introgression for further BW improvement.

Management of ash/impurity ratio in sugarcane: relative effects of genotypes, and N and K fertiliser rates

In sugarcane juice or raw sugar, ash refers to soluble inorganic salts. The ratio of ash/impurity is important because high levels reduce sucrose extraction in sugar mills and the market value of raw sugar. The aim of research reported here was to examine, through a series of field experiments, the effects of genotypes and varying N and K fertiliser application rates on ash and ash/impurity levels. Ash levels were estimated via conductivity measurements, following prior studies indicating close relationships between conductivity and ash. Significant variation due to genotypes for conductivity/impurity levels was observed, with a range of about ±25% around the mean. Despite this variation, broad-sense heritability of conductivity/impurity levels on unselected genotypes on the basis of measurements in one environment were low (0.20), suggesting that selection in early phases of selection systems in breeding programs would probably be of limited value. However, it was recommended that measurements on conductivity/impurity ratio be made in multi-environment trials for genotypes being tested for commercial release, to assist in comprehensive economic evaluation. On average it was found that conductivity/impurity levels increased by 15% per 100 kg/ha of applied K, highlighting potential costs of high rates of K fertiliser. Increased N rates had a significant but small effect on reducing conductivity/impurity levels by ∼10% per additional 100 kg/ha of applied N. The information reported here may be used to help develop optimal strategies for cultivar selection in sugarcane breeding programs and for developing recommendations for optimal fertiliser management, and some guidelines in relation to this are discussed.