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Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide. Fhb1 is the most widely utilized and the only isolated gene for FHB resistance, while Sr2 is a durable stem rust resistance gene used in rust-prone areas. The two loci are closely linked on the short arm of chromosome 3B and the two genes are in repulsion phase among cultivars. With climate change and the shift in Fusarium populations, it is imperative to develop wheat cultivars resistant to both diseases. The present study was dedicated to developing wheat germplasm combining Fhb1 and Sr2 resistance alleles in the International Maize and Wheat Improvement Center (CIMMYT)’s elite cultivars’ backgrounds. Four recombinant inbred lines (RILs) in Hartog background that have the resistant Fhb1 and Sr2 alleles in coupled phase linkage were crossed with seven CIMMYT bread wheat lines, resulting in 208 lines. Molecular markers for both genes were employed in addition to the use of pseudo-black chaff (PBC) as a phenotypic marker for the selection of Sr2. At various stages of the selection process, progeny lines were assessed for FHB index, Fusarium damaged kernels (FDK), stem rust, and PBC expression as well as other diseases of interest (stripe rust and leaf spotting diseases). The 25 best lines were selected for CIMMYT’s wheat breeding program. In addition to expressing resistance to FHB, most of these 25 lines have an acceptable level of resistance to other tested diseases. These lines will be useful for wheat breeding programs worldwide and potentially speed up the resistance breeding efforts against FHB and stem rust.

Fusarium head blight (FHB) and stem rust are among the most devastating diseases of wheat worldwide.

Leptochloa dubia (Kunth) Nees es una gramínea forrajera perenne, nativa del centro-norte de México, adaptada a zonas de escaza precipitación, su número cromosómico básico es x= 10 y su nivel de ploidía desde diploide (2n= 2x= 20) a octoploide (2n= 2x= 80). El objetivo fue determinar el número cromosómico y nivel de ploidía de una colección de 67 poblaciones de pasto Gigante, recolectadas durante 2009 en el Altiplano Mexicano entre 19o a 28o latitud norte y 1 500 a 2 450 msnm. Los conteos cromosómicos se realizaron en ápices de raíces en crecimiento activo (5 a 10 mm), tratadas con 8-hidroxiquinolina (2 mM) por 3.5 h, fijadas en solución (3:1 v/v alcohol absoluto y ácido acético glacial) y se conservaron a 4 oC, hasta el momento de su evaluación. El recuento de cromosomas se efectúo en microscopio compuesto de contraste de fases. Se observaron células en metafase, por lo menos, cinco preparaciones y 10 células por preparación, para cada planta y población. El 96% de las plantas analizadas fueron tetraploides 2n= 4x= 40 y 4% diploides 2n= 2x= 20. Las plantas diploides fueron originarias de seis poblaciones de Hidalgo, Guanajuato y de la zona limítrofe entre Aguascalientes, Jalisco y Guanajuato, las plantas tetraploides se encontraron en todas las poblaciones evaluadas; sin embargo, no se encontraron diferencias significativas entre localidades (p< 0.05), de acuerdo a su nivel de ploidía. Los niveles encontrados son indicativos del amplio centro de origen de esta especie.

The loss of genetic diversity in bread wheat (Triticum aestivum L.) due to bottlenecks from polyploidy, domestication, and modern plant breeding can be compensated by introgressing exotic germplasm. A successful approach to capture genetic diversity is the production of primary synthetic bread wheats, which are contemporary reconstitutions of the ancestral genomes of wheat from diverse wild relatives. However, this diverse germplasm has many undesirable characters, making direct use in breeding programs difficult. To increase the speed of introgression of exotic germplasm, genomic selection approaches could be applied to enable rapid cycles of selection. To test this, selected lines from double haploid and recombinant inbred line populations between six different primary synthetics and the elite cultivar ‘Opata M85’ were evaluated for grain yield and other important agronomic traits. Field trials were conducted at CIMMYT (International Center for Maize and Wheat Improvement) over 2 yr in irrigated, heat, and drought-stressed environments. Several synthetic-derived lines outperformed the elite parent Opata M85 in all environments, indicating that the primary synthetics contribute alleles increasing yield. Whole-genome profiles were generated using genotyping-by-sequencing. Five different whole-genome prediction models that can be applied for genomic selection were evaluated for prediction accuracy using cross validation. Overall, the prediction models had moderate predictive ability, slightly lower than expected based on the heritability of the traits. While a viable approach, rapid cycle genomic selection for introgression of exotic alleles might be restricted with synthetic-derived wheat due to complex and confounding physiological effects.

Until now, genomic prediction (GP) in plant breeding has only used information from individuals that have been genotyped. Information from nongenotyped relatives of genotyped individuals can also be used. Single-step GP combines marker and pedigree information into a single relationship matrix to perform GP. The objective of this study was to evaluate single-step GP in a wheat breeding program. We compared the performance of pedigree-based, marker-based, and single-step models (ABLUP, GBLUP, and HBLUP, respectively). Data consisted of 1176 genotyped (via genotyping-by-sequencing) and 11,131 nongenotyped wheat lines replicated in five management environments at the CIMMYT experiment station in Obregon, Mexico. Analyses involved three scenarios: (i) all lines had pedigree information but only some were genotyped, with phenotypes from one or two environments in the 2011–2012 season, (ii) all lines had genotype and pedigree information and phenotypes from four or five environments in the 2012–2013 season, and (iii) the combination of Scenarios 1 and 2. Prediction accuracies were calculated by five-fold cross validation on plant height, maturity, heading date, and grain yield. The single-step HBLUP outperformed GBLUP and pedigree-based ABLUP in all cases. We conclude that the single-step procedure combining pedigree and genomic marker data should be favored where appropriate data is available for GP in wheat breeding programs.

Awns were linked to larger grain size, improved seedlot quality, and yield in less favourable environments but trade-offs in grain number reduced much of their benefit in more favourable environments., Genotypic variation in ear morphology is linked to differences in photosynthetic potential to influence grain yield in winter cereals. Awns contribute to photosynthesis, particularly under water-limited conditions when canopy assimilation is restricted. We assessed performance of up to 45 backcross-derived, awned–awnletted NILs representing four diverse genetic backgrounds in 25 irrigated or rainfed, and droughted environments in Australia and Mexico. Mean environment grain yields were wide-ranging (1.38–7.93 t ha−1) with vegetative and maturity biomass, plant height, anthesis date, spike number, and harvest index all similar (P >0.05) for awned and awnletted NILs. Overall, grain yields of awned–awnletted sister-NILs were equivalent, irrespective of yield potential and genetic background. Awnletted wheats produced significantly more grains per unit area (+4%) and per spike (+5%) reflecting more fertile spikelets and grains in tertiary florets. Increases in grain number were compensated for by significant reductions in grain size (–5%) and increased frequency (+0.8%) of small, shrivelled grains (‘screenings’) to reduce seed-lot quality of awnletted NILs. Post-anthesis canopies of awnletted NILs were marginally warmer over all environments (+0.27 °C) but were not different and were sometimes cooler than awned NILs at cooler air temperatures. Awns develop early and represented up to 40% of total spikelet biomass prior to ear emergence. We hypothesize that the allocation of assimilate to large and rapidly developing awns decreases spikelet number and floret fertility to reduce grain number, particularly in distal florets. Individual grain size is increased to reduce screenings and to increase test weight and milling quality, particularly in droughted environments. Despite the average reduction in grain size, awnless lines could be identified that combined higher grain yield with larger grain size, increased grain protein concentration, and reduced screenings.

Fusarium head blight (FHB), also known as head scab, is a devastating fungal disease of bread and durum wheat worldwide. It reduces yield, lowers seed germination, reduces grain quality, and renders grain unsuitable for human or animal consumption due to mycotoxin contamination. Use of host resistance in commercially cultivated wheat varieties is an economical, effective and environmentally friendly method to manage FHB. In order to map loci underlying FHB resistance in synthetic-derived bread wheat line SYN1, a doubled haploid (DH) population of 169 lines was developed through hybridizing SYN1 with FHB-susceptible line Ocoroni. The DH population was evaluated in spray-inoculated field nurseries in the 2010 and 2011 cropping seasons at the El Batan Experiment Station of the International Maize and Wheat Improvement Center, Mexico. Ten marked spikes from each plot were scored for disease response and an FHB index was subsequently calculated. The population was genotyped with 1391 genotyping by sequencing and 106 simple-sequence repeat (SSR) loci and 28 linkage groups were constructed. These linkage groups were anchored by SSRs to all chromosomes, except 4D, 5D and 6D. Using the inclusive composite interval mapping algorithm, three genomic regions were associated with FHB resistance, including a major QTL on chromosome 2D accounting for 25 % of the phenotypic variation explained (PVE) and two minor QTLs on chromosomes 1B (4.7 % PVE) and 7A (4.2 % PVE), with all favorable alleles contributed by SYN1. The average FHB index of lines with all three SYN1 alleles was substantially lower (61.4 %) than that of those with Ocoroni alleles.

Genomic selection (GS) models use genome-wide genetic information to predict genetic values of candidates of selection. Originally, these models were developed without considering genotype × environment interaction(G×E). Several authors have proposed extensions of the single-environment GS model that accommodate G×E using either covariance functions or environmental covariates. In this study, we model G×E using a marker × environment interaction (M×E) GS model; the approach is conceptually simple and can be implemented with existing GS software. We discuss how the model can be implemented by using an explicit regression of phenotypes on markers or using co-variance structures (a genomic best linear unbiased prediction-type model). We used the M×E model to analyze three CIMMYT wheat data sets (W1, W2, and W3), where more than 1000 lines were genotyped using genotyping-by-sequencing and evaluated at CIMMYT’s research station in Ciudad Obregon, Mexico, under simulated environmental conditions that covered different irrigation levels, sowing dates and planting systems. We compared the M×E model with a stratified (i.e., within-environment) analysis and with a standard (across-environment) GS model that assumes that effects are constant across environments (i.e., ignoring G×E). The prediction accuracy of the M×E model was substantially greater of that of an across-environment analysis that ignores G×E. Depending on the prediction problem, the M×E model had either similar or greater levels of prediction accuracy than the stratified analyses. The M×E model decomposes marker effects and genomic values into components that are stable across environments (main effects) and others that are environment-specific (interactions). Therefore, in principle, the interaction model could shed light over which variants have effects that are stable across environments and which ones are responsible for G×E. The data set and the scripts required to reproduce the analysis are publicly available as Supporting Information.

Spot blotch, caused by Cochliobolus sativus, is an important foliar disease of wheat in warmer wheat-growing regions leading to significant reductions in grain yield and quality. Although inoculum levels can be reduced by planting disease-free seed, treatment of plants with fungicides and crop rotation, genetic resistance is likely to be a robust, economical and environmentally friendly tool in the control of spot blotch. The spot blotch resistant synthetic derivative ‘SYN1’ was developed from a cross between two resistance sources, Mayoor and the primary synthetic bread wheat Tksn1081/Ae. squarrosa (222) that are likely to form an important component of resistance in many elite CIMMYT bread wheats. In order to map the loci underlying the resistance of ‘SYN1’, a doubled-haploid population produced from a cross between ‘SYN1’ and the susceptible CIMMYT-derived variety Ocoroni-86 was evaluated in artificially inoculated field nurseries in the 2010–2011 and 2011–2012 crop seasons at CIMMYT’s research station in Agua Fria, Mexico. Disease assessment was performed on three or four occasions and subsequently area under disease progress curve (AUDPC) calculated. Genotyping was with genotyping by sequencing and simple sequence repeat markers. Using inclusive composite interval mapping, three genomic regions were found to have a significant effect on spot blotch AUDPC in each of the 2 years of trials with phenotypic variation explained by QSb.cim-1B of 8.5 %, 17.6 % by QSb.cim-3B and 12.3 % by QSb.cim-5A. The quantitative trait loci (QTL) mapping results showed that the favorable alleles of QSb.cim-1B, QSb.cim-3B and QSb.cim-5A were derived from the synthetic-derived bread wheat SYN1. Genotypes of the parents of SYN1 indicated that the favorable alleles at these three QTLs were all inherited from Mayoor.

Pearson’s correlation coefficient (ρ) is the most commonly reported metric of the success of prediction in genomic selection (GS). However, in real breeding ρ may not be very useful for assessing the quality of the regression in the tails of the distribution, where individuals are chosen for selection. This research used 14 maize and 16 wheat data sets with different trait–environment combinations. Six different models were evaluated by means of a cross-validation scheme (50 random partitions each, with 90% of the individuals in the training set and 10% in the testing set). The predictive accuracy of these algorithms for selecting individuals belonging to the best α=10, 15, 20, 25, 30, 35, 40% of the distribution was estimated using Cohen’s kappa coefficient (κ) and an ad hoc measure, which we call relative efficiency (RE), which indicates the expected genetic gain due to selection when individuals are selected based on GS exclusively. We put special emphasis on the analysis for α=15%, because it is a percentile commonly used in plant breeding programmes (for example, at CIMMYT). We also used ρ as a criterion for overall success. The algorithms used were: Bayesian LASSO (BL), Ridge Regression (RR), Reproducing Kernel Hilbert Spaces (RHKS), Random Forest Regression (RFR), and Support Vector Regression (SVR) with linear (lin) and Gaussian kernels (rbf). The performance of regression methods for selecting the best individuals was compared with that of three supervised classification algorithms: Random Forest Classification (RFC) and Support Vector Classification (SVC) with linear (lin) and Gaussian (rbf) kernels. Classification methods were evaluated using the same cross-validation scheme but with the response vector of the original training sets dichotomised using a given threshold. For α=15%, SVC-lin presented the highest κ coefficients in 13 of the 14 maize data sets, with best values ranging from 0.131 to 0.722 (statistically significant in 9 data sets) and the best RE in the same 13 data sets, with values ranging from 0.393 to 0.948 (statistically significant in 12 data sets). RR produced the best mean for both κ and RE in one data set (0.148 and 0.381, respectively). Regarding the wheat data sets, SVC-lin presented the best κ in 12 of the 16 data sets, with outcomes ranging from 0.280 to 0.580 (statistically significant in 4 data sets) and the best RE in 9 data sets ranging from 0.484 to 0.821 (statistically significant in 5 data sets). SVC-rbf (0.235), RR (0.265) and RHKS (0.422) gave the best κ in one data set each, while RHKS and BL tied for the last one (0.234). Finally, BL presented the best RE in two data sets (0.738 and 0.750), RFR (0.636) and SVC-rbf (0.617) in one and RHKS in the remaining three (0.502, 0.458 and 0.586). The difference between the performance of SVC-lin and that of the rest of the models was not so pronounced at higher percentiles of the distribution. The behaviour of regression and classification algorithms varied markedly when selection was done at different thresholds, that is, κ and RE for each algorithm depended strongly on the selection percentile. Based on the results, we propose classification method as a promising alternative for GS in plant breeding.

Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required.Heredity advance online publication, 10 April 2013; doi:10.1038/hdy.2013.16.

Agriculture is the single largest geo-engineering initiative that humans have initiated on planet Earth, largely through the introduction of unprecedented amounts of reactive nitrogen (N) into ecosystems. A major portion of this reactive N applied as fertilizer leaks into the environment in massive amounts, with cascading negative effects on ecosystem health and function. Natural ecosystems utilize many of the multiple pathways in the N cycle to regulate N flow. In contrast, the massive amounts of N currently applied to agricultural systems cycle primarily through the nitrification pathway, a single inefficient route that channels much of this reactive N into the environment. This is largely due to the rapid nitrifying soil environment of present-day agricultural systems.In this Viewpoint paper, the importance of regulating nitrification as a strategy to minimize N leakage and to improve N-use efficiency (NUE) in agricultural systems is highlighted. The ability to suppress soil nitrification by the release of nitrification inhibitors from plant roots is termed 'biological nitrification inhibition' (BNI), an active plant-mediated natural function that can limit the amount of N cycling via the nitrification pathway. The development of a bioassay using luminescent Nitrosomonas to quantify nitrification inhibitory activity from roots has facilitated the characterization of BNI function. Release of BNIs from roots is a tightly regulated physiological process, with extensive genetic variability found in selected crops and pasture grasses. Here, the current status of understanding of the BNI function is reviewed using Brachiaria forage grasses, wheat and sorghum to illustrate how BNI function can be utilized for achieving low-nitrifying agricultural systems. A fundamental shift towards ammonium (NH4(+))-dominated agricultural systems could be achieved by using crops and pastures with high BNI capacities. When viewed from an agricultural and environmental perspective, the BNI function in plants could potentially have a large influence on biogeochemical cycling and closure of the N loop in crop-livestock systems.

Emmer wheat (Triticum dicoccon Schrank) is still largely cultivated in India, and highly appreciated for the preparation of traditional dishes. Moreover, its nutritional characteristics could justify a development of its cultivation. The perspective of genetic improvement however requires a good knowledge of the genetic diversity existing within the eco-geographic group of Indian emmer wheats. A set of 48 emmer wheat accessions from India including 28 from a local collection and 20 Indian accessions obtained from CIMMYT, Mexico, was assessed for genetic variability using 47 microsatellite (SSR) markers, distributed over all the 14 chromosomes. The number of alleles per locus ranged from 2 to 9, with an average of 3.87 alleles per locus. A total of 201 alleles were detected at 52 loci with average polymorphic information content of 0.35 per locus and a mean resolving power of 1. The pair-wise similarity coefficients calculated from binary data matrix based on presence or absence of alleles varied from 0.15 to 0.98, but was greater than 0.5 for most accessions, indicating a high level of similarity. A cluster analysis based on the similarity matrix identified nine distinct accessions and three clusters. All the recently developed commercial varieties were distinctly different from the clusters. Based on the analysis, it appears that Indian emmer wheats are not very diverse. Consequently, there is a need to increase the diversity within the Indian emmer wheat eco-geographic group, by introducing diversity from other eco-geographic groups, or even from other wheat species.

Reductions in plant height are associated with genotypic increases in lodging resistance, harvest index and wheat yields worldwide. Historically, the largest single increase in harvest index and yield was seen in development of semi-dwarf wheats through introgression of the gibberellic acid (GA)-insensitive, Rht-B1b and Rht-D1b dwarfing alleles. A suite of GA-sensitive dwarfing genes including Rht8 are also available and their neutral effects on seedling vigour suggest their potential in being deployed singly, or in combination with GA-insensitive dwarfing alleles. Five biparental and backcross populations each comprising between 44 and 124 progeny were developed from commercial parents varying for alleles at either the Rht-B1 or Rht-D1 and the Rht8 dwarfing gene loci. Progeny was grown together in multiple environments, and assessed for agronomic performance and coleoptile growth. Genotypic variation was large and significant ( P Rht8c and either Rht-B1b or Rht-D1b dwarfing alleles averaged 8 and 17%, respectively. The Rht8c + Rht-B1b/D1b sesqui-dwarfs were significantly ( P Rht8c dwarfing allele did not appear epistatic with either Rht-B1b or Rht-D1b alleles in effects on plant growth. Coleoptile lengths were similar for sesqui- and Rht-B1b/D1b single-dwarfs and both shorter than for Rht8c and tall lines. Together with their pleiotropic effects on harvest index and availability of linked molecular markers, simultaneous selection of Rht8c + Rht-B1b or Rht-D1b sesqui-dwarfs in early generations may facilitate rapid development of high-yielding varieties targeting favourable and unfavourable environments alike.

Improved ability to establish well when sowing at depth, into crop residues or hard soils should lead to increased yields in these situations. The semi-dwarfing Rht-B1b and Rht-D1b genes reduce plant height and increase grain number and yield in favourable environments. However, these genes are associated with reduced coleoptile length and leaf length extension to slow leaf area and biomass accumulation especially when seed are sown deep. Preliminary evidence indicates the potential of Rht4 , Rht5 , Rht8 , Rht12 and Rht13 gibberellin-responsive (GAR) dwarfing genes to reduce plant height without affecting seedling vigour. Four large, inbred populations were generated varying for presence of one or more GAR-dwarfing genes. Lines were genotyped with molecular markers linked to each dwarfing gene and grown in multiple environments to evaluate seedling growth and agronomic performance. Genotypic variation was large for plant height, aerial biomass, grain yield and its components, grain number and size. Height reduction was greatest for Rht5 (−55%), Rht12 (−45%), Rht13 (−34%), Rht4 (−17%), and to a lesser extent Rht8 (−7%). In comparison, height reductions associated with Rht-B1b averaged 23%. Reduced height was genetically correlated with reduced lodging score ( r g = 0.84–0.93), increased dry-matter partitioning to grain (i.e. harvest index; r g = −0.46** to −0.86**) and increased grain number ( r g = −0.22* to −0.73**). Most dwarfing genes were associated with increased grain number: Rht13 (+27%), Rht4 (+19%), Rht12 (+19%), and Rht-B1b (+9%). Rht8 had little effect on grain number (−1%) whereas later maturity associated with Rht5 contributed to reduced grain number (−66%). The influence of dwarfing genes on aerial biomass was negligible, with some Rht4 , Rht12 and Rht13 semi-dwarf lines identified combining greater partitioning and aerial biomass to increase grain yield. Compared to tall siblings, coleoptile lengths and seedling leaf breadths were largely unaffected by GAR-dwarfing genes but leaf length was on average smaller in lines containing Rht5 or Rht12 . These studies demonstrate the potential of GAR-dwarfing genes for increasing grain number and yield without compromising aerial biomass or coleoptile length in bread wheat.

Realistic experimental protocols to screen for drought adaptation in controlled conditions are crucial if high throughput phenotyping is to be used for the identification of high performance lines, and is especially important in the evaluation of transgenes where stringent biosecurity measures restrict the frequency of open field trials. Transgenic DREB1A-wheat events were selected under greenhouse conditions by evaluating survival and recovery under severe drought (SURV) as well as for water use efficiency (WUE). Greenhouse experiments confirmed the advantages of transgenic events in recovery after severe water stress. Under field conditions, the group of transgenic lines did not generally outperform the controls in terms of grain yield under water deficit. However, the events selected for WUE were identified as lines that combine an acceptable yield-even higher yield (WUE-11) under well irrigated conditions-and stable performance across the different environments generated by the experimental treatments.

The green-revolution Rht-B1b and Rht-D1b dwarfing alleles are usually associated with increased wheat yields but are linked to reduced early growth and poor emergence if sowing conditions are unfavourable. Other dwarfing genes are available but not used in commercial breeding. The Rht13 bread wheat donor, Magnif M1, produces uniquely short peduncle and penultimate internodes to reduce plant height. A set of near-isogenic (NILs) and recombinant inbred (RILs) lines varying for height were developed from the cross of Magnif M1 and the Rht8c -containing Chuan-mai 18, and evaluated for a range of agronomic characteristics across favourable environments. Reductions in plant height were associated with increased grain number ( r 2 = 0.35**) and harvest index ( r 2 = 0.62**) in the NILs. Reduced-height RILs containing the Rht13 -linked, Xgwm577 M microsatellite marker were significantly shorter, produced greater biomass, yield and harvest index, and increased spike and grain number than lines without the marker. Approximately 74 and 7% of the total phenotypic variance in plant height was accounted for by allelic differences in Xgwm577 and Rht8 loci, respectively. The peduncle and penultimate peduncle internodes of Rht13 -containing lines were proportionately shorter than Rht8c -containing sibs and lines containing the Rht-B1b dwarfing allele. The unique height-reducing phenotype, increased grain number and yield associated with Rht13 indicate considerable potential for use of this dwarfing allele for improving wheat performance.

To introduce new genetic diversity into the bread wheat gene pool from its progenitor, Aegilops tauschii (Coss.) Schmalh, 33 primary synthetic hexaploid wheat genotypes (SYN) were crossed to 20 spring bread wheat (BW) cultivars at the International Wheat and Maize Improvement Center. Modified single seed descent was used to develop 97 populations with 50 individuals per population using first back-cross, biparental, and three-way crosses. Individuals from each cross were selected for short stature, early heading, flowering and maturity, minimal lodging, and free threshing. Yield trials were conducted under irrigated, drought, and heat-stress conditions from 2011 to 2014 in Ciudad Obregon, Mexico. Genomic estimated breeding values (GEBVs) of parents and synthetic derived lines (SDLs) were estimated using a genomic best linear unbiased prediction (GBLUP) model with markers in each trial. In each environment, there were SDLs that had higher GEBVs than their recurrent BW parent for yield. The GEBVs of BW parents for yield ranged from -0.32 in heat to 1.40 in irrigated trials. The range of the SYN parent GEBVs for yield was from -2.69 in the irrigated to 0.26 in the heat trials and were mostly negative across environments. The contribution of the SYN parents to improved grain yield of the SDLs was highest under heat stress, with an average GEBV for the top 10% of the SDLs of 0.55 while the weighted average GEBV of their corresponding recurrent BW parents was 0.26. Using the pedigree-based model, the accuracy of genomic prediction for yield was 0.42, 0.43, and 0.49 in the drought, heat and irrigated trials, respectively, while for the marker-based model these values were 0.43, 0.44, and 0.55. The SYN parents introduced novel diversity into the wheat gene pool. Higher GEBVs of progenies were due to introgression and retention of some positive alleles from SYN parents.

Wheat is a staple food for the major part of the world’s population. For wheat and other crops, it is generally agreed that in order to meet future challenges in food production, multifaceted breeding approaches are needed, including the use of current available genomics resources. Since more than three decades, molecular markers have acted as a versatile genomics tool for fast and unambiguous genetic analysis of plant species of both diploid and polyploid origin. Together with decreasing marker assay costs and interconnected genotyping service facilities, the opportunity to apply marker-assisted selection (MAS) strategies is becoming accessible to more and more breeding programs. We describe the use of molecular markers in wheat breeding with emphasis on the status of MAS in the CIMMYT global wheat program and will share our experience on recently developed prediction methods using genome-wide markers to archive genetic gain for more complex traits.

The height-reducing gene Rht8 was introduced into Italian wheats by breeder Nazareno Strampelli from the Japanese landrace Akakomugi, and has been widely used in wheats adapted to southern and eastern European conditions. Following identification of a close linkage to Rht8, microsatellite marker Gwm261 has been used extensively to screen large numbers of diverse international germplasm. A 192bp allele at this locus has been taken as “diagnostic” for Rht8 and used to infer the international distribution of Rht8. In this paper, we report several instances of cultivars and mapping populations that vary for the presence of the 192bp allele at the Xgwm261 locus (Xgwm261 192 ), but with no associated reduction in height, suggesting a lack of association with Rht8. For instance, in the population derived from a cross between Sunco (Rht-B1b, Xgwm261 165 ) and Tasman (Rht-D1b, Xgwm261 192 ), there were significant height differences associated with the segregation of Rht-B1b and Rht-D1b, but no height differences between Xgwm261 genotypes. Similar results were obtained in a population derived from the cross between Molineux (Rht-B1b, Xgwm261 192 ) and Trident (Rht-D1b Xgwm261 208 ). In contrast, the cross between Trident and Chuanmai 18 (Xgwm261 192 ) gave significant height effects at both the Rht-D1 and Xgwm261 loci, with no epistatic interaction between loci. Chuanmai 18 is closely related to the Strampelli wheat Mara (ancestrally derived from Akakomugi) and is therefore likely to carry Rht8. The old Japanese cultivar Norin 10, used by Norman Borlaug to introduce Rht-B1b and Rht-D1b into Mexican wheats, also has a 192bp allele at the Xgwm261 locus, and the sequence of the amplified product is identical to that of Akakomugi. We suggest that the widespread use of Norin 10-derived germplasm during and after the Green Revolution introduced a second haplotype into international germplasm, in which Xgwm261 192 has no association with Rht8. Therefore, the presence of Xgwm261 192 is only indicative of Rht8 in wheat cultivars that have inherited this allele from Akakomugi or a Strampelli wheat ancestor.

Breeders face many complex choices in the design of effi cient crossing and selection strategies aimed at combining desired alleles into a single target genotype. Both population genetic theory and a breeding simulation tool were used to study the effects of different strategies on population size and number of marker assays required to recover a target genotype in wheat (Triticum aestivum L.). Enriching the frequency of desirable alleles in the F 2 of single-cross and in the F 1 of backcross and topcross populations greatly reduced the minimum required population size, but the gain from another enrichment selection is minor. General equations were developed to determine appropriate crossing strategies, and sequential culling was proposed to minimize total marker screening costs. For a topcross of three adapted lines from an existing breeding program, simulation of changes in allele frequencies at nine target genes (seven unlinked) showed that population size was minimized with a three-stage selection strategy in the F 1 generation of the topcross (TCF 1 ), the F 2 generation of the topcross (TCF 2 ), and doubled haploid lines (DHs). Enrichment of allelic frequencies in TCF 2 reduced the total number of lines screened from >3500 to 0.97 after selection, while the tin reduced-tillering allele was only at 0.77 in the fi nal selected population due to its strong repulsion-phase linkage to the grain quality gene Glu-A3 in this cross and the incomplete linkage of the tin marker. Therefore, the presence of the tin gene needs to be further confi rmed by other methods.

Successful plant establishment is critical to the development of high-yielding crops. Short coleoptiles can reduce seedling emergence particularly when seed is sown deep as occurs when moisture necessary for germination is deep in the subsoil. Detailed molecular maps for a range of wheat doubled-haploid populations (Cranbrook/Halberd, Sunco/Tasman, CD87/Katepwa and Kukri/Janz) were used to identify genomic regions affecting coleoptile characteristics length, cross-sectional area and degree of spiralling across contrasting soil temperatures. Genotypic variation was large and distributions of genotype means were approximately normal with evidence for transgressive segregation. Narrow-sense heritabilities were high for coleoptile length and cross-sectional area indicating a strong genetic basis for differences among progeny. In contrast, heritabilities for coleoptile spiralling were small. Molecular marker analyses identified a number of significant quantitative trait loci (QTL) for coleoptile growth. Many of the coleoptile growth QTL mapped directly to the Rht-B1 or Rht-D1 dwarfing gene loci conferring reduced cell size through insensitivity to endogenous gibberellins. Other QTL for coleoptile growth were identified throughout the genome. Epistatic interactions were small or non-existent, and there was little evidence for any QTL x temperature interaction. Gene effects at significant QTL were approximately one-half to one-quarter the size of effects at the Rht-B1 and Rht-D1 regions. However, selection at these QTL could together alter coleoptile length by up to 50 mm. In addition to Rht-B1b and Rht-D1b, genomic regions on chromosomes 2B, 2D, 4A, 5D and 6B were repeatable across two or more populations suggesting their potential value for use in breeding and marker-aided selection for greater coleoptile length and improved establishment.

Journal of Experimental Botany, 66 (18), ISSN:1460-2431, ISSN:0022-0957

Chromosomal translocations in wheat derived from alien species are a valuable source of genetic diversity that have provided increases in resistance to various diseases and improved tolerance to abiotic stresses in wheat. These alien genomic segments can also affect multiple traits, with a concomitant ability to alter yield potential in either a positive or negative fashion. The aim of this work was to characterize the effects on yield of two types of translocations, namely T4-derived translocations from Thinopyrum ponticum, carrying the leaf rust resistance gene Lr19, and the TC14 translocation from Th. intermedium, carrying the barley yellow dwarf virus resistance gene Bdv2, in Australian adapted genetic backgrounds and under Australian conditions. A large range of germplasm was developed by crossing donor sources of the translocations into 24 Australian adapted varieties producing 340 genotypes. Yield trials were conducted in 14 environments to identify effects on yield and yield components. The T4 translocations had a positive effect on yield in one high yielding environment, but negatively affected yield in low-yielding environments. The TC14 translocation was generally benign, however, it was associated with a negative impact on yield and reduced height in two genetic backgrounds. The translocation was also associated with a delayed maturity in several backgrounds. The T4 translocations results were consistent with previously published data, whilst this is the first time that such an investigation has been undertaken on the TC14 translocation. Our data suggests a limited role for each of these translocations in Australia. The T4 translocations may be useful in high yielding environments, such as under irrigation in NSW and in the more productive high rainfall regions of south-eastern Australia. Traits associated with the TC14 translocation, such as BYDV resistance and delayed maturity, would make this translocation useful in BYDV-prone areas that experience a less pronounced terminal drought (e.g., south-eastern Australia).

Although molecular markers allow more accurate selection in early generations than conventional screens, large numbers can make selection impracticable while screening in later generations may provide little or no advantage over conventional selection techniques. Investigation of different crossing strategies and consideration of when to screen, what proportion to retain and the impacts of dominant vs. codominant marker expression revealed important choices in the design of marker-assisted selection programs that can produce large efficiency gains. Using F2 enrichment increased the frequency of selected alleles allowing large reductions in minimum population size for recovery of target genotypes (commonly around 90%) and/or selection at a greater number of loci. Increasing homozygosity by inbreeding from F2 to F2:3 also reduced population size by around 90% in some crosses with smaller incremental reductions in subsequent generations. Backcrossing was found to be a useful strategy to reduce population size compared with a biparental population where one parent contributed more target alleles than the other and was complementary to F2 enrichment and increasing homozygosity. Codominant markers removed the need for progeny testing reducing the number of individuals that had to be screened to identify a target genotype. However, although codominant markers allow target alleles to be fixed in early generations, minimum population sizes are often so large in F2 that it is not efficient to do so at this stage. Formulae and tables for calculating genotypic frequencies and minimum population sizes are provided to allow extension to different breeding systems, numbers of target loci, and probabilities of failure. Principles outlined are applicable to implementation of markers for both quantitative trait loci (QTL) and major genes.

Incorporation of genetic diversity into elite wheat (Triticum aestivum L., 2n1⁄4 6x1⁄4 42, AABBDD) cultivars has long been recognized as a means of improving wheat productivity and securing global wheat supply. Synthetic hexaploid wheat (SHW) genotypes recreated from its two progenitor species, the tetraploid, Triticum turgidum (2n1⁄4 4x1⁄4 28, AABB) and its diploid wild relative, Aegilops tauschii (2n1⁄4 2x1⁄4 14, DD) are a useful resource of new genes for hexaploidwheat improvement. These include many productivity traits such as abiotic (drought, heat, salinity/sodicity, andwaterlogging) and biotic (rusts, septoria, barley yellow dwarfvirus (BYDV), crownrot, tan spot, spot blotch, nematodes,powderymildew, and fusarium head blight) stress resistance/tolerances as well as novel grain quality traits. Numerous SHWs have been produced globally by various institutions including CIMMYT-Mexico, ICARDA-Syria, Department of Primary Industries (DPI), Victoria-Australia, IPK-Germany, Kyoto University-Japan, and USDAARS. This review examines the varied aspects in the utilization of synthetics for wheat improvement including the traits and genes identified, mapped, and transferred to common wheat. It has also been demonstrated that synthetic backcross-derived lines (SBLs, i.e., when SHW is crossed to adapted local bread varieties) show significant yield increases and thus, enhanced yield performance across a diverse range of environments, demonstrating their potential for improving wheat productivity worldwide. This is particularly evident in moisturelimited environments. The use of SBLs, advanced backcross QTL analysis, chromosome introgression lines, and whole genome association mapping is contributing to the elucidation of the genetic architecture of some of the traits. The contribution of transgressive segregation to enhanced phenotypes and the mechanisms including its genetic and physiological basis are yet to be elucidated. 36 FRANCIS C. OGBONNAYA ET AL.

Genetic diversity is paramount for cultivated crops genetic improvement, and for wheat this resides in three gene pools of the Triticeae. In wheat, access to this diversity and its exploitation is based upon the genetic distance of the wild species relatives from the wheat genomes. For several decades, these wide crosses have been a reservoir of novel variation for wheat improvement. Among these, close relatives of the primary gene pool have been preferred since this ensures successful gene transfer as they permit homologous genetic exchanges to occur between related genomes, as exemplified by the A and D genome diploid progenitors. One strategy has been based upon first producing genetic stocks that capture the potential of the diploids via bridge crossing where the D genome synthetic hexaploid wheats (2n = 6x = 42, AABBDD) are exploited. The synthetics are products of crosses between elite durum wheat cultivars (Triticum turgidum) and various Aegilops tauschii accessions. Similarly, the diversity of the A and B genomes has also been assembled as AABBAA (T. turgidum/A genome diploids Triticum boeoticum, Triticum monococcum, Triticum urartu) and AABBBB (SS) (T. turgidum/Aegilops speltoides). The utilization of these useful diversity for various biotic/abiotic stresses including in the development of molecular tools for enhancing breeding efficiency has been in the forefront of wheat improvement over the past two decades. Additional strategy employed includes the direct crosses between parental diploids and recipient wheat cultivars extended to give even swifter products by top- or backcrossing the F1 combinations with either durum or bread wheats. Relatively less progress has been made in the use of genes from tertiary gene pool often involving “intergeneric crosses.” The potency of potentially useful diversity in tertiary gene pool warrants further exploitation of this resource. Presented here are major facets of intergeneric hybridization embracing a taxonomic consideration of genetic diversity within the Triticeae, the exploitation protocols, prebreeding strategies, and some of the outputs from distant hybridization with a major focus on wheat/alien chromosomal exchanges classed as “translocations” such as T1BL.1RS and to a lesser degree the T1AL.1RS Robertsonian translocations. This chapter also attempts to relate the exploitation of the Triticeae genetic diversity with wheat productivity as a means of addressing diverse stress constraints that if pursued will provide yield enhancing outputs necessary for overriding environmental limitations of climate change, unpredictable incidences of biotic stresses, and catalyzing gains for food security with wheat.

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation ; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.

Human activity has had the single largest influence on the global nitrogen (N) cycle by introducing unprecedented amounts of reactive-N into ecosystems. A major portion of this reactive-N, applied as fertilizer to crops, leaks into the environment with cascading negative effects on ecosystem functions and contributes to global warming. Natural ecosystems use multiple pathways of the N-cycle to regulate the flow of this element. By contrast, the large amounts of N currently applied in agricultural systems cycle primarily through the nitrification process, a single inefficient route that allows much of the reactive-N to leak into the environment. The fact that present agricultural systems do not channel this reactive-N through alternate pathways is largely due to uncontrolled soil nitrifier activity, creating a rapid nitrifying soil environment. Regulating nitrification is therefore central to any strategy for improving nitrogen-use efficiency. Biological nitrification inhibition (BNI) is an active plant-mediated natural function, where nitrification inhibitors released from plant roots suppress soil-nitrifying activity, thereby forcing N into other pathways. This review illustrates the presence of detection methods for variation in physiological regulation of BNI-function in field crops and pasture grasses and analyzes the potential for its genetic manipulation. We present a conceptual framework utilizing a BNI-platform that integrates diverse crop science disciplines with ecological principles. Sustainable agriculture will require development of production systems that include new crop cultivars capable of controlling nitrification (i.e., high BNI-capacity) and improved agronomic practices to minimize leakage of reactive-N during the N-cycle, a critical requirement for increasing food production while avoiding environmental damage.

Theoretical considerations suggest that wheat yield potential could be increased by up to 50% through the genetic improvement of radiation use efficiency (RUE). However, to achieve agronomic impacts, structural and reproductive aspects of the crop must be improved in parallel. A Wheat Yield Consortium (WYC) has been convened that fosters linkage between ongoing research platforms in order to develop a cohesive portfolio of activities that will maximize the probability of impact in farmers' fields. Attempts to increase RUE will focus on improving the performance and regulation of Rubisco, introduction of C(4)-like traits such as CO(2)-concentrating mechanisms, improvement of light interception, and improvement of photosynthesis at the spike and whole canopy levels. For extra photo-assimilates to translate into increased grain yield, reproductive aspects of growth must be tailored to a range of agro-ecosystems to ensure that stable expression of a high harvest index (HI) is achieved. Adequate partitioning among plant organs will be critical to achieve favourable expression of HI, and to ensure that plants with heavier grain have strong enough stems and roots to avoid lodging. Trait-based hybridization strategies will aim to achieve their simultaneous expression in elite agronomic backgrounds, and wide crossing will be employed to augment genetic diversity where needed; for example, to introduce traits for improving RUE from wild species or C(4) crops. Genomic selection approaches will be employed, especially for difficult-to-phenotype traits. Genome-wide selection will be evaluated and is likely to complement crossing of complex but complementary traits by identifying favourable allele combinations among progeny. Products will be delivered to national wheat programmes worldwide via well-established international nursery systems and are expected to make a significant contribution to global food security.

Plant breeders simultaneously select for qualitative traits controlled by one or a small number of major genes, as well as for polygenic traits controlled by multiple genes that may be detected as quantitative trait loci (QTL). In this study, we applied computer simulation to investigate simultaneous selection for alleles at both major and minor gene (as QTL) loci in breeding populations of two wheat parental lines, HM14BS and Sunstate. Loci targeted for selection included six major genes affecting plant height, disease resistance, and grain quality, plus 6 known and 11 "unidentified" QTL affecting coleoptile length (CL). Parental line HM14BS contributed the target alleles at two of the major gene loci, while parental line Sunstate contributed target alleles at four loci. The parents have similar plant height, but HM14BS has a longer coleoptile, a desirable attribute for deep sowing in rainfed environments. Including the wild-type allele at the major reduced-height locus Rht-D1, HM14BS was assumed to have 13 QTL for increased CL, and Sunstate four; these assumptions being derived from mapping studies and empirical data from an actual HM14BS/Sunstate population. Simulation indicated that compared to backcross populations, a single biparental F(1) cross produced the highest frequency of target genotypes (six desired alleles at major genes plus desired QTL alleles for long CL). From 1,000 simulation runs, an average of 2.4 individuals with the target genotype were present in unselected F(1)-derived doubled haploid (DH) or recombinant inbred line (RIL) populations of size 200. A selection scheme for the six major genes increased the number of target individuals to 19.1, and additional marker-assisted selection (MAS) for CL increased the number to 23.0. Phenotypic selection (PS) of CL outperformed MAS in this study due to the high heritability of CL, incompletely linked markers for known QTL, and the existence of unidentified QTL. However, a selection scheme combining MAS and PS was equally as efficient as PS and would result in net savings in production and time to delivery of long coleoptile wheats containing the six favorable alleles.

The height-reducing gene Rht8 was introduced by breeder Nazareno Strampelli from the Japanese landrace ‘Akakomugi’ and has been widely used in wheats adapted to southern and eastern Europe ∈dent Definitive identification of Rht8 is difficult because it does not make seedlings insensitive to gibberellin application and its height effect may be confounded with other genes affecting plant height or flowering time. Following identification of a close linkage between microsatellite WMS261 and Rht8, the marker has been used extensively to screen large numbers of diverse international germplasm. A 192bp allele at the WMS261 locus was assumed to be ‘diagnostic’ for Rht8 and its international distribution was inferred from the marker data ∈dent We report several instances of cultivars and mapping populations which vary for the presence of the Xgwm261-192bp allele, but with no associated reduction in height, suggesting a lack of linkage with Rht8 ∈dent Our studies have identified that Norin10, used by Norman Borlaug to introduce Rht-B1b and Rht-D1b into Mexican wheats, also carries WMS261-192bp, and this allele was retained in some of his varieties. The widespread use of Norin10-derived germplasm during and after the green revolution represents a second source of WMS261-192bp microsatellite allele in international germplasm, with no linkage to Rht8. Therefore, the presence of this allele can only be indicative of Rht8 in wheat varieties with a clear pedigree relationship to Akakomugi or Strampelli

Molecular markers make it possible for breeders to combine desirable alleles at a greater number of loci and at earlier generations than is possible with conventional breeding methodologies. With an increasing number of markers for important traits, marker assisted selection (MAS) strategies that minimize population sizes and assay numbers while ensuring important alleles are not lost become increasingly important. In practical breeding, strategies will often have to balance MAS with the need to retain variability for important traits that are selected partly or wholly by conventional means This paper will discuss strategies to maximize the number of traits that can be combined in a single breeding cycle taking account of practical limits such as reasonable population sizes that can be managed in a breeding program. Examples from our breeding program and mapping populations will be used to illustrate the effects of different MAS strategies on population size and levels of residual genetic variation at unselected loci. It is these unselected loci that become important where conventional selection follows MAS

Wheat crops with greater early vigour shade the soil surface more rapidly and reduce water loss. Evaporative losses affect water-use efficiency particularly in drier regions where most of the rainfall occurs early in the growing season before canopy closure. Greater seedling leaf area and longer coleoptiles are major determinants of increased vigour and better crop establishment. A previously developed high vigour breeding line ‘Vigour 18’ was used to establish a large recombinant inbred family and framework map to identify a QTL on chromosome 6A that accounted for up to 8% of the variation for coleoptile length, 14% of seedling leaf width and was associated with increased plant height. The SSR marker NW3106, nearest to the 6A QTL, was also associated with greater leaf width in a breeding population that was also derived from a cross involving the high vigour donor line ‘Vigour18’. The association between the NW3106 marker and coleoptile length was validated in a second breeding population which was developed using an unrelated long coleoptile donor line. The ‘Vigour18’ allele of the QTL on chromosome 6A promoted coleoptile length and leaf width during early plant growth but was also associated with increased plant height at maturity. Markers linked to the QTL are being used to increase the frequency of increased vigour and long coleoptile alleles in early generations of breeding populations.

Genes that reduce height without compromising seedling vigour or coleoptile length have great potential for wheat improvement. We therefore investigated the effects of various reduced height (Rht) genes on the early stages of plant development, using a combination of near isogenic, recombinant, mutant and wild type comparisons. Gibberellin (GA) insensitivity caused by Rht-B1b or Rht-D1b was associated with reduced leaf elongation rate and coleoptile length. Similar results were found for two other sources of dwarfing, Rht11 and Rht17. We found one class of Rht genes (e.g. Rht8) which had no effect on coleoptile length, leaf elongation rate or responsiveness to GA, indicating that these dwarfing genes may act later in wheat development to reduce height and increase harvest index, without affecting early growth. A third class of Rht genes was found in three durum backgrounds. These had reduced coleoptile lengths and leaf elongation rates, but had a greater response to GA than the corresponding tall varieties. We discuss these results in relation to the possible mechanisms underlying the reduction in height and the suitability of the different Rht genes for wheat improvement.

Post-anthesis water deficit and increasing vapour pressure deficit are common and can result in reduced grain yield and the development of small or shrivelled wheat kernels (screenings) that reduce grain value. Previous studies suggest incorporation of a tiller inhibition (tin) gene to restrict tiller number and thereby slow water use and promote the development of larger, fertile spikes to increase kernel weight. This paper reports on the influence of the tin gene on grain yield and screenings in multiple wheat genetic backgrounds assessed in field experiments in 2005 and 2006. Across environments, grain yield ranged from 0.90 to 5.50 t/ha and screenings from 4 to 20%. The effect of tin on grain yield and screenings varied with environment and genetic background. Grain yield was unchanged in tin lines derived from varieties Brookton, Chara, and Wyalkatchem assessed in southern Australian environments. However, there was a 31 and 10% advantage of free-tillering over tin-containing Silverstar lines for the 2005 western and 2006 northern experiments, respectively, resulting in an average 12% reduction in grain yield of Silverstar tin lines. In northern experiments, where screenings ranged from 4 to 12%, Silverstar-based tin lines produced significantly fewer screenings than free-tillering sister lines. Reduction in screenings was associated with a higher kernel weight (+10%) and a tendency for lower grain yield, although individual Silverstar tin progeny with grain yield equivalent to the parent were readily identified. The incorporation of the tin gene has considerable potential to reduce the incidence of screenings in commercial wheat crops. Variation in grain yield associated with the tin gene was dependent on genetic background, with potential for selection of higher yielding tin progeny for commercial line development.

The Norin-10 dwarfing genes, Rht-B1b (Rht1) and Rht-D1b (Rht2), are commonly used to reduce plant height and increase grain yield in wheat breeding programs. These dwarfing genes lower sensitivity of vegetative tissue to endogenous gibberellin to reduce cell and subsequent stem elongation. This reduction in cell elongation capacity reportedly results in a concomitant reduction in coleoptile length and early vigour (leaf area) thereby affecting seedling establishment and growth. A detailed genetic map from a cross between tall Halberd (Rht-B1a) and semidwarf Cranbrook (Rht-B1b) wheat cultivars was used to assess genetic factors affecting seedling growth. Parental and 150 doubled haploid progeny lines were characterised for seedling and height-related traits in controlled and field environments. Genotypic variation was large and predominantly under additive genetic control with evidence for transgressive segregation for some traits. Narrow-sense heritabilities were moderate to high (h2 = 0.31–0.91) indicating a strong genetic basis for differences between progeny. Molecular marker analyses identified a number of significant (P < 0.05) quantitative trait loci (QTL) for each trait. A major QTL, mapping directly to the Rht-B1 locus on chromosome arm 4BS, accounted for up to 49% of the genotypic variance in peduncle length and plant height, and 27–45% of the genotypic variance in coleoptile length across different temperatures. Another QTL, located close to the RFLP marker XksuC2 on the long arm of chromosome 4B, accounted for 15–27% of the genotypic variance in coleoptile length. The influence of the XksuC2-linked QTL on coleoptile length was greatest at 19˚C and decreased with cooler temperatures. The same QTL affected reductions in leaf size, and both coleoptile tiller size and presence to affect overall seedling vigour. There was also some evidence for epistatic interactions influencing coleoptile tiller growth. Reductions in plant size at the Rht-B1b and XksuC2 loci were associated with presence of the Cranbrook 4B allele. The negative genetic effect of the Rht-B1b dwarfing gene on early growth of wheat confirms phenotypic evidence of a pleiotropic effect of Rht-B1b on establishment and early vigour. Genetic increases in coleoptile length and early leaf area development are likely to be limited in wheat populations containing the Rht-B1b dwarfing gene.