Suchismita Mondal

Canopy temperature and vegetation indices from high-throughput phenotyping improve accuracy of pedigree and genomic selection for grain yield in wheat

Genomic selection can be applied prior to phenotyping, enabling shorter breeding cycles and greater rates of genetic gain relative to phenotypic selection. Traits measured using high-throughput phenotyping based on proximal or remote sensing could be useful for improving pedigree and genomic prediction model accuracies for traits not yet possible to phenotype directly. We tested if using aerial measurements of canopy temperature, and green and red normalized difference vegetation index as secondary traits in pedigree and genomic best linear unbiased prediction models could increase accuracy for grain yield in wheat, Triticum aestivum L., using 557 lines in five environments. Secondary traits on training and test sets, and grain yield on the training set were modeled as multivariate, and compared to univariate models with grain yield on the training set only. Cross validation accuracies were estimated within and across-environment, with and without replication, and with and without correcting for days to heading. We observed that, within environment, with unreplicated secondary trait data, and without correcting for days to heading, secondary traits increased accuracies for grain yield by 56% in pedigree, and 70% in genomic prediction models, on average. Secondary traits increased accuracy slightly more when replicated, and considerably less when models corrected for days to heading. In across-environment prediction, trends were similar but less consistent. These results show that secondary traits measured in high-throughput could be used in pedigree and genomic prediction to improve accuracy. This approach could improve selection in wheat during early stages if validated in early-generation breeding plots.

Harnessing Diversity in Wheat to Enhance Grain Yield, Climate Resilience, Disease and Insect Pest Resistance and Nutrition Through Conventional and Modern Breeding Approaches

Current trends in population growth and consumption patterns continue to increase the demand for wheat, a key cereal for global food security. Further, multiple abiotic challenges due to climate change and evolving pathogen and pests pose a major concern for increasing wheat production globally. Triticeae species comprising of primary, secondary, and tertiary gene pools represent a rich source of genetic diversity in wheat. The conventional breeding strategies of direct hybridization, backcrossing and selection have successfully introgressed a number of desirable traits associated with grain yield, adaptation to abiotic stresses, disease resistance, and bio-fortification of wheat varieties. However, it is time consuming to incorporate genes conferring tolerance/resistance to multiple stresses in a single wheat variety by conventional approaches due to limitations in screening methods and the lower probabilities of combining desirable alleles. Efforts on developing innovative breeding strategies, novel tools and utilizing genetic diversity for new genes/alleles are essential to improve productivity, reduce vulnerability to diseases and pests and enhance nutritional quality. New technologies of high-throughput phenotyping, genome sequencing and genomic selection are promising approaches to maximize progeny screening and selection to accelerate the genetic gains in breeding more productive varieties. Use of cisgenic techniques to transfer beneficial alleles and their combinations within related species also offer great promise especially to achieve durable rust resistance.

Genetic yield gains in CIMMYT’s international elite Spring Wheat yield trials by modeling the Genotype X environment interaction

We calculated the annual genetic gains for grain yield (GY) of wheat (Triticum aestivum L.) achieved over 8 yr of international Elite Spring Wheat Yield Trials (ESWYT), from 2006–2007 (27th ESWYT) to 2014–2015 (34th ESWYT). In total, 426 locations were classified within three main megaenvironments (MEs): ME1 (optimally irrigated environments), ME4 (drought-stressed environments), and ME5 (heat-stressed environments). By fitting a factor analytical structure for modeling the genotype × environment (G × E) interaction, we measured GY gains relative to the widely grown cultivar Attila (GYA) and to the local checks (GYLC). Genetic gains for GYA and GYLC across locations were 1.67 and 0.53% (90.1 and 28.7 kg ha–1 yr–1), respectively. In ME1, genetic gains were 1.63 and 0.72% (102.7 and 46.65 kg ha–1 yr–1) for GYA and GYLC, respectively. In ME4, genetic gains were 2.7 and 0.41% (88 and 15.45 kg ha–1 yr–1) for GYA and GYLC, respectively. In ME5, genetic gains were 0.31 and 1.0% (11.28 and 36.6 kg ha–1 yr–1) for GYA and GYLC, respectively. The high GYA in ME1 and ME4 can be partially attributed to yellow rust races that affect Attila. When G × E interactions were not modeled, genetic gains were lower. Analyses showed that CIMMYT’s location at Ciudad Obregon, Mexico, is highly correlated with locations in other countries in ME1. Lines that were top performers in more than one ME and more than one country were identified. CIMMYT’s breeding program continues to deliver improved and widely adapted germplasm for target environments.

Functionality of Gliadin Proteins in Wheat Flour Tortillas

Gliadins are monomeric proteins that are encoded by the genes at the loci Gli 1 and Gli 2 present on the short arm of homologous wheat chromosomes 1 and 6, respectively. Studies have suggested that gliadins may play an important role in determining the functional properties of wheat flour. The main objective of this study was to understand the functionality of gliadins with respect to tortilla quality. The important tortilla quality attributes are diameter, opacity, and shelf stability, designated here as rollability or the ability to roll or fold the tortilla without cracking. In this study gliadin functionality in tortilla quality was studied using near-isogenic wheat lines that have deletions in either Gli A1, Gli D1, Gli A2, or Gli D2 gliadin loci. The deletion lines are designated by the same abbreviations. Dough and tortillas were prepared from the parent line used to derive these deletion lines, each individual deletion line, and a control commercial tortilla flour. Quantitative and qualitative evaluations were performed on the dough and tortillas derived from the flour from each of these lines. None of the deletions in the gliadin loci altered the shelf stability versus that found for the parent to the deletion lines or control tortilla flour. However, deletions in the Gli 2 loci, in particular Gli A2 reduced the relative proportion of alpha- and beta-gliadins with a greater cysteine amino acid content and gluten cross-link function versus the chain-terminating omega-gliadins in Gli 1, which were still present. As such, the dough and gluten matrix appeared to have greater extensibility, which improved the diameter and overall quality of the tortillas while not altering the rollability. Deletions in the Gli 1 loci had the opposite result with increased cross-linking of alpha- and beta-gliadins, polymeric protein content, and a stronger dough that decreased the diameter and overall quality of the tortillas. The data suggest that altering certain Gli 2 loci through null alleles could be a viable strategy to develop cultivars improved for the specific functionality requirements needed for the rapidly growing tortilla market.

Grain yield, adaptation and progress in breeding for early-maturing and heat-tolerant wheat lines in South Asia

Highlights • Each year from 2009 to 2014, 28 newly developed early-maturing high-yielding CIMMYT wheat lines were evaluated across locations in South Asia.• Maximum temperatures in ME5 (continual high temperature stress regions) and minimum temperature in ME1 (terminal high temperature stress regions) had significant impact on grain yield in South Asia.• Significant negative genetic correlations of grain yield with days to heading.• Early maturity has the potential to improve adaptation and maintenance of genetic gains in South Asia.

Identification of quantitative trait loci (QTLs) associated with maintenance of wheat (Triticum aestivum Desf.) quality characteristics under heat stress conditions

The goal of this study was to identify quantitative trait loci (QTLs) associated with the maintenance of wheat grain quality following post-anthesis heat stress in a recombinant inbred line (RIL) population. The response to heat stress was measured using the sodium dodecyl sulfate sedimentation test (SDSS), a significant predictor of bread baking quality. SDSS scores were used to identify QTLs associated with grain quality and QTLs associated with quality stability were identified based on percent change in SDSS score between the heat stress and control treatments. Four QTLs were identified, located one each on linkage groups 1B, 1D, 4A, and 7A. The 1B, 1D, and 4A QTLs were associated with grain quality; the QTL on linkage group 7A was associated with quality stability. To confirm the detected QTLs, eighty advanced lines grown at three Texas nurseries were tested for relationships between allelic polymorphism at QTL linked markers and quality traits. Quality trait stability in the advanced lines was estimated using the coefficient of variability (CV%) of quality traits between nurseries. The analysis supported the relationship of the predicted QTLs on linkage groups 1B, 1D, and 4A with quality traits. The confirmed QTLs may be used in marker assisted selection (MAS) to develop wheat lines possessing superior quality traits. In addition, identification of genetic regions associated with this trait will aid the identification of the underlying genes.

Combining High-Throughput Phenotyping and Genomic Information to Increase Prediction and Selection Accuracy in Wheat Breeding

Wheat breeding High throughput phenotyping Genomic selection Yield prediction modeling

Prediction of multiple-trait and multiple-environment genomic data using recommender systems

In genomic-enabled prediction, the task of improving the accuracy of the prediction of lines in environments is difficult because the available information is generally sparse and usually has low correlations between traits. In current genomic selection, although researchers have a large amount of information and appropriate statistical models to process it, there is still limited computing efficiency to do so. Although some statistical models are usually mathematically elegant, many of them are also computationally inefficient, and they are impractical for many traits, lines, environments, and years because they need to sample from huge normal multivariate distributions. For these reasons, this study explores two recommender systems: item-based collaborative filtering (IBCF) and the matrix factorization algorithm (MF) in the context of multiple traits and multiple environments. The IBCF and MF methods were compared with two conventional methods on simulated and real data. Results of the simulated and real data sets show that the IBCF technique was slightly better in terms of prediction accuracy than the two conventional methods and the MF method when the correlation was moderately high. The IBCF technique is very attractive because it produces good predictions when there is high correlation between items (environment–trait combinations) and its implementation is computationally feasible, which can be useful for plant breeders who deal with very large data sets.

Genetic resources and breeding methodologies for improving drought tolerance in wheat

ABSTRACT Yield gains from rain-fed wheat (Triticum aestivum L.) production, particularly in areas experiencing intermittent and terminal dry spells, can be realized through integrated breeding with promising genetic and genomic resources using appropriate methodologies. This enables targeted recombination of novel genes for drought tolerance and selection of desirable genotypes. Continuous exploration of new sources of genetic variation and introgression of suitable genes into elite drought-susceptible genotypes, including via transgenic approaches, and the use of genome editing could offer exciting future prospects in acquiring drought-tolerant wheat genotypes. This review highlights the available genetic resources, the major wheat genebanks and databases, as well as the breeding methodologies for drought tolerance in wheat, including prebreeding, conventional breeding, hybrid breeding, and genomics-assisted breeding. The potential of genetic modification through the transgenic and genome-editing approaches is also discussed. Emphasis is placed on how best these breeding methods can be brought together to develop strategies aimed at improving drought tolerance in wheat.

Early Maturity in Wheat for Adaptation to High Temperature Stress

High temperatures pose a serious threat to productivity maintenance and enhancement in wheat. A strategy that has come forward in the CIMMYT breeding program is the development of high yielding early maturing lines that are adapted to high temperature stress especially for South Asia. The high temperature stress in South Asia is classified into terminal high temperature stress where the high temperatures stress occurs during grain filling stages, and continual high temperature stress, where high temperature persists across the wheat growing season. The new high yielding, early maturing and heat tolerant CIMMYT wheat lines were evaluated for grain yield and adaptation across diverse locations in South Asia and Mexico. Trials were conducted for three consecutive years 2009–2010, 2010–2011, and 2011–2012. The results suggest that CIMMYT lines with high yields and early maturity, selected under normal and late sown condition in Cd. Obregon, Mexico, have the potential to adapt and outperform normal maturing check varieties under terminal and continual high temperature stress in South Asia. Earliness favored the plants to escape terminal high temperature stress and also promoted an efficient utilization of available resources under continual high temperature stress to achieve higher grain yield. The simultaneous enhancement of grain yield potential and heat stress tolerance of early maturing wheat lines is likely to be beneficial in enhancing productivity under high temperature stress across South Asia.