Amir M. H. Ibrahim

Increased food and ecosystem security via perennial grains

Perennial grains hold promise, especially for marginal landscapes or with limited resources where annual versions struggle. Despite doubling of yields of major grain crops since the 1950s, more than one in seven people suffer from malnutrition (1). Global population is growing; demand for food, especially meat, is increasing; much land most suitable for annual crops is already in use; and production of nonfood goods (e.g., biofuels) increasingly competes with food production for land (2). The best lands have soils at low or moderate risk of degradation under annual grain production but make up only 12.6% of global land area (16.5 million km2) (3). Supporting more than 50% of world population is another 43.7 million km2 of marginal lands (33.5% of global land area), at high risk of degradation under annual grain production but otherwise capable of producing crops (3). Global food security depends on annual grains—cereals, oilseeds, and legumes—planted on almost 70% of croplands, which combined supply a similar portion of human calories (4, 5). Annual grain production, though, often compromises essential ecosystem services, pushing some beyond sustainable boundaries (5). To ensure food and ecosystem security, farmers need more options to produce grains under different, generally less favorable circumstances than those under which increases in food security were achieved this past century. Development of perennial versions of important grain crops could expand options.

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1—the summer 2015 and winter 2016 growing seasons–of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project’s goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and most comprehensive project of its kind to date, these lessons are particularly salient to researchers embarking on agricultural research with UAVs.

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

Population Genomics Related to Adaptation in Elite Oat Germplasm

An oat association‐mapping panel contributed by active breeding programs worldwide. Characterized population structure and found subdivisions related to adaptation Characterized genome‐wide and chromosome‐specific linkage disequilibrium Performed association‐mapping and post hoc modeling of heading date Found several consistently associated QTL

Family-based QTL mapping of heat stress tolerance in primitive tetraploid wheat (Triticum turgidum L.)

Identification of quantitative trait loci (QTL) and markers associated with heat and drought tolerance is warranted for marker-assisted selection in wheat (Triticum aestivum L.) breeding programs in areas prone to these abiotic stresses. Our study used a family-based mapping approach in which 19 families consisting of 384 individuals were developed by three-way crosses involving the heat tolerant, tetraploid cultivated emmer (Triticum turgidum L. var dicoccum) genotype IG45069 and ten heat susceptible tetraploid genotypes, IG44999, IG44961, IG45413, IG83047, IG45441, IG127682, IG45448, IG110572, IG88723 and IG54073, in order to detect QTL and markers associated with heat tolerance. The 384 individuals were phenotyped for physiological traits associated with heat tolerance and genotyped by SSR markers. The QTL associated with heat stress tolerance, as measured by chlorophyll content, flag leaf temperature depression (FLTD) and individual kernel weight (IKW) were mapped on chromosomes 1B (QChlc.tamu-1B), 2B (QFlt.tamu-2B), and 5A (QIkw.tamu-5A), respectively, using linkage analysis. Alleles from IG45069 possessed the highest associations with the phenotypic data for the studied traits. This study demonstrates that a family-based mapping approach can be utilized in rapid detection of QTL associated with heat tolerance in wheat based on linkage and association analyses.

A QTL on chromosome 2DS of ‘Sumai 3’ increases susceptibility to Fusarium head blight in wheat

Much effort has been invested in identifying molecular markers in wheat (Triticum aestivum L.) linked to quantitative trait loci (QTL) that confer resistance to Fusarium head blight (FHB) caused by Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schwein) Petch]. Even after several generations of crossing and selection by many wheat breeding programs, resistance of the Chinese spring wheat cultivar ‘Sumai 3’ (PI 481542) remains among the most effective. It therefore seems that undocumented resistance QTL present in Sumai 3 were not detected in various mapping studies. Using an extremely susceptible Tibetan landrace (‘Y1193-6’; unknown pedigree) in the creation of a mapping population with Sumai 3, the objective of this research was to identify undocumented resistance QTL in Sumai 3. This was accomplished through collecting disease index (DI) and Fusarium damaged kernel (FDK) phenotypic values along with 305 Diversity Array Technology (DArT) and 52 Simple Sequence Repeat (SSR) marker genotypes on 160 F2:6 recombinant inbred lines (RILs). Disease response evaluations were based on four (two greenhouse and two field) experiments where spray inoculation methods were used. Three QTL were identified on chromosome arms 3BS, 6BL and 2DS explaining 26.1, 10.7 and 18.9% of the phenotypic variation for DI, respectively. The same QTL were also significantly associated with reduced FDK scores and explained 28.0, 11.0 and 23.0% of phenotypic variation. Lines within the mapping population were placed in eight categories with respect to their various QTL combinations. Lines with no QTL were the most susceptible, whereas those with the Sumai 3-derived 3BS and 6BL QTL combined with the 2DS QTL from Y1193-6 were the most resistant. Though the 3BS and 6BL QTL are well-documented, the 2DS resistance QTL, which was contributed by the susceptible parent, confers increased susceptibility when derived from Sumai 3. In this study no new FHB QTL from Sumai 3 was discovered, but results suggest that Sumai 3 contains a QTL for susceptibility on chromosome arm 2DS. Selection against this QTL may potentially increase resistance levels among Sumai 3-derived populations.

Wild Tetraploid Wheat (Triticum turgidum L.) Response to Heat Stress

Identifying reliable screening tools and characterizing tolerant germplasm sources are essential for developing wheat (Triticum aestivum L.) varieties suited for the hot areas of the world. Our objective was to evaluate heat tolerance of promising wild tetraploid wheat (Triticum turgidum L.) accessions that could be used as sources of heat tolerance in common- and durum-wheat (Triticum durum) breeding programs. We screened 16 wild tetraploid wheat accessions and two common wheat checks for their response to heat stress by measuring damage to the thylakoid membranes, flag leaf temperature depression (FLTD), and spike temperature depression (STD) during exposure to heat stress for 16 days post-anthesis (DPA). Measurements were taken on the day of anthesis then 4, 8, 12, 16 DPA under controlled optimum and heat-stress conditions. Individual kernel weight (IKW) and heat susceptibility index (HSI) measurements were also obtained. Prolonged exposure to heat stress was associated with increased damage to thylakoid membranes, as indicated by the high ratio of constant fluorescence (O) to peak variable fluorescence (P). Some wild tetraploid wheat accessions exhibited a better HSI than the common heat-tolerant wheat cultivar ‘Kauz.’ A positive and significant correlation was found between O/P ratio and each of FLTD and STD under heat-stress conditions. A negative and significant correlation was found between FLTD and HSI and between STD and HSI based on the second and third measurements (4 and 8 DPA). Correlations obtained after the third measurement were not significant because of heat-induced, accelerated maturity and a lack of green leaf tissue. This study identified potential heat-tolerant wild tetraploid wheat germplasm that can be incorporated into wheat breeding programs to improve heat tolerance in cultivated common and durum wheat.

Effect of High-Molecular-Weight Glutenin Subunit Allelic Composition on Wheat Flour Tortilla Quality

ABSTRACT Wheat cultivars possessing quality attributes needed to produce optimum quality tortillas have not been identified. This study investigated the effect of variations in high-molecular-weight glutenin subunits encoded at the Glu-1 loci (Glu-A1, Glu-B1, and Glu-D1) on dough properties and tortilla quality. Flour protein profiles, dough texture, and tortilla physical quality attributes were evaluated. Deletion at Glu-D1 resulted in reduced insoluble polymeric protein content of flour, reduced dough compression force, and large dough extensibility. These properties produced very large tortillas (181 mm diameter) compared with a control made with commercial tortilla wheat flour (161 mm). Presence of a 7 + 9 allelic pair at Glu-B1 increased dough strength (largest compression force, reduced extensibility, and small-diameter tortillas). Deletion at Glu-A1 produced large tortillas (173 mm) but with unacceptable flexibility during storage (score <3.0 at day 16). In general, presence of 2* at Glu-A1, in com...

Ethylene-inhibiting compound 1-MCP delays leaf senescence in cotton plants under abiotic stress conditions

Cotton (Gossypium hirsutum L.) plants produce more ethylene when subjected to abiotic stresses, such as high temperatures and drought, which result in premature leaf senescence, reduced photosynthetic efficiency, and thus decreased yield. This study was conducted to test the hypothesis that the ethylene-inhibiting compound 1-methylcyclopropene (1-MCP) treatment of cotton plants can delay leaf senescence under high temperature, drought, and the aging process in controlled environmental conditions. Potted cotton plants were exposed to 1-MCP treatment at the early square stage of development. The protective effect of 1-MCP against membrane damage was found on older compared to younger leaves, indicating 1-MCP could lower the stress level caused by aging. Application of 1-MCP resulted in reduction of lipid peroxidation, membrane leakage, soluble sugar content, and increased chlorophyll content, in contrast to the untreated plants under heat stress, suggesting that 1-MCP treatment of cotton plants may also have the potential to reduce the effect of heat stress in terms of delayed senescence. Application of 1-MCP caused reductions of lipid peroxidation, membrane leakage, and soluble sugar content, together with increases in water use efficiency (WUE), water potential, chlorophyll content, and fluorescence quantum efficiency, compared to the untreated plants under drought, suggesting that 1-MCP treatment of cotton plants may also have the ability to reduce the level of stress under drought conditions. In conclusion, 1-MCP treatment of cotton should have the potential to delay senescence under heat and drought stress, and the aging process. Additionally, 1-MCP is more effective under stress than under non-stress conditions.

Comparative Systems Biology Reveals Allelic Variation Modulating Tocochromanol Profiles in Barley (Hordeum vulgare L.)

Tocochromanols are recognized for nutritional content, plant stress response, and seed longevity. Here we present a systems biological approach to characterize and develop predictive assays for genes affecting tocochromanol variation in barley. Major QTL, detected in three regions of a SNP linkage map, affected multiple tocochromanol forms. Candidate genes were identified through barley/rice orthology and sequenced in genotypes with disparate tocochromanol profiles. Gene-specific markers, designed based on observed polymorphism, mapped to the originating QTL, increasing R2 values at the respective loci. Polymorphism within promoter regions corresponded to motifs known to influence gene expression. Quantitative PCR analysis revealed a trend of increased expression in tissues grown at cold temperatures. These results demonstrate utility of a novel method for rapid gene identification and characterization, and provide a resource for efficient development of barley lines with improved tocochromanol profiles.