Amir M. H. Ibrahim

Bio: Amir M. H. Ibrahim is an academic researcher from Texas A&M University. The author has contributed to research in topics: Population & Quantitative trait locus. The author has an hindex of 25, co-authored 126 publications receiving 2945 citations. Previous affiliations of Amir M. H. Ibrahim include Hospital Corporation of America & South Dakota State University.

Increased food and ecosystem security via perennial grains

Abstract: 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 (eg, 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 126% of global land area (165 million km2) ( 3 ) Supporting more than 50% of world population is another 437 million km2 of marginal lands (335% 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

Supporting Online Material for Increased Food and Ecosystem Security via Perennial Grains

Abstract: Increased Food and Ecosystem Security via Perennial Grains J. D. Glover,* J. P. Reganold, L. W. Bell, J. Borevitz, E. C. Brummer, E. S. Buckler, C. M. Cox, T. S. Cox, T. E. Crews, S. W. Culman, L. R. DeHaan, D. Eriksson, B. S. Gill, J. Holland, F. Hu, B. S. Hulke, A. M. H. Ibrahim, W. Jackson, S. S. Jones, S. C. Murray, A. H. Paterson, E. Ploschuk, E. J. Sacks, S. Snapp, D. Tao, D. L. Van Tassel, L. J. Wade, D. L. Wyse, Y. Xu

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

Abstract: 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.

QTL associated with heat susceptibility index in wheat (Triticum aestivum L.) under short-term reproductive stage heat stress.

Abstract: Heat stress adversely affects wheat production in many regions of the world and is particularly detrimental during reproductive development and grain-filling. The objective of this study was to identify quantitative trait loci (QTL) associated with heat susceptibility index (HSI) of yield components in response to a short-term heat shock during early grain-filling in wheat. The HSI was used as an indicator of yield stability and a proxy for heat tolerance. A recombinant inbred line (RIL) population derived from the heat tolerant cultivar ‘Halberd’ and heat sensitive cultivar ‘Cutter’ was evaluated for heat tolerance over 2 years in a controlled environment. The RILs and parental lines were grown in the greenhouse and at 10 days after pollination (DAP) half the plants for each RIL received a three-day heat stress treatment at 38°C/18°C day/night, while half were kept at control conditions of 20°C/18°C day/night. At maturity, the main spike was harvested and used to determine yield components. A significant treatment effect was observed for most yield components and a HSI was calculated for individual components and used for QTL mapping. QTL analysis identified 15 and 12 QTL associated with HSI in 2005 and 2006, respectively. Five QTL regions were detected in both years, including QTL on chromosomes 1A, 2A, 2B, and 3B. These same regions were commonly associated with QTL for flag leaf length, width, and visual wax content, but not with days to flowering. Pleiotropic trade-offs between the maintenance of kernel number versus increasing single kernel weight under heat stress were present at some QTL regions. The results of this study validate the use of the main spike for detection of QTL for heat tolerance and identify genomic regions associated with improved heat tolerance that can be targeted for future studies.

Evaluating physiological traits to complement empirical selection for wheat in warm environments

Abstract: The response of spring wheat to heat stress has been determined in several hot wheat growing environments worldwide on different types of germplasm. Physiological data has been collected to identify potential traits to assist in the empirical breeding for heat tolerance. Initial studies focused on 10 established varieties to determine genetic diversity for heat tolerance, identify association between heat tolerance and traits measured, and evaluate genotype by environment interaction (G × E). Yields from over 40 hot environments were analysed for G x E, and relative humidity (RH) was identified as the major factor determining relative genotype ranking. Further analysis focused on 16 environments: those with low RH and relatively high yields, i.e., over 2.5 t ha−1. For these environments, mean yield of lines correlated with a number of physiological traits measured in Mexico, including canopy temperature depression (CTD), membrane thermostability, leaf conductance and photosynthetic rate at heading, chlorophyll content during grainfilling, leaf internal CO2 concentration, and dark respiration. Morphological traits were measured in all environments and the following showed associations with yield: above ground biomass at maturity, days from emergence to anthesis and to maturity, grain number m−2, and ground cover estimated visually after heading. Subsequent studies focused on breeding material, namely recombinant inbred lines derived from crosses between parents of contrasting heat tolerance, and 60 advanced breeding lines selected for performance under heat stress. The genetic basis for association between heat tolerance and CTD was established by demonstrating a correlation between the two traits in RILs (recombinant inbred lines). Data from RILs, as well as from the 60 advanced lines grown at several international locations, indicated CTD to be a powerful and robust selection criterion for heat tolerance.

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

A User’s Guide

Abstract: OUTPU T 29 OUTPU T 30 OUTPU T 31 OUTPU T 32 OUTPU T 25 OUTPU T 26 OUTPU T 27 OUTPU T 28 OUTPU T 21 OUTPU T 22 OUTPU T 23 OUTPU T 24 OUTPU T 17 OUTPU T 18 OUTPU T 19 OUTPU T 20 OUTPU T 13 OUTPU T 14 OUTPU T 15 OUTPU T 16 OUTPU T 9 OUTPU T 10 OUTPU T 11 OUTPU T 12 OUTPU T 5 OUTPU T 6 OUTPU T 7 OUTPU T 8 OUTPU T 1 OUTPU T 2 OUTPU T 3 OUTPU T 4 29 30 31 32 25 26 27 28 21 22 23 24 17 18 19 20 13 14 15 16 9

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

Abstract: High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.

Crop Production under Drought and Heat Stress: Plant Responses and Management Options

Abstract: Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought stress are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.

Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops

Abstract: Global warming is predicted to have a general negative effect on plant growth due to the damaging effect of high temperatures on plant development. The increasing threat of climatological extremes including very high temperatures might lead to catastrophic loss of crop productivity and result in wide spread famine. In this review, we assess the impact of global climate change on the agricultural crop production. There is a differential effect of climate change both in terms of geographic location and the crops that will likely show the most extreme reductions in yield as a result of expected extreme fluctuations in temperature and global warming in general. High temperature stress has a wide range of effects on plants in terms of physiology, biochemistry and gene regulation pathways. However, strategies exist to crop improvement for heat stress tolerance. In this review, we present recent advances of research on all these levels of investigation and focus on potential leads that may help to understand more fully the mechanisms that make plants tolerant or susceptible to heat stress. Finally, we review possible procedures and methods which could lead to the generation of new varieties with sustainable yield production, in a world likely to be challenged both by increasing population, higher average temperatures and larger temperature fluctuations.