Agriculture Commons^™

Can Bangladesh Produce Enough Cereals To Meet Future Demand?, J. Timsina, J. Wolf, N. Guilpart, L.G.J. Van Bussel, P. Grassini, J. Van Wart, A. Hossain, H. Rashid, S. Islam, M.K. Van Ittersum

Department of Agronomy and Horticulture: Faculty Publications

Bangladesh faces huge challenges in achieving food security due to its high population, diet changes, and limited room for expanding cropland and cropping intensity. The objective of this study is to assess the degree to which Bangladesh can be self-sufficient in terms of domestic maize, rice and wheat production by the years 2030 and 2050 by closing the existing gap (Yg) between yield potential (Yp) and actual farm yield (Ya), accounting for possible changes in cropland area. Yield potential and yield gaps were calculated for the three crops using well-validated crop models and site-specific weather,management and soil data, and upscaled …

Doublethink And Scale Mismatch Polarize Policies For An Invasive Tree, Caleb P. Roberts, Daniel R. Uden, Craig R. Allen, Dirac L. Twidwell Jr.

Department of Agronomy and Horticulture: Faculty Publications

Mismatches between invasive species management policies and ecological knowledge can lead to profound societal consequences. For this reason, natural resource agencies have adopted the scientifically-based density-impact invasive species curve to guide invasive species management. We use the density-impact model to evaluate how well management policies for a native invader (Juniperus virginiana) match scientific guidelines. Juniperus virginiana invasion is causing a sub-continental regime shift from grasslands to woodlands in central North America, and its impacts span collapses in endemic diversity, heightened wildfire risk, and crashes in grazing land profitability. We (1) use land cover data to identify the stage …

Unlocking The Novel Genetic Diversity And Population Structure Of Synthetic Hexaploid Wheat, Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, Jesse Poland, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Background: Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for broadening the genetic base of elite bread wheat (BW) germplasm (T. aestivum L). Understanding the diversity and population structure of SHWs will facilitate their use in wheat breeding programs. Our objectives were to understand the genetic diversity and population structure of SHWs and compare the genetic diversity of SHWs with elite BW cultivars and demonstrate the potential of SHWs to broaden the genetic base …

Water Productivity Of Rainfed Maize And Wheat: A Local To Global Perspective, Juan I. Rattalino Edreira, Nicolas Guilpart, Victor Sadras, Kenneth G. Cassman, Martin K. Van Ittersum, Rene L.M. Schils, Patricio Grassini

Department of Agronomy and Horticulture: Faculty Publications

Water productivity (WP) is a robust benchmark for crop production in relation to available water supply across spatial scales. Quantifying water-limited potential (WPw) and actual on-farm (WPa) WP to estimate WP gaps is an essential first step to identify the most sensitive factors influencing production capacity with limited water supply. This study combines local weather, soil, and agronomic data, and crop modeling in a spatial framework to determine WPw and WPa at local and regional levels for rainfed cropping systems in 17 (maize) and 18 (wheat) major grain-producing countries representing a wide range of cropping systems, from intensive, highyield maize …

Isolation And Analysis Of Microbial Communities In Soil, Rhizosphere, And Roots In Perennial Grass Experiments, Morgan R. Mcpherson, Peng Wang, Robert B. Mitchell, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Plant and soil microbiome studies are becoming increasingly important for understanding the roles microorganisms play in agricultural productivity. The purpose of this manuscript is to provide detail on how to rapidly sample soil, rhizosphere, and endosphere of replicated field trials and analyze changes that may occur in the microbial communities due to sample type, treatment, and plant genotype. The experiment used to demonstrate these methods consists of replicated field plots containing two, pure, warm-season grasses (Panicum virgatum and Andropogon gerardii) and a low-diversity grass mixture (A. gerardii, Sorghastrum nutans, and Bouteloua curtipendula). Briefly, plants …

Managing Grazing Lands To Improve Soils And Promote Climate Change Adaptation And Mitigation: A Global Synthesis, Marcia Delonge, Andrea D. Basche

Department of Agronomy and Horticulture: Faculty Publications

The potential to improve soils to help farmers and ranchers adapt to and mitigate climate change has generated significant enthusiasm. Within this discussion, grasslands have surfaced as being particularly important, due to their geographic range, their capacity to store substantial quantities of carbon relative to cultivated croplands and their potential role in mitigating droughts and floods. However, leveraging grasslands for climate change mitigation and adaptation will require a better understanding of how farmers and ranchers who rely on them for their livelihoods can improve management and related outcomes. To investigate opportunities for such improvements, we conducted a meta-analysis of field …

Hunger In The Land Of Plenty: Local Responses To Food Insecurity In Iowa, Gabrielle E. Roesch-Mcnally, Jacqueline Ann Nester, Andrea D. Basche, Eric Christianson, Emily Zimmerman

Department of Agronomy and Horticulture: Faculty Publications

Story County (estimated population 92,406 in 2013) lies in the heart of central Iowa, a state renowned for its remarkable agricultural productivity. Iowa leads all states for production of corn, soybean, and hogs. Revenues from agricultural products in Iowa total more than $30 billion annually according the 2012 Agricultural Census (USDA-NASS 2014). This productivity stems from a favorable natural and political environment. The temperate climate, productive soils, and gentle topography are ideal for our production system of commodity agriculture facilitated by federal policies, which include subsidized crop insurance and commodity payments (Horrigan, Lawrence, and Walker 2002). Despite this productivity and …

Empirical Comparisons Of Different Statistical Models To Identify And Validate Kernel Row Number-Associated Variants From Structured Multi-Parent Mapping Populations Of Maize, Jinliang Yang, Cheng-Ting Yeh, Raghuprakash Kastoori Ramamurthy, Xinshuai Qi, Rohan L. Fernando, Jack C. M. Dekkers, Dorian J. Garrick, Dan Nettleton, Patrick Schnable

Department of Agronomy and Horticulture: Faculty Publications

Advances in next generation sequencing technologies and statistical approaches enable genomewide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from the …

Optimising The Identification Of Causal Variants Across Varying Genetic Architectures In Crops, Chenyong Miao, Jinliang Yang, James C. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures and linkage disequilibrium patterns. We demonstrate that different GWAS statistical approaches provide favourable trade-offs between power and accuracy for traits controlled by different types of genetic architectures. FarmCPU provides …

Maize Genomes To Fields: 2014 And 2015 Field Season Genotype, Phenotype, Environment, And Inbred Ear Image Datasets, Naser Alkhalifah, Darwin A. Campbell, Celeste M. Falcon, Jack M. Gardiner, Nathan D. Miller, Maria Cinta Romay, Ramona Walls, Renee Walton, Cheng-Ting Yeh, Martin Bohn, Jessica Bubert, Edward S. Buckler, Ignacio Ciampitti, Sherry Flint-Garcia, Michael A. Gore, Christopher Graham, Candice Hirsch, James B. Holland, David Hooker, Shawn Kaeppler, Joseph Knoll, Nick Lauter, Elizabeth C. Lee, Aaron Lorenz, Jonathan P. Lynch, Stephen P. Moose, Seth C. Murray, Rebecca Nelson, Torbert Rocheford, Oscar Rodriguez, James C. Schnable, Brian Scully, Margaret Smith, Nathan Springer, Peter Thomison, Mitchell Tuinstra, Randall J. Wisser, Wenwei Xu, David Ertl, Patrick S. Schnable, Natalia De Leon, Edgar P. Spalding, Jode Edwards, Carolyn J. Lawrence-Dill

Department of Agronomy and Horticulture: Faculty Publications

Objectives: Crop improvement relies on analysis of phenotypic, genotypic, and environmental data. Given large, well-integrated, multi-year datasets, diverse queries can be made: Which lines perform best in hot, dry environments? Which alleles of specific genes are required for optimal performance in each environment? Such datasets also can be leveraged to predict cultivar performance, even in uncharacterized environments. The maize Genomes to Fields (G2F) Initiative is a multi-institutional organization of scientists working to generate and analyze such datasets from existing, publicly available inbred lines and hybrids. G2F’s genotype by environment project has released 2014 and 2015 datasets to the public, with …

Linked Read Technology For Assembling Large Complex And Polyploid Genomes, Alina Ott, James C. Schnable, Cheng-Ting Yeh, Linjiang Wu, Chao Liu, Heng-Cheng Hu, Clifton L. Dalgard, Soumik Sarkar, Patrick Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly.

Results: Here we describe a de novo maize B73 genome assembly …

Genomic Prediction Accuracy For Switchgrass Traits Related To Bioenergy Within Differentiated Populations, Jason D. Fiedler, Christina Lanzatella, Serge J. Edme, Nathan A. Palmer, Gautam Sarath, Rob Mitchell, Christian M. Tobias

Department of Agronomy and Horticulture: Faculty Publications

Background: Switchgrass breeders need to improve the rates of genetic gain in many bioenergy-related traits in order to create improved cultivars that are higher yielding and have optimal biomass composition. One way to achieve this is through genomic selection. However, the heritability of traits needs to be determined as well as the accuracy of prediction in order to determine if efficient selection is possible.

Results: Using five distinct switchgrass populations comprised of three lowland, one upland and one hybrid accession, the accuracy of genomic predictions under different cross-validation strategies and prediction methods was investigated. Individual genotypes were collected using GBS …