Agricultural Science Commons^™

Identification Of Positive Yield Qtl Alleles From Exotic Soybean Germplasm In Two Backcross Populations, K.-S. Kim, B. W. Diers, D. L. Hyten, M. A. Rouf Mian, J. G. Shannon, R. L. Nelson

Department of Agronomy and Horticulture: Faculty Publications

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC₂F₃-derived lines developed using ‘‘Elgin’’ as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC₃F …

Molecular Mapping Of Soybean Rust Resistance In Soybean Accession Pi 561356 And Snp Haplotype Analysis Of The Rpp1 Region In Diverse Germplasm, Ki-Seung Kim, Jair R. Unfried, D. L. Hyten, Reid D. Frederick, Glen L. Hartman, Randall L. Nelson, Qijian Song, Brian W. Diers

Department of Agronomy and Horticulture: Faculty Publications

Soybean rust (SBR), caused by Phakopsora pachyrhizi Sydow, is one of the most economically important and destructive diseases of soybean [Glycine max (L.) Merr.] and the discovery of novel SBR resistance genes is needed because of virulence diversity in the pathogen. The objectives of this research were to map SBR resistance in plant introduction (PI) 561356 and to identify single nucleotide polymorphism (SNP) haplotypes within the region on soybean chromosome 18 where the SBR resistance gene Rpp1 maps. One-hundred F_2:3 lines derived from a cross between PI 561356 and the susceptible experimental line LD02-4485 were genotyped with genetic …

The Application Of A Visual Data Mining Framework To Determine Soil, Climate And Land-Use Relationships, Yunous Vagh

Research outputs 2012

In this research study, the methodology of action research dynamics and a case study was employed in constructing a visual data mining framework for the processing and analysis of geographic land-use data in an agricultural context. The geographic data was made up of a digital elevation model (DEM), soil and land use profiles that were juxtaposed with previously captured climatic data from fixed weather stations in Australia. In this pilot study, monthly rainfall profiles for a selected study area were used to identify areas of soil variability. The rainfall was sampled for the beginning (April) of the rainy season for …

Development And Application Of Methods Used To Source Prehistoric Southwestern Maize: A Review, Larry Benson

United States Geological Survey: Staff Publications

Archaeological cobs free of mineral contaminants should be used to source the soils in which they were grown. Mineral contaminants often contain much higher concentrations of metals than vegetal materials and can alter a cob’s apparent metal and heavy-isotope content. Cleaning a cob via immersion in an acid solution for more than a few minutes will result in the incongruent and sometimes complete leaching of metals, including strontium (Sr), from the cob. When using ⁸⁷Sr/⁸⁶Sr to determine the location of potential agriculture fields, it is best to either integrate several depth-integrated soil samples or to integrate several …

A Mutagenesis-Derived Broad-Spectrum Disease Resistance Locus In Wheat, Jackie Campbell, Hongtao Zhang, Michael J. Giroux, Leila Feiz, Yue Jin, Meinan Wang, Xianming Chen, Li Huang

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Wheat leaf rust, stem rust, stripe rust, and powdery mildew caused by the fungal pathogens Puccinia triticina, P. graminis f. sp. tritici, P. striiformis f. sp. tritici, and Blumeria graminis f. sp. tritici, respectively, are destructive diseases of wheat worldwide. Breeding durable disease resistance cultivars rely largely on continually introgressing new resistance genes, especially the genes with different defense mechanisms, into adapted varieties. Here, we describe a new resistance gene obtained by mutagenesis. The mutant, MNR220 (mutagenesis-derived new resistance), enhances resistance to three rusts and powdery mildew, with the characteristics of delayed disease …

Brown Midrib2 (Bmr2) Encodes The Major 4-Coumarate: Coenzyme A Ligase Involved In Lignin Biosynthesis In Sorghum (Sorghum Bicolor (L.) Moench), Ana Saballos, Scott Sattler, Emiliano Sanchez, Timothy P. Foster, Zhanguo Xin, Chulhee Kang, Jeffrey F. Pedersen, Wilfred Vermerris

Department of Agronomy and Horticulture: Faculty Publications

Successful modification of plant cell-wall composition without compromising plant integrity is dependent on being able to modify the expression of specific genes, but this can be very challenging when the target genes are members of multigene families. 4-coumarate:CoA ligase (4CL) catalyzes the formation of 4-coumaroyl CoA, a precursor of both flavonoids and monolignols, and is an attractive target for transgenic down-regulation aimed at improving agro-industrial properties. Inconsistent phenotypes of transgenic plants have been attributed to variable levels of down-regulation of multiple 4CL genes. Phylogenetic analysis of the sorghum genome revealed 24 4CL(-like) proteins, five of which cluster with bona fide …

Advances In Genome Sequencing And Genotyping Technology For Soybean Diversity Analysis, David L. Hyten

Department of Agronomy and Horticulture: Faculty Publications

The completion of a soybean draft whole genome sequence along with advances in sequencing and genotyping technologies are creating a revolution in soybean genomics. The draft whole genome sequence of soybean is allowing researchers to fully take advantage of this new technology and is rapidly changing how soybean germ plasm is mined. Genetic markers such as SNPs can be quickly identified by using next generation sequencing and assayed on a large number of materials using advanced technologies that can genotype tens of thousands of markers on thousands of individuals very rapidly. This ability to qUickly identify and genotype genetic diversity …

Inheritance Of Grain Polyphenol Oxidase (Ppo) Activity In Multiple Wheat (Triticum Aestivum L.) Genetic Backgrounds, Somrudee Nilthong, Robert A. Graybosch, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Grain polyphenol oxidase (PPO) activity can cause discoloration of wheat (Triticum aestivum L.) food products. Five crosses (PI 117635/Antelope; Fielder/ NW03681; Fielder/Antelope; NW07OR1070/Antelope; NW07OR1066/OR2050272H) were selected to study the genetic inheritance of PPO activity. STS markers, PPO18, PPO29 and STS01, were used to identify lines with putative alleles at the Ppo-A1 and Ppo-D1 loci conditioning low or high PPO activity. ANOVA showed significant genotypic effects on PPO activity (P\0.0001) in all populations. The generations and generation 9 genotype effects were not significant in any population. A putative third (null) genotype at Ppo-A1 (no PCR fragments for PPO18) was discovered …

Identification And Characterization Of Four Missense Mutations In Brown Midrib 12 (Bmr12), The Caffeic O-Methyltranferase (Comt) Of Sorghum, Scott E. Sattler, Nathan A. Palmer, Ana Saballos, Ann M. Greene, Zhanguo Xin, Gautam Sarath, Wilfred Vermerris, Jeffrey F. Pedersen

Department of Agronomy and Horticulture: Faculty Publications

Modifying lignin content and composition are targets to improve bioenergy crops for cellulosic conversion to biofuels. In sorghum and other C4 grasses, the brown midrib mutants have been shown to reduce lignin content and alter its composition. Bmr12 encodes the sorghum caffeic O-methyltransferase, which catalyzes the penultimate step in monolignol biosynthesis. From an EMS-mutagenized TILLING population, four bmr12 mutants were isolated. DNA sequencing identified the four missense mutations in the Bmr12 coding region, which changed evolutionarily conserved amino acids Ala71Val, Pro150Leu, Gly225Asp, and Gly325Ser. The previously characterized bmr12 mutants all contain premature stop codons. These newly identified mutants, along …

Cultivating A Movement: Excerpts From An Oral History Of Organic Farming And Sustainable Agriculture On California’S Central Coast [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Edited by I. Reti and S. Rabkin, 2011. University of California, Santa Cruz, Library, Santa Cruz, California, United States. 299 p., US$19.95, ISBN 9-780972-33431, paper.

Often the most compelling evidence for success of organic farming comes from the personal stories of farmers. Coupled with reports on the application of science in organics, the practical knowledge of people in the field provides a rich foundation for the ongoing growth of this intriguing sector of the food system. This collection of interviews by the staff of the Regional History Project is one unique activity of the University of California, Santa Cruz library, …

Agriculture And Food In Crisis: Conflict, Resistance, And Renewal [Book Review], Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

Edited by Fred Magdoff and Brian Tokar. 2010. Monthly Review Press, New York, New York, United States. 348 p. Paperback, cloth US$ 75.00, paper US$ 18.95, ISBN-13 978-1-58367-226-6.

That doubling of food production over the next four decades will be needed to adequately nourish our human population is not news, but the incredible steps essential to achieve that goal and their political and social implications are less well reported. In this series of 16 essays edited by Fred Magdoff and Brian Tokar, several thoughtful specialists in global food issues explore the historical, biological, economic, energy, political and social dimensions of …

Estimating Construction Costs For A Low-Cost Quonset-Style Greenhouse, David P. Lambe, Stacy A. Adams, Ellen T. Paparozzi

Department of Agronomy and Horticulture: Faculty Publications

Double polyethylene Quonset-style greenhouses offergrowers and farmers a more cost-effective structure than glass- or acrylic-covered structures for growing plants off-season. These greenhouses are especially applicablefor producing off-season high value crops such as fruits and vegetables for local markets. To support this production alternative, this publication contains a list of greenhouse components, the start-up costs associated with these items and an estimate of the number of person hours required to assemble and outfit a 24-foot-by-72-foot double polyethylene, air-inflated greenhouse structure. As there are many options available for building double polyethylene greenhouses, the main purpose of this publication is to identify the …

Cover Crop Mixtures For The Western Corn Belt: Opportunities For Increased Productivity And Stability, Samuel E. Wortman, Charles A. Francis, John L. Lindquist

Department of Agronomy and Horticulture: Faculty Publications

Achieving agronomic and environmental benefits associated with cover crops oft en depends on reliable establishment of a highly productive cover crop community. The objective of this study was to determine if cover crop mixtures can increase productivity and stability compared to single species cover crops, and to identify those components most active in contributing to or detracting from mixture productivity. A rainfed field experiment was conducted near Mead, Nebraska, United States, in 2010 and 2011. Eight individual cover crop species (in either the Brassicaceae [mustard] or Fabaceae [legume] family) and four mixtures of these species (two, four, six, and eight …

Structural Variants In The Soybean Genome Localize To Clusters Of Biotic Stress-Response Genes, Leah K. Mchale, William J. Haun, Wayne W. Xu, Pudota B. Bhaskar, Justin E. Anderson, D. L. Hyten, Daniel J. Gerhardt, Jeffrey A. Jeddeloh, Robert M. Stupar

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide structural and gene content variations are hypothesized to drive important phenotypic variation within a species. Structural and gene content variations were assessed among four soybean (Glycine max) genotypes using array hybridization and targeted resequencing. Many chromosomes exhibited relatively low rates of structural variation (SV) among genotypes. However, several regions exhibited both copy number and presence-absence variation, the most prominent found on chromosomes 3, 6, 7, 16, and 18. Interestingly, the regions most enriched for SV were specifically localized to gene-rich regions that harbor clustered multigene families. The most abundant classes of gene families associated with these regions …

High-Resolution Mapping Of Open Chromatin In The Rice Genome, Wenli Zhang, Yufeng Wu, James C. Schnable, Zixian Zeng, Michael Freeling, Gregory E. Crawford, Jiming Jiang

Department of Agronomy and Horticulture: Faculty Publications

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promoters, indicating that the vast majority of the gene regulatory elements in rice are not located in promoter regions. We found 58% more DH sites in …