Agricultural Science Commons^™

Intragenic Meiotic Crossovers Generate Novel Alleles With Transgressive Expression Levels, Sanzhen Liu, James C. Schnable, Alina Ott, Cheng-Ting Yeh, Nathan M. Springer, Jianming Yu, Gary Muehlbauer, Marja C. P. Timmermans, Michael J. Scanlon, Patrick S. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5' ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed …

Phosphate Deficiency Negatively Affects Early Steps Of The Symbiosis Between Common Bean And Rhizobia, Mariel C. Isidra-Arellano, Maria Del Rocio Reyero-Saavedra, Maria Del Socorro Sanchez-Correa, Lise Pingault, Sidharth Sen, Trupti Joshi, Lourdes Girard, Norma A. Castro-Guerrero, David G. Mendoza-Cozatl, Marc Libault, Oswaldo Valdes-Lopez

Department of Agronomy and Horticulture: Faculty Publications

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression …

Increasing Predictive Ability By Modeling Interactions Between Environments, Genotype And Canopy Coverage Image Data For Soybeans, Diego Jarquin, Reka Howard, Alencar Xavier, Sruti Das Choudhury

Department of Agronomy and Horticulture: Faculty Publications

Phenomics is a new area that offers numerous opportunities for its applicability in plant breeding. One possibility is to exploit this type of information obtained from early stages of the growing season by combining it with genomic data. This opens an avenue that can be capitalized by improving the predictive ability of the common prediction models used for genomic prediction. Imagery (canopy coverage) data recorded between days 14–71 using two collection methods (ground information in 2013 and 2014; aerial information in 2014 and 2015) on a soybean nested association mapping population (SoyNAM) was used to calibrate the prediction models together …

Long-Term Winter Wheat (Triticum Aestivum L.) Seasonal Irrigation Amount, Evapotranspiration, Yield, And Water Productivity Under Semiarid Climate, Koffi Djaman, Michael O'Neill, Curtis K. Owen, Daniel Smeal, Margaret West, Dallen Begay, Samuel Allen, Komlan Koudahe, Suat Irmak, Kevin Lombard

Department of Agronomy and Horticulture: Faculty Publications

A long-term field experiment was conducted from 2002 to 2014 for the evaluation of yield and water productivity of three winter wheat varieties—Kharkof, Scout 66, and TAM107—under sprinkler irrigation at New Mexico State University Agricultural Science Center at Farmington, NM. Winter wheat daily evapotranspiration was estimated following the United Nations Food and Agriculture Organization FAO crop coefficient approach (ETc = Kc ETo), and crop water use efficiency (CWUE), evapotranspiration water use efficiency (ETWUE), and irrigation water use efficiency (IWUE) were estimated for each growing season. There was inter-annual variation in seasonal precipitation and irrigation amounts. Seasonal irrigation amounts varied from …

Genome-Wide Association Study Reveals Novel Genomic Regions For Grain Yield And Yield-Related Traits In Drought-Stressed Synthetic Hexaploid Wheat, Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Synthetic hexaploid wheat (SHW; 2n = 6x = 42, AABBDD, Triticum aestivum L.) is produced from an interspecific cross between durum wheat (2n = 4x = 28, AABB, T. turgidum L.) and goat grass (2n = 2x = 14, DD, Aegilops tauschii Coss.) and is reported to have significant novel alleles-controlling biotic and abiotic stresses resistance. A genome-wide association study (GWAS) was conducted to unravel these loci [marker–trait associations (MTAs)] using 35,648 genotyping-by-sequencing-derived single nucleotide polymorphisms in 123 SHWs. We identified 90 novel MTAs (45, 11, and 34 on the A, B, and D …

Wheat Height Estimation Using Lidar In Comparison To Ultrasonic Sensor And Uas, Wenan Yuan, Jiating Li, Madhav Bhatta, Yeyin Shi, P. Stephen Baenziger, Yufeng Ge

Department of Agronomy and Horticulture: Faculty Publications

As one of the key crop traits, plant height is traditionally evaluated manually, which can be slow, laborious and prone to error. Rapid development of remote and proximal sensing technologies in recent years allows plant height to be estimated in more objective and efficient fashions, while research regarding direct comparisons between different height measurement methods seems to be lagging. In this study, a ground-based multi-sensor phenotyping system equipped with ultrasonic sensors and light detection and ranging (LiDAR) was developed. Canopy heights of 100 wheat plots were estimated five times during a season by the ground phenotyping system and an unmanned …

Genetic Architecture Of Common Bunt Resistance In Winter Wheat Using Genome-Wide Association Study, Amira M. I. Mourad, Ahmed Sallam, Vikas Belamkar, Ezzat Mahdy, Bahy Bakheit, Atif Abo El-Wafaa, P. Stephen Baenziger

Department of Agronomy and Horticulture: Faculty Publications

Background: Common bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative.

Results: To identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine …

Root And Shoot Contribution To Carbon And Nitrogen Inputs In The Topsoil Layer In No-Tillage Crop Systems Under Subtropical Conditions, Marciel Redin, Sylvie Recous, Celso Aita, Bruno Chaves, Ismael Cristiano Pfeifer, Leonardo Mendes Bastos, Getulio Elias Pilecco, Sandro Jose Giacomini

Department of Agronomy and Horticulture: Faculty Publications

Recycling of carbon (C) and nitrogen (N) from plants into soils is decisive for maintaining soil organic matter and soil fertility. Therefore, we quantified plant biomass and C and N in the shoots and roots from the topsoil layer for a wide range of annual crops grown under subtropical conditions. We grew 26 species, 13 main crops, and 13 cover crops, in the field in standard sowing arrangements. Root biomass was recovered from the 0.00-0.20 m soil layer at flowering, and shoot biomass was measured at flowering for all crops and at maturity only for the main crops. Root dry …

Improving Fertilizer Recommendations For Nepalese Farmers With The Help Of Soil-Testing Mobile Van, Sunil Pandey, Netra Prasad Bhatta, Prakash Paudel, Rajan Pariyar, Kiran Hari Maskey, Janardan Khadka, Tuk Bahadur Thapa, Balaram Rijal, Dinesh Panday

Department of Agronomy and Horticulture: Faculty Publications

Smallholder farmers dominate agriculture in Nepal. These farmers have poor knowledge about agriculture and lack of support for soil management and integrated plant-nutrient systems. Focusing on the importance and need for soil-fertility management, a soil-testing mobile van program has recently been introduced in Nepal by Soil Management Directorate, Hariharbhawan. With the introduction of the mobile lab, famers can get their soil tested for nutrient deficiencies and fertilizer requirements at their doorsteps. Using mobile lab, spatial distributions of chemical properties, including pH, organic matter (OM), total nitrogen (N), available phosphorus (as P₂O₅), and available potassium (as K …

Genotype Imputation In Winter Wheat Using First-Generation Haplotype Map Snps Improves Genome-Wide Association Mapping And Genomic Prediction Of Traits, Moses Nyine, Shichen Wang, Kian Kiani, Katherine Jordan, Shuyu Liu, Patrick Byrne, Scott Haley, Stephen Baenziger, Shiaoman Chao, Robert Bowden, Eduard Akhunov

Department of Agronomy and Horticulture: Faculty Publications

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study …

Genome-Wide Association Study Reveals Novel Genomic Regions Associated With 10 Grain Minerals In Synthetic Hexaploid Wheat, Madhav Bhatta, P. Stephen Baenziger, Brian M. Waters, Rachana Poudel, Vikas Belamkar, Jesse Poland, Alexey Morgounov

Department of Agronomy and Horticulture: Faculty Publications

Synthetic hexaploid wheat (SHW; Triticum durum L. x Aegilops tauschii Coss.) is a means of introducing novel genes/genomic regions into bread wheat (T. aestivum L.) and a potential genetic resource for improving grain mineral concentrations. We quantified 10 grain minerals (Ca, Cd, Cu, Co, Fe, Li, Mg, Mn, Ni, and Zn) using an inductively coupled mass spectrometer in 123 SHWs for a genome-wide association study (GWAS). A GWAS with 35,648 single nucleotide polymorphism (SNP) markers identified 92 marker-trait associations (MTAs), of which 60 were novel and 40 were within genes, and the genes underlying 20 MTAs had annotations suggesting …

Stolon Development And Cultural Production Practices Of Winter-Grown Strawberries, Donna M. Morrison, Erin Blankenship, Paul Read, Ellen Paparozzi

Department of Agronomy and Horticulture: Faculty Publications

The four experiments described here are part of a 5-year program focused on determining whether day-neutral and short-day strawberries would be suitable for commercial offseason/ winter (temperate climate) production in greenhouses. All research was performed using container-grown plants fertigated through a capillary mat production system with heat supplied under the benches. The first experiment focused on stolon development. The second experiment investigated the influence of stolon removal on berry production and included the removal of flowers for the first three weeks. The third and fourth experiments were conducted as a comparison of university research (experiment 3) versus a commercial operation …

Wildland Fire Science Literacy: Education, Creation, And Application, Devan Allen Mcgranahan, Carissa L. Wonkka

Department of Agronomy and Horticulture: Faculty Publications

Wildland fire science literacy is the capacity for wildland fire professionals to understand and communicate three aspects of wildland fire: (1) the fundamentals of fuels and fire behavior, (2) the concept of fire as an ecological regime, and (3) multiple human dimensions of wildland fire and the socio-ecological elements of fire regimes. Critical to wildland fire science literacy is a robust body of research on wildland fire. Here, we describe how practitioners, researchers, and other professionals can study, create, and apply robust wildland fire science. We begin with learning and suggest that the conventional fire ecology canon include detail on …

An Exome-Seq Based Tool For Mapping And Selection Of Candidate Genes In Maize Deletion Mutants, Shangang Jia, Kyla Morton, Chi Zhang, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 X Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA …

Genetic Architecture Of Soybean Yield And Agronomic Traits, Brian W. Diers, Jim Specht, Katy Martin Rainey, Perry Cregan, Qijian Song, Vishnu Ramasubramanian, George Graef, Randall L. Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah Mchale, Stella K. Kantartzi, Alencar Xavier, Rouf Mian, Robert M. Stupar, Jean-Michel Michno, Yong-Qiang Charles An, Wolfgang Goettel, Russell Ward, Carolyn Fox, Alexander E. Lipka, David Hyten, Troy Cary, William D. Beavis

Department of Agronomy and Horticulture: Faculty Publications

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. …

Influence Of Harvest Date On Seed Yield And Quality In Forage Kochia, Cody F. Creech, Blair L. Waldron, Corey V. Ransom, Dale R. Zobell, Joseph Earl Creech

Department of Agronomy and Horticulture: Faculty Publications

Forage kochia (Bassia prostrata) is used for rangeland reclamation and livestock and wildlife forage, but limited research has been conducted on its seed production. Therefore, this research evaluated the effect of harvest date on seed weight, germination, and seed yield of forage kochia subspecies virescens and grisea. Seed was harvested from individual plants for 3 years during October, November, and December. October harvest had the lightest 100-seed weights, with the November harvest slightly heavier than December, for most accessions. Cultivar Snowstorm and breeding line Sahsel, both subsp. grisea, had the greatest 100-seed weights in November, 155 …

Maize And Soybean Root Front Velocity And Maximum Depth In Iowa, Usa, Raziel A. Ordóñez, Michael J. Castellano, J. L. Hatfield, M. J. Helmers, Mark A. Licht, Matt Liebman, Ranae Dietzel, Rafael Martinez-Feria, Javed Iqbal, Laila A. Puntel, S. Carolina Córdova, Kaitlin Togliatti, Emily E. Wright, Sotirios V. Archontoulis

Department of Agronomy and Horticulture: Faculty Publications

Quantitative measurements of root traits can improve our understanding of how crops respond to soil and weather conditions, but such data are rare. Our objective was to quantify maximum root depth and root front velocity (RFV) for maize (Zea mays) and soybean (Glycine max) crops across a range of growing conditions in the Midwest USA. Two sets of root measurements were taken every 10–15 days: in the crop row (in-row) and between two crop rows (center-row) across six Iowa sites having different management practices such as planting dates and drainage systems, totaling 20 replicated experimental treatments. …

Sequences Involved In Plant Yield And Methods Of Using, Harkamal Walia, Dante Placido, Thomas E. Clemente

Department of Agronomy and Horticulture: Faculty Publications

Nucleic acid sequences involved in plant yield are provided, as are methods of using such nucleic acid sequences .

Building Resilience In Social-Ecological Food Systems In Vermont, Kristine Lien Skog, Stine Elisabeth Eriksen, Christy Anderson Brekken, Charles A. Francis

Department of Agronomy and Horticulture: Faculty Publications

There is an expanding interest in Local Food Systems (LFSs) in Vermont, United States, along with a growing effort to create adaptive governance to facilitate action. In this case study, we investigate how adaptive governance of LFS can provide ideas and act as a catalyst for creating resilience in other social-ecological systems (SESs). By participating in meetings and interviewing stakeholders inside and outside the Vermont LFS network, we found that consumers were highly motivated to participate by supporting environmental issues, the local economy, and interactive communities, as well as building social relationships. Farmers experienced better income and increased respect in …

Identification Of Quantitative Trait Loci Conferring Resistance To Tan Spot In A Biparental Population Derived From Two Nebraska Hard Red Winter Wheat Cultivars, Gayan K. Kariyawasam, Waseem Hussain, Amanda Easterly, Mary Guttieri, Vikas Belamkar, Jesse Poland, Jorge Venegas, Stephen Baenziger, Francois Marais, Jack B. Rasmussen, Zhaohui Liu

Department of Agronomy and Horticulture: Faculty Publications

Tan spot, caused by Pyrenophora triticirepentis (Ptr), is a destructive foliar disease in all types of cultivated wheat worldwide. Genetics of tan spot resistance in wheat is complex, involving insensitivity to fungal-produced necrotrophic effectors (NEs), major resistance genes, and quantitative trait loci (QTL) conferring race-nonspecific and race-specific resistance. The Nebraska hard red winter wheat (HRWW) cultivar ‘Wesley’ is insensitive to Ptr ToxA and highly resistant to multiple Ptr races, but the genetics of resistance in this cultivar is unknown. In this study, we used a recombinant inbred line (RIL) population derived from a cross between Wesley and another …