Agriculture Commons^™

Plasticity Of Sorghum Biomass And Inflorescence Traits In Response To Nitrogen Application, Kyle M. Linders

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Nitrogen is an essential nutrient required for growth and development in plants. Insufficient nitrogen availability can reduce vegetative growth and grain yield. However, nitrogen is a costly input for farmers, is energy intensive to manufacture, and runoff of excess nitrogen fertilizer impacts water quality. Compared to its close relative, maize, sorghum has much greater resilience to nitrogen and water deficit, and heat stress, allowing sorghum to be grown with fewer inputs and on marginal land. Variation in total biomass accumulation and grain yield between sorghum accessions, as well as between nitrogen conditions, can be largely explained by differences in vegetative …

Seedextractor: An Open-Source Gui For Seed Image Analysis, Feiyu Zhu, Puneet Paul, Waseem Hussain, Kyle Wallman, Balpreet K. Dhatt, Jaspreet Sandhu, Larissa Irvin, Gota Morota, Hongfeng Yu, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes 2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it …

Genome-Wide Association Mapping And Genomic Prediction Of Anther Extrusion In Cimmyt Hybrid Wheat Breeding Program Via Modeling Pedigree, Genomic Relationship, And Interaction With The Environment, Anil Adhikari, Bhoja Raj Basnet, Jose Crossa, Susanne Dreisigacker, Fatima Camarillo, Pradeep Kumar Bhati, Diego Jarquin, Yann Manes, Amir M.H. Ibrahim

Department of Agronomy and Horticulture: Faculty Publications

Anther extrusion (AE) is the most important male floral trait for hybrid wheat seed production. AE is a complex quantitative trait that is difficult to phenotype reliably in field experiments not only due to high genotype-by-environment effects but also due to the short expression window in the field condition. In this study, we conducted a genome-wide association scan (GWAS) and explored the possibility of applying genomic prediction (GP) for AE in the CIMMYT hybrid wheat breeding program. An elite set of male lines (n = 603) were phenotype for anther count (AC) and anther visual score (VS) across three field …

Perspectives On Low Temperature Tolerance And Vernalization Sensitivity In Barley: Prospects For Facultative Growth Habit, Maria Munoz-Amatriain, Javier Hernandez, Dustin Herb, P Stephen Baenziger, Anne Marie Bochard, Flavio Capettini, Ana Casas, Alfonso Cuesta-Marcos, Claus Einfeldt, Scott Fisk, Amelie Genty, Laura Helgerson, Markus Herz, Gongshe Hu, Ernesto Igartua, Ildiko Karsai, Toshiki Nakamura, Kazuhiro Sato, Kevin Smith, Eric Stockinger, William Thomas, Patrick Hayes

Department of Agronomy and Horticulture: Faculty Publications

One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known …

Gwas: Fast-Forwarding Gene Identification And Characterization In Temperate Cereals: Lessons From Barley – A Review, Ahmad M. Alqudah, Ahmed Sallam, P. Stephen Baenziger, Andreas Börner

Department of Agronomy and Horticulture: Faculty Publications

Understanding the genetic complexity of traits is an important objective of small grain temperate cereals yield and adaptation improvements. Bi-parental quantitative trait loci (QTL) linkage mapping is a pow- erful method to identify genetic regions that co-segregate in the trait of interest within the research pop- ulation. However, recently, association or linkage disequilibrium (LD) mapping using a genome-wide association study (GWAS) became an approach for unraveling the molecular genetic basis underlying the natural phenotypic variation. Many causative allele(s)/loci have been identified using the power of this approach which had not been detected in QTL mapping populations. In barley (Hordeum …

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 …

Substantial Contribution Of Genetic Variation In The Expression Of Transcription Factors To Phenotypic Variation Revealed By Erd-Gwas, Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton, Patrick S. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

Results: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes. In contrast, transcription factors are depleted among genes whose expression is either highly stable or highly variable across genotypes. We developed a …

Genome-Wide Characterization Of Non-Reference Transposable Element Insertion Polymorphisms Reveals Genetic Diversity In Tropical And Temperate Maize, Xianjun Lai, James C. Schnable, Zhengqiao Liao, Jie Xu, Gengyun Zhang, Chuan Li, Erliang Hu, Tingzhao Rong, Yunbi Xu, Yanli Li

Department of Agronomy and Horticulture: Faculty Publications

Background: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of …

Identification And Verification Of Qtl Associated With Frost Tolerance Using Linkage Mapping And Gwas In Winter Faba Bean, Ahmed Sallam, Mustapha Arbaoui, Mohamed El-Esawi, Nathan Abshire

Department of Agronomy and Horticulture: Faculty Publications

Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the …

A Genome-Wide Association Study Of Seed Protein And Oil Content In Soybean, Eun-Young Hwang, Qijian Song, Gaofeng Jia, James E. Specht, David L. Hyten, Jose Costa, Perry B. Cregan

Department of Agronomy and Horticulture: Faculty Publications

Background: Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of …