Plant Breeding and Genetics Commons^™

Maize Leaf Angle Genetic Gain Is Slowing Down In The Last Decades, Elvis F. Elli, Jode Edwards, Jianming Yu, Slobodan Trifunovic, Douglas M. Eudy, Kevin R. Kosola, Patrick S. Schnable, Kendall R. Lamkey, Sotirios V. Archontoulis

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Quantifying historical changes in maize leaf angle and factors affecting it can enhance our understanding of canopy architecture and light capture, and hence crop productivity. Our objectives were to (1) quantify leaf angle genetic gain per canopy position in Bayer's legacy maize (Zea mays L.) hybrids; (2) dissect the contribution of breeding from plant density on historical changes in leaf angle; and (3) synthesize our findings with literature to determine leaf angle changes over a century of breeding. We measured leaf angle in 78 maize hybrids released between 1980 and 2020 across eight environments in the US Corn Belt. …

Summaries Of Arkansas Cotton Research 2022, Fred Bourland

Arkansas Agricultural Experiment Station Research Series

The current economic environment continues to drive the need to produce record or near-record yields to be profitable. Price volatility in 2022 added another level of difficulty in the quest for being profitable. The cotton market saw significant movement after reaching a $1.5802 per pound high in May 2022, cotton prices corrected and more than halved in value at the October 2022 low, and then consolidated around the 80 cents per pound level in December 2022 (Cotton is Consolidating). Great uncertainties still exist for the upcoming season, most of which are outside of our control. These include, but are not …

Exome-Based New Allele-Specific Pcr Markers And Transferability For Sodicity Tolerance In Bread Wheat (Triticum Aestivum L.), Roopali Bhoite, Rosemary Smith, Urmil Bansal, Mirza Dowla, Harbans Bariana, Darshan L. Sharma

Grain and Other Field Crops Research Articles

Targeted exome-based genotype by sequencing (t-GBS), a sequencing technology that tags SNPs and haplotypes in gene-rich regions was used in previous genome-wide association studies (GWAS) for sodicity tolerance in bread wheat. Thirty-nine novel SNPs including 18 haplotypes for yield and yield-components were identified. The present study aimed at developing SNP-derived markers by precisely locating new SNPs on ~180 bp allelic sequence of t-GBS, marker validation, and SNP functional characterization based on its exonic location. We identified unknown locations of significant SNPs/haplotypes by aligning allelic sequences on to IWGSC RefSeqv1.0 on respective chromosomes. Eighteen out of the target 39 SNP locations …

Induction Of Ploidy Level On Three Patchouli (Pogostemon Cablin Benth) Cultivars By Colchicine In Vitro, Suseno Amien, Nikkita Putri Darmawan, Daniya Fathya

Jurnal Kultivasi

Patchouli plants produce essential oils and are used as a raw material and fixative agent for perfumes. The most widely cultivated patchouli plant in Indonesia is Aceh patchouli. Sexual propagation in Aceh patchouli plants is impossible as it does not flower. Genetic diversity can be elevated through another method, such as polyploidy induction using colchicine. This research aimed to evaluate the state-of-the-art application of polyploidization techniques as a breeding tool for callus-based explants. A completely randomized design with a factorial pattern was used in this experiment consisting of two factors, patchouli cultivars (Sidikalang, Tapak Tuan, and Lhokseumawe) and colchicine concentration …

Isolation Of Arabidopsis Thaliana Plants Homozygous For An Insertional Inactivation Mutation Within Atprp4., Sydney Raitz, Timothy D. Trott

Research in Biology

The AtPRP4 gene in Arabidopsis thaliana has been shown to function in several specific parts of the plant’s cell wall. It is shown to be expressed in the seeds, radicles, roots, leaves, inflorescences, and embryos of Arabidopsis thaliana. These patterns have suggested unique functions for ATPRP4 in determining cell-type-specific wall structure during the development of a plant as well as contributing to defense reactions against physical damage to the plant and pathogen infection within the plant. In this study, a simple DNA prep was performed on the true leaves of Arabidopsis thaliana. Subsequent PCR reactions were performed using …

Testing Of Resistance To Downy Mildew On Several Sweet Corn Inbred Lines Of 7th Generation, Heri Kustanto

Jurnal Kultivasi

Sweet corn is one of the most well-known horticultural crop commodities and can adapt to various climates and environments. Efforts to control downy mildew disease continue to be carried out in collaboration with various parties in different ways, including genetic improvement of the varieties planted. The purpose of this study was to test the resistance of the 7th generation of sweet corn inbred lines to downy mildew and to find out the phenotypic characters that affect downy mildew. The new inbred lines obtained from the results of a long breeding process will be better tested for resistance to downy mildew …

Breeding Cotton For Determinate Growth Habit: Increasing Cotton Fiber Yield By Remobilization Of End-Of-Season Perennial Reserves, Salman Naveed

All Dissertations

Cotton (Gossypium spp.) is a major export commodity for the U.S. Despite advances in plant breeding and management practices, the cotton yield gains in the U.S. have stagnated. Therefore, to increase cotton fiber yield, we undertook a novel approach by altering the growth habit of cotton from perennial to annual. In this effort, eight genotypes showing strong expression alleles for five floral induction and meristem identity genes were selected from 44 Upland cotton mini-core collection genotypes and genetically crossed in various combinations to stack the strong expression alleles in a genotype. These efforts have allowed us to develop high-yielding, …

Identifying Genetic Sources Of Anthracnose Resistance In Global Sorghum Lines, Mary-Frances Behnke

All Theses

Anthracnose of sorghum (causal agent: Colletotrichum sublineola) is the most detrimental disease of sorghum (Sorghum bicolor) worldwide, significantly reducing grain yield. This study includes a literature review of the disease and a meta-analysis of genome-wide association studies (GWAS) of anthracnose-resistance in sorghum as means to elucidate genetic sources of the trait. The meta-analysis includes genotypic and phenotypic data from 5 unique studies and 1,071 sorghum lines. Original genotyping-by-sequencing data from were obtained primarily from National Center for Biotechnology Information’s Sequence Read Archive (NCBI-SRA) and prepared and processed using the Tassel 5 GBS v2. pipeline. Phenotypic data were …

B. R. Wells Arkansas Rice Research Studies 2022, J. Hardke, X. Sha, N. Bateman

Arkansas Agricultural Experiment Station Research Series

Arkansas is the leading rice producer in the United States. The state represents 50.1% of total U.S. rice production and 49.8% of the total acres planted to rice in 2022. Rice cultural practices vary across the state and across the U.S. However, these practices are also dynamic and continue to evolve in response to changing political, environmental, and economic times. This survey was initiated in 2002 to monitor and record changes in the way Arkansas rice producers approach their livelihood. The survey was conducted by polling county extension agents in each of the counties in Arkansas that produce rice. Questions …

Genetic Dissection Of Alkalinity Tolerance In Rice (Oryza Sativa L.), Lovepreet Singh

LSU Doctoral Dissertations

Alkaline stress is a major threat to rice production globally. The resources for genetic improvement of alkalinity tolerance in rice are limited. We performed genome-wide association study (GWAS) and QTL mapping integrated with whole genome sequencing and expression analysis to identify and confirm QTLs and candidate genes. We developed a near-isogenic line (NIL) population to fine map the two important QTLs. In GWAS experiment, we genotyped and phenotyped a panel of indica and japonica genotypes for alkalinity tolerance and identified genomic regions and candidate genes conferring alkalinity tolerance. Principal component analysis revealed that alkalinity tolerance score, shoot dry weight, and …

Genetic Resources And Precise Gene Editing For Targeted Improvement Of Barley Abiotic Stress Tolerance, Sakura Karunarathne, Esther Walker, Darshan Sharma, Chengdao Li, Yong Han

Grain and Other Field Crops Research Articles

Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about …

Arkansas Corn And Grain Sorghum Research Studies 2022, Victor Ford, Jason Kelley, Nathan Mckinney Ii

Arkansas Agricultural Experiment Station Research Series

The 2022 edition of the Arkansas Corn and Grain Sorghum Research Studies Series includes research results on topics pertaining to corn and grain sorghum production, including weed, disease, and insect management; economics; sustainability; irrigation; post-harvest drying; soil fertility; mycotoxins; cover crop management; and research verification program results. Our objective is to capture and broadly distribute the results of research projects funded by the Arkansas Corn and Grain Sorghum Board. The intended audience includes producers and their advisors, current investigators, and future researchers. The Series serves as a citable archive of research results.

Reports in this publication are 2–3 year summaries. …

Likelihood-Based Tests Of Species Tree Hypotheses, Richard Adams, Michael Degiorgio

Entomology and Plant Pathology Faculty Publications and Presentations

Likelihood-based tests of phylogenetic trees are a foundation of modern systematics. Over the past decade, an enormous wealth and diversity of model-based approaches have been developed for phylogenetic inference of both gene trees and species trees. However, while many techniques exist for conducting formal likelihood-based tests of gene trees, such frameworks are comparatively underdeveloped and underutilized for testing species tree hypotheses. To date, widely used tests of tree topology are designed to assess the fit of classical models of molecular sequence data and individual gene trees and thus are not readily applicable to the problem of species tree inference. To …

Development And Issues Of Biotech Seed Industry In China, Peijuan Chi, Hualing Xie, Ping Zhao, Fang Chen, Ning Wu, Zhixi Tian, Weicai Yang, Yanping Yang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biotech seed industry is a strategic core industry. Biotechnology combined with digital technology has promoted the seed industry into an intelligent era, and the breeding paradigm has changed from “experimental selection” to “computational selection”. Biotech seed industry has become a research and development intensive industry, and the market is highly concentrated, which is controlled by large multinational enterprises. The scientific and technological output of China and the United States is in the first echelon, and the number of papers and authorized patents ranks among the top two in the world. From the perspective of core competitiveness, the United States is …

Genomic Approaches To Enhance Adaptive Plasticity To Cope With Soil Constraints Amidst Climate Change In Wheat, Roopali Bhoite, Yong Han, Alamuru Krishna Chaitanya, Rajeev K. Varshney, Darshan L. Sharma

Grain and Other Field Crops Research Articles

Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints—acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)—are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics …

International Rice Outlook: International Rice Baseline Projections 2022-2032, A. Durand-Morat, S. Bairagi, W. Mulimbi

AAES Research Reports and Research Bulletins

Rice prices in Asia increased since the Summer of 2022 mainly due to worries about a reduction in rice production in India caused by an abnormal monsoon season (Fig. 1). The upward trend in export prices solidified after India implemented a 20% export tariff on brown and milled long-grain rice, and a complete ban on exports of broken rice, in September 2022 to curve down exports and release the pressure on domestic rice prices. India’s rice export prices increased since then and proportionally to the value of the export tax. The latest estimates put rice production at 128 million metric …

Fluidity And Inconstancy: Australian Bush Tomatoes As An Exemplar Of Non-Normative Sex Expression, Christopher T. Martine

Faculty Journal Articles

Solanum, a genus of ~1500 global species, is one of the more interesting plant groups in which to study reproductive biology and ecology. Overwhelmingly, species in this group express full cosexuality, where individual plants have flowers containing both fully-functioning “male” (staminate) and “female” (carpellate) organs. However, there have been multiple and widespread evolutionary transitions within the genus to non-normative variations on this ancestral condition. Australian bush tomatoes (ca. 40 species) are especially diverse in this regard, with uncommon variation and combinations of unisexuality and cosexuality -- including, most notably, two sexual systems known as dioecy (unisexual male or female …

Arkansas Soybean Performance Tests 2022, J. F. Carlin, R. B. Mulloy, R. D. Bond

Arkansas Agricultural Experiment Station Research Series

Soybean variety and strain performance tests are conducted each year in Arkansas by the University of Arkansas System Division of Agriculture’s Arkansas Crop Variety Improvement Program. The tests provide information to companies developing varieties and/ or marketing seed within the state, and aid the Arkansas Cooperative Extension Service in formulating variety recommendations for soybean producers.

Genome-Wide Association Identifies Key Loci Controlling Blackberry Postharvest Quality, T. Mason Chizk, John R. Clark, Carmen Johns, Lacy Nelson, Hamid Ashrafi, Rishi Aryal, Margaret Worthington

Horticulture Faculty Publications and Presentations

Introduction: Blackberry (Rubus subgenus Rubus) is a soft-fruited specialty crop that often suffers economic losses due to degradation in the shipping process. During transportation, fresh-market blackberries commonly leak, decay, deform, or become discolored through a disorder known as red drupelet reversion (RDR). Over the past 50 years, breeding programs have achieved better fruit firmness and postharvest quality through traditional selection methods, but the underlying genetic variation is poorly understood.

Methods: We conducted a genome-wide association of fruit firmness and RDR measured in 300 tetraploid fresh-market blackberry genotypes from 2019-2021 with 65,995 SNPs concentrated in genic regions of the …

Exploring The Potential Of Heterosis To Improve Nitrogen Use Efficiency In Popcorn Plants, Talles De Oliveira Santos, Antônio Teixeira Do Amaral Junior, Rosimeire Barboza Bispo, Wallace De Paula Bernado, Bruna Rohem Simão, Valter Jário De Lima, Marta Simone Mendonça Freitas, Freddy Mora-Poblete, Roberto Dos Santos Trindade, Samuel Henrique Kamphorst, Weverton Pereira Rodrigues, Eliemar Campostrini, Flávia Nicácio Viana, Cosme Damião Cruz

Center for Plant Science Innovation: Faculty Publications

Nitrogen is crucial for plant growth and development, and improving nitrogen use efficiency (NUE) is a viable strategy for reducing dependence on nitrogen inputs and promoting sustainability. While the benefits of heterosis in corn are well known, the physiological mechanisms underlying this phenomenon in popcorn are less understood. We aimed to investigate the effects of heterosis on growth and physiological traits in four popcorn lines and their hybrids under two contrasting nitrogen conditions. We evaluated morpho-agronomic and physiological traits such as leaf pigments, the maximum photochemical efficiency of PSII, and leaf gas exchange. Components associated with NUE were also evaluated. …

Reaction-Diffusion System On Irregular Boundaries Reproduces Multiple Generations Of Petal Spot Patterns In Monkeyflower Hybrids, Emily Simmons

Biology and Medicine Through Mathematics Conference

No abstract provided.

Genome-Wide Association Study For Agronomic Traits In Bermudagrass (Cynodon Spp.), Lovepreet Singh

Theses and Dissertations

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. A germplasm collection of 206 bermudagrass accessions from 29 countries was genotyped with high-throughput genotyping-by-sequencing technique. Genomic diversity in this diverse germplasm panel was assessed with multifaceted approaches including population structure, phylogenetic analysis, principal component analysis, and genetic diversity parameters. This study revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs. Another critical issue in turfgrass breeding is the lack of information regarding the genetic …

Evaluation Of Early Maturing Cultivars, Optimal Harvest Timing, And Canopy Reflectance Of Peanut To Maximize Grade And Yield, Joseph Bryan Whittenton

Theses and Dissertations

Peanut digging timing is difficult to predict due to indeterminate growth and peanut pods maturing underground, resulting in the need to research methods that provide consistent measurements, while reducing time and effort for farmers and researchers. Experiments were conducted to evaluate the accuracy of the Maturity Index 1 and Maturity Index 2 in predicting peanut grade, the accuracy of the North Carolina 2 degree day method in predicting peanut yield, and remote sensing vegetative indices sensitivity equivalence (SEq) to peanut Maturity Index 2 and harvest grade (TSMK) for cultivars IPG-914 and Georgia-06G in Mississippi.

Maturity Index 1 and …

Investigating Effect Of Seed Source And Developing Germination Protocols To Improve Success In Restoration Of Arkansas Tallgrass Prairies, Rhiannon Spencerosa

Graduate Theses and Dissertations

American tallgrass prairie has faced losses estimated at 87-98% of original land area since European settlement. Native seeds are often used to supplement struggling or extinct plant populations in tallgrass prairie restoration and establishment sites. Two main considerations in restoration and establishment are from where to source seed and how to obtain high germination rates. In order to determine the effect of seed source, a common garden experiment was performed in Fayetteville, Arkansas in 2022 with five prairie species: Andropogon gerardii (big bluestem), Bouteloua curtipendula (sideoats grama), Panicum virgatum (switchgrass), Schizachyrium scoparium (little bluestem), and Sorghastrum nutans (Indiangrass). Seed was …

A Genome-Wide Association Study And Genomic Prediction For Phakopsora Pachyrhizi Resistance In Soybean, Haizheng Xiong, Yilin Chen, Yong-Bao Pan, Jinshe Wang, Weiguo Lu, Ainong Shi

Horticulture Faculty Publications and Presentations

Soybean brown rust (SBR), caused by Phakopsora pachyrhizi, is a devastating fungal disease that threatens global soybean production. This study conducted a genome-wide association study (GWAS) with seven models on a panel of 3,082 soybean accessions to identify the markers associated with SBR resistance by 30,314 high quality single nucleotide polymorphism (SNPs). Then five genomic selection (GS) models, including Ridge regression best linear unbiased predictor (rrBLUP), Genomic best linear unbiased predictor (gBLUP), Bayesian least absolute shrinkage and selection operator (Bayesian LASSO), Random Forest (RF), and Support vector machines (SVM), were used to predict breeding values of SBR resistance using …

In-Situ Characterization Of Jatigede Local Roid Banana (Musa Spp.) Based On Morphological And Agronomical Characteristics, Ade Ismail, Vika Faraditha Pratiwi, Haris Maulana, Ichsan Nurul Bari, Yani Maharani, Fajar Maulana Wijaya Kusumah

Jurnal Kultivasi

Banana (Musa spp.) is one of the agricultural commodities that’s widely cultivated and used by the local community. Currently, only 101 types of local varieties of bananas are registered in Indonesia; one of them is the Roid banana from Jatigede District. Roid bananas grow wild without any mandatory special care. Continuous use without any conservation and preservation efforts can lead to scarcity of Roid banana germplasm as a genetic resource. Therefore, it is necessary to identify the distribution and diversity of Roid bananas through in situ exploration and characterization activities. This study aimed to identify the potential for genetic diversity …

Complete Genome Sequences Of Chop, Delrio, And Grandslam, Three Gordonia Phages Isolated From Soil In Central Arkansas, Heidi N. Mathes, Elijah I. Christenson, John H. Crum, Emme M. Edmondson, Kassidy E. Gray, Luke W. Lawson, Lauren E. Lee, Michael P. Lee, Jackson A. Lipscomb, Morgan E. Masengale, Hannah G. Matthews, Charles M. Mcclain 4th, Tuesday N. Melton, Trace H. Morrow, Alexis M. Perry, David R. Rainwater, Grace E. Renois, Maryann F. Rettig, Duncan C. Troup, Allie J. Wilson, Nathan S. Reyna, Ruth Plymale

School of Dentistry Faculty Publications

Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.

Genetic Variability, Heritability, And Path Analysis For Agronomic Characters In Hybrid Maize, Slamet Bambang Priyanto, Roy Efendi, Bunyamin Zainuddin

Jurnal Kultivasi

Genetic parameters, which include genetic variability, heritability, and correlation between characters, are essential factors in the selection process. This study aims to: 1) determine the genetic variability and heritability for agronomic characters in hybrid maize and 2) determine the characteristics that directly affect hybrid maize yield. The experiment was conducted at Indonesian Cereal Research Institute (ICERI) Maros from June to October 2021. Fourteen maize hybrids genotypes were arranged in a randomized block design (RBD) with four replications. The observed traits were plant height, ear height, stalk diameter, leaf angle, leaf length, leaf width, days to anthesis, days to silking, days …

Protease Inhibitor Asp Enhances Freezing Tolerance By Inhibiting Protein Degradation In Kumquat, Hua Yang, Ke-Wei Qiao, Jin-Jing Teng, Jia-Bei Chen, Ying-Li Zhong, Li-Qun Rao, Xing-Yao Xiong, Huang Li

Center for Plant Science Innovation: Faculty Publications

Cold acclimation is a complex biological process leading to the development of freezing tolerance in plants. In this study, we demonstrated that cold-induced expression of protease inhibitor FmASP in a Citrus-relative species kumquat [Fortunella margarita (Lour.) Swingle] contributes to its freezing tolerance by minimizing protein degradation. Firstly, we found that only cold-acclimated kumquat plants, despite extensive leaf cellular damage during freezing, were able to resume their normal growth upon stress relief. To dissect the impact of cold acclimation on this anti-freezing performance, we conducted protein abundance assays and quantitative proteomic analysis of kumquat leaves subjected to cold acclimation …

Characterization Of Physical And Biochemical Traits In Wheat And Corn Plants Using High Throughput Image Analysis, Kantilata Thapa

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Plant phenotyping has been recognized as a rapidly growing field of research due to the labor-intensive, destructive, and time-consuming nature of traditional phenotyping methods. These phenotyping bottlenecks can be addressed by advancements in image-based phenotyping like RGB and hyperspectral imaging for the assessment of plant traits important for breeding purposes. This study aims (1) to characterize the physical and biochemical traits of wheat and corn plants using RGB and hyperspectral imaging in the greenhouse, and (2) to estimate leaf nitrogen (N), phosphorus (P), and potassium (K) content using hyperspectral imaging and an analytical spectral device (ASD spectrometer) and compare the …