Horticulture Commons^™

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 …

Skim Resequencing Finely Maps The Downy Mildew Resistance Loci Rpf2 And Rpf3 In Spinach Cultivars Whale And Lazio, Gehendra Bhattarai, Ainong Shi, Beiquan Mou, James C. Correll

Horticulture Faculty Publications and Presentations

Commercial production of spinach (Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance (R) genes. Progeny populations segregating for RPF2 locus derived from resistant differential …

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 …

Evaluating Species-Specific Replenishment Solution Effects On Plant Growth And Root Zone Nutrients With Hydroponic Arugula (Eruca Sativa L.) And Basil (Ocimum Basilicum L.), Lauren L. Houston, Ryan W. Dickson, Matthew B. Bertucci, Trenton L. Roberts

Horticulture Faculty Publications and Presentations

Managing nutrients in recirculating solutions can be challenging in hydroponic production, and poor management practices can rapidly result in root zone nutrient imbalances in reduced yield. Using mass balance principles to formulate hydroponic replenishment solutions is a proposed strategy to reduce nutrient imbalances and the need to periodically replace the hydroponic solution. Objectives were to (1) formulate species-specific nutrient replenishment solutions for arugula (Eruca sativa L.) and basil (Ocimum basilicum L.) using mass balance principles and (2) evaluate the effects of using these replenishment solutions on plant growth and root zone nutrients over time. In the first experiment, …

A Genome-Wide Association Study And Genomic Prediction For Fiber And Sucrose Contents In A Mapping Population Of Lcp 85-384 Sugarcane, Haizheng Xiong, Yilin Chen, Yong-Bao Pan, Ainong Shi

Horticulture Faculty Publications and Presentations

Sugarcane (Saccharum spp. hybrids) is an economically important crop for both sugar and biofuel industries. Fiber and sucrose contents are the two most critical quantitative traits in sugarcane breeding that require multiple-year and multiple-location evaluations. Marker-assisted selection (MAS) could significantly reduce the time and cost of developing new sugarcane varieties. The objectives of this study were to conduct a genome-wide association study (GWAS) to identify DNA markers associated with fiber and sucrose contents and to perform genomic prediction (GP) for the two traits. Fiber and sucrose data were collected from 237 self-pollinated progenies of LCP 85-384, the most popular …

Mapping And Selection Of Downy Mildew Resistance In Spinach Cv. Whale By Low Coverage Whole Genome Sequencing, Gehendra Bhattarai, Dotun Olaoye, Beiquan Mou, James C. Correll, Ainong Shi

Horticulture Faculty Publications and Presentations

Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes …

Genetic Dissection Of Nitrogen Induced Changes In The Shoot And Root Biomass Of Spinach, Vijay Joshi, Ainong Shi, Amit Kumar Mishra, Haramrit Gill, James Dipiazza

Horticulture Faculty Publications and Presentations

Efficient partitioning of above and below-ground biomass in response to nitrogen (N) is critical to the productivity of plants under sub-optimal conditions. It is particularly essential in vegetable crops like spinach with shallow root systems, a short growth cycle, and poor nitrogen use efficiency. In this study, we conducted a genome-wide association study (GWAS) to explore N-induced changes using spinach accessions with diverse genetic backgrounds. We evaluated phenotypic variations as percent changes in the shoot and root biomass in response to N using 201 spinach accessions grown in randomized complete blocks design in a soilless media under a controlled environment. …

Identification Of Candidate Genes And Genomic Selection For Seed Protein In Soybean Breeding Pipeline, Jun Qin, Fengmin Wang, Qingsong Zhao, Ainong Shi, Tiantian Zhao, Qijian Song, Waltram Ravelombola, Hongzhou An, Long Yan, Chunyan Yang, Mengchen Zhang

Horticulture Faculty Publications and Presentations

Soybean is a primary meal protein for human consumption, poultry, and livestock feed. In this study, quantitative trait locus (QTL) controlling protein content was explored via genome-wide association studies (GWAS) and linkage mapping approaches based on 284 soybean accessions and 180 recombinant inbred lines (RILs), respectively, which were evaluated for protein content for 4 years. A total of 22 single nucleotide polymorphisms (SNPs) associated with protein content were detected using mixed linear model (MLM) and general linear model (GLM) methods in Tassel and 5 QTLs using Bayesian interval mapping (IM), single-trait multiple interval mapping (SMIM), single-trait composite interval mapping maximum …

Genome-Wide Association Study And Genomic Prediction For Bacterial Wilt Resistance In Common Bean (Phaseolus Vulgaris) Core Collection, Bazgha Zia, Ainong Shi, Dotun Olaoye, Haizheng Xiong, Waltram Ravelombola, Paul Gepts, Howard F. Schwartz, Mark A. Brick, Kristen Otto, Barry Ogg, Senyu Chen

Horticulture Faculty Publications and Presentations

Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 …

Glutathione S-Transferase: A Candidate Gene For Berry Color In Muscadine Grapes (Vitis RotundifoliA), Aruna Varanasi, Margaret Worthington, Lacy Nelson, Autumn Brown, Thomas Mason Chizk, Renee Threlfall, Luke Howard, Patrick Conner, Rosa Figueroa-Balderas, Melanie Massonnet, Dario Cantu, John R. Clark

Horticulture Faculty Publications and Presentations

Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline …

Genetic Diversity Of Wild And Cultivated Muscadine Grapes (Vitis Rotundifolia Michx.), Kenneth Buck, Margaret Worthington

Horticulture Faculty Publications and Presentations

The muscadine (Vitis rotundifolia syn. Muscadinia rotundifolia) is an American grape species native to the southeastern United States that has been cultivated for centuries. Muscadines are one of three grape species in subgenus Muscadinia with a chromosome number of 2n = 40 (V. rotundifolia, Vitis munsoniana, and Vitis popenoei), making them genetically distinct from the European wine and table grape (Vitis vinifera) and other species in subgenus Euvitis. Crop improvement efforts have been continuous since the late 19th century, yet the germplasm that served as the foundation for early muscadine …

Genetic Architecture Of Salt Tolerance In A Multi-Parent Advanced Generation Inter-Cross (Magic) Cowpea Population, Waltram Ravelombola, Ainong Shi, Boa-Lam Huynh, Jun Qin, Haizheng Xiong, Aurora Manley, Lingdi Dong, Dotun Olaoye, Gehendra Bhattarai, Bazgha Zia, Huda Alshaya, Ibtisam Alatawi

Horticulture Faculty Publications and Presentations

Background

Previous reports have shown that soil salinity is a growing threat to cowpea production, and thus the need for breeding salt-tolerant cowpea cultivars. A total of 234 Multi-Parent Advanced Generation Inter-Cross (MAGIC) lines along with their 8 founders were evaluated for salt tolerance under greenhouse conditions. The objectives of this study were to evaluate salt tolerance in a multi-parent advanced generation inter-cross (MAGIC) cowpea population, to identify single nucleotide polymorphism (SNP) markers associated with salt tolerance, and to assess the accuracy of genomic selection (GS) in predicting salt tolerance, and to explore possible epistatic interactions affecting salt tolerance in …

Population Structure And Genetic Diversity Analysis In Sugarcane (Saccharum Spp. Hybrids) And Six Related Saccharum Species, Haizheng Xiong, Yilin Chen, San-Ji Gao, Yong-Bao Pan, Ainong Shi

Horticulture Faculty Publications and Presentations

Sugarcane (Saccharum spp. hybrids) is one of the most important commercial crops for sugar, ethanol, and other byproducts production; therefore, it is of great significance to carry out genetic research. Assessing the genetic population structure and diversity plays a vital role in managing genetic resources and gene mapping. In this study, we assessed the genetic diversity and population structure among 196 Saccharum accessions, including 34 S. officinarum, 69 S. spontaneum, 17 S. robustum, 25 S. barberi, 13 S. sinense, 2 S. edule, and 36 Saccharum spp. hybrids. A total of 624 polymorphic SSR …

Evaluation Of Peat Blended With Pine Wood Components For Effects On Substrate Physical Properties, Nitrogen Immobilization, And Growth Of Petunia (Petunia X Hybrida Vilm.-Andr.), Ryan W. Dickson, Kalyn M. Helms, Brian E. Jackson, Leala M. Machesney, Jung Ae Lee

Horticulture Faculty Publications and Presentations

The first objective was to evaluate wood components for differences in nitrogen (N) immobilization and effects on substrate physical properties. The second objective was to evaluate peat substrates amended with pine wood components for effects on plant growth, shoot tissue N, and fertigation practices during production. Substrates consisted of a coarse sphagnum peat blended with four types of processed pine wood at rates of 15%, 30%, 45%, and 60% (by volume). For comparison, peat was also blended with an aged pine bark, perlite, and coconut coir. Nitrogen immobilization was measured for individual components, except perlite. Individual components and blended substrates …

Genome-Wide Association Study And Genomic Prediction Of White Rust Resistance In Usda Grin Spinach Germplasm, Ainong Shi, Gehendra Bhattarai, Haizheng Xiong, Carlos A. Avila, Chunda Feng, Bo Liu, Vijay Joshi, Larry Stein, Beiquan Mou, Lindsey J. Du Toit, James C. Corell

Horticulture Faculty Publications and Presentations

White rust, caused by Albugo occidentalis, is one of the major yield-limiting diseases of spinach (Spinacia oleracea) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. …

Resequencing Worldwide Spinach Germplasm For Identification Of Field Resistance Qtls To Downy Mildew And Assessment Of Genomic Selection Methods, Gehendra Bhattarai, Ainong Shi, Beiquan Mou, James C. Correll

Horticulture Faculty Publications and Presentations

Downy mildew, commercially the most important disease of spinach, is caused by the obligate oomycete Peronospora effusa. In the past two decades, new pathogen races have repeatedly overcome the resistance used in newly released cultivars, urging the need for more durable resistance. Commercial spinach cultivars are bred with major R genes to impart resistance to downy mildew pathogens and are effective against some pathogen races/isolates. This work aimed to evaluate the worldwide USDA spinach germplasm collections and commercial cultivars for resistance to downy mildew pathogen in the field condition under natural inoculum pressure and conduct genome wide association analysis …

Genetic Diversity, Structure, And Selective Sweeps In Spinacia Turkestanica Associated With The Domestication Of Cultivated Spinach, Sanjaya Gyawali, Gehendra Bhattarai, Ainong Shi, Chris Kik, Lindsey J. Du Toit

Horticulture Faculty Publications and Presentations

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica …

Silicon Foliar Spray And Substrate Drench Effects On Plant Growth, Morphology, And Resistance To Wilting With Container-Grown Edible Species, Joshua Tebow, Lauren L. Houston, Ryan W. Dickson

Horticulture Faculty Publications and Presentations

The objective of this study was to evaluate silicon (Si) foliar spray and substrate drench effects on plant growth and morphology for container-grown edible crops during greenhouse production, as well as resistance to plant wilting during post-production. In the first greenhouse experiment, basil received Si foliar sprays at 0, 50, 100, 200, and 400 mg∙L^–1 Si. In the second greenhouse experiment, Si was applied as either a foliar spray (500 mg∙L–1 Si) or substrate drench (100 mg∙L^–1 Si) with six edible crop species. Supplemental Si increased shoot Si levels but had minimal effects on plant growth and morphology, …

Dormant Sprigging Of Bermudagrass And Zoysiagrass, Juming Zhang, Michael Richardson, Douglas Karcher, John Mccalla, Jingwen Mai, Hanfu Luo

Horticulture Faculty Publications and Presentations

Many bermudagrass (Cynodon sp.) and zoysiagrass (Zoysia sp.) cultivars are not available as seed and are commonly planted vegetatively using sprigs, especially for sod production or in sand-based systems. Sprig planting is typically done in late spring or early summer, but this can result in an extended grow-in period and delay the use of the turf in the first growing season. The objective of this study was to determine if sprigs of bermudagrass and zoysiagrass could be planted earlier in the year, during the dormancy phase, to hasten establishment. A field study was carried out in Fayetteville, AR, …

Genome-Wide Association Study And Genomic Selection For Yield And Related Traits In Soybean, Waltram Second Ravelombola, Jun Qin, Ainong Shi, Qijian Song, Jin Yuan, Fengmin Wang, Pengyin Chen, Long Yan, Yan Feng, Tiantian Zhao, Yaning Meng, Kexin Guan, Chunyan Yang, Mengchen Zhang

Horticulture Faculty Publications and Presentations

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and …

Fertilizer And Plant Growth Regulator Strategies For Improving Consumer Performance Of Container-Grown Petunia, Jonathan Ebba, Ryan W. Dickson, Paul R. Fisher, Crysta N. Harris, Todd Guerdat, Sofia Flores

Horticulture Faculty Publications and Presentations

The overall goal was to evaluate fertilizer options for greenhouse producers, with or without a plant growth regulator (PGR) application, to improve subsequent performance of container-grown annuals. Petunia (Petunia × hybrida) was the model container-grown crop in simulated production and consumer environments. The first experiment at two locations (New Hampshire and Florida) compared strategies using water-soluble fertilizer [WSF (17N–1.8P–14.1K)], controlled-release fertilizers (CRF), and slow-release fertilizers (SRF) that were either applied throughout or at the end of the 8-week production phase [point of shipping (POS)] for petunia rooted cuttings grown in 8-inch azalea containers. In the subsequent simulated “consumer” …

High Resolution Mapping And Candidate Gene Identification Of Downy Mildew Race 16 Resistance In Spinach, Gehendra Bhattarai, Wei Yang, Ainong Shi, Chunda Feng, Braham Dhillon, James C. Correll, Beiquan Mou

Horticulture Faculty Publications and Presentations

Background

Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was …

Genome-Wide Simple Sequence Repeats (Ssr) Markers Discovered From Whole-Genome Sequence Comparisons Of Multiple Spinach Accessions, Gehendra Bhattarai, Ainong Shi, Devi R. Kandel, Nora Solis-Garcia, Jorge Alberto Da Silva, Carlos A. Avila

Horticulture Faculty Publications and Presentations

The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences …

Loci Discovery, Network-Guided Approach, And Genomic Prediction For Drought Tolerance Index In A Multi-Parent Advanced Generation Intercross (Magic) Cowpea Population, Waltram Ravelombola, Ainong Shi, Boa-Lam Huynh

Horticulture Faculty Publications and Presentations

Cowpea is a nutrient-dense legume that significantly contributes to the population’s diet in sub-Saharan Africa and other regions of the world. Improving cowpea cultivars to be more resilient to abiotic stress such as drought would be of great importance. The use of a multi-parent advanced generation intercross (MAGIC) population has been shown to be efficient in increasing the frequency of rare alleles that could be associated with important agricultural traits. In addition, drought tolerance index has been reported to be a reliable parameter for assessing crop tolerance to water-deficit conditions. Therefore, the objectives of this study were to evaluate the …

Testing Flowering Perennial Plants In A Bermudagrass (Cynodon Spp.) Lawn, Paige Elizabeth Boyle, Michelle Wisdom

Horticulture Faculty Publications and Presentations

Most pollinating insects require a season-long succession of floral resources to fulfill life-cycle requirements. Incorporating forbs into turfgrass sites may create a season-long sequence of flowers to support foraging pollinators. However, persistence of forbs in warm-season turfgrasses such as bermudagrass (Cynodon spp.) may be affected by the competitive nature of the turfgrass and routine management practices such as mowing. A 2-year study was conducted to evaluate seven forbs (Bellis perennis L., Lotus corniculatus L., Prunella vulgaris L., Trifolium fragiferum L. ‘Fresa’, Trifolium repens L. ‘Durana’ and ‘Resolute’, Trifolium subterraneum L.) for persistence and ability to produce floral resources …