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Shrestha SL, Tobias CM, Bhandari HS, Bragg J, Nayak S, Goddard K, Allen F. Mapping quantitative trait loci for biomass yield and yield-related traits in lowland switchgrass (Panicum virgatum L.) multiple populations. G3 (BETHESDA, MD.) 2023; 13:jkad061. [PMID: 36947434 PMCID: PMC10151402 DOI: 10.1093/g3journal/jkad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/15/2022] [Accepted: 03/09/2023] [Indexed: 03/23/2023]
Abstract
Switchgrass can be used as an alternative source for bioenergy production. Many breeding programs focus on the genetic improvement of switchgrass for increasing biomass yield. Quantitative trait loci (QTL) mapping can help to discover marker-trait associations and accelerate the breeding process through marker-assisted selection. To identify significant QTL, this study mapped 7 hybrid populations and one combined of 2 hybrid populations (30-96 F1s) derived from Alamo and Kanlow genotypes. The populations were evaluated for biomass yield, plant height, and crown size in a simulated-sward plot with 2 replications at 2 locations in Tennessee from 2019 to 2021. The populations showed significant genetic variation for the evaluated traits and exhibited transgressive segregation. The 17,251 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) were used to construct a linkage map using a fast algorithm for multiple outbred families. The linkage map spanned 1,941 cM with an average interval of 0.11 cM between SNPs. The QTL analysis was performed on evaluated traits for each and across environments (year and location) that identified 5 QTL for biomass yield (logarithm of the odds, LOD 3.12-4.34), 4 QTL for plant height (LOD 3.01-5.64), and 7 QTL for crown size (LOD 3.0-4.46) (P ≤ 0.05). The major QTL for biomass yield, plant height, and crown size resided on chromosomes 8N, 6N, and 8K explained phenotypic variations of 5.6, 5.1, and 6.6%, respectively. SNPs linked to QTL could be incorporated into marker-assisted breeding to maximize the selection gain in switchgrass breeding.
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Affiliation(s)
- Surya L Shrestha
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Christian M Tobias
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
- Plant Systems-Production, USDA National Institute of Food and Agriculture (NIFA), Beacon Complex, USA
| | - Hem S Bhandari
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Jennifer Bragg
- United States Department of Agriculture (USDA) Agricultural Research Service (ARS), Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Santosh Nayak
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
- USDA ARS, Crop Improvement and Protection Research Unit, 1636 E Alisal Street, Salinas, CA 93905, USA
| | - Ken Goddard
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
| | - Fred Allen
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building, Knoxville, TN 37996-4500, USA
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Razar RM, Qi P, Devos KM, Missaoui AM. Genotyping-by-Sequencing and QTL Mapping of Biomass Yield in Two Switchgrass F 1 Populations (Lowland x Coastal and Coastal x Upland). FRONTIERS IN PLANT SCIENCE 2022; 13:739133. [PMID: 35665173 PMCID: PMC9162799 DOI: 10.3389/fpls.2022.739133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
The prevalence of genetic diversity in switchgrass germplasm can be exploited to capture favorable alleles that increase its range of adaptation and biomass yield. The objectives of the study were to analyze the extent of polymorphism and patterns of segregation distortion in two F1 populations and use the linkage maps to locate QTL for biomass yield. We conducted genotyping-by-sequencing on two populations derived from crosses between the allotetraploid lowland genotype AP13 (a selection from "Alamo") and coastal genotype B6 (a selection from PI 422001) with 285 progeny (AB population) and between B6 and the allotetraploid upland VS16 (a selection from "Summer") with 227 progeny (BV population). As predictable from the Euclidean distance between the parents, a higher number of raw variants was discovered in the coastal × upland BV cross (6 M) compared to the lowland × coastal AB cross (2.5 M). The final number of mapped markers was 3,107 on the BV map and 2,410 on the AB map. More segregation distortion of alleles was seen in the AB population, with 75% distorted loci compared to 11% distorted loci in the BV population. The distortion in the AB population was seen across all chromosomes in both the AP13 and B6 maps and likely resulted from zygotic or post-zygotic selection for increased levels of heterozygosity. Our results suggest lower genetic compatibility between the lowland AP13 and the coastal B6 ecotype than between B6 and the upland ecotype VS16. Four biomass QTLs were mapped in the AB population (LG 2N, 6K, 6N, and 8N) and six QTLs in the BV population [LG 1N (2), 8N (2), 9K, and 9N]. The QTL, with the largest and most consistent effect across years, explaining between 8.4 and 11.5% of the variation, was identified on 6N in the AP13 map. The cumulative effect of all the QTLs explained a sizeable portion of the phenotypic variation in both AB and BV populations and the markers associated with them may potentially be used for the marker-assisted improvement of biomass yield. Since switchgrass improvement is based on increasing favorable allele frequencies through recurrent selection, the transmission bias within individuals and loci needs to be considered as this may affect the genetic gain if the favorable alleles are distorted.
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Affiliation(s)
- Rasyidah M. Razar
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Genetic Resources and Improvement Unit, RRIM Research Station, Malaysian Rubber Board, Selangor, Malaysia
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Ali M. Missaoui
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Yu S, Fang T, Dong H, Yan L, Martin DL, Moss JQ, Fontanier CH, Wu Y. Genetic and QTL mapping in African bermudagrass. THE PLANT GENOME 2021; 14:e20073. [PMID: 33660431 DOI: 10.1002/tpg2.20073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Cynodon transvaalensis Burtt-Davy is frequently used to cross with C. dactylon Pers. in the creation of F1 hybrid cultivars that are some of the most widely used in the worldwide turf industry. However, molecular resource development in this species is limited. Accordingly, the objectives of this study were to construct a high-density genetic map, and to identify genomic regions associated with establishment rate. In this study, we constructed the first high-density linkage map for African bermudagrass using a genotyping by sequencing approach based on 109 S1 progenies. A total of 1,246 single nucleotide polymorphisms and 32 simple sequence repeat markers were integrated in the linkage map. The total length of nine linkage groups was 882.3 cM, with an average distance of 0.69 cM per interval. Four genomic regions were identified to be associated with sod establishment rate. The results provide important genetic resources towards understanding the genome as well as marker-assisted selection for improving the establishment rate in bermudagrass breeding.
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Affiliation(s)
- Shuhao Yu
- Dept. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Tilin Fang
- Dept. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Hongxu Dong
- Dept. of Plant and Soil Sciences, Mississippi State Univ., 358 Dorman Hall, Starkville, Mississippi, 39762, USA
| | - Liuling Yan
- Dept. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Dennis L Martin
- Dept. of Horticulture and Landscape Architecture, Oklahoma State Univ., 358 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Justin Q Moss
- Dept. of Horticulture and Landscape Architecture, Oklahoma State Univ., 358 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Charles H Fontanier
- Dept. of Horticulture and Landscape Architecture, Oklahoma State Univ., 358 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
| | - Yanqi Wu
- Dept. of Plant and Soil Sciences, Oklahoma State Univ., 371 Agriculture Hall, Stillwater, Oklahoma, 74078, USA
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Luo Y, Zhang X, Xu J, Zheng Y, Pu S, Duan Z, Li Z, Liu G, Chen J, Wang Z. Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum. BMC Genet 2020; 21:86. [PMID: 32787786 PMCID: PMC7425169 DOI: 10.1186/s12863-020-00892-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions. RESULTS Based on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h = 0.47, I = 0.66) and ISSR markers (h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers. CONCLUSIONS Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.
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Affiliation(s)
- Ying Luo
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Xiujie Zhang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Yao Zheng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Shouqin Pu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Zhizhen Duan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Zhihao Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Guodao Liu
- Chinese Academy of Tropical Agricultural Science, Haikou, 570228, People's Republic of China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China.
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China.
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China.
- Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, People's Republic of China.
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Reasor EH, Brosnan JT, Staton ME, Lane T, Trigiano RN, Wadl PA, Conner JA, Schwartz BM. Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass [ Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] putting greens using genotyping-by-sequencing and morphological characterization. Hereditas 2017; 155:8. [PMID: 28827983 PMCID: PMC5563029 DOI: 10.1186/s41065-017-0043-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/09/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Interspecific hybrid bermudagrass [Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt-Davy] is one of the most widely used grasses on golf courses, with cultivars derived from 'Tifgreen' or 'Tifdwarf' particularly used for putting greens. Many bermudagrass cultivars established for putting greens can be genetically unstable and lead to the occurrence of undesirable off-type grasses that vary in phenotype. The objective of this research was to genetically and phenotypically differentiate off-type grasses and hybrid cultivars. Beginning in 2013, off-type and desirable hybrid bermudagrass samples were collected from golf course putting greens in the southeastern United States and genetically and phenotypically characterized using genotyping-by-sequencing and morphology. RESULTS Genotyping-by-sequencing determined that 11% (5) of off-type and desirable samples from putting greens were genetically divergent from standard cultivars such as Champion, MiniVerde, Tifdwarf, TifEagle, and Tifgreen. In addition, genotyping-by-sequencing was unable to genetically distinguish all standard cultivars from one another due to their similar origin and clonal propagation; however, over 90,000 potentially informative nucleotide variants were identified among the triploid hybrid cultivars. CONCLUSIONS Although few genetic differences were found in this research, samples harvested from golf course putting greens had variable morphology and were clustered into three distinct phenotypic groups. The majority of off-type grasses in hybrid bermudagrass putting greens were genetically similar with variable morphological traits. Off-type grasses within golf course putting greens have the potential to compromise putting surface functionality and aesthetics.
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Affiliation(s)
- Eric H. Reasor
- Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, 32 Creelman Street, Mississippi State University, Mississippi State, MS 39762 USA
| | - James T. Brosnan
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., 252 Ellington Plant Sciences Bldg., Knoxville, TN 37996 USA
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E.J. Chapman Dr., 370 Plant Biotechnology Bldg, Knoxville, TN 37996 USA
| | - Thomas Lane
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E.J. Chapman Dr., 370 Plant Biotechnology Bldg, Knoxville, TN 37996 USA
| | - Robert N. Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E.J. Chapman Dr., 370 Plant Biotechnology Bldg, Knoxville, TN 37996 USA
| | - Phillip A. Wadl
- United States Department of Agriculture, Agriculture Research Service, United States Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414 USA
| | - Joann A. Conner
- Department of Horticulture, University of Georgia, 2360 Rainwater Rd, Tifton, GA 31794 USA
| | - Brian M. Schwartz
- Department of Crop and Soil Sciences, University of Georgia, University of Georgia, 2360 Rainwater Rd, Tifton, GA 31794 USA
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Reasor EH, Brosnan JT, Trigiano RN, Elsner JE, Henry GM, Schwartz BM. The genetic and phenotypic variability of interspecific hybrid bermudagrasses (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) used on golf course putting greens. PLANTA 2016; 244:761-73. [PMID: 27448290 PMCID: PMC5018024 DOI: 10.1007/s00425-016-2573-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/16/2016] [Indexed: 05/29/2023]
Abstract
MAIN CONCLUSION Some interspecific hybrid bermudagrass cultivars used on golf course putting greens are genetically unstable, which has caused phenotypically different off-type grasses to occur in production nurseries and putting surfaces. Management practices to reduce the occurrence of off-type grasses in putting green surfaces and the effect they can have on putting quality and performance need to be researched until genetically stable cultivars are developed. Golf course putting green surfaces in subtropical and tropical climates are typically planted with an interspecific hybrid bermudagrass (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy), because of the superior putting quality and performance of these cultivars. 'Tifgreen' was one of the first interspecific hybrids developed for putting green use in lieu of common bermudagrass. However, off-type grasses began appearing in established Tifgreen stands soon after commercial release. Off-type grasses are those with different morphology and performance when compared to the surrounding, desirable cultivar. Off-types have the potential to decrease surface uniformity, which negatively affects putting surface quality. However, several unique off-types from Tifgreen have been selected as commercial cultivars, the first being 'Tifdwarf'; then 'Floradwarf', 'MS-Supreme', 'Pee Dee-102', and 'TL-2', identified later. The cultivars 'Champion Dwarf', 'P-18', 'RJT', and 'Emerald Dwarf' were subsequently selected as off-types in Tifdwarf. The naturally occurring off-types and cultivars that have been identified within the Tifgreen family have widely differing phenotypes; however, they are reported to be genetically similar, supporting the hypothesis that their occurrence is a result of somatic mutations. Genetic instability in currently available commercial cultivars is likely to lead to the continued presence of off-types in production nurseries and putting greens. Additional research is needed to understand the nature of genetic instability in Tifgreen-derived cultivars and how to manage its consequences to develop new cultivars, but also strategies for eradication of off-types in pedigree nursery production and end-site putting greens.
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Affiliation(s)
- Eric H Reasor
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., 252 Ellington Plant Sciences Bldg., Knoxville, TN, 37996, USA.
| | - James T Brosnan
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Dr., 252 Ellington Plant Sciences Bldg., Knoxville, TN, 37996, USA
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, 2505 E.J. Chapman Dr., 370 Plant Biotechnology Bldg., Knoxville, TN, 37996, USA
| | - J Earl Elsner
- Georgia Seed Development Commission, 2420 S. Milledge Ave., Athens, GA, 30605, USA
| | - Gerald M Henry
- Department of Crop and Soil Sciences, University of Georgia, 3111 Miller Plant Sciences Bldg., Athens, GA, 30602, USA
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, 2360 Rainwater Rd., Tifton, GA, 31794, USA
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