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Tilhou NW, Poudel HP, Lovell J, Mamidi S, Schmutz J, Daum C, Zane M, Yoshinaga Y, Lipzen A, Casler MD. Genomic prediction of switchgrass winter survivorship across diverse lowland populations. G3 (Bethesda) 2023; 13:jkad014. [PMID: 36648238 PMCID: PMC9997553 DOI: 10.1093/g3journal/jkad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023]
Abstract
In the North-Central United States, lowland ecotype switchgrass can increase yield by up to 50% compared with locally adapted but early flowering cultivars. However, lowland ecotypes are not winter tolerant. The mechanism for winter damage is unknown but previously has been associated with late flowering time. This study investigated heading date (measured for two years) and winter survivorship (measured for three years) in a multi-generation population generated from two winter-hardy lowland individuals and diverse southern lowland populations. Sequencing data (311,776 markers) from 1,306 individuals were used to evaluate genome-wide trait prediction through cross-validation and progeny prediction (n = 52). Genetic variance for heading date and winter survivorship was additive with high narrow-sense heritability (0.64 and 0.71, respectively) and reliability (0.68 and 0.76, respectively). The initial negative correlation between winter survivorship and heading date degraded across generations (F1r = -0.43, pseudo-F2r = -0.28, pseudo-F2 progeny r = -0.15). Within-family predictive ability was moderately high for heading date and winter survivorship (0.53 and 0.52, respectively). A multi-trait model did not improve predictive ability for either trait. Progeny predictive ability was 0.71 for winter survivorship and 0.53 for heading date. These results suggest that lowland ecotype populations can obtain sufficient survival rates in the northern United States with two or three cycles of effective selection. Despite accurate genomic prediction, naturally occurring winter mortality successfully isolated winter tolerant genotypes and appears to be an efficient method to develop high-yielding, cold-tolerant switchgrass cultivars.
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Affiliation(s)
- Neal W Tilhou
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
| | - Hari P Poudel
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, T1J 4B1 Canada
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christopher Daum
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Matthew Zane
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Yuko Yoshinaga
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Lawrence, CA 94704, USA
| | - Michael D Casler
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI 53706, USA
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Tilhou NW, Casler MD. Subsampling and DNA pooling can increase gains through genomic selection in switchgrass. Plant Genome 2021; 14:e20149. [PMID: 34626166 DOI: 10.1002/tpg2.20149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Genomic selection (GS) can accelerate breeding cycles in perennial crops such as the bioenergy grass switchgrass (Panicum virgatum L.). The sequencing costs of GS can be reduced by pooling DNA samples in the training population (TP), only sequencing TP phenotypic outliers, or pooling candidate population (CP) samples. These strategies were simulated for two traits (spring vigor and anthesis date) in three breeding populations. Sequencing only the outlier 50% of the TP phenotype distribution resulted in a penalty of <5% of the predictive ability, measured using cross-validation. Predictive ability also decreased when sequencing progressively fewer TP DNA pools, but TPs constructed from only two phenotypically contrasting DNA samples retained a mean of >80% predictive ability relative to individual TP sequencing. Novel group testing methods allowed greater than one CP individual to be screened per sequenced DNA sample but resulted in a predictive ability penalty. To determine the impact of reduced sequencing, genetic gain was calculated for seven GS scenarios with variable sequencing budgets. Reduced TP sequencing and most CP pooling methods were superior to individual sequence-based GS when sequencing resources were restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was superior to individual sequencing when sequencing budgets were large (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes for reduced sequencing costs in GS.
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Affiliation(s)
- Neal Wepking Tilhou
- Department of Agronomy, University of Wisconsin, 1575 Linden Dr, Madison, WI, 53706, USA
| | - Michael D Casler
- U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr, Madison, WI, 53706-1108, USA
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Poudel HP, Tilhou NW, Sanciangco MD, Vaillancourt B, Kaeppler SM, Buell CR, Casler MD. Genetic loci associated with winter survivorship in diverse lowland switchgrass populations. Plant Genome 2021; 14:e20159. [PMID: 34661986 DOI: 10.1002/tpg2.20159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
High winter mortality limits biomass yield of lowland switchgrass (Panicum virgatum L.) planted in the northern latitudes of North America. Breeding of cold tolerant switchgrass cultivars requires many years due to its perennial growth habit and the unpredictable winter selection pressure that is required to identify winter-hardy individuals. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 populations with differential winter survivorship were used for BSA. A maximum of 10% of the individuals (8-20) were bulked to create survivor and nonsurvivor DNA pools from each population and location. The DNA pools were evaluated using exome capture sequencing, and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine quatitative trait loci (QTL) from tetraploid populations and seven QTL from octoploid populations. Many QTL were population-specific, but some were identified in multiple populations that originated across a broad geographic landscape. Four QTL (at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N) were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.
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Affiliation(s)
- Hari P Poudel
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Neal W Tilhou
- Dep. of Agronomy, Univ. of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | - C Robin Buell
- Dep. of Plant Biology, Michigan State Univ., East Lansing, MI, USA
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Stock MN, Arriaga FJ, Vadas PA, Good LW, Casler MD, Karthikeyan KG, Zopp Z. Fall Tillage Reduced Nutrient Loads from Liquid Manure Application during the Freezing Season. J Environ Qual 2019; 48:889-898. [PMID: 31589665 DOI: 10.2134/jeq2018.11.0417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reducing agricultural runoff is important year round, particularly on landscapes that receive wintertime applications of manure. No-tillage systems are typically associated with reduced runoff loads during the growing season, but surface roughness from fall tillage may aid infiltration on frozen soils by providing surface depressional storage. The timing of winter manure applications may also affect runoff, depending on snow and soil frost conditions. Therefore, the objective of this study was to evaluate runoff and nutrient loads during the freezing season from combinations of tillage and manure application timings. Six management treatments were tested in south-central Wisconsin during the winters of 2015-2016 and 2016-2017 with a complete factorial design: two tillage treatments (fall chisel plow vs. no-tillage) and three manure application timings (early December, late January, and unmanured). Nutrient loads from winter manure application were lower on chisel-plowed versus untilled soils during both monitoring years. Loads were also lower from manure applied to soils with less frost development. Wintertime manure applications pose a risk of surface nutrient losses, but fall tillage and timing applications to thawed soils can help reduce loads.
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Poudel HP, Sanciangco MD, Kaeppler SM, Buell CR, Casler MD. Quantitative Trait Loci for Freezing Tolerance in a Lowland x Upland Switchgrass Population. Front Plant Sci 2019; 10:372. [PMID: 30984223 PMCID: PMC6450214 DOI: 10.3389/fpls.2019.00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
Low-temperature related abiotic stress is an important factor affecting winter survival in lowland switchgrass when grown in northern latitudes in the United States. A better understanding of the genetic architecture of freezing tolerance in switchgrass will aid the development of lowland switchgrass cultivars with improved winter survival. The objectives of this study were to conduct a freezing tolerance assessment, generate a genetic map using single nucleotide polymorphism (SNP) markers, and identify QTL (quantitative trait loci) associated with freezing tolerance in a lowland × upland switchgrass population. A pseudo-F2 mapping population was generated from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. The segregating progenies were screened for freezing tolerance in a controlled-environment facility. Two clonal replicates of each genotype were tested at six different treatment temperatures ranging from -15 to -5°C at an interval of 2°C for two time periods. Tiller emergence (days) and tiller number were recorded following the recovery of each genotype with the hypothesis that upland genotype is the source for higher tiller number and early tiller emergence. Survivorship of the pseudo-F2 population ranged from 89% at -5°C to 5% at -15°C with an average LT50 of -9.7°C. Genotype had a significant effect on all traits except tiller number at -15°C. A linkage map was constructed from bi-allelic single nucleotide polymorphism markers generated using exome capture sequencing. The final map consisted of 1618 markers and 2626 cM, with an average inter-marker distance of 1.8 cM. Six significant QTL were identified, one each on chromosomes 1K, 5K, 5N, 6K, 6N, and 9K, for the following traits: tiller number, tiller emergence days and LT50. A comparative genomics study revealed important freezing tolerance genes/proteins, such as COR47, DREB2B, zinc finger-CCCH, WRKY, GIGANTEA, HSP70, and NRT2, among others that reside within the 1.5 LOD confidence interval of the identified QTL.
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Affiliation(s)
- Hari P. Poudel
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - Millicent D. Sanciangco
- Department of Plant Biology, Plant Resilience Institute, and MSU AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin–Madison, Madison, WI, United States
| | - C. Robin Buell
- Department of Plant Biology, Plant Resilience Institute, and MSU AgBioResearch, Michigan State University, East Lansing, MI, United States
| | - Michael D. Casler
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
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Ramstein GP, Casler MD. Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample. G3 (Bethesda) 2019; 9:789-805. [PMID: 30651285 PMCID: PMC6404615 DOI: 10.1534/g3.118.200969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 01/10/2019] [Indexed: 11/18/2022]
Abstract
Genomic prediction is a useful tool to accelerate genetic gain in selection using DNA marker information. However, this technology typically relies on standard prediction procedures, such as genomic BLUP, that are not designed to accommodate population heterogeneity resulting from differences in marker effects across populations. In this study, we assayed different prediction procedures to capture marker-by-population interactions in genomic prediction models. Prediction procedures included genomic BLUP and two kernel-based extensions of genomic BLUP which explicitly accounted for population heterogeneity. To model population heterogeneity, dissemblance between populations was either depicted by a unique coefficient (as previously reported), or a more flexible function of genetic distance between populations (proposed herein). Models under investigation were applied in a diverse switchgrass sample under two validation schemes: whole-sample calibration, where all individuals except selection candidates are included in the calibration set, and cross-population calibration, where the target population is entirely excluded from the calibration set. First, we showed that using fixed effects, from principal components or putative population groups, appeared detrimental to prediction accuracy, especially in cross-population calibration. Then we showed that modeling population heterogeneity by our proposed procedure resulted in highly significant improvements in model fit. In such cases, gains in accuracy were often positive. These results suggest that population heterogeneity may be parsimoniously captured by kernel methods. However, in cases where improvement in model fit by our proposed procedure is null-to-moderate, ignoring heterogeneity should probably be preferred due to the robustness and simplicity of the standard genomic BLUP model.
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Affiliation(s)
| | - Michael D Casler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI 53706
- Agricultural Research Service, United States Department of Agriculture, Madison, WI 53706
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Clifton‐Brown J, Harfouche A, Casler MD, Dylan Jones H, Macalpine WJ, Murphy‐Bokern D, Smart LB, Adler A, Ashman C, Awty‐Carroll D, Bastien C, Bopper S, Botnari V, Brancourt‐Hulmel M, Chen Z, Clark LV, Cosentino S, Dalton S, Davey C, Dolstra O, Donnison I, Flavell R, Greef J, Hanley S, Hastings A, Hertzberg M, Hsu T, Huang LS, Iurato A, Jensen E, Jin X, Jørgensen U, Kiesel A, Kim D, Liu J, McCalmont JP, McMahon BG, Mos M, Robson P, Sacks EJ, Sandu A, Scalici G, Schwarz K, Scordia D, Shafiei R, Shield I, Slavov G, Stanton BJ, Swaminathan K, Taylor G, Torres AF, Trindade LM, Tschaplinski T, Tuskan GA, Yamada T, Yeon Yu C, Zalesny RS, Zong J, Lewandowski I. Breeding progress and preparedness for mass-scale deployment of perennial lignocellulosic biomass crops switchgrass, miscanthus, willow and poplar. Glob Change Biol Bioenergy 2019; 11:118-151. [PMID: 30854028 PMCID: PMC6392185 DOI: 10.1111/gcbb.12566] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/18/2018] [Indexed: 05/07/2023]
Abstract
Genetic improvement through breeding is one of the key approaches to increasing biomass supply. This paper documents the breeding progress to date for four perennial biomass crops (PBCs) that have high output-input energy ratios: namely Panicum virgatum (switchgrass), species of the genera Miscanthus (miscanthus), Salix (willow) and Populus (poplar). For each crop, we report on the size of germplasm collections, the efforts to date to phenotype and genotype, the diversity available for breeding and on the scale of breeding work as indicated by number of attempted crosses. We also report on the development of faster and more precise breeding using molecular breeding techniques. Poplar is the model tree for genetic studies and is furthest ahead in terms of biological knowledge and genetic resources. Linkage maps, transgenesis and genome editing methods are now being used in commercially focused poplar breeding. These are in development in switchgrass, miscanthus and willow generating large genetic and phenotypic data sets requiring concomitant efforts in informatics to create summaries that can be accessed and used by practical breeders. Cultivars of switchgrass and miscanthus can be seed-based synthetic populations, semihybrids or clones. Willow and poplar cultivars are commercially deployed as clones. At local and regional level, the most advanced cultivars in each crop are at technology readiness levels which could be scaled to planting rates of thousands of hectares per year in about 5 years with existing commercial developers. Investment in further development of better cultivars is subject to current market failure and the long breeding cycles. We conclude that sustained public investment in breeding plays a key role in delivering future mass-scale deployment of PBCs.
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Affiliation(s)
- John Clifton‐Brown
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antoine Harfouche
- Department for Innovation in Biological, Agrofood and Forest systemsUniversity of TusciaViterboItaly
| | | | - Huw Dylan Jones
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | | | - Lawrence B. Smart
- Horticulture Section, School of Integrative Plant ScienceCornell UniversityGenevaNew York
| | - Anneli Adler
- SweTree Technologies ABUmeåSweden
- Institute of Crop Production EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Chris Ashman
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Danny Awty‐Carroll
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Sebastian Bopper
- Department of Seed Science and Technology, Institute of Plant Breeding, Seed Science and Population GeneticsUniversity of HohenheimStuttgartGermany
| | - Vasile Botnari
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | | | - Zhiyong Chen
- Insitute of MiscanthusHunan Agricultural UniversityHunan ChangshaChina
| | - Lindsay V. Clark
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Salvatore Cosentino
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Sue Dalton
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Chris Davey
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Oene Dolstra
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Iain Donnison
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | | | - Joerg Greef
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | | | - Astley Hastings
- Institute of Biological and Environmental ScienceUniversity of AberdeenAberdeenUK
| | | | - Tsai‐Wen Hsu
- Taiwan Endemic Species Research Institute (TESRI)Nantou CountyTaiwan
| | - Lin S. Huang
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Antonella Iurato
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Elaine Jensen
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Xiaoli Jin
- Department of Agronomy & The Key Laboratory of Crop Germplasm Resource of Zhejiang ProvinceZhejiang UniversityHangzhouChina
| | - Uffe Jørgensen
- Department of AgroecologyAarhus University Centre for Circular BioeconomyTjeleDenmark
| | - Andreas Kiesel
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
| | - Do‐Soon Kim
- Department of Plant Sciences, Research Institute of Agriculture & Life Sciences, CALSSeoul National UniversitySeoulKorea
| | - Jianxiu Liu
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Jon P. McCalmont
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Bernard G. McMahon
- Natural Resources Research InstituteUniversity of Minnesota – DuluthDuluthMinnesota
| | | | - Paul Robson
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Erik J. Sacks
- Department of Crop Sciences & Center for Advanced Bioenergy and Bioproducts Innovation, 279 Edward R Madigan LaboratoryUniversity of IllinoisUrbanaIllinois
| | - Anatolii Sandu
- Institute of Genetics, Physiology and Plant Protection (IGFPP) of Academy of Sciences of MoldovaChisinauMoldova
| | - Giovanni Scalici
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Kai Schwarz
- Julius Kuhn‐Institut (JKI)Bundesforschungsinstitut fur KulturpflanzenBraunschweigGermany
| | - Danilo Scordia
- Dipartimento di Agricoltura Alimentazione e AmbienteUniversità degli Studi di CataniaCataniaItaly
| | - Reza Shafiei
- James Hutton InstituteUniversity of DundeeDundeeUK
| | | | | | | | | | - Gail Taylor
- Biological SciencesUniversity of SouthamptonSouthamptonUK
| | - Andres F. Torres
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Luisa M. Trindade
- Plant BreedingWageningen University & ResearchWageningenThe Netherlands
| | - Timothy Tschaplinski
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Gerald A. Tuskan
- The Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTennessee
| | - Toshihiko Yamada
- Field Science Centre for the Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chang Yeon Yu
- College of Agriculture and Life Sciences 2Kangwon National UniversityChuncheonSouth Korea
| | | | - Junqin Zong
- Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingChina
| | - Iris Lewandowski
- Department of Biobased Products and Energy Crops, Institute of Crop ScienceUniversity of HohenheimStuttgartGermany
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Ramstein GP, Evans J, Nandety A, Saha MC, Brummer EC, Kaeppler SM, Buell CR, Casler MD. Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass ( Panicum virgatum L.) Identified by Genome-Wide Association Analyses. Plant Genome 2018; 11:180002. [PMID: 30512032 DOI: 10.3835/plantgenome2018.01.0002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes. We performed association analyses based on exome capture sequencing and tested 439,170 markers for marginal effects, 83,290 markers for marker × ecotype interactions, and up to 311,445 marker pairs for pairwise interactions. Analyses of pairwise interactions focused on subsets of marker pairs preselected on the basis of marginal marker effects, gene ontology annotation, and pairwise marker associations. Our tests identified 12 significant effects. Homology and gene expression information corroborated seven effects and indicated plausible causal pathways: flowering time and lignin synthesis for plant height; plant growth and senescence for C content and mineral concentration. Four pairwise interactions were detected, including three interactions preselected on the basis of pairwise marker correlations. Furthermore, a marker × ecotype interaction and a pairwise interaction were confirmed in an independent switchgrass panel. Our analyses identified reliable candidate variants for important bioenergy traits. Moreover, they exemplified the importance of interactive effects for depicting genetic bases and illustrated the usefulness of preselecting marker pairs for identifying pairwise marker interactions in association studies.
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Taylor M, Tornqvist CE, Zhao X, Grabowski P, Doerge R, Ma J, Volenec J, Evans J, Ramstein GP, Sanciangco MD, Buell CR, Casler MD, Jiang Y. Genome-Wide Association Study in Pseudo-F 2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates. Front Plant Sci 2018; 9:1250. [PMID: 30271414 PMCID: PMC6146286 DOI: 10.3389/fpls.2018.01250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 08/06/2018] [Indexed: 06/01/2023]
Abstract
Switchgrass (Panicum virgatum) is a native prairie grass and valuable bio-energy crop. The physiological change from juvenile to reproductive adult can draw important resources away from growth into producing reproductive structures, thereby limiting the growth potential of early flowering plants. Delaying the flowering of switchgrass is one approach by which to increase total biomass. The objective of this research was to identify genetic variants and candidate genes for controlling heading and anthesis in segregating switchgrass populations. Four pseudo-F2 populations (two pairs of reciprocal crosses) were developed from lowland (late flowering) and upland (early flowering) ecotypes, and heading and anthesis dates of these populations were collected in Lafayette, IN and DeKalb, IL in 2015 and 2016. Across 2 years, there was a 34- and 73-day difference in heading and a 52- and 75-day difference in anthesis at the Lafayette and DeKalb locations, respectively. A total of 37,901 single nucleotide polymorphisms obtained by exome capture sequencing of the populations were used in a genome-wide association study (GWAS) that identified five significant signals at three loci for heading and two loci for anthesis. Among them, a homolog of FLOWERING LOCUS T on chromosome 5b associated with heading date was identified at the Lafayette location across 2 years. A homolog of ARABIDOPSIS PSEUDO-RESPONSE REGULATOR 5, a light modulator in the circadian clock associated with heading date was detected on chromosome 8a across locations and years. These results demonstrate that genetic variants related to floral development could lend themselves to a long-term goal of developing late flowering varieties of switchgrass with high biomass yield.
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Affiliation(s)
- Megan Taylor
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Carl-Erik Tornqvist
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Xiongwei Zhao
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Paul Grabowski
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Rebecca Doerge
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- Department of Biology and Department of Statistics, Mellon College of Science, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Jeffrey Volenec
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Joseph Evans
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Guillaume P. Ramstein
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
| | - Millicent D. Sanciangco
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - C. Robin Buell
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Michael D. Casler
- U.S. Department of Energy, Great Lakes Bioenergy Research Center and Department of Agronomy, University of Wisconsin-Madison, Madison, WI, United States
- U.S. Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
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Eckberg JO, Johnson GA, Seefeldt LL, Felton AJ, Casler MD, Shaw RG. Competitive effects of cultivar and wild switchgrass on other native grasses. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1711-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tornqvist CE, Taylor M, Jiang Y, Evans J, Buell CR, Kaeppler SM, Casler MD. Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F2 Population. Plant Genome 2018; 11. [PMID: 30025023 DOI: 10.3835/plantgenome2017.10.0093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Flowering is an important developmental event in switchgrass (), as the time to complete the life cycle affects overall biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify quantitative trait loci (QTL) associated with flowering time. A pseudo-F population was created by crossing two siblings derived from an initial cross between the lowland population Ellsworth and the upland cultivar Summer. Heading and anthesis dates were collected for 2 yr at two locations: DeKalb, IL and Lafayette, IN. Nine QTL for flowering time were detected, two of which were heading-associated, four anthesis-associated, and three associated with both heading and anthesis. One QTL on linkage group (LG) 2a was detected for heading and anthesis in each location and year when environments were analyzed separately, and in a combined analysis across both locations and years. The effect on heading and anthesis of the QTL on LG 2a ranged from 4 to 13 and 5 to 9 d, respectively, depending on environment. Our findings validate QTL for switchgrass flowering time from previous research and identified additional QTL. Based on the switchgrass reference genome version 1.1, flowering time gene homologs reside near the LG 2a QTL and include PSEUDO RESPONSE REGULATOR 5, SUPPRESSOR OF FRIGIDA 4, and APETALA 1, respectively involved in the circadian clock, vernalization, and floral meristem identity. Markers linked to the QTL can be used to improve the efficiency of breeding switchgrass for delayed flowering to increase biomass yield.
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Yang X, Zhao H, Zhang T, Zeng Z, Zhang P, Zhu B, Han Y, Braz GT, Casler MD, Schmutz J, Jiang J. Amplification and adaptation of centromeric repeats in polyploid switchgrass species. New Phytol 2018; 218:1645-1657. [PMID: 29577299 DOI: 10.1111/nph.15098] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 05/24/2023]
Abstract
Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.
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Affiliation(s)
- Xueming Yang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Pingdong Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yonghua Han
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Guilherme T Braz
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Michael D Casler
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI, 53706, USA
| | - Jeremy Schmutz
- Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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Arojju SK, Conaghan P, Barth S, Milbourne D, Casler MD, Hodkinson TR, Michel T, Byrne SL. Genomic prediction of crown rust resistance in Lolium perenne. BMC Genet 2018; 19:35. [PMID: 29843601 PMCID: PMC5975627 DOI: 10.1186/s12863-018-0613-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 04/18/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Here, we used a large perennial ryegrass population to assess the accuracy of using genome wide markers to predict crown rust resistance and to investigate the factors affecting predictive ability. RESULTS Using these data, predictive ability for crown rust resistance in the complete population reached a maximum of 0.52. Much of the predictive ability resulted from the ability of markers to capture genetic relationships among families within the training set, and reducing the marker density had little impact on predictive ability. Using permutation based variable importance measure and genome wide association studies (GWAS) to identify and rank markers enabled the identification of a small subset of SNPs that could achieve predictive abilities close to those achieved using the complete marker set. CONCLUSION Using a GWAS to identify and rank markers enabled a small panel of markers to be identified that could achieve higher predictive ability than the same number of randomly selected markers, and predictive abilities close to those achieved with the entire marker set. This was particularly evident in a sub-population characterised by having on-average higher genome-wide linkage disequilibirum (LD). Higher predictive abilities with selected markers over random markers suggests they are in LD with QTL. Accuracy due to genetic relationships will decay rapidly over generations whereas accuracy due to LD will persist, which is advantageous for practical breeding applications.
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Affiliation(s)
- Sai Krishna Arojju
- Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12 Ireland
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Patrick Conaghan
- Teagasc, Grassland Science Research Department, Animal and Grassland Research and Innovation Centre, Oak Park, Carlow, R93 XE12 Ireland
| | - Susanne Barth
- Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12 Ireland
| | - Dan Milbourne
- Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12 Ireland
| | - Michael D. Casler
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI53706 USA
- Agricultural Research Service, United State Department of Agriculture, Madison, WI53706 USA
| | - Trevor R. Hodkinson
- Department of Botany, School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Thibauld Michel
- Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12 Ireland
| | - Stephen L. Byrne
- Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12 Ireland
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Evans J, Sanciangco MD, Lau KH, Crisovan E, Barry K, Daum C, Hundley H, Jenkins J, Kennedy M, Kunde-Ramamoorthy G, Vaillancourt B, Acharya A, Schmutz J, Saha M, Kaeppler SM, Brummer EC, Casler MD, Buell CR. Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. Plant Genome 2018; 11. [PMID: 29505643 DOI: 10.3835/plantgenome2017.06.0055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Switchgrass ( is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals. In total, over 37 million single nucleotide polymorphisms (SNPs) were identified and a set of 1.9 million high-confidence SNPs were obtained from 1169 individuals from 140 populations (67 upland, 65 lowland, 8 admixed) were used in downstream analyses of genetic diversity and population structure. Seven separate population groups were identified with moderate genetic differentiation [mean fixation index (Fst) estimate of 0.06] between the lowland and the upland populations. Ecotype-specific and population-specific SNPs were identified for use in germplasm evaluations. Relative to rice ( L.), maize ( L.), soybean [ (L.) Merr.], and Gaertn., analyses of nucleotide diversity revealed a high degree of genetic diversity (0.0135) across all individuals, consistent with the outcrossing mode of reproduction and the polyploidy of switchgrass. This study supports the hypothesis that repeated glaciation events, ploidy barriers, and restricted gene flow caused by flowering time differences have resulted in distinct gene pools across ecotypes and geographic regions. These data provide a resource to associate alleles with traits of interest for forage, restoration, and biofuel feedstock efforts in switchgrass.
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Sripathi R, Conaghan P, Grogan D, Casler MD. Spatial Variability Effects on Precision and Power of Forage Yield Estimation. Crop Science 2017; 57:1383-1393. [PMID: 0 DOI: 10.2135/cropsci2016.08.0645] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Raghuveer Sripathi
- Dep. of Agronomy; Univ. of Wisconsin-Madison; 1575 Linden Dr. Madison 53706
| | - Patrick Conaghan
- Animal and Grassland Research and Innovation Centre, Teagasc; Oak Park Carlow Ireland
| | - Dermot Grogan
- Dep. of Agriculture, Food and the Marine; Davis St. Tipperary Town Ireland
| | - Michael D. Casler
- USDA-ARS; US Dairy Forage Research Center; 1925 Linden Dr. Madison WI 53706-1108
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Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y, Casler MD. Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data. New Phytol 2017; 213:154-169. [PMID: 27443672 DOI: 10.1111/nph.14101] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/10/2016] [Indexed: 05/20/2023]
Abstract
Flowering time is a major determinant of biomass yield in switchgrass (Panicum virgatum), a perennial bioenergy crop, because later flowering allows for an extended period of vegetative growth and increased biomass production. A better understanding of the genetic regulation of flowering time in switchgrass will aid the development of switchgrass varieties with increased biomass yields, particularly at northern latitudes, where late-flowering but southern-adapted varieties have high winter mortality. We use genotypes derived from recently published exome-capture sequencing, which mitigates challenges related to the large, highly repetitive and polyploid switchgrass genome, to perform genome-wide association studies (GWAS) using flowering time data from a switchgrass association panel in an effort to characterize the genetic architecture and genes underlying flowering time regulation in switchgrass. We identify associations with flowering time at multiple loci, including in a homolog of FLOWERING LOCUS T and in a locus containing TIMELESS, a homolog of a key circadian regulator in animals. Our results suggest that flowering time variation in switchgrass is due to variation at many positions across the genome. The relationship of flowering time and geographic origin indicates likely roles for genes in the photoperiod and autonomous pathways in generating switchgrass flowering time variation.
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Affiliation(s)
- Paul P Grabowski
- US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA
| | - Joseph Evans
- DuPont Pioneer, Johnston, IA, 50131, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Chris Daum
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | - Kerrie W Barry
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Megan Kennedy
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Guillaume Ramstein
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA
| | - Shawn M Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Dr, Madison, WI, 53706, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, 53726, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
| | - Michael D Casler
- US Dairy Forage Research Center, USDA-ARS, 1925 Linden Dr. W, Madison, WI, 53706, USA
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Chen S, Kaeppler SM, Vogel KP, Casler MD. Selection Signatures in Four Lignin Genes from Switchgrass Populations Divergently Selected for In Vitro Dry Matter Digestibility. PLoS One 2016; 11:e0167005. [PMID: 27893787 PMCID: PMC5125650 DOI: 10.1371/journal.pone.0167005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022] Open
Abstract
Switchgrass is undergoing development as a dedicated cellulosic bioenergy crop. Fermentation of lignocellulosic biomass to ethanol in a bioenergy system or to volatile fatty acids in a livestock production system is strongly and negatively influenced by lignification of cell walls. This study detects specific loci that exhibit selection signatures across switchgrass breeding populations that differ in in vitro dry matter digestibility (IVDMD), ethanol yield, and lignin concentration. Allele frequency changes in candidate genes were used to detect loci under selection. Out of the 183 polymorphisms identified in the four candidate genes, twenty-five loci in the intron regions and four loci in coding regions were found to display a selection signature. All loci in the coding regions are synonymous substitutions. Selection in both directions were observed on polymorphisms that appeared to be under selection. Genetic diversity and linkage disequilibrium within the candidate genes were low. The recurrent divergent selection caused excessive moderate allele frequencies in the cycle 3 reduced lignin population as compared to the base population. This study provides valuable insight on genetic changes occurring in short-term selection in the polyploid populations, and discovered potential markers for breeding switchgrass with improved biomass quality.
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Affiliation(s)
- Shiyu Chen
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
| | - Kenneth P. Vogel
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Lincoln, Nebraska, United States of America
- Department of Agronomy & Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Michael D. Casler
- Department of Energy, Great Lakes Bioenergy Research Center, Madison, Wisconsin, United States of America
- USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America
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Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR. Diversity and population structure of northern switchgrass as revealed through exome capture sequencing. Plant J 2015; 84:800-15. [PMID: 26426343 DOI: 10.1111/tpj.13041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 05/11/2023]
Abstract
Panicum virgatum L. (switchgrass) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuel feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype, composed of tetraploid and octoploid accessions, and a southern lowland ecotype, composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data, we identified ~27 million single-nucleotide polymorphisms (SNPs), of which 1 590 653 high-confidence SNPs were used in downstream analyses of diversity within and between the populations. From the 66 populations, we identified five primary population groups within the upland and lowland ecotypes, a result that was further supported through genetic distance analysis. We identified conserved, ecotype-restricted, non-synonymous SNPs that are predicted to affect the protein function of CONSTANS (CO) and EARLY HEADING DATE 1 (EHD1), key genes involved in flowering, which may contribute to the phenotypic differences between the two ecotypes. We also identified, relative to the near-reference Kanlow population, 17 228 genes present in more copies than in the reference genome (up-CNVs), 112 630 genes present in fewer copies than in the reference genome (down-CNVs) and 14 430 presence/absence variants (PAVs), affecting a total of 9979 genes, including two upland-specific CNV clusters. In total, 45 719 genes were affected by an SNP, CNV, or PAV across the panel, providing a firm foundation to identify functional variation associated with phenotypic traits of interest for biofuel feedstock production.
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Affiliation(s)
- Joseph Evans
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Chris Daum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Aruna Nandety
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Chew Yee Ngan
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Brieanne Vaillancourt
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chia-Lin Wei
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shawn M Kaeppler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI, 53706, USA
- USDA-ARS, U.S. Dairy Forage Research Center, 1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - Carol Robin Buell
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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Lipka AE, Lu F, Cherney JH, Buckler ES, Casler MD, Costich DE. Accelerating the switchgrass (Panicum virgatum L.) breeding cycle using genomic selection approaches. PLoS One 2014; 9:e112227. [PMID: 25390940 PMCID: PMC4229143 DOI: 10.1371/journal.pone.0112227] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 09/30/2014] [Indexed: 11/28/2022] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass undergoing development as a biofuel feedstock. One of the most important factors hindering breeding efforts in this species is the need for accurate measurement of biomass yield on a per-hectare basis. Genomic selection on simple-to-measure traits that approximate biomass yield has the potential to significantly speed up the breeding cycle. Recent advances in switchgrass genomic and phenotypic resources are now making it possible to evaluate the potential of genomic selection of such traits. We leveraged these resources to study the ability of three widely-used genomic selection models to predict phenotypic values of morphological and biomass quality traits in an association panel consisting of predominantly northern adapted upland germplasm. High prediction accuracies were obtained for most of the traits, with standability having the highest ten-fold cross validation prediction accuracy (0.52). Moreover, the morphological traits generally had higher prediction accuracies than the biomass quality traits. Nevertheless, our results suggest that the quality of current genomic and phenotypic resources available for switchgrass is sufficiently high for genomic selection to significantly impact breeding efforts for biomass yield.
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Affiliation(s)
- Alexander E. Lipka
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- * E-mail:
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Jerome H. Cherney
- Department of Crop and Soil Sciences, Cornell University, Ithaca, New York, United States of America
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, United States of America
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Michael D. Casler
- Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
- Department of Agronomy, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Denise E. Costich
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, United States of America
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Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR. Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum. Plant J 2014; 79:993-1008. [PMID: 24947485 PMCID: PMC4309430 DOI: 10.1111/tpj.12601] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/31/2014] [Accepted: 06/09/2014] [Indexed: 05/23/2023]
Abstract
Switchgrass (Panicum virgatum) is a polyploid, outcrossing grass species native to North America and has recently been recognized as a potential biofuel feedstock crop. Significant phenotypic variation including ploidy is present across the two primary ecotypes of switchgrass, referred to as upland and lowland switchgrass. The tetraploid switchgrass genome is approximately 1400 Mbp, split between two subgenomes, with significant repetitive sequence content limiting the efficiency of re-sequencing approaches for determining genome diversity. To characterize genetic diversity in upland and lowland switchgrass as a first step in linking genotype to phenotype, we designed an exome capture probe set based on transcript assemblies that represent approximately 50 Mb of annotated switchgrass exome sequences. We then evaluated and optimized the probe set using solid phase comparative genome hybridization and liquid phase exome capture followed by next-generation sequencing. Using the optimized probe set, we assessed variation in the exomes of eight switchgrass genotypes representing tetraploid lowland and octoploid upland cultivars to benchmark our exome capture probe set design. We identified ample variation in the switchgrass genome including 1,395,501 single nucleotide polymorphisms (SNPs), 8173 putative copy number variants and 3336 presence/absence variants. While the majority of the SNPs (84%) detected was bi-allelic, a substantial number was tri-allelic with limited occurrence of tetra-allelic polymorphisms consistent with the heterozygous and polyploid nature of the switchgrass genome. Collectively, these data demonstrate the efficacy of exome capture for discovery of genome variation in a polyploid species with a large, repetitive and heterozygous genome.
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Affiliation(s)
- Joseph Evans
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Jeongwoon Kim
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Brieanne Vaillancourt
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Emily Crisovan
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Aruna Nandety
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | | | | | | | - Shawn M Kaeppler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- Department of Agronomy, University of Wisconsin-Madison1575 Linden Drive, Madison, WI, 53706, USA
| | - Michael D Casler
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, 53706, USA
- US Dairy Forage Research Center, USDA-ARS1925 Linden Dr., Madison, WI, 53706-1108, USA
| | - C Robin Buell
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
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Grabowski PP, Morris GP, Casler MD, Borevitz JO. Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass. Mol Ecol 2014; 23:4059-73. [PMID: 24962137 PMCID: PMC4142443 DOI: 10.1111/mec.12845] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/09/2023]
Abstract
Geographic patterns of genetic variation are shaped by multiple evolutionary processes, including genetic drift, migration and natural selection. Switchgrass (Panicum virgatum L.) has strong genetic and adaptive differentiation despite life history characteristics that promote high levels of gene flow and can homogenize intraspecific differences, such as wind-pollination and self-incompatibility. To better understand how historical and contemporary factors shape variation in switchgrass, we use genotyping-by-sequencing to characterize switchgrass from across its range at 98 042 SNPs. Population structuring reflects biogeographic and ploidy differences within and between switchgrass ecotypes and indicates that biogeographic history, ploidy incompatibilities and differential adaptation each have important roles in shaping ecotypic differentiation in switchgrass. At one extreme, we determine that two Panicum taxa are not separate species but are actually conspecific, ecologically divergent types of switchgrass adapted to the extreme conditions of coastal sand dune habitats. Conversely, we identify natural hybrids among lowland and upland ecotypes and visualize their genome-wide patterns of admixture. Furthermore, we determine that genetic differentiation between primarily tetraploid and octoploid lineages is not caused solely by ploidy differences. Rather, genetic diversity in primarily octoploid lineages is consistent with a history of admixture. This suggests that polyploidy in switchgrass is promoted by admixture of diverged lineages, which may be important for maintaining genetic differentiation between switchgrass ecotypes where they are sympatric. These results provide new insights into the mechanisms shaping variation in widespread species and provide a foundation for dissecting the genetic basis of adaptation in switchgrass.
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Affiliation(s)
- Paul P Grabowski
- U.S. Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA; Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
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Affiliation(s)
- Michael D. Casler
- USDA‐ARSU.S. Dairy Forage Research Center1925 Linden Dr.MadisonWI53706‐1108
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Nelson MF, Anderson NO, Casler MD, Jakubowski AR. Population genetic structure of N. American and European Phalaris arundinacea L. as inferred from inter-simple sequence repeat markers. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0525-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 2013. [PMID: 23349638 DOI: 10.1371/journalpgen1003215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Switchgrass (Panicum virgatum L.) is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS) and genomic selection (GS). All of the 840 individuals were then genotyped using genotyping by sequencing (GBS), generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid) species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP) discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK). Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L.) P. Beauv.), two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics of switchgrass.
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Affiliation(s)
- Fei Lu
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA
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Price DL, Casler MD. Simple regression models as a threshold for selecting AFLP loci with reduced error rates. BMC Bioinformatics 2012; 13:268. [PMID: 23072295 PMCID: PMC3534328 DOI: 10.1186/1471-2105-13-268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 10/09/2012] [Indexed: 11/15/2022] Open
Abstract
Background Amplified fragment length polymorphism is a popular DNA marker technique that has applications in multiple fields of study. Technological improvements and decreasing costs have dramatically increased the number of markers that can be generated in an amplified fragment length polymorphism experiment. As datasets increase in size, the number of genotyping errors also increases. Error within a DNA marker dataset can result in reduced statistical power, incorrect conclusions, and decreased reproducibility. It is essential that error within a dataset be recognized and reduced where possible, while still balancing the need for genomic diversity. Results Using simple regression with a second-degree polynomial term, a model was fit to describe the relationship between locus-specific error rate and the frequency of present alleles. This model was then used to set a moving error rate threshold that varied based on the frequency of present alleles at a given locus. Loci with error rates greater than the threshold were removed from further analyses. This method of selecting loci is advantageous, as it accounts for differences in error rate between loci of varying frequencies of present alleles. An example using this method to select loci is demonstrated in an amplified fragment length polymorphism dataset generated from the North American prairie species big bluestem. Within this dataset the error rate was reduced from 12.5% to 8.8% by removal of loci with error rates greater than the defined threshold. By repeating the method on selected loci, the error rate was further reduced to 5.9%. This reduction in error resulted in a substantial increase in the amount of genetic variation attributable to regional and population variation. Conclusions This paper demonstrates a logical and computationally simple method for selecting loci with a reduced error rate. In the context of a genetic diversity study, this method resulted in an increased ability to detect differences between populations. Further application of this locus selection method, in addition to error-reducing methodological precautions, will result in amplified fragment length polymorphism datasets with reduced error rates. This reduction in error rate should result in greater power to detect differences and increased reproducibility.
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Affiliation(s)
- David L Price
- Department of Agronomy, University of Wisconsin-Madison, 53706, USA.
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Ersoz ES, Wright MH, Pangilinan JL, Sheehan MJ, Tobias C, Casler MD, Buckler ES, Costich DE. SNP discovery with EST and NextGen sequencing in switchgrass (Panicum virgatum L.). PLoS One 2012; 7:e44112. [PMID: 23049744 PMCID: PMC3458043 DOI: 10.1371/journal.pone.0044112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 07/31/2012] [Indexed: 11/18/2022] Open
Abstract
Although yield trials for switchgrass (Panicum virgatum L.), a potentially high value biofuel feedstock crop, are currently underway throughout North America, the genetic tools for crop improvement in this species are still in the early stages of development. Identification of high-density molecular markers, such as single nucleotide polymorphisms (SNPs), that are amenable to high-throughput genotyping approaches, is the first step in a quantitative genetics study of this model biofuel crop species. We generated and sequenced expressed sequence tag (EST) libraries from thirteen diverse switchgrass cultivars representing both upland and lowland ecotypes, as well as tetraploid and octoploid genomes. We followed this with reduced genomic library preparation and massively parallel sequencing of the same samples using the Illumina Genome Analyzer technology platform. EST libraries were used to generate unigene clusters and establish a gene-space reference sequence, thus providing a framework for assembly of the short sequence reads. SNPs were identified utilizing these scaffolds. We used a custom software program for alignment and SNP detection and identified over 149,000 SNPs across the 13 short-read sequencing libraries (SRSLs). Approximately 25,000 additional SNPs were identified from the entire EST collection available for the species. This sequencing effort generated data that are suitable for marker development and for estimation of population genetic parameters, such as nucleotide diversity and linkage disequilibrium. Based on these data, we assessed the feasibility of genome wide association mapping and genomic selection applications in switchgrass. Overall, the SNP markers discovered in this study will help facilitate quantitative genetics experiments and greatly enhance breeding efforts that target improvement of key biofuel traits and development of new switchgrass cultivars.
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Affiliation(s)
- Elhan S. Ersoz
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- * E-mail: (DC); (ESE)
| | - Mark H. Wright
- Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Jasmyn L. Pangilinan
- Joint Genome Institute, Department of Energy, Walnut Creek, California, United States of America
| | - Moira J. Sheehan
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Christian Tobias
- USDA-ARS, Western Regional Research Center, Albany, California, United States of America
| | - Michael D. Casler
- USDA-ARS, U.S. Dairy Forage Research Center, Madison, Wisconsin, United States of America
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- USDA-ARS, Robert Holley Center, Ithaca, New York, United States of America
| | - Denise E. Costich
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- USDA-ARS, Robert Holley Center, Ithaca, New York, United States of America
- * E-mail: (DC); (ESE)
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Jakubowski AR, Casler MD, Jackson RD. Genetic evidence suggests a widespread distribution of native North American populations of reed canarygrass. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0300-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Plant breeders have played an essential role in improving agricultural crops, and their efforts will be critical to meet the increasing demand for cellulosic bioenergy feedstocks. However, a major concern is the potential development of novel invasive species that result from breeders' efforts to improve agronomic traits in a crop. We use reed canarygrass as a case study to evaluate the potential of plant breeding to give rise to invasive species. Reed canarygrass has been improved by breeders for use as a forage crop, but it is unclear whether breeding efforts have given rise to more vigorous populations of the species. We evaluated cultivars, European wild, and North American invader populations in upland and wetland environments to identify differences in vigor between the groups of populations. While cultivars were among the most vigorous populations in an agricultural environment (upland soils with nitrogen addition), there were no differences in above- or below-ground production between any populations in wetland environments. These results suggest that breeding has only marginally increased vigor in upland environments and that these gains are not maintained in wetland environments. Breeding focuses on selection for improvements of a specific target population of environments, and stability across a wide range of environments has proved elusive for even the most intensively bred crops. We conclude that breeding efforts are not responsible for wetland invasion by reed canarygrass and offer guidelines that will help reduce the possibility of breeding programs releasing cultivars that will become invasive.
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Affiliation(s)
- Andrew R Jakubowski
- Department of Agronomy, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
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Zhang Y, Zalapa JE, Jakubowski AR, Price DL, Acharya A, Wei Y, Brummer EC, Kaeppler SM, Casler MD. Post-glacial evolution of Panicum virgatum: centers of diversity and gene pools revealed by SSR markers and cpDNA sequences. Genetica 2011; 139:933-48. [PMID: 21786028 DOI: 10.1007/s10709-011-9597-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 07/04/2011] [Indexed: 12/01/2022]
Abstract
Switchgrass (Panicum virgatum), a central and Eastern USA native, is highly valued as a component in tallgrass prairie and savanna restoration and conservation projects and a potential bioenergy feedstock. The purpose of this study was to identify regional diversity, gene pools, and centers-of-diversity of switchgrass to gain an understanding of its post-glacial evolution and to identify both the geographic range and potential overlap between functional gene pools. We sampled a total of 384 genotypes from 49 accessions that included the three main taxonomic groups of switchgrass (lowland 4x, upland 4x, and upland 8x) along with one accession possessing an intermediate phenotype. We identified primary centers of diversity for switchgrass in the eastern and western Gulf Coast regions. Migration, drift, and selection have led to adaptive radiation in switchgrass, creating regional gene pools within each of the main taxa. We estimate that both upland-lowland divergence and 4x-to-8x polyploidization within switchgrass began approximately 1.5-1 M ybp and that subsequent ice age cycles have resulted in gene flow between ecotype lineages and between ploidy levels. Gene flow has resulted in "hot spots" of genetic diversity in the southeastern USA and along the Atlantic Seaboard.
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Affiliation(s)
- Yunwei Zhang
- Grassland Institute, China Agricultural University, Beijing, China
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Gregos J, Casler MD, Stier JC. Resistance of Closely Mown Fine Fescue and Bentgrass Species to Snow Mold Pathogens. Plant Dis 2011; 95:847-852. [PMID: 30731740 DOI: 10.1094/pdis-11-10-0791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Creeping bentgrass (Agrostis stolonifera) is the primary species used on golf courses in temperate regions but requires prophylactic fungicide treatment to prevent snow mold diseases. We hypothesized that fine fescues (Festuca spp.) and colonial bentgrass (A. capillaris) have superior resistance to snow mold diseases compared with creeping bentgrass. Our objective was to compare the resistance of fine fescues, colonial bentgrass, and creeping bentgrass to snow mold diseases caused by Microdochium nivale and Typhula spp. Field plots were established in two separate years on fairways of three golf courses in Wisconsin to encompass the geographic distribution of snow mold pathogens. The experimental design was a split-split-split plot arrangement with three replications. Whole plots were pathogen species, host genus were subplots, host cultivars were sub-subplots, and inoculated versus noninoculated treatments were sub-sub-subplots. Plots were visually evaluated each spring for disease, turf quality, and Poa annua infestation. Data were analyzed using planned contrasts. Inoculation effects depended on pathogen type and location. Creeping bentgrass always had the most snow mold damage. Fine fescues had less snow mold damage than colonial bentgrass except for one year-location but did not provide acceptable year-long turf quality due to P. annua invasion.
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Affiliation(s)
- Jeff Gregos
- former Research Assistant, Department of Plant Pathology, University of Wisconsin-Madison 53706
| | - M D Casler
- United States Department of Agriculture-Agricultural Research Service, U.S. Dairy Forage Research Center, Madison, WI 53706-1108
| | - J C Stier
- Professor, Department of Horticulture, University of Wisconsin-Madison
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Zalapa JE, Price DL, Kaeppler SM, Tobias CM, Okada M, Casler MD. Hierarchical classification of switchgrass genotypes using SSR and chloroplast sequences: ecotypes, ploidies, gene pools, and cultivars. Theor Appl Genet 2011; 122:805-17. [PMID: 21104398 DOI: 10.1007/s00122-010-1488-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/22/2010] [Indexed: 05/07/2023]
Abstract
Switchgrass (Panicum virgatum L.) is an important crop for bioenergy feedstock development. Switchgrass has two main ecotypes: the lowland ecotype being exclusively tetraploid (2n = 4x = 36) and the upland ecotype being mainly tetraploid and octaploid (2n = 8x = 72). Because there is a significant difference in ploidy, morphology, growth pattern, and zone of adaptation between and within the upland and lowland ecotypes, it is important to discriminate switchgrass plants belonging to different genetic pools. We used 55 simple sequence repeats (SSR) loci and six chloroplast sequences to identify patterns of variation between and within 18 switchgrass cultivars representing seven lowland and 11 upland cultivars from different geographic regions and of varying ploidy levels. We report consistent discrimination of switchgrass cultivars into ecotype membership and demonstrate unambiguous molecular differentiation among switchgrass ploidy levels using genetic markers. Also, SSR and chloroplast markers identified genetic pools related to the geographic origin of the 18 cultivars with respect to ecotype, ploidy, and geographical, and cultivar sources. SSR loci were highly informative for cultivar fingerprinting and to classify plants of unknown origin. This classification system is the first step toward developing switchgrass complementary gene pools that can be expected to provide a significant heterotic increase in biomass yield.
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Affiliation(s)
- J E Zalapa
- USDA-ARS, Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, USA.
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Jakubowski AR, Casler MD, Jackson RD. The Benefits of Harvesting Wetland Invaders for Cellulosic Biofuel: An Ecosystem Services Perspective. Restor Ecol 2010. [DOI: 10.1111/j.1526-100x.2010.00738.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Digman MF, Shinners KJ, Casler MD, Dien BS, Hatfield RD, Jung HJG, Muck RE, Weimer PJ. Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production. Bioresour Technol 2010; 101:5305-5314. [PMID: 20202834 DOI: 10.13031/2013.30051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 02/01/2010] [Accepted: 02/04/2010] [Indexed: 05/22/2023]
Abstract
Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.
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Affiliation(s)
- Matthew F Digman
- United States Department of Agriculture, Agricultural Research Service, US Dairy Forage Research Center, Madison, WI 53706, United States.
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36
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Digman MF, Shinners KJ, Casler MD, Dien BS, Hatfield RD, Jung HJG, Muck RE, Weimer PJ. Optimizing on-farm pretreatment of perennial grasses for fuel ethanol production. Bioresour Technol 2010; 101:5305-14. [PMID: 20202834 DOI: 10.1016/j.biortech.2010.02.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 02/01/2010] [Accepted: 02/04/2010] [Indexed: 05/24/2023]
Abstract
Switchgrass (Panicum virgatum L.) and reed canarygrass (Phalaris arundinacea L.) were pretreated under ambient temperature and pressure with sulfuric acid and calcium hydroxide in separate experiments. Chemical loadings from 0 to 100g (kg DM)(-1) and durations of anaerobic storage from 0 to 180days were investigated by way of a central composite design at two moisture contents (40% or 60% w.b.). Pretreated and untreated samples were fermented to ethanol by Saccharomyces cerevisiae D5A in the presence of a commercially available cellulase (Celluclast 1.5L) and beta-glucosidase (Novozyme 188). Xylose levels were also measured following fermentation because xylose is not metabolized by S. cerevisiae. After sulfuric acid pretreatment and anaerobic storage, conversion of cell wall glucose to ethanol for reed canarygrass ranged from 22% to 83% whereas switchgrass conversions ranged from 16% to 46%. Pretreatment duration had a positive effect on conversion but was mitigated with increased chemical loadings. Conversions after calcium hydroxide pretreatment and anaerobic storage ranged from 21% to 55% and 18% to 54% for reed canarygrass and switchgrass, respectively. The efficacy of lime pretreatment was found to be highly dependent on moisture content. Moreover, pretreatment duration was only found to be significant for reed canarygrass. Although significant levels of acetate and lactate were observed in the biomass after storage, S. cerevisiae was not found to be inhibited at a 10% solids loading.
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Affiliation(s)
- Matthew F Digman
- United States Department of Agriculture, Agricultural Research Service, US Dairy Forage Research Center, Madison, WI 53706, United States.
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El-Nashaar HM, Banowetz GM, Griffith SM, Casler MD, Vogel KP. Genotypic variability in mineral composition of switchgrass. Bioresour Technol 2009; 100:1809-14. [PMID: 19019672 DOI: 10.1016/j.biortech.2008.09.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2007] [Revised: 09/25/2008] [Accepted: 09/25/2008] [Indexed: 05/04/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a warm season perennial grass with great potential as an energy crop in the USA. It is widely adapted to many regions of the country, produces large amounts of biomass, serves as a useful forage grass, and provides ecosystem services that benefit soil and water quality and wildlife. Biological and thermochemical technologies are being developed to convert herbaceous biomass, including switchgrass, to energy. The objective of this research was to determine the effect of genotype and production environment on the concentration of minerals that affect the suitability of switchgrass for thermochemical conversion and to quantify the amount of potassium (K) and phosphorus (P) removed from the production system by harvest of the aboveground biomass, a measure of the sustainability of the practice. Straw dry biomass contained from 1.3 to 6.4 kg Mg(-1) and from 6.2 to 15.8 kg Mg(-1) of P and K, respectively. Variability in aluminum (Al), calcium (Ca), chloride (Cl), K, P, silicon (Si), and sulfur (S) concentrations across locations was relatively high, ranging from twofold (Al) to eightfold (Cl). Location had a strong impact on mineral concentrations among switchgrass genotypes evaluated in this study. Latitude of origin impacted the Cl and Si concentrations measured in plant tissues, but none of the other minerals analyzed in this study. Upland and lowland cytotypes explained some of the observed differences, but populationxlocation interactions were the primary source of variability in the concentration of these minerals.
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Affiliation(s)
- Geoffrey E. Brink
- USDA‐ARSUnited States Dairy Forage Research Center1925 Linden Drive WestMadisonWI53706
| | - Michael D. Casler
- USDA‐ARSUnited States Dairy Forage Research Center1925 Linden Drive WestMadisonWI53706
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Casler MD, Brummer EC. Theoretical Expected Genetic Gains for Among-and-Within-Family Selection Methods in Perennial Forage Crops. Crop Science 2008; 48:890. [PMID: 0 DOI: 10.2135/cropsci2007.09.0499] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Abstract
Federal and state regulations are being promulgated under the Clean Air Act to reduce hazardous air emissions from livestock operations. Few data are available on emissions from livestock facilities in the USA and the management practices that may minimize emissions. The objective of this study was to measure seasonal and bedding impacts on ammonia emissions from tie-stall dairy barns located in central Wisconsin. Four chambers each housed four Holstein dairy heifers (approximately 17 mo of age; body weights, 427-522 kg) for three 28-d trial periods corresponding to winter, summer, and fall. A 4x4 Latin Square statistical design was used to evaluate four bedding types (manure solids, chopped newspaper, pine shavings, and chopped wheat straw) in each chamber for a 4-d ammonia monitoring period. Average ammonia-N emissions (g heifer(-1) d(-1)) during summer (20.4) and fall (21.0) were similar and twice the emissions recorded during winter (10.1). Ammonia-N emissions accounted for approximately 4 to 7% of consumed feed N, 4 to 10% of excreted N, and 9 to 20% of manure ammonical N. Cooler nighttime temperatures did not result in lower ammonia emissions than daytime temperatures. Ammonia emissions (g heifer(-1) d(-1)) from chambers that contained manure solids (20.0), newspaper (18.9), and straw (18.9) were similar and significantly greater than emissions using pine shavings (15.2). Chamber N balances, or percent difference between the inputs feed N and bedding N, and the outputs manure N, body weight N, and ammonia N were 105, 90, and 89% for the winter, summer, and fall trials, respectively. Relatively high chamber N balances and favorable comparisons of study data with published values of ammonia emissions, feed N intake, and manure N excretion provided confidence in the accuracy of the study results.
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Affiliation(s)
- J M Powell
- USDA-ARS U.S. Dairy Forage Resh. Center, Madison, WI 53706, USA.
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Chakraborty N, Curley J, Warnke S, Casler MD, Jung G. Mapping QTL for dollar spot resistance in creeping bentgrass (Agrostis stolonifera L.). Theor Appl Genet 2006; 113:1421-35. [PMID: 16969681 DOI: 10.1007/s00122-006-0387-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Accepted: 08/03/2006] [Indexed: 05/11/2023]
Abstract
Dollar spot caused by Sclerotinia homoeocarpa F. T. Bennett is the most economically important turf disease on golf courses in North America. Dollar spot resistance in a creeping bentgrass cultivar would greatly reduce the frequency, costs, and environmental impacts of fungicide application. Little work has been done to understand the genetics of resistance to dollar spot in creeping bentgrass. Therefore, QTL analysis was used to determine the location, number and effects of genomic regions associated with dollar spot resistance in the field. To meet this objective, field inoculations using a single isolate were performed over 2 years and multiple locations using progeny of a full sib mapping population '549 x 372'. Dollar spot resistance seems to be inherited quantitatively and broad sense heritability for resistance was estimated to be 0.88. We have detected one QTL with large effect on linkage group 7.1 with LOD values ranging from 3.4 to 8.6 and explaining 14-36% of the phenotypic variance. Several smaller effect QTL specific to rating dates, locations and years were also detected. The association of the tightly linked markers with the LG 7.1 QTL based on 106 progeny was further examined by single marker analysis on all 697 progeny. The high significance of the QTL on LG 7.1 at a sample size of 697 (P < 0.0001), along with its consistency across locations, years and ratings dates, indicated that it was stable over environments. Markers tightly linked to the QTL can be utilized for marker-assisted selection in future bentgrass breeding programs.
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Affiliation(s)
- N Chakraborty
- Department of Crop Sciences, University of Illinois, Urbana Champaign, IL 61801, USA
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Abstract
Neutral detergent fiber (NDF) is considered the single best laboratory predictor of voluntary intake by ruminant livestock, creating interest in using NDF as a selection criterion in forage breeding programs. Because genetic reductions in NDF lead to increases in dry matter digestibility but not to changes in digestibility of the NDF fraction, we postulated that low-NDF plants do not have altered compositions of their cell walls. We tested this hypothesis using clones of smooth bromegrass (Bromus inermis Leyss.) with divergent NDF concentrations. High-NDF and low-NDF plants did not differ in cell wall concentrations or in the concentrations of any cell wall component (fucose, arabinose, rhamnose, galactose, glucose, xylose, mannose, uronic acids, and lignin). Instead, low-NDF plants had a cell wall that was more susceptible to solubilization in neutral detergent solution, suggesting that their cell walls were less well-developed as compared to high-NDF plants. NDF should not be used as a substitute for cell wall concentration in forage plants.
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Affiliation(s)
- M D Casler
- U.S. Dairy Forage Research Center, Agricultural Research Service, U.S. Department of Agriculture, 1925 Linden Drive West, Madison, WI 53706-1108, USA.
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Casler MD, Buxton DR, Vogel KP. Genetic modification of lignin concentration affects fitness of perennial herbaceous plants. Theor Appl Genet 2002; 104:127-131. [PMID: 12579437 DOI: 10.1007/s001220200015] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Populations of four perennial herbaceous species that were genetically modified for altered lignin content (or associated forage digestibility) by conventional plant breeding were evaluated for two agricultural fitness traits, plant survival and plant biomass, in three Northcentral USA environments for more than 4 years. Reduced lignin concentration or increased digestibility resulted in increased winter mortality in two of four species and reduced biomass in one species. Results from other experiment indicate that these apparent genetic correlations may be ephemeral, suggesting that selection for fitness can be successful within high-digestibility or low-lignin germplasm. Results indicate that perennial plants genetically engineered with altered lignin concentration or composition for use in livestock, pulp and paper, or bioenergy production should be evaluated for fitness in field environments prior to use in agriculture.
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Affiliation(s)
- M D Casler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706-1597, USA.
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Abstract
A rust fungus was observed on smooth brome grass (Bromus inermis Leyss.) leaves growing in the fields of the University of Wisconsin (UW) Agricultural Research Station at Arlington, WI. The population (WPc-95A) was classified as Puccinia coronata Corda. Reports of P. coronata on B. inermis are rare, so a study of the pathogen host range, alternate host, and morphology of urediniospores and teliospores was undertaken. Fourteen grass species representing 10 genera were inoculated with P. coronata WPc-95A, which was maintained with repeated inoculations on B. inermis cv. PL-BDR1. Seventy-two 30-day-old seedlings of B. inermis were inoculated with urediniospores of the fungus. Infection type, pustule density, and disease incidence were recorded 15 days after inoculation. The same grass cultivars were also inoculated with aecio-spores collected from Rhamnus cathartica L. located on the UW campus. To test for host specificity, urediniospores produced on aeciospore-susceptible grass species were used to reinoculate plants of B. inermis and the host species from which the urediniospores were derived. B. inermis, B. riparius Rehm., Festuca pratensis Huds., and Lolium perenne L. were susceptible to P. coronata WPc-95A. The two Bromus spp. had the highest disease incidence. R. cathartica was found to be an alternate host of P. coronata WPc-95A, as it is for P. coronata isolates found on F. pratensis. However, cross-inoculations with urediniospores from R. cathartica-derived aeciospore infections indicated that only urediniospores of B. inermis origin were capable of infecting B. inermis. Thus, P. coronata WPc-95A appears to belong to a forma speciales previously undescribed in North America.
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Affiliation(s)
| | | | - M D Casler
- Department of Agronomy, University of Wisconsin, Madison 53706
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Abstract
Common smooth bromegrass (Bromus inermis Leyss.) is octoploid, 2n = 8x = 56, with a genome structure of AAAAB1B1B2B2. Tetrasomic inheritance patterns have been observed in smooth bromegrass, but disomic inheritance is also expected from cytologic observations. Smooth bromegrass is susceptible to the crown rust fungus (Puccinia coronata Corda.). The objective of this study was to determine the inheritance of smooth bromegrass resistance to P. coronata. Seven smooth bromegrass clones, three susceptible and four resistant, were selfed and crossed in a diallel with bulked reciprocals. Inoculations were made with a population of P. coronata from PL-BDR1 smooth bromegrass. Resistance of smooth bromegrass to this population of P. coronata is complex. At least three genes appear to be involved in this host-pathogen interaction, one tetrasomic dominant gene which determines susceptibility (S) and two dominant genes (R1 and R2) that may be complementary and could be inherited either tetrasomically or disomically. Other genes may be involved in the smooth bromegrass-P. coronata interaction, possibly accounting for the lack of fit to expected ratios of some progeny. Heterogeneity for avirulence phenotype in the pathogen population may also have contributed to lack of fit of some progeny. Multiple resistance genes were detected because a pathogen population, likely consisting of genotypes with different genes for virulence, was used to challenge the host.
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Affiliation(s)
- N J Delgado
- Department of Agronomy, University of Wisconsin, Madison 53706, USA
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Abstract
The nutrient contents of perennial ryegrass (Lolium perenne L.) and alfalfa (Medicago sativa L.) are reasonably similar. Despite similarities, the lactation performance of dairy cows fed perennial ryegrass has not been compared with the lactation performance of dairy cows fed alfalfa. The present study was implemented to compare the performance of lactating cows fed alfalfa or perennial ryegrass silage. Alfalfa and perennial ryegrass were harvested at late bud and boot stages of maturity, respectively, and ensiled in separate 4.9- x 18.3-m concrete silos. The experimental silages were supplemented with a concentrate mix at 31.1% of dietary dry matter and fed to 18 multiparous Holstein cows in early lactation in a crossover experimental design with 28-d periods. Digestibility and rate of passage of experimental diets were also measured using rare earth markers. The perennial ryegrass contained 3.0 percentage units more neutral detergent fiber than did alfalfa, but in vitro digestibility of neutral detergent fiber was 8.8 percentage units higher for perennial ryegrass. In vitro digestibility of dry matter was also higher for perennial ryegrass. Cows fed alfalfa silage produced more milk (31.8 kg/d) than did cows fed perennial ryegrass silage (30.2 kg/d). Cows fed perennial ryegrass silage ate less feed (2.2 kg/d) than did cows fed alfalfa. Because dry matter intake was lower, diet digestibilities were higher, and rate of passage was slower, for cows consuming perennial ryegrass. Based on laboratory evaluations, perennial ryegrass silage has high nutritional quality, but performance of lactating cows indicated that the forage was suboptimal for supporting high milk production when compared with alfalfa. The perennial ryegrass silage was suboptimal because it did not stimulate high amounts of dry matter intake in lactating cows.
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Affiliation(s)
- P C Hoffman
- Department of Dairy Science, University of Wisconsin, Madison 53706, USA
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Casler MD. Genetic variation and covariation in a population of tetraploid Dactylis L. accessions. Theor Appl Genet 1991; 81:253-264. [PMID: 24221211 DOI: 10.1007/bf00215731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/1990] [Accepted: 07/25/1990] [Indexed: 06/02/2023]
Abstract
Efficient utilization of divergent germ plasm sources in breeding cultivated Dactylis glomerata L. ssp. glomerata Domin depends on knowledge of quantitative variation within and among accessions. This study was undertaken to quantify variation and covariation for forage yield, maturity, disease reaction, and ground cover within a population of tetraploid Dactylis accessions. Variation was observed among families within the population for each variable. Most genetic variation (73%-93% of the family sums of squares) was within country sources or within accessions. Thus, country boundaries, which are traditionally important factors used in defining limits of plant exploration expeditions, have limited expected use in targeting future exploration for specific sources of high yield, disease resistance, or ground cover. Maturity was the exception to this; late-maturing accessions were identified as originating exclusively from the USSR. Some relationships among traits, such as that for yield and disease reaction, differed for accessions and cultivars. Several accessions and families within accessions were identified to have performance superior to most or all cultivars included in this study. Existing germ plasm from several countries was identified to have potential in breeding orchardgrass, while that from other countries appeared to have little or no potential in supplying germ plasm for hay production in humid-temperate environments.
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Affiliation(s)
- M D Casler
- Department of Agronomy, University of Wisconsin-Madison, 53706-1597, Madison, WI, USA
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