Online citations, reference lists, and bibliographies.
Please confirm you are human
(Sign Up for free to never see this)
← Back to Search

Investigation Of Genomic Organization In Switchgrass (Panicum Virgatum L.) Using DNA Markers

A. Missaoui, A. Paterson, J. Bouton
Published 2005 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
We report an early investigation into genomic organization and chromosomal transmission in switchgrass based on restriction fragment length polymorphism (RFLP) markers. The segregation of 224 single dose restriction fragments (SDRF) in 85 full-sib progeny of a cross between the genotypes Alamo (AP13) and Summer (VS16) was used to determine linkage associations in each parent. In the seed parent AP13, 11 cosegregation groups were identified by 45 SDRF markers with a cumulative recombination length of 412.4 cM. In the pollen parent VS16, 57 SDRF markers were assigned to 16 cosegregation groups covering a length of 466.5 cM. SDRF markers identified by the same probes and mapping to different cosegregation groups were used to combine the two maps and identify homology groups. Eight homology groups were identified among the nine haploid linkage groups expected in switchgrass. The high incidence of repulsion phase associations indicates that preferential pairing between homologous chromosomes is predominant in switchgrass. Based on marker distribution in the paternal map (VS16), we estimated the recombinational length of switchgrass genome to be 4,617 cM. In order to link 95% of the genome to a marker at a 15-cM distance, a minimum of 459 markers will be required. Using information from the ratio of repulsion to coupling linkages, we infer that switchgrass is an autotetraploid with a high degree of preferential pairing. The information presented in this study establishes a foundation for extending genetic mapping in this crop and constitutes a framework for basic and applied genetic studies.
This paper references
10.1016/0960-8524(95)00176-X
Switchgrass as a sustainable bioenergy crop
M. Sanderson (1996)
Manual of grasses of the United States, vol II
AS Hitchcock (1971)
10.1086/333978
Meiotic Phenomena in Certain Gramineae. II. Paniceae and Andropogoneae
G. L. Church (1929)
Switchgrass as a sustainable bioenergy source
WR Osumpaugh (1996)
10.1007/s001220050033
Identification and molecular mapping of loci controlling fruit ripening time in tomato
S. Doğanlar (2000)
10.1016/S0022-2836(75)80083-0
Detection of specific sequences among DNA fragments separated by gel electrophoresis.
E. M. Southern (1975)
10.1007/s001220200008
Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions
R. Yadav (2002)
10.1038/NG1296-380
Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence
Andrew H. Paterson (1996)
10.1002/J.1537-2197.1954.TB14297.X
APOMIXIS IN PANICUM MAXIMUM
H. E. Warmke (1954)
Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes.
R. Ming (1998)
10.1001/jama.1951.03670250085036
The measurement of linkage in heredity
H. M. Slatis (1952)
The number of polymorphic DNA clones required to map the human genome. In: Wier BS (ed) Statistical analysis of DNA sequence data
DT Bishop (1983)
10.1007/BF00303919
Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs
J. Beckmann (2004)
10.1007/s001220100647
Detecting and mapping repulsion-phase linkage in polyploids with polysomic inheritance
L. Qu (2001)
10.1007/s001220100621
Seed quality QTLs identified in a molecular map of early maturing soybean
G. Csanádi (2001)
10.1007/s001220100541
Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench)
H. Kebede (2001)
Comparative genome mapping of Sorghum and maize.
R. Whitkus (1992)
A high density recombination map
JH Bowers (2003)
10.1046/J.1365-313X.1996.09010013.X
Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time.
U. Lagercrantz (1996)
10.1007/s001220050054
QTL analysis of leaf morphology in tetraploid Gossypium (cotton)
C. Jiang (2000)
parative mapping in Arabidopsis and Brassica , congruence of genes controlling flowering time
U Lagercrantz (1996)
10.1007/s001220050906
Anchor probes for comparative mapping of grass genera
A. Van Deynze (1998)
Methods of Genome Analysis in Plants
P. Jauhar (1996)
10.1139/G93-103
RFLP linkage map and genome analysis of Saccharum spontaneum.
J. Silva (1993)
A general polyploid model for analyzing gene segregation in outcrossing tetraploid species.
R. Wu (2001)
10.2135/CROPSCI1983.0011183X002300040029X
Estimates of Genetic Parameters in Switchgrass 1
L. Talbert (1983)
10.1016/S0304-4238(01)00309-0
Inheritance of RAPD markers in an interspecific F1 hybrid of grape between Vitis quinquangularis and V. vinifera
S. Luo (2002)
10.1023/A:1022308414864
Common Features of Segregation Distortion in Plants and Animals
D. Taylor (2004)
Saturated molecular map of the rice genome based on an interspecific backcross population.
M. Causse (1994)
10.1007/BF00019160
Nomad DNA — A model for movement and duplication of DNA sequences in plant genomes
E. Pichersky (2004)
The number of polymorphic DNA clones required to map the human genome
DT Bishop (1983)
10.1007/s00122-002-0970-9
Chromosomal regions associated with segregation distortion in maize
H. Lu (2002)
10.1007/s001220051324
A molecular marker linkage map of tetraploid alfalfa (Medicago sativa L.)
D. J. Brouwer (1999)
10.2307/3670396
Cytological and Morphological Variation in Panicum virgatum L.
J. N. Brunken (1975)
10.1002/J.1537-2197.1948.TB08097.X
A CYTOLOGICAL STUDY IN THE GRAMINEAE
W. V. Brown (1948)
10.1007/s001220051013
Genetic linkage map in sour cherry using RFLP markers
D. Wang (1998)
10.1073/PNAS.84.8.2363
Construction of multilocus genetic linkage maps in humans.
E. Lander (1987)
10.1093/NAR/8.19.4321
Rapid isolation of high molecular weight plant DNA.
M. G. Murray (1980)
10.1016/0003-2697(83)90418-9
A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity.
Andrew P. Feinberg (1983)
10.2135/CROPSCI1996.0011183X003600040039X
Chloroplast DNA and nuclear DNA content variations among cultivars of switchgrass
Sherry J. Hultquist (1996)
10.1007/BF00145628
Induction of a mutation in the male fertility gene of the preferentially transmitted Aegilops sharonensis chromosome 4S1 and its application for hybrid wheat production
I. King (2004)
10.2307/2418908
Exomorphological, Anatomical, and Cytological Studies in Panicum validum (Poaceae: Panicoideae: Paniceae): Its Systematic Position within the Genus
F. Zuloaga (1989)
10.1002/J.1537-2197.1940.TB14682.X
Cytotaxonomic studies in the Gramineae, Spartina, Andropogon, and Panicum.
G. L. Church (1940)
10.1007/BF00224092
The effect of genome and sex on recombination rates in Pennisetum species
C. Liu (2004)
Quan - titative trait loci influencing drought tolerance in grain sorghum ( Sorghum bicolor L Moench )
H Kebede (2001)
How many polymorphic genes will it take to span the human genome?
K. Lange (1982)
10.2135/CROPSCI2002.1800
Incompatibility Systems in Switchgrass
J. M. Martínez-Reyna (2002)
Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization.
S. Kowalski (1994)
Molecular investigation of the genetic variation and polymorphism in switchgrass (Panicum virgatum L) cultivars and development of a DNA marker for the classification of switchgrass germplasm
AM Missaoui (2003)
10.1007/BF00224274
The detection and estimation of linkage in polyploids using single-dose restriction fragments
K. Wu (2004)
10.1002/J.1537-2197.1942.TB14228.X
A CYTOLOGICAL STUDY OF SOME SPECIES IN THE TRIBE PANICEAE
G. Burton (1942)
Analysis of variation in Panicum virgatum
EL Nielson (1944)
10.5962/bhl.title.19358
Manual of the grasses of the United States
A. Hitchcock (1935)
10.2135/CROPSCI1967.0011183X000700040005X
Meiosis and Pollen Stainability in Switchgrass, Panicum virgatum L1
F. Barnett (1967)
10.1023/A:1022870917230
A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers
A. Kriegner (2004)
10.1016/S1360-1385(00)01629-0
Colinearity and gene density in grass genomes.
B. Keller (2000)
A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses.
J. Bowers (2003)
Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms.
S. Hulbert (1988)
RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid.
L. Grivet (1996)
10.1007/s001220051470
Molecular marker assisted genetic analysis of head shattering in six-rowed barley
N. Kandemir (2000)
10.2307/1935646
An Analysis of Variation Between Upland and Lowland Switchgrass, Panicum Virgatum L., in Central Oklahoma
C. Porter (1966)
10.2135/CROPSCI1992.0011183X003200050003X
Development and application of RFLPs in polyploids.
M. Sorrells (1992)
10.1006/TPBI.2002.1608
A bivalent polyploid model for linkage analysis in outcrossing tetraploids.
R. Wu (2002)
10.1016/S1360-1385(98)01240-0
Marker-assisted selection: new tools and strategies
J. Ribaut (1998)
10.2135/CROPSCI1996.0011183X003600050021X
Chromosome number and nuclear DNA content of several switchgrass populations
A. Hopkins (1996)
10.1038/NG0397-322
Erratum: Toward a unified genetic map of higher plants, transcending the monocot–dicot divergence
A. Paterson (1997)
A maximum likelihood method for estimating genome length using genetic linkage data.
A. Chakravarti (1991)
10.1016/S0168-9452(02)00327-8
Evolution of switchgrass (Panicum virgatum L.) based on sequences of the nuclear gene encoding plastid acetyl-CoA carboxylase☆
S. Huang (2003)
10.1007/BF02672016
Nuclear DNA content of some important plant species
K. Arumuganathan (2007)
10.1139/G93-112
Segregation of random amplified polymorphic DNA markers and strategies for molecular mapping in tetraploid alfalfa.
K. Yu (1993)
10.1111/J.1469-1809.1943.TB02321.X
The estimation of map distances from recombination values.
D. D. Kosambi (1943)
Linkage analysis in polyploids using molecular markers
Da Silva JAG (1996)
10.2135/CROPSCI2001.4151579X
Meiotic Stability, Chloroplast DNA Polymorphisms, and Morphological Traits of Upland × Lowland Switchgrass Reciprocal Hybrids
J. M. Martínez-Reyna (2001)
10.1007/BF00224524
Chromosome assortment in Saccharum
S. M. Aljanabi (2004)
10.1016/0888-7543(87)90010-3
MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations.
E. Lander (1987)
10.1007/s001220050847
Autotetraploids and genetic mapping using common AFLP markers: the R2 allele conferring resistance to Phytophthora infestans mapped on potato chromosome 4
X. Li (1998)
Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea.
T. Lan (2000)



This paper is referenced by
10.1007/s00122-012-1790-1
SSR-based genetic maps of Miscanthus sinensis and M. sacchariflorus, and their comparison to sorghum
C. Kim (2012)
10.1007/s00122-011-1568-x
Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers
S. Andru (2011)
10.1007/s11627-009-9215-9
A multiple species approach to biomass production from native herbaceous perennial feedstocks
J. González-Hernández (2009)
10.1371/journal.pone.0033892
A Genome-Wide Survey of Switchgrass Genome Structure and Organization
M. K. Sharma (2012)
10.1007/s12155-011-9166-y
Prospects for Hybrid Breeding in Bioenergy Grasses
Andrea Arias Aguirre (2011)
Genetic Transformation of Switchgrass (Panicum Virgatum L.) with Endoglucanase Gene and Characterization of Plants with Endoglucanase Transgene
Madhavi Suresh Dere (2012)
10.1016/J.GDE.2007.08.012
Molecular breeding of switchgrass for use as a biofuel crop.
J. Bouton (2007)
10.1016/J.SCIENTA.2011.05.016
Selection and characterization of a new switchgrass (Panicum virgatum L.) line with high somatic embryogenic capacity for genetic transformation.
B. Xu (2011)
A Comprehensive Analysis of Rust Disease Resistance in the Bioenergy Plant Switchgrass (Panicum virgatum L.)
T. Frazier (2016)
10.1007/s12155-013-9364-x
Production of Autopolyploid Lowland Switchgrass Lines Through In Vitro Chromosome Doubling
Zhiyong Yang (2013)
10.1534/g3.111.001503
A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass
L. Liu (2012)
10.3835/plantgenome2008.08.0003
Comparative Genomics in Switchgrass Using 61,585 High‐Quality Expressed Sequence Tags
C. Tobias (2008)
10.1007/s12155-013-9315-6
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes
D. Serba (2013)
10.1016/J.BIOMBIOE.2010.11.025
High throughput Agrobacterium-mediated switchgrass transformation
Ruyu Li (2011)
Genomes in the evolution of polyploid crop species and hybrids
Farah Badakshi (2014)
10.1142/S233954781540004X
Switchgrass as a bioenergy feedstock: advances in breeding and genomics research
Hem S. Bhandari (2015)
10.1007/s11032-007-9083-0
A genetic map of tetraploid Paspalum notatum Flügge (bahiagrass) based on single-dose molecular markers
J. Stein (2007)
10.1007/s12155-015-9629-7
QTLs for Biomass and Developmental Traits in Switchgrass (Panicum virgatum)
D. B. Lowry (2015)
10.3835/plantgenome2015.01.0001
Genomic Characterization of Interspecific Hybrids and an Admixture Population Derived from Panicum amarum × P. virgatum
Christopher Heffelfinger (2015)
10.1002/BBB.1418
Developments in crops and management systems to improve lignocellulosic feedstock production
B. Coulman (2013)
10.1101/GR.3725905
Grains of knowledge: genomics of model cereals.
A. Paterson (2005)
10.7282/T3SX6BG7
Evaluation of switchgrass (Panicum virgatum L.) as a bioenergy feedstock for the Northeastern and Mid-Atlantic USA
Laura M. Cortese (2014)
10.1104/pp.105.065136
Toward Sequencing the Sorghum Genome. A U.S. National Science Foundation-Sponsored Workshop Report[w]
S. Kresovich (2005)
10.1007/s12155-010-9081-7
Dihaploid Stocks of Switchgrass Isolated by a Screening Approach
H. A. Young (2010)
10.1111/J.1471-8286.2006.01187.X
Genic microsatellite markers derived from EST sequences of switchgrass (Panicum virgatum L.)
C. Tobias (2006)
10.1186/1754-6834-6-77
Advances in biotechnology and genomics of switchgrass
M. Nageswara-Rao (2013)
10.1101/2020.05.23.112961
Functional analysis of the teosinte branched 1 gene in the tetraploid switchgrass (Panicum virgatum L.) by CRISPR/Cas9-directed mutagenesis
Y. Liu (2020)
10.1016/J.FCR.2014.07.016
Variance components and heritability of biomass yield in switchgrass (Panicum virgatum L.) grown in the Southern Great Plains
Qingzhen Jiang (2014)
10.1534/genetics.110.113910
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions
M. Okada (2010)
10.1007/s12010-008-8168-5
Cell-Wall Composition and Accessibility to Hydrolytic Enzymes is Differentially Altered in Divergently Bred Switchgrass (Panicum virgatum L.) Genotypes
G. Sarath (2008)
Ploidy Number for Panicum virgatum (switchgrass) from the Long Island Sound Coastal Lowland compared to Upland and Lowland Cultivars.
T. Williams (2014)
10.1071/FP19086
Photosynthesis capacity diversified by leaf structural and physiological regulation between upland and lowland switchgrass in different growth stages.
Xin Cui (2019)
See more
Semantic Scholar Logo Some data provided by SemanticScholar