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

Genetic Linkage Mapping And Transmission Ratio Distortion In A Three-Generation Four-Founder Population Of Panicum Virgatum (L.)

Guifen Li, D. Serba, M. Saha, J. Bouton, Christina L. Lanzatella, C. Tobias
Published 2014 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
Switchgrass (Panicum virgatum L.), a warm season, C4, perennial grass, is one of the predominant grass species of the North American tall grass prairies. It is viewed as a high-potential bioenergy feedstock species because it can produce large amounts of lignocellulosic material with relatively few inputs. The objectives of this project were to develop an advanced switchgrass population and use it for the construction of genetic linkage maps and trait characterization. A three-generation, four-founder population was created and a total of 182 progeny of this advanced population were genotyped, including a mixture of self-pollinated and hybrid individuals. The female map integrated both subpopulations and covered 1629 cM of the switchgrass genome, with an average map length of 91 cM per linkage group. The male map of the hybrid progeny covered 1462 cM, with an average map length of 81 cM per linkage group. Average marker density of the female and male maps was 3.9 and 3.5 cM per marker interval, respectively. Based on the parental maps, the genome length of switchgrass was estimated to be 1776 cM and 1596 cM for the female map and male map, respectively. The proportion of the genome within 5 cM of a mapped locus was estimated to be 92% and 93% for the female map and male map, respectively. Thus, the linkage maps have covered most of the switchgrass genome. The assessment of marker transmission ratio distortion found that 26% of the genotyped markers were distorted from either 1:1 or 3:1 ratios expected for segregation of single dose markers in one or both parents, respectively. Several regions affected by transmission ratio distortion were found, with linkage groups Ib-m and VIIIa-f most affected.
This paper references
10.1046/J.1471-8278.2000.00013.X
Isolation and characterization of polymorphic microsatellite loci in Rubus alceifolius Poir. (Rosaceae), an invasive weed in La Réunion island
L. Amsellem (2001)
10.1093/OXFORDJOURNALS.JHERED.A111175
On the use of the classical tests for detecting linkage.
A. García-Dorado (1992)
Estimates of genetic parameters in switchgrass
J. W. VanOoijen (2006)
10.3923/RJAGR.2010.78.83
Progress of Segregation Distortion in Genetic Mapping of Plants
X. Liu (2010)
10.1016/J.PLANTSCI.2009.09.003
Tolerance of switchgrass to extreme soil moisture stress: Ecological implications
J. Barney (2009)
10.3835/plantgenome2011.01.0004
Reference Genome‐Directed Resolution of Homologous and Homeologous Relationships within and between Different Oat Linkage Maps
Juan J Gutierrez-Gonzalez (2011)
10.1007/BF00220999
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations
M. Lorieux (2004)
Meiotic Drive in Natural Populations of Drosophila Melanogaster. I. the Cytogenetic Basis of Segregation-Distortion.
L. Sandler (1959)
10.2135/CROPSCI1983.0011183X002300040029X
Estimates of Genetic Parameters in Switchgrass 1
L. Talbert (1983)
10.1186/1471-2164-12-380
Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map
K. Alheit (2011)
10.1007/BF00222097
Development of an RFLP map in diploid alfalfa
E. C. Brummer (2004)
Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers.
D. Grattapaglia (1994)
10.1007/s00122-003-1277-1
Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines
G. Fazio (2003)
10.2135/CROPSCI2005.0388
Ecotypic Variation among Switchgrass Populations from the Northern USA
M. Casler (2005)
10.1093/JHERED/93.1.77
MapChart: software for the graphical presentation of linkage maps and QTLs.
R. Voorrips (2002)
10.1007/s00122-011-1560-5
Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system
M. Muraya (2011)
10.1101/GR.10.3.350
A fast and scalable radiation hybrid map construction and integration strategy.
R. Agarwala (2000)
Switchgrass variety choice in Europe
H. W. Elbersen (2001)
Excess heterozygosity contributes to genetic map expansion in pea recombinant inbred populations.
M. Knox (2002)
10.1007/BF00037152
Universal primers for amplification of three non-coding regions of chloroplast DNA
P. Taberlet (2004)
A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions.
L. Fishman (2001)
Differential Zygotic Lethality in a Tomato Species Hybrid.
Charles M. Rick (1963)
10.1139/G87-026
Differential zygotic abortion in an interspecific Lycopersicon cross
I. Gadish (1987)
The Expression of Mendelian Factors in the Gametophyte of Maize.
P. Mangelsdorf (1926)
10.2134/JEQ2004.0329
Herbaceous vegetation productivity, persistence, and metals uptake on a biosolids-amended mine soil.
G. Evanylo (2005)
10.18637/JSS.V022.I09
simecol : An Object-Oriented Framework for Ecological Modeling in R
T. Petzoldt (2007)
10.1007/s00122-005-1935-6
Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers
A. Missaoui (2005)
10.1111/J.1469-1809.1943.TB02321.X
The estimation of map distances from recombination values.
D. D. Kosambi (1943)
Switchgrass, Big Bluestem, and Indiangrass
L. E. Moser (1995)
10.1038/nbt.2196
Reference genome sequence of the model plant Setaria
J. Bennetzen (2012)
A maximum likelihood method for estimating genome length using genetic linkage data.
A. Chakravarti (1991)
10.18637/JSS.V022.I08
Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (R Package qualV)
Stefanie Jachner (2007)
10.1007/978-0-387-70805-8_11
Improvement of Switchgrass as a Bioenergy Crop
J. Bouton (2008)
10.1016/J.BIOMBIOE.2005.10.006
Long-term yield potential of switchgrass-for-biofuel systems.
J. Fike (2006)
10.1534/genetics.110.113910
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions
M. Okada (2010)
10.1038/72708
An economic method for the fluorescent labeling of PCR fragments
M. Schuelke (2000)
10.1534/genetics.105.054791
Distribution of Microsatellites in the Genome of Medicago truncatula: A Resource of Genetic Markers That Integrate Genetic and Physical Maps
J. Mun (2006)
10.1371/journal.pone.0005795
An Integrated Genetic and Cytogenetic Map of the Cucumber Genome
Y. Ren (2009)
10.2135/CROPSCI1996.0011183X003600040039X
Chloroplast DNA and nuclear DNA content variations among cultivars of switchgrass
Sherry J. Hultquist (1996)
10.1186/1471-2164-12-369
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits
C. Saski (2011)
10.2135/CROPSCI2004.4430
Genetic Variability and Trait Relationships in Switchgrass
M. Das (2004)
10.1111/J.1365-313X.1993.00739.X
Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP.
P. Stam (1993)
10.2135/CROPSCI1998.0011183X003800030042X
Controlled Hybridization Technique for Switchgrass
J. M. Martínez-Reyna (1998)
Abortion of male and female gametes in the tomato determined by allelic interaction.
Charles M. Rick (1966)
Software for the calculation of genetic linkage maps
J. V. Ooijen (2001)
10.2135/CROPSCI2011.02.0104
Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass
Y. Zhang (2011)
Estimates of genetic parameters in switchgrass
L E Talbert (1983)
JoinMap v.4: Software for the calculation of genetic linkage maps in experimental populations
J W Vanooijen (2006)
10.4141/P06-136
Switchgrass as a biofuels feedstock in the USA
M. Sanderson (2006)
10.1007/s12155-011-9173-z
Identification of a Selfing Compatible Genotype and Mode of Inheritance in Switchgrass
L. Liu (2011)
10.1007/s00122-011-1617-5
Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications
X. Li (2011)
10.1093/dnares/dsr017
Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives
N. Ramchiary (2011)
10.1007/BF00220998
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations
M. Lorieux (2004)
10.2135/CROPSCI1995.0011183X003500050030X
Integration of Simple Sequence Repeat DNA Markers into a Soybean Linkage Map
M. Akkaya (1995)
10.2135/CROPSCI1996.0011183X003600050021X
Chromosome number and nuclear DNA content of several switchgrass populations
A. Hopkins (1996)
10.1007/s00122-002-0970-9
Chromosomal regions associated with segregation distortion in maize
H. Lu (2002)
10.1016/S0168-9525(97)01008-1
Simple sequence repeats as a source of quantitative genetic variation.
Y. Kashi (1997)
10.2135/CROPSCI2002.1800
Incompatibility Systems in Switchgrass
J. M. Martínez-Reyna (2002)
10.1007/s12155-013-9367-7
Lowland Switchgrass Plants in Populations Set Completely Outcrossed Seeds Under Field Conditions as Assessed with SSR Markers
L. Liu (2013)
10.1007/s00122-003-1370-5
High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae)
M. V. Ashley (2003)
10.1038/sj.hdy.6800173
Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps
C. Hackett (2003)
10.1007/s12155-013-9315-6
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes
D. Serba (2013)
10.1079/9780851996011.0059
Association mapping in plant populations.
J. Jannink (2001)
Statistical Genetics of Quantitative Traits: Linkage, Maps and QTL
R. Wu (2007)
10.1006/TPBI.2002.1577
Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species.
R. Wu (2002)
10.1534/g3.111.001503
A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass
L. Liu (2012)
10.1007/BF02191823
Characterization and genetic mapping of simple repeat sequences in the tomato genome
P. Broun (2005)
10.1007/s001220050952
An RFLP linkage map of Upland cotton, Gossypium hirsutum L.
Z. W. Shappley (1998)
10.2135/CROPSCI2004.2930
Latitudinal Adaptation of Switchgrass Populations
M. Casler (2004)
Switchgrass, big bluestem, and indiangrass, pp. 409-420 in An Introduction to Grassland Agriculture
L E Moser (1995)
10.18637/JSS.V022.I04
The ade4 Package: Implementing the Duality Diagram for Ecologists
S. Dray (2007)



This paper is referenced by
10.1007/s12155-017-9867-y
Breeding for Biomass Yield in Switchgrass Using Surrogate Measures of Yield
M. Casler (2017)
10.1186/s12864-016-3377-8
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency
D. Serba (2016)
10.3835/plantgenome2018.01.0002
Candidate Variants for Additive and Interactive Effects on Bioenergy Traits in Switchgrass (Panicum virgatum L.) Identified by Genome‐Wide Association Analyses
Guillaume P Ramstein (2018)
10.3389/fpls.2020.00615
Analysis of Crossover Events and Allele Segregation Distortion in Interspecific Citrus Hybrids by Single Pollen Genotyping
Miguel Garavello (2020)
10.1371/journal.pone.0208838
Efficient algorithms for Longest Common Subsequence of two bucket orders to speed up pairwise genetic map comparison
Lisa De Mattéo (2018)
10.4995/thesis/10251/149567
Análisis del nivel de ploidía y estructura genética de gametos de mandarino
M. F. Garavello (2020)
10.1007/s12892-017-0175-0
Breeding of Lignocellulosic Bioethanol Feedstock
Yong Suk Chung (2017)
10.1534/g3.118.200969
Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample
Guillaume P Ramstein (2019)
10.1007/s12155-019-09978-5
Identification of Quantitative Trait Loci for Plant Height, Crown Diameter, and Plant Biomass in a Pseudo-F2 Population of Switchgrass
M. Taylor (2019)
10.3835/plantgenome2014.10.0075
Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA‐Seq Analysis
Desalegn D. Serba (2015)
10.3835/plantgenome2014.10.0065
High‐Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping‐by‐Sequencing
Jason D. Fiedler (2015)
10.1534/g3.115.024950
Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium
Guillaume P Ramstein (2016)
10.1101/124081
Extensions of BLUP models for genomic prediction in heterogeneous populations: Application in a diverse switchgrass sample
Guillaume P Ramstein (2017)
10.1017/9781108377737
Integer Linear Programming in Computational and Systems Biology: An Entry-Level Text and Course
D. Gusfield (2019)
10.1007/s12155-016-9768-5
QTL and Drought Effects on Leaf Physiology in Lowland Panicum virgatum
S. H. Taylor (2016)
Semantic Scholar Logo Some data provided by SemanticScholar