Genetic Linkage Mapping and Transmission Ratio Distortion in a Three-Generation Four-Founder Population of Panicum virgatum (L.)

Li, Guifen; Serba, Desalegn D.; Saha, Malay C.; Bouton, Joseph H.; Lanzatella, Christina L.; Tobias, Christian M.

doi:10.1534/g3.113.010165

**Genetic Linkage Mapping and Transmission Ratio Distortion in a Three-Generation Four-Founder Population of Panicum virgatum (L.)**

Journal Article · Mon Mar 17 00:00:00 EDT 2014 · G3

DOI:https://doi.org/10.1534/g3.113.010165· OSTI ID:1627948

Li, Guifen ^[1]; Serba, Desalegn D. ^[2]; Saha, Malay C. ^[2]; Bouton, Joseph H. ^[2]; Lanzatella, Christina L. ^[3]; Tobias, Christian M. ^[3]

Samuel Roberts Noble Foundation, Ardmore, OK (United States); DOE/OSTI
Samuel Roberts Noble Foundation, Ardmore, OK (United States)
US Department of Agriculture (USDA), Albany, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Samuel Roberts Noble Foundation, Ardmore, OK (United States); US Department of Agriculture (USDA), Albany, CA (United States)

Sponsoring Organization:: USDOE

OSTI ID:: 1627948

Journal Information:: G3, Journal Name: G3 Journal Issue: 5 Vol. 4; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

References (55)

Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations Lorieux, M.; Goffinet, B.; Perrier, X. Theoretical and Applied Genetics, Vol. 90, Issue 1 https://doi.org/10.1007/bf00220998	journal	January 1995
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations Lorieux, M.; Perrier, X.; Goffinet, B. Theoretical and Applied Genetics, Vol. 90, Issue 1 https://doi.org/10.1007/bf00220999	journal	January 1995
Characterization and genetic mapping of simple repeat sequences in the tomato genome Broun, Pierre; Tanksley, Steven D. Molecular and General Genetics MGG, Vol. 250, Issue 1 https://doi.org/10.1007/bf02191823	journal	January 1996
Chromosomal regions associated with segregation distortion in maize Lu, H.; Romero-Severson, J.; Bernardo, R. Theoretical and Applied Genetics, Vol. 105, Issue 4 https://doi.org/10.1007/s00122-002-0970-9	journal	September 2002
High variability and disomic segregation of microsatellites in the octoploid Fragaria virginiana Mill. (Rosaceae) Ashley, M. V.; Wilk, J. A.; Styan, S. M. N. Theoretical and Applied Genetics, Vol. 107, Issue 7 https://doi.org/10.1007/s00122-003-1370-5	journal	August 2003
Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers Missaoui, A. M.; Paterson, A. H.; Bouton, J. H. Theoretical and Applied Genetics, Vol. 110, Issue 8 https://doi.org/10.1007/s00122-005-1935-6	journal	April 2005
Wild sorghum from different eco-geographic regions of Kenya display a mixed mating system Muraya, Moses M.; Mutegi, Evans; Geiger, Hartwig H. Theoretical and Applied Genetics, Vol. 122, Issue 8 https://doi.org/10.1007/s00122-011-1560-5	journal	March 2011
Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications Li, Xuehui; Wang, Xiaojuan; Wei, Yanling Theoretical and Applied Genetics, Vol. 123, Issue 4 https://doi.org/10.1007/s00122-011-1617-5	journal	May 2011
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes Serba, Desalegn; Wu, Limin; Daverdin, Guillaume BioEnergy Research, Vol. 6, Issue 3 https://doi.org/10.1007/s12155-013-9315-6	journal	March 2013
Simple sequence repeats as a source of quantitative genetic variation Kashi, Yechezkel; King, David; Soller, Morris Trends in Genetics, Vol. 13, Issue 2 https://doi.org/10.1016/s0168-9525(97)01008-1	journal	February 1997
An economic method for the fluorescent labeling of PCR fragments Schuelke, Markus Nature Biotechnology, Vol. 18, Issue 2 https://doi.org/10.1038/72708	journal	February 2000
Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives Ramchiary, N.; Nguyen, V. D.; Li, X. DNA Research, Vol. 18, Issue 5 https://doi.org/10.1093/dnares/dsr017	journal	July 2011
A maximum likelihood method for estimating genome length using genetic linkage data. Chakravarti, A.; Lasher, L. K.; Reefer, J. E. Genetics, Vol. 128, Issue 1 https://doi.org/10.1093/genetics/128.1.175	journal	May 1991
Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Grattapaglia, D.; Sederoff, R. Genetics, Vol. 137, Issue 4 https://doi.org/10.1093/genetics/137.4.1121	journal	August 1994
A Genetic Map in the Mimulus guttatus Species Complex Reveals Transmission Ratio Distortion due to Heterospecific Interactions Fishman, Lila; Kelly, Alan J.; Morgan, Emily Genetics, Vol. 159, Issue 4 https://doi.org/10.1093/genetics/159.4.1701	journal	December 2001
Meiotic Drive in Natural Populations of Drosophila Melanogaster. i. the Cytogenetic Basis of Segregation-Distortion Sandler, L.; Hiraizumi, Yuichiro; Sandler, Iris Genetics, Vol. 44, Issue 2 https://doi.org/10.1093/genetics/44.2.233	journal	March 1959
Differential Zygotic Lethality in a Tomato Species Hybrid Rick, Charles M. Genetics, Vol. 48, Issue 11 https://doi.org/10.1093/genetics/48.11.1497	journal	November 1963
Abortion of male and Female Gametes in the Tomato Determined by Allelic Interaction Rick, Charles M. Genetics, Vol. 53, Issue 1 https://doi.org/10.1093/genetics/53.1.85	journal	January 1966
On the Use of the Classical Tests for Detecting Linkage Garcia-Dorado, A.; Gallego, A. Journal of Heredity, Vol. 83, Issue 2 https://doi.org/10.1093/oxfordjournals.jhered.a111175	journal	March 1992
A Fast and Scalable Radiation Hybrid Map Construction and Integration Strategy Agarwala, R. Genome Research, Vol. 10, Issue 3 https://doi.org/10.1101/gr.10.3.350	journal	March 2000
Differential zygotic abortion in an interspecific Lycopersicon cross Gadish, I.; Zamir, D. Genome, Vol. 29, Issue 1 https://doi.org/10.1139/g87-026	journal	February 1987
New genomic resources for switchgrass: a BAC library and comparative analysis of homoeologous genomic regions harboring bioenergy traits Saski, Christopher A.; Li, Zhigang; Feltus, Frank A. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-369	journal	July 2011
An Integrated Genetic and Cytogenetic Map of the Cucumber Genome Ren, Yi; Zhang, Zhonghua; Liu, Jinhua PLoS ONE, Vol. 4, Issue 6 https://doi.org/10.1371/journal.pone.0005795	journal	June 2009
Distribution of Microsatellites in the Genome of Medicago truncatula : A Resource of Genetic Markers That Integrate Genetic and Physical Maps Mun, Jeong-Hwan; Kim, Dong-Jin; Choi, Hong-Kyu Genetics, Vol. 172, Issue 4 https://doi.org/10.1534/genetics.105.054791	journal	April 2006
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions Okada, Miki; Lanzatella, Christina; Saha, Malay C. Genetics, Vol. 185, Issue 3 https://doi.org/10.1534/genetics.110.113910	journal	April 2010
Herbaceous Vegetation Productivity, Persistence, and Metals Uptake on a Biosolids-Amended Mine Soil Evanylo, G. K.; Abaye, A. O.; Dundas, C. Journal of Environmental Quality, Vol. 34, Issue 5 https://doi.org/10.2134/jeq2004.0329	journal	September 2005
Chromosome Number and Nuclear DNA Content of Several Switchgrass Populations Hopkins, Andrew A.; Taliaferro, Charles M.; Murphy, Christopher D. Crop Science, Vol. 36, Issue 5 https://doi.org/10.2135/cropsci1996.0011183x003600050021x	journal	January 1996
Simultaneous Maximum Likelihood Estimation of Linkage and Linkage Phases in Outcrossing Species Wu, Rongling; Ma, Chang-Xing; Painter, Ian Theoretical Population Biology, Vol. 61, Issue 3 https://doi.org/10.1006/tpbi.2002.1577	journal	May 2002
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations Lorieux, M.; Goffinet, B.; Perrier, X. Theoretical and Applied Genetics, Vol. 90, Issue 1 https://doi.org/10.1007/BF00220998	journal	January 1995
Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations Lorieux, M.; Perrier, X.; Goffinet, B. Theoretical and Applied Genetics, Vol. 90, Issue 1 https://doi.org/10.1007/BF00220999	journal	January 1995
Characterization and genetic mapping of simple repeat sequences in the tomato genome Broun, Pierre; Tanksley, Steven D. Molecular and General Genetics MGG, Vol. 250, Issue 1 https://doi.org/10.1007/BF02191823	journal	January 1996
Genetic mapping and QTL analysis of horticultural traits in cucumber (Cucumis sativus L.) using recombinant inbred lines Fazio, G.; Staub, J. E.; Stevens, M. R. Theoretical and Applied Genetics, Vol. 107, Issue 5 https://doi.org/10.1007/s00122-003-1277-1	journal	June 2003
Identification of a Selfing Compatible Genotype and Mode of Inheritance in Switchgrass Liu, Linglong; Wu, Yanqi BioEnergy Research, Vol. 5, Issue 3 https://doi.org/10.1007/s12155-011-9173-z	journal	December 2011
Simple sequence repeats as a source of quantitative genetic variation Kashi, Yechezkel; King, David; Soller, Morris Trends in Genetics, Vol. 13, Issue 2 https://doi.org/10.1016/S0168-9525(97)01008-1	journal	February 1997
Long-term yield potential of switchgrass-for-biofuel systems Fike, John H.; Parrish, David J.; Wolf, Dale D. Biomass and Bioenergy, Vol. 30, Issue 3 https://doi.org/10.1016/j.biombioe.2005.10.006	journal	March 2006
Tolerance of switchgrass to extreme soil moisture stress: Ecological implications Barney, Jacob N.; Mann, J. Jeremiah; Kyser, Guy B. Plant Science, Vol. 177, Issue 6 https://doi.org/10.1016/j.plantsci.2009.09.003	journal	December 2009
Reference genome sequence of the model plant Setaria Bennetzen, Jeffrey L.; Schmutz, Jeremy; Wang, Hao Nature Biotechnology, Vol. 30, Issue 6 https://doi.org/10.1038/nbt.2196	journal	May 2012
Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps Hackett, C. A.; Broadfoot, L. B. Heredity, Vol. 90, Issue 1 https://doi.org/10.1038/sj.hdy.6800173	journal	January 2003
Isolation and characterization of polymorphic microsatellite loci in Rubus alceifolius Poir. (Rosaceae), an invasive weed in La Réunion island: PRIMER NOTE Amsellem, L.; Dutech, C.; Billotte, N. Molecular Ecology Notes, Vol. 1, Issue 1-2 https://doi.org/10.1046/j.1471-8278.2000.00013.x	journal	March 2001
The Expression of Mendelian Factors in the Gametophyte of Maize Mangelsdorf, P. C.; Jones, D. F. Genetics, Vol. 11, Issue 5 https://doi.org/10.1093/genetics/11.5.423	journal	September 1926
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs Voorrips, R. E. Journal of Heredity, Vol. 93, Issue 1 https://doi.org/10.1093/jhered/93.1.77	journal	January 2002
Construction of integrated genetic linkage maps by means of a new computer package: Join Map Stam, Piet The Plant Journal, Vol. 3, Issue 5 https://doi.org/10.1111/j.1365-313X.1993.00739.x	journal	May 1993
The Estimation of map Distances from Recombination Values Kosambi, D. D. Annals of Eugenics, Vol. 12, Issue 1 https://doi.org/10.1111/j.1469-1809.1943.tb02321.x	journal	January 1943
Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay ( R Package qualV ) Jachner, Stefanie; Boogaart, Gerald; Petzoldt, Thomas Journal of Statistical Software, Vol. 22, Issue 8 https://doi.org/10.18637/jss.v022.i08	journal	January 2007
Estimates of Genetic Parameters in Switchgrass1 Talbert, L. E.; Timothy, D. H.; Burns, J. C. Crop Science, Vol. 23, Issue 4 https://doi.org/10.2135/cropsci1983.0011183X002300040029x	journal	January 1983
Integration of Simple Sequence Repeat DNA Markers into a Soybean Linkage Map Akkaya, Mahinur S.; Shoemaker, Randy C.; Specht, James E. Crop Science, Vol. 35, Issue 5 https://doi.org/10.2135/cropsci1995.0011183X003500050030x	journal	September 1995
Chloroplast DNA and Nuclear DNA Content Variations among Cultivars of Switchgrass, Panicum virgatum L. Hultquist, Sherry J.; Vogel, K. P.; Lee, D. J. Crop Science, Vol. 36, Issue 4 https://doi.org/10.2135/cropsci1996.0011183X003600040039x	journal	January 1996
Chromosome Number and Nuclear DNA Content of Several Switchgrass Populations Hopkins, Andrew A.; Taliaferro, Charles M.; Murphy, Christopher D. Crop Science, Vol. 36, Issue 5 https://doi.org/10.2135/cropsci1996.0011183X003600050021x	journal	January 1996
Incompatibility Systems in Switchgrass Martínez-Reyna, J. M.; Vogel, K. P. Crop Science, Vol. 42, Issue 6 https://doi.org/10.2135/cropsci2002.1800	journal	January 2002
Latitudinal Adaptation of Switchgrass Populations Casler, M. D.; Vogel, K. P.; Taliaferro, C. M. Crop Science, Vol. 44, Issue 1 https://doi.org/10.2135/cropsci2004.2930	journal	January 2004
Genetic Variability and Trait Relationships in Switchgrass Das, Modan K.; Fuentes, Roger G.; Taliaferro, Charles M. Crop Science, Vol. 44, Issue 2 https://doi.org/10.2135/cropsci2004.4430	journal	January 2004
Ecotypic Variation among Switchgrass Populations from the Northern USA Casler, M. D. Crop Science, Vol. 45, Issue 1 https://doi.org/10.2135/cropsci2005.0388	journal	January 2005
Natural Hybrids and Gene Flow between Upland and Lowland Switchgrass Zhang, Yunwei; Zalapa, Juan; Jakubowski, Andrew R. Crop Science, Vol. 51, Issue 6 https://doi.org/10.2135/cropsci2011.02.0104	journal	January 2011
Reference Genome-Directed Resolution of Homologous and Homeologous Relationships within and between Different Oat Linkage Maps Gutierrez-Gonzalez, Juan J.; Garvin, David F. The Plant Genome, Vol. 4, Issue 3 https://doi.org/10.3835/plantgenome2011.01.0004	journal	November 2011
Switchgrass as a biofuels feedstock in the USA Sanderson, M. A.; Adler, P. R.; Boateng, A. A. Canadian Journal of Plant Science, Vol. 86, Issue Special Issue https://doi.org/10.4141/P06-136	journal	December 2006

Cited By (3)

Extensions of BLUP Models for Genomic Prediction in Heterogeneous Populations: Application in a Diverse Switchgrass Sample Ramstein, Guillaume P.; Casler, Michael D. G3 Genes\|Genomes\|Genetics, Vol. 9, Issue 3 https://doi.org/10.1534/g3.118.200969	journal	March 2019
Integer Linear Programming in Computational and Systems Biology: Tutorial Gusfield, Dan BCB '19: 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics https://doi.org/10.1145/3307339.3343179	conference	September 2019
Transcriptome analysis in switchgrass discloses ecotype difference in photosynthetic efficiency Serba, Desalegn D.; Uppalapati, Srinivasa Rao; Krom, Nick BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-3377-8	journal	December 2016

Similar Records

A Saturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous with the Medicago truncatula Genome

Journal Article · Wed Aug 20 20:00:00 EDT 2014 · G3 · OSTI ID:1627951

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Journal Article · Tue Jun 30 20:00:00 EDT 2015 · The Plant Genome · OSTI ID:1616040

A New Genetic Linkage Map of the Zygomycete Fungus Phycomyces blakesleeanus

Journal Article · Wed Mar 13 20:00:00 EDT 2013 · PLoS ONE · OSTI ID:1627590

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
allopolyploid
biofuel
biomass
feedstock