High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass
Abstract
Abstract Switchgrass ( Panicum virgatum L.), a native warm‐season perennial grass, is being considered as a feedstock for biofuel production in the United States. To expedite its genetic improvement and enhance genetic gain per selection cycle, application of marker‐assisted selection is indispensable. A high‐density linkage map was constructed in a pseudo‐F 1 testcross mapping population of AP13×VS16, consisting of 349 progenies. A total of 8,757 single nucleotide polymorphism (SNP) markers generated through genotype‐by‐sequencing (GBS) were used to construct the linkage map. The total map length spans up to 2,540.2 cM with the marker density of one marker in every 0.25–0.34 cM. Spring green‐up (SG), days to flowering (FL), and the vegetative growth period (VP) data were analyzed and used for quantitative trait loci (QTL) mapping. The population showed significant variations and exhibited transgressive segregation for SG, FL, and VP. QTL analyses were performed using trait mean of each year and location along with BLUP (best linear unbiased prediction) values of the traits. A total of 35, 37, and 34 QTL for SG, FL, and VP, respectively, were identified. Phenotypic variability explained by each QTL ranged from 11.29% to 27.85%. The additive genetic effects of individual QTL ranged from −1.81 to 2.40, −6.12more »
- Authors:
-
- Noble Research Institute, LLC. Ardmore Oklahoma
- Kansas State University, AG Research Centers‐Hays Hays Kansas
- Hudson Alpha Institute for Biotechnology Huntsville Alabama
- Department of Energy Joint Genome Institute Walnut Creek California
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1504288
- Alternate Identifier(s):
- OSTI ID: 1504289
- Resource Type:
- Journal Article: Published Article
- Journal Name:
- Global Change Biology. Bioenergy
- Additional Journal Information:
- Journal Name: Global Change Biology. Bioenergy Journal Volume: 11 Journal Issue: 5; Journal ID: ISSN 1757-1693
- Publisher:
- Wiley-Blackwell
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Ali, Shahjahan, Serba, Desalegn D., Jenkins, Jerry, Kwon, Soonil, Schmutz, Jeremy, and Saha, Malay C. High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass. United Kingdom: N. p., 2019.
Web. doi:10.1111/gcbb.12592.
Ali, Shahjahan, Serba, Desalegn D., Jenkins, Jerry, Kwon, Soonil, Schmutz, Jeremy, & Saha, Malay C. High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass. United Kingdom. https://doi.org/10.1111/gcbb.12592
Ali, Shahjahan, Serba, Desalegn D., Jenkins, Jerry, Kwon, Soonil, Schmutz, Jeremy, and Saha, Malay C. 2019.
"High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass". United Kingdom. https://doi.org/10.1111/gcbb.12592.
@article{osti_1504288,
title = {High‐density linkage map reveals QTL underlying growth traits in AP13×VS16 biparental population of switchgrass},
author = {Ali, Shahjahan and Serba, Desalegn D. and Jenkins, Jerry and Kwon, Soonil and Schmutz, Jeremy and Saha, Malay C.},
abstractNote = {Abstract Switchgrass ( Panicum virgatum L.), a native warm‐season perennial grass, is being considered as a feedstock for biofuel production in the United States. To expedite its genetic improvement and enhance genetic gain per selection cycle, application of marker‐assisted selection is indispensable. A high‐density linkage map was constructed in a pseudo‐F 1 testcross mapping population of AP13×VS16, consisting of 349 progenies. A total of 8,757 single nucleotide polymorphism (SNP) markers generated through genotype‐by‐sequencing (GBS) were used to construct the linkage map. The total map length spans up to 2,540.2 cM with the marker density of one marker in every 0.25–0.34 cM. Spring green‐up (SG), days to flowering (FL), and the vegetative growth period (VP) data were analyzed and used for quantitative trait loci (QTL) mapping. The population showed significant variations and exhibited transgressive segregation for SG, FL, and VP. QTL analyses were performed using trait mean of each year and location along with BLUP (best linear unbiased prediction) values of the traits. A total of 35, 37, and 34 QTL for SG, FL, and VP, respectively, were identified. Phenotypic variability explained by each QTL ranged from 11.29% to 27.85%. The additive genetic effects of individual QTL ranged from −1.81 to 2.40, −6.12 to 7.58, and −16.01 to 6.38 for SG, FL, and VP, respectively. Comparing major QTL regions in the switchgrass genome, 20 candidate genes were identified which were reported to be involved in growth‐, development‐, and flowering‐related traits in switchgrass.},
doi = {10.1111/gcbb.12592},
url = {https://www.osti.gov/biblio/1504288},
journal = {Global Change Biology. Bioenergy},
issn = {1757-1693},
number = 5,
volume = 11,
place = {United Kingdom},
year = {Tue Jan 29 00:00:00 EST 2019},
month = {Tue Jan 29 00:00:00 EST 2019}
}
Web of Science
Works referenced in this record:
MINISEED3 (MINI3), a WRKY family gene, and HAIKU2 (IKU2), a leucine-rich repeat (LRR) KINASE gene, are regulators of seed size in Arabidopsis
journal, November 2005
- Luo, M.; Dennis, E. S.; Berger, F.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 48
Switchgrass selection as a “model” bioenergy crop: A history of the process
journal, June 2010
- Wright, Lynn; Turhollow, Anthony
- Biomass and Bioenergy, Vol. 34, Issue 6
Changes in forage quality, ingestive mastication, and digesta kinetics resulting from switchgrass maturity.
journal, January 1997
- Burns, J. C.; Pond, K. R.; Fisher, D. S.
- Journal of Animal Science, Vol. 75, Issue 5
QTL × environment interactions in rice. I. Heading date and plant height
journal, September 2003
- Li, Z. K.; Yu, S. B.; Lafitte, H. R.
- Theoretical and Applied Genetics, Vol. 108, Issue 1
Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations
journal, February 2006
- Feltus, F. A.; Hart, G. E.; Schertz, K. F.
- Theoretical and Applied Genetics, Vol. 112, Issue 7
MYB108 Acts Together with MYB24 to Regulate Jasmonate-Mediated Stamen Maturation in Arabidopsis
journal, December 2008
- Mandaokar, Ajin; Browse, John
- Plant Physiology, Vol. 149, Issue 2
Forage Quality and Digestion Kinetics of Switchgrass Herbage and Morphological Components
journal, January 1988
- Twidwell, E. K.; Johnson, K. D.; Cherney, J. H.
- Crop Science, Vol. 28, Issue 5
Joint analysis for heading date QTL in small interconnected barley populations
journal, October 2007
- Cuesta-Marcos, Alfonso; Casas, Ana M.; Yahiaoui, Samia
- Molecular Breeding, Vol. 21, Issue 3
TRANSPARENT TESTA GLABRA2 , a Trichome and Seed Coat Development Gene of Arabidopsis, Encodes a WRKY Transcription Factor
journal, June 2002
- Johnson, Cameron S.; Kolevski, Ben; Smyth, David R.
- The Plant Cell, Vol. 14, Issue 6
Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations
journal, August 2013
- Spindel, Jennifer; Wright, Mark; Chen, Charles
- Theoretical and Applied Genetics, Vol. 126, Issue 11
QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize
journal, January 2017
- Maschietto, Valentina; Colombi, Cinzia; Pirona, Raul
- BMC Plant Biology, Vol. 17, Issue 1
A Homolog of NO APICAL MERISTEM Is an Immediate Target of the Floral Homeotic Genes APETALA3/PISTILLATA
journal, January 1998
- Sablowski, Robert W. M.; Meyerowitz, Elliot M.
- Cell, Vol. 92, Issue 1
Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol
journal, January 2013
- Lu, Fei; Lipka, Alexander E.; Glaubitz, Jeff
- PLoS Genetics, Vol. 9, Issue 1
Validation of QTL for Grain Yield-Related Traits on Wheat Chromosome 3A Using Recombinant Inbred Chromosome Lines
journal, January 2012
- Mengistu, Neway; Baenziger, P. S.; Eskridge, K. M.
- Crop Science, Vol. 52, Issue 4
A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass
journal, March 2012
- Liu, Linglong; Wu, Yanqi; Wang, Yunwen
- G3: Genes|Genomes|Genetics, Vol. 2, Issue 3
Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions
journal, April 2010
- Okada, Miki; Lanzatella, Christina; Saha, Malay C.
- Genetics, Vol. 185, Issue 3
Development of 1,030 genomic SSR markers in switchgrass
journal, October 2010
- Wang, Y. W.; Samuels, T. D.; Wu, Y. Q.
- Theoretical and Applied Genetics, Vol. 122, Issue 4
Regulation of plant biomass production
journal, June 2010
- Demura, Taku; Ye, Zheng-Hua
- Current Opinion in Plant Biology, Vol. 13, Issue 3
The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana
journal, October 2007
- Andersen, Stig Uggerhøj; Algreen-Petersen, Randi Groslier; Hoedl, Martina
- Journal of Experimental Botany, Vol. 58, Issue 13
Effects of Strain Source and Management Practice on Forage Yields of Two Warm-Season Prairie Grasses1
journal, January 1968
- Newell, L. C.
- Crop Science, Vol. 8, Issue 2
Location of major effect genes in sorghum (Sorghum bicolor (L.) Moench)
journal, June 2010
- Mace, E. S.; Jordan, D. R.
- Theoretical and Applied Genetics, Vol. 121, Issue 7
PsbP Protein, But Not PsbQ Protein, Is Essential for the Regulation and Stabilization of Photosystem II in Higher Plants
journal, October 2005
- Ifuku, Kentaro; Yamamoto, Yumiko; Ono, Taka-aki
- Plant Physiology, Vol. 139, Issue 3
An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping
journal, January 2013
- Sonah, Humira; Bastien, Maxime; Iquira, Elmer
- PLoS ONE, Vol. 8, Issue 1
Roles of arabidopsis WRKY18, WRKY40 and WRKY60 transcription factors in plant responses to abscisic acid and abiotic stress
journal, January 2010
- Chen, Han; Lai, Zhibing; Shi, Junwei
- BMC Plant Biology, Vol. 10, Issue 1
Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding
journal, September 2014
- He, Jiangfeng; Zhao, Xiaoqing; Laroche, André
- Frontiers in Plant Science, Vol. 5
Linkage Maps of Lowland and Upland Tetraploid Switchgrass Ecotypes
journal, March 2013
- Serba, Desalegn; Wu, Limin; Daverdin, Guillaume
- BioEnergy Research, Vol. 6, Issue 3
Inhibition of Leaf Senescence by Autoregulated Production of Cytokinin
journal, December 1995
- Gan, S.; Amasino, R. M.
- Science, Vol. 270, Issue 5244
Precision mapping of quantitative trait loci.
journal, April 1994
- Zeng, Z. B.
- Genetics, Vol. 136, Issue 4
Unravelling the genetic control of flowering time in the bioenergy grass Miscanthus
journal, July 2008
- Jensen, E.; Thomas-Jones, S.; Farrar, K.
- Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology, Vol. 150, Issue 3
Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods
journal, August 2012
- Zou, Guihua; Zhai, Guowei; Feng, Qi
- Journal of Experimental Botany, Vol. 63, Issue 15
The Mg-Chelatase H Subunit of Arabidopsis Antagonizes a Group of WRKY Transcription Repressors to Relieve ABA-Responsive Genes of Inhibition
journal, June 2010
- Shang, Yi; Yan, Lu; Liu, Zhi-Qiang
- The Plant Cell, Vol. 22, Issue 6
Heterosis and Reciprocal-cross Effects in Tetraploid Switchgrass
journal, January 2014
- Casler, Michael D.
- Crop Science, Vol. 54, Issue 5
QTL Mapping for Fusarium Ear Rot and Fumonisin Contamination Resistance in Two Maize Populations
journal, January 2006
- Robertson-Hoyt, Leilani A.; Jines, Michael P.; Balint-Kurti, Peter J.
- Crop Science, Vol. 46, Issue 4
Targets of AtWRKY6 regulation during plant senescence and pathogen defense
journal, May 2002
- Robatzek, S.
- Genes & Development, Vol. 16, Issue 9
Quantitative trait locus analysis for days-to-heading and morphological traits in an RIL population derived from an extremely late flowering F1 hybrid of sorghum
journal, June 2012
- Takai, Tomoyuki; Yonemaru, Jun-ichi; Kaidai, Hirokazu
- Euphytica, Vol. 187, Issue 3
QTLs for Biomass and Developmental Traits in Switchgrass (Panicum virgatum)
journal, June 2015
- Lowry, David B.; Taylor, Samuel H.; Bonnette, Jason
- BioEnergy Research, Vol. 8, Issue 4
Genetic Improvement of Sorghum as a Biofuel Feedstock: I. QTL for Stem Sugar and Grain Nonstructural Carbohydrates
journal, January 2008
- Murray, Seth C.; Sharma, Arun; Rooney, William L.
- Crop Science, Vol. 48, Issue 6
Estimates of Genetic Parameters in Switchgrass1
journal, January 1983
- Talbert, L. E.; Timothy, D. H.; Burns, J. C.
- Crop Science, Vol. 23, Issue 4
Genetic Variation for Biomass and Residue Production in Lentil: II. Factors Determining Seed and Straw Yield
journal, January 1998
- Kusmenoglu, Ismail; Muehlbauer, Fred J.
- Crop Science, Vol. 38, Issue 4
Selection Response and Developmental Basis for Early and Late Panicle Emergence in Alamo Switchgrass
journal, January 1998
- Van Esbroeck, G. A.; Hussey, M. A.; Sanderson, M. A.
- Crop Science, Vol. 38, Issue 2
Structural and Functional Analysis of VQ Motif-Containing Proteins in Arabidopsis as Interacting Proteins of WRKY Transcription Factors
journal, April 2012
- Cheng, Yuan; Zhou, Yuan; Yang, Yan
- Plant Physiology, Vol. 159, Issue 2
Genotyping-by-Sequencing for Plant Breeding and Genetics
journal, January 2012
- Poland, Jesse A.; Rife, Trevor W.
- The Plant Genome Journal, Vol. 5, Issue 3
Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach
journal, February 2012
- Poland, Jesse A.; Brown, Patrick J.; Sorrells, Mark E.
- PLoS ONE, Vol. 7, Issue 2
QTL Mapping for Reproductive Maturity in Lowland Switchgrass Populations
journal, July 2015
- Dong, Hongxu; Thames, Shuiyi; Liu, Linglong
- BioEnergy Research, Vol. 8, Issue 4
Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis
journal, August 2004
- Miao, Y.; Laun, T.; Zimmermann, P.
- Plant Molecular Biology, Vol. 55, Issue 6
Correlations and QTL detection in maize family per se and testcross progenies for plant height and ear height: QTL detection of plant and ear height in maize
journal, June 2011
- Zhang, Yan; Li, Yongxiang; Wang, Yang
- Plant Breeding, Vol. 130, Issue 6
Leaf and Stem Forage Quality of Big Bluestem and Switchgrass1
journal, January 1983
- Griffin, J. L.; Jung, G. A.
- Agronomy Journal, Vol. 75, Issue 5
Investigation of genomic organization in switchgrass (Panicum virgatum L.) using DNA markers
journal, April 2005
- Missaoui, A. M.; Paterson, A. H.; Bouton, J. H.
- Theoretical and Applied Genetics, Vol. 110, Issue 8
An Abscisic Acid-Induced Protein, HVA22, Inhibits Gibberellin-Mediated Programmed Cell Death in Cereal Aleurone Cells
journal, June 2008
- Guo, Woei-Jiun; David Ho, Tuan-Hua
- Plant Physiology, Vol. 147, Issue 4
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
journal, May 2011
- Elshire, Robert J.; Glaubitz, Jeffrey C.; Sun, Qi
- PLoS ONE, Vol. 6, Issue 5, Article No. e19379
TSO1 is a novel protein that modulates cytokinesis and cell expansion in Arabidopsis
journal, May 2000
- Hauser, B. A.; He, J. Q.; Park, S. O.
- Development, Vol. 127, Issue 10
Cell Wall Composition and Underlying QTL in an F1 Pseudo-Testcross Population of Switchgrass
journal, April 2016
- Serba, Desalegn D.; Sykes, Robert W.; Gjersing, Erica L.
- BioEnergy Research, Vol. 9, Issue 3
Growth and biomass productivity of kenaf (Hibiscus cannabinus, L.) under different agricultural inputs and management practices in central Greece
journal, November 2010
- Danalatos, N. G.; Archontoulis, S. V.
- Industrial Crops and Products, Vol. 32, Issue 3
Quantitative Trait Loci (QTL) Underlying Biomass Yield and Plant Height in Switchgrass
journal, August 2014
- Serba, Desalegn D.; Daverdin, Guillaume; Bouton, Joseph H.
- BioEnergy Research, Vol. 8, Issue 1
Activation of the Ethylene Gas Response Pathway in Arabidopsis by the Nuclear Protein ETHYLENE-INSENSITIVE3 and Related Proteins
journal, June 1997
- Chao, Qimin; Rothenberg, Madge; Solano, Roberto
- Cell, Vol. 89, Issue 7, p. 1133-1144
Improving linkage analysis in outcrossed forest trees – an example from Acacia mangium
journal, May 2002
- Butcher, P.; Williams, E.; Whitaker, D.
- Theoretical and Applied Genetics, Vol. 104, Issue 6