Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length

Hilley, Josie L.; Weers, Brock D.; Truong, Sandra K.; McCormick, Ryan F.; Mattison, Ashley J.; McKinley, Brian A.; Morishige, Daryl T.; Mullet, John E.

doi:10.1038/s41598-017-04609-5

Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length

Journal Article · Tue Jul 04 00:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-017-04609-5· OSTI ID:1466831

Hilley, Josie L. ^[1]; Weers, Brock D. ^[2]; ^[3]; McCormick, Ryan F. ^[3]; Mattison, Ashley J. ^[3]; McKinley, Brian A. ^[2]; Morishige, Daryl T. ^[2]; Mullet, John E. ^[4]

Texas A & M Univ., College Station, TX (United States). Interdisciplinary Program in Genetics; Texas A&M Univ., College Station, TX (United States)
Texas A & M Univ., College Station, TX (United States).Dept. of Biochemistry and Biophysics
Texas A & M Univ., College Station, TX (United States). Interdisciplinary Program in Genetics
Texas A & M Univ., College Station, TX (United States). Interdisciplinary Program in Genetics and Dept. of Biochemistry and Biophysics

Sorghum is an important C4 grass crop grown for grain, forage, sugar, and bioenergy production. While tall, late flowering landraces are commonly grown in Africa, short early flowering varieties were selected in US grain sorghum breeding programs to reduce lodging and to facilitate machine harvesting. Four loci have been identified that affect stem length (Dw1-Dw4). Subsequent research showed that Dw3 encodes an ABCB1 auxin transporter and Dw1 encodes a highly conserved protein involved in the regulation of cell proliferation. In this study, Dw2 was identified by fine-mapping and further confirmed by sequencing the Dw2 alleles in Dwarf Yellow Milo and Double Dwarf Yellow Milo, the progenitor genotypes where the recessive allele of dw2 originated. Furthermore, the Dw2 locus was determined to correspond to Sobic.006G067700, a gene that encodes a protein kinase that is homologous to KIPK, a member of the AGCVIII subgroup of the AGC protein kinase family in Arabidopsis.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: FC02-07ER64494

OSTI ID:: 1466831

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 7; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (67)

Plant evolution: AGC kinases tell the auxin tale Galván-Ampudia, Carlos S.; Offringa, Remko Trends in Plant Science, Vol. 12, Issue 12 https://doi.org/10.1016/j.tplants.2007.10.004	journal	December 2007
Growth signalling pathways in Arabidopsis and the AGC protein kinases Bögre, L. Trends in Plant Science, Vol. 8, Issue 9 https://doi.org/10.1016/s1360-1385(03)00188-2	journal	September 2003
Structural and Functional Insights into the Regulation of Arabidopsis AGC VIIIa Kinases Zegzouti, Hicham; Li, Wei; Lorenz, Todd C. Journal of Biological Chemistry, Vol. 281, Issue 46 https://doi.org/10.1074/jbc.m605167200	journal	September 2006
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
Non-structural carbohydrate partitioning in grass stems: a target to increase yield stability, stress tolerance, and biofuel production Slewinski, T. L. Journal of Experimental Botany, Vol. 63, Issue 13 https://doi.org/10.1093/jxb/ers124	journal	June 2012
Resolution of Genetic Map Expansion Caused by Excess Heterozygosity in Plant Recombinant Inbred Populations Truong, Sandra K.; McCormick, Ryan F.; Morishige, Daryl T. G3: Genes\|Genomes\|Genetics, Vol. 4, Issue 10 https://doi.org/10.1534/g3.114.012468	journal	August 2014
RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK McCormick, Ryan F.; Truong, Sandra K.; Mullet, John E. G3: Genes\|Genomes\|Genetics, Vol. 5, Issue 4 https://doi.org/10.1534/g3.115.017012	journal	February 2015
A simple regression-based method to map quantitative trait loci underlying function-valued phenotypes Kwak, Il-Youp; Moore, Candace R.; Spalding, Edgar P. arXiv https://doi.org/10.48550/arxiv.1403.3048	text	January 2014
From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline Auwera, Geraldine A.; Carneiro, Mauricio O.; Hartl, Christopher Current Protocols in Bioinformatics, Vol. 43, Issue 1 https://doi.org/10.1002/0471250953.bi1110s43	journal	October 2013
High biomass yield energy sorghum: developing a genetic model for C4 grass bioenergy crops: Modeling and Analysis: Developing a genetic model for C4 grass bioenergy crops Olson, Sara N.; Ritter, Kimberley; Rooney, William Biofuels, Bioproducts and Biorefining, Vol. 6, Issue 6 https://doi.org/10.1002/bbb.1357	journal	September 2012
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton Notredame, Cédric; Higgins, Desmond G.; Heringa, Jaap Journal of Molecular Biology, Vol. 302, Issue 1 https://doi.org/10.1006/jmbi.2000.4042	journal	September 2000
Identification of genomic regions affecting plant height in sorghum and maize Pereira, M. G.; Lee, M. Theoretical and Applied Genetics, Vol. 90, Issue 3-4 https://doi.org/10.1007/BF00221980	journal	March 1995
Growth signalling pathways in Arabidopsis and the AGC protein kinases Bögre, L. Trends in Plant Science, Vol. 8, Issue 9 https://doi.org/10.1016/S1360-1385(03)00188-2	journal	September 2003
Dynamic control of auxin transport-dependent growth by AGCVIII protein kinases Barbosa, Inês CR; Schwechheimer, Claus Current Opinion in Plant Biology, Vol. 22 https://doi.org/10.1016/j.pbi.2014.09.010	journal	December 2014
AGCVIII kinases: at the crossroads of cellular signaling Zhang, Yan; McCormick, Sheila Trends in Plant Science, Vol. 14, Issue 12 https://doi.org/10.1016/j.tplants.2009.09.006	journal	December 2009
‘Green revolution’ genes encode mutant gibberellin response modulators Peng, Jinrong; Richards, Donald E.; Hartley, Nigel M. Nature, Vol. 400, Issue 6741 https://doi.org/10.1038/22307	journal	July 1999
A framework for variation discovery and genotyping using next-generation DNA sequencing data DePristo, Mark A.; Banks, Eric; Poplin, Ryan Nature Genetics, Vol. 43, Issue 5 https://doi.org/10.1038/ng.806	journal	April 2011
Clustering of a kinesin-14 motor enables processive retrograde microtubule-based transport in plants Jonsson, Erik; Yamada, Moé; Vale, Ronald D. Nature Plants, Vol. 1, Issue 7 https://doi.org/10.1038/nplants.2015.87	journal	June 2015
A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.) Seki, Kousuke; Komatsu, Kenji; Tanaka, Keisuke Horticulture Research, Vol. 7, Issue 1 https://doi.org/10.1038/s41438-020-0241-4	journal	February 2020
Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland Furtwängler, Anja; Rohrlach, A. B.; Lamnidis, Thiseas C. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-15560-x	journal	April 2020
A sand fly salivary protein acts as a neutrophil chemoattractant Guimaraes-Costa, Anderson B.; Shannon, John P.; Waclawiak, Ingrid Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23002-5	journal	May 2021
Mapping the genetic basis of diabetes mellitus in the Australian Burmese cat (Felis catus) Samaha, Georgina; Wade, Claire M.; Beatty, Julia Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-76166-3	journal	November 2020
Why does the Aβ peptide of Alzheimer share structural similarity with antimicrobial peptides? Pastore, Annalisa; Raimondi, Francesco; Rajendran, Lawrence Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-0865-9	journal	March 2020
Sorghum Dw1, an agronomically important gene for lodging resistance, encodes a novel protein involved in cell proliferation Yamaguchi, Miki; Fujimoto, Haruka; Hirano, Ko Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep28366	journal	June 2016
Structure of the complex of a mitotic kinesin with its calcium binding regulator Vinogradova, M. V.; Malanina, G. G.; Reddy, A. S. N. Proceedings of the National Academy of Sciences, Vol. 106, Issue 20 https://doi.org/10.1073/pnas.0811131106	journal	May 2009
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum Murphy, R. L.; Klein, R. R.; Morishige, D. T. Proceedings of the National Academy of Sciences, Vol. 108, Issue 39, p. 16469-16474 https://doi.org/10.1073/pnas.1106212108	journal	September 2011
Population genomic and genome-wide association studies of agroclimatic traits in sorghum Morris, G. P.; Ramu, P.; Deshpande, S. P. Proceedings of the National Academy of Sciences, Vol. 110, Issue 2 https://doi.org/10.1073/pnas.1215985110	journal	December 2012
Dissecting repulsion linkage in the dwarfing gene Dw3 region for sorghum plant height provides insights into heterosis Li, Xin; Li, Xianran; Fridman, Eyal Proceedings of the National Academy of Sciences, Vol. 112, Issue 38 https://doi.org/10.1073/pnas.1509229112	journal	September 2015
Interaction of a Kinesin-like Calmodulin-binding Protein with a Protein Kinase Day, Irene S.; Miller, Cindy; Golovkin, Maxim Journal of Biological Chemistry, Vol. 275, Issue 18 https://doi.org/10.1074/jbc.275.18.13737	journal	April 2000
Structural and Functional Insights into the Regulation of Arabidopsis AGC VIIIa Kinases Zegzouti, Hicham; Li, Wei; Lorenz, Todd C. Journal of Biological Chemistry, Vol. 281, Issue 46 https://doi.org/10.1074/jbc.M605167200	journal	September 2006
R/qtl: QTL mapping in experimental crosses Broman, K. W.; Wu, H.; Sen, S. Bioinformatics, Vol. 19, Issue 7 https://doi.org/10.1093/bioinformatics/btg112	journal	May 2003
Positional Cloning of Rice Semidwarfing Gene, sd-1: Rice "Green Revolution Gene" Encodes a Mutant Enzyme Involved in Gibberellin Synthesis Monna, L. DNA Research, Vol. 9, Issue 1 https://doi.org/10.1093/dnares/9.1.11	journal	January 2002
Brachytic2/ZmABCB1 functions in IAA export from intercalary meristems Knöller, Anne Sophie; Blakeslee, Joshua J.; Richards, Elizabeth L. Journal of Experimental Botany, Vol. 61, Issue 13 https://doi.org/10.1093/jxb/erq180	journal	June 2010
Energy Sorghum--a genetic model for the design of C4 grass bioenergy crops Mullet, J.; Morishige, D.; McCormick, R. Journal of Experimental Botany, Vol. 65, Issue 13 https://doi.org/10.1093/jxb/eru229	journal	June 2014
PERK–KIPK–KCBP signalling negatively regulates root growth in Arabidopsis thaliana Humphrey, Tania V.; Haasen, Katrina E.; Aldea-Brydges, May Grace Journal of Experimental Botany, Vol. 66, Issue 1 https://doi.org/10.1093/jxb/eru390	journal	September 2014
An update on cell surface proteins containing extensin-motifs Borassi, Cecilia; Sede, Ana R.; Mecchia, Martin A. Journal of Experimental Botany, Vol. 67, Issue 2 https://doi.org/10.1093/jxb/erv455	journal	October 2015
An Improved General Amino Acid Replacement Matrix Le, S. Q.; Gascuel, O. Molecular Biology and Evolution, Vol. 25, Issue 7 https://doi.org/10.1093/molbev/msn067	journal	April 2008
MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0 Tamura, Koichiro; Stecher, Glen; Peterson, Daniel Molecular Biology and Evolution, Vol. 30, Issue 12 https://doi.org/10.1093/molbev/mst197	journal	October 2013
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
The Genetics of Sorghum Improvement Quinby, J. R. Journal of Heredity, Vol. 66, Issue 2 https://doi.org/10.1093/oxfordjournals.jhered.a108582	journal	March 1975
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data McKenna, A.; Hanna, M.; Banks, E. Genome Research, Vol. 20, Issue 9 https://doi.org/10.1101/gr.107524.110	journal	July 2010
Predicting Deleterious Amino Acid Substitutions Ng, P. C.; Henikoff, S. Genome Research, Vol. 11, Issue 5 https://doi.org/10.1101/gr.176601	journal	May 2001
Multidrug Resistance-like Genes of Arabidopsis Required for Auxin Transport and Auxin-Mediated Development Noh, B. THE PLANT CELL ONLINE, Vol. 13, Issue 11 https://doi.org/10.1105/tpc.13.11.2441	journal	November 2001
Plasma membrane-associated proline-rich extensin-like receptor kinase 4, a novel regulator of Ca ²⁺ signalling, is required for abscisic acid responses in Arabidopsis thaliana Bai, Ling; Zhang, Guozeng; Zhou, Yun The Plant Journal, Vol. 60, Issue 2 https://doi.org/10.1111/j.1365-313X.2009.03956.x	journal	October 2009
Dynamics of biomass partitioning, stem gene expression, cell wall biosynthesis, and sucrose accumulation during development of Sorghum bicolor McKinley, Brian; Rooney, William; Wilkerson, Curtis The Plant Journal, Vol. 88, Issue 4 https://doi.org/10.1111/tpj.13269	journal	September 2016
Loss of an MDR Transporter in Compact Stalks of Maize br2 and Sorghum dw3 Mutants Multani, D. S. Science, Vol. 302, Issue 5642 https://doi.org/10.1126/science.1086072	journal	October 2003
MUSCLE: a multiple sequence alignment method with reduced time and space complexity Edgar, Robert C. BMC Bioinformatics, Vol. 5, Issue 1, p. 113 https://doi.org/10.1186/1471-2105-5-113	journal	August 2004
Digital genotyping of sorghum -- a diverse plant species with a large repeat-rich genome Morishige, Daryl T.; Klein, Patricia E.; Hilley, Josie L. BMC Genomics, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2164-14-448	journal	January 2013
CONSTANS is a photoperiod regulated activator of flowering in sorghum Yang, Shanshan; Weers, Brock D.; Morishige, Daryl T. BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/1471-2229-14-148	journal	January 2014
Normalizing a large number of quantitative traits using empirical normal quantile transformation Peng, Bo; Yu, Robert K.; DeHoff, Kevin L. BMC Proceedings, Vol. 1, Issue S1 https://doi.org/10.1186/1753-6561-1-s1-s156	journal	December 2007
Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production Thurber, Carrie S.; Ma, Justin M.; Higgins, Race H. Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-r68	journal	June 2013
Plant Kinesin-Like Calmodulin Binding Protein Employs Its Regulatory Domain for Dimerization Vinogradova, Maia V.; Malanina, Galina G.; Waitzman, Joshua S. PLoS ONE, Vol. 8, Issue 6 https://doi.org/10.1371/journal.pone.0066669	journal	June 2013
Extensive Variation in the Density and Distribution of DNA Polymorphism in Sorghum Genomes Evans, Joseph; McCormick, Ryan F.; Morishige, Daryl PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0079192	journal	November 2013
Identification of Dw1, a Regulator of Sorghum Stem Internode Length Hilley, Josie; Truong, Sandra; Olson, Sara PLOS ONE, Vol. 11, Issue 3 https://doi.org/10.1371/journal.pone.0151271	journal	March 2016
Efficient Mapping of Plant Height Quantitative Trait Loci in a Sorghum Association Population With Introgressed Dwarfing Genes Brown, Patrick J.; Rooney, William L.; Franks, Cleve Genetics, Vol. 180, Issue 1 https://doi.org/10.1534/genetics.108.092239	journal	August 2008
A Model Selection Approach for the Identification of Quantitative Trait Loci in Experimental Crosses, Allowing Epistasis Manichaikul, Ani; Moon, Jee Young; Sen, Śaunak Genetics, Vol. 181, Issue 3 https://doi.org/10.1534/genetics.108.094565	journal	December 2008
A Simple Regression-Based Method to Map Quantitative Trait Loci Underlying Function-Valued Phenotypes Kwak, Il-Youp; Moore, Candace R.; Spalding, Edgar P. Genetics, Vol. 197, Issue 4 https://doi.org/10.1534/genetics.114.166306	journal	June 2014
Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor Truong, Sandra K.; McCormick, Ryan F.; Rooney, William L. Genetics, Vol. 201, Issue 3 https://doi.org/10.1534/genetics.115.178608	journal	August 2015
Inheritance of Height in Sorghum1 Quinby, J. R.; Karper, R. E. Agronomy Journal, Vol. 46, Issue 5 https://doi.org/10.2134/agronj1954.00021962004600050007x	journal	January 1954
Effect of a Single Height (Dw) Gene of Sorghum on Grain Yield, Grain Yield Components, and Test Weight1 Cassady, A. J. Crop Science, Vol. 5, Issue 5 https://doi.org/10.2135/cropsci1965.0011183X000500050002x	journal	January 1965
Effect of Height on Yield and Yield Components of Two Isogenic Lines of Sorghum vulgare Pers.1 Graham, Doyce; Lessman, K. J. Crop Science, Vol. 6, Issue 4 https://doi.org/10.2135/cropsci1966.0011183X000600040024x	journal	January 1966
The Effect of Tropical Sorghum Conversion and Inbred Development on Genome Diversity as Revealed by High-Resolution Genotyping Klein, Robert R.; Mullet, John E.; Jordan, David R. Crop Science, Vol. 48, Issue Supplement_1 https://doi.org/10.2135/cropsci2007.06.0319tpg	journal	January 2008
Genetic Improvement of Sorghum as a Biofuel Feedstock: I. QTL for Stem Sugar and Grain Nonstructural Carbohydrates Murray, Seth C.; Sharma, Arun; Rooney, William L. Crop Science, Vol. 48, Issue 6 https://doi.org/10.2135/cropsci2008.01.0016	journal	January 2008
Registration of the BTx623/IS3620C Recombinant Inbred Mapping Population of Sorghum Burow, G. B.; Klein, R. R.; Franks, C. D. Journal of Plant Registrations, Vol. 5, Issue 1 https://doi.org/10.3198/jpr2010.04.0219crmp	journal	January 2011
Evolutionary Adaptations of Plant AGC Kinases: From Light Signaling to Cell Polarity Regulation Rademacher, Eike H.; Offringa, Remko Frontiers in Plant Science, Vol. 3 https://doi.org/10.3389/fpls.2012.00250	journal	January 2012
Orchestration of microtubules and the actin cytoskeleton in trichome cell shape determination by a plant-unique kinesin Tian, Juan; Han, Libo; Feng, Zhidi eLife, Vol. 4 https://doi.org/10.7554/eLife.09351	journal	August 2015

Cited By (9)

Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development Casto, Anna L.; McKinley, Brian A.; Yu, Ka Man Jasmine Plant Direct, Vol. 2, Issue 11 https://doi.org/10.1002/pld3.85	journal	November 2018
Functional principal component based time-series genome-wide association in sorghum Miao, Chenyong; Xu, Yuhang; Liu, Sanzhen https://doi.org/10.1101/2020.02.16.951467	posted_content	February 2020
Genotyping by Sequencing of 393 Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection Kong, WenQian; Kim, Changsoo; Zhang, Dong G3: Genes\|Genomes\|Genetics, Vol. 8, Issue 8 https://doi.org/10.1534/g3.118.200173	journal	May 2018
Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments Boyles, Richard E.; Brenton, Zachary W.; Kresovich, Stephen The Plant Journal, Vol. 97, Issue 1 https://doi.org/10.1111/tpj.14113	journal	December 2018
Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought Spindel, Jennifer E.; Dahlberg, Jeffery; Colgan, Matthew BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5055-5	journal	September 2018
Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection Cuevas, Hugo E.; Prom, Louis K. BMC Genomics, Vol. 21, Issue 1 https://doi.org/10.1186/s12864-020-6489-0	journal	January 2020
Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population Marla, Sandeep R.; Burow, Gloria; Chopra, Ratan G3: Genes\|Genomes\|Genetics, Vol. 9, Issue 12 https://doi.org/10.1534/g3.119.400353	journal	October 2019
QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants Lin, Fan; Lazarus, Elena Z.; Rhee, Seung Y. G3: Genes\|Genomes\|Genetics, Vol. 10, Issue 7 https://doi.org/10.1534/g3.120.401122	journal	May 2020
Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations Miao, Chenyong; Pages, Alejandro; Xu, Zheng Plant Phenomics, Vol. 2020 https://doi.org/10.34133/2020/4216373	journal	February 2020

Similar Records

The AGCVIII kinase Dw2 modulates cell proliferation, endomembrane trafficking, and MLG/xylan cell wall localization in elongating stem internodes of Sorghum bicolor

Journal Article · Wed Nov 18 19:00:00 EST 2020 · The Plant Journal · OSTI ID:1764856

The genetic architecture of biomechanical traits in sorghum

Journal Article · Sun Mar 08 20:00:00 EDT 2020 · Crop Science · OSTI ID:1803390

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Sorghum Dw2 Encodes a Protein Kinase Regulator of Stem Internode Length

Citation Formats

References (67)

Cited By (9)

Similar Records

Related Subjects