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

Genetic Analysis Of Inflorescence And Plant Height Components In Sorghum (Panicoidae) And Comparative Genetics With Rice (Oryzoidae)

Dong Zhang, W. Kong, J. Robertson, V. Goff, Ethan Epps, A. Kerr, Gabriel Mills, Jay Cromwell, Yelena Lugin, C. Phillips, A. Paterson
Published 2015 · Biology, Medicine

Save to my Library
Download PDF
Analyze on Scholarcy
Share
BackgroundDomestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice.ResultsWe performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum.ConclusionsIntersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.
This paper references
Resolution of quantitative traits into Mendelian factors by using a complete RFLP linkage
AH Paterson (1988)
10.1093/bioinformatics/btm308
TASSEL: software for association mapping of complex traits in diverse samples
P. Bradbury (2007)
10.1371/journal.pgen.1000551
A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana
P. Kover (2009)
10.1007/s00122-010-1312-y
Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench
A. Shiringani (2010)
10.1038/335721A0
Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms
A. Paterson (1988)
Discovery and utilization of sorghum genes (MA5/MA6)
JE Mullet (2012)
10.1186/1939-8433-6-4
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Y. Kawahara (2012)
10.1038/nature07723
The Sorghum bicolor genome and the diversification of grasses
A. Paterson (2009)
10.1038/nature05911
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
P. Burton (2007)
10.1038/nature11532
A map of rice genome variation reveals the origin of cultivated rice
X. Huang (2012)
10.1105/tpc.105.038430
Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice[W][OA]
M. Sweeney (2006)
10.1007/s00425-010-1301-z
A rice β-1,3-glucanase gene Osg1 is required for callose degradation in pollen development
L. Wan (2010)
10.2135/CROPSCI2010.03.0179
Genetic Support for Phenotype‐based Racial Classification in Sorghum
P. Brown (2011)
10.1038/nrg3097
Crop genomics: advances and applications
P. Morrell (2012)
10.2135/CROPSCI2000.0008BR
World Economic Plants: A Standard Reference
L. Merrick (2000)
10.1073/pnas.1201700109
Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1
Yuye Wu (2012)
10.1038/ncomms3320
Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum
E. Mace (2013)
10.1007/s00122-006-0232-3
Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations
F. A. Feltus (2006)
10.1007/s001220100541
Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench)
H. Kebede (2001)
10.1534/genetics.109.111831
Flavonoid Phytoalexin-Dependent Resistance to Anthracnose Leaf Blight Requires a Functional yellow seed1 in Sorghum bicolor
F. Ibraheem (2010)
10.1186/gb-2013-14-6-r68
Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production
C. Thurber (2013)
10.1093/bioinformatics/bts444
GAPIT: genome association and prediction integrated tool
A. Lipka (2012)
10.1038/ng1702
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
J. Yu (2006)
10.1371/journal.pone.0059714
Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources
C. Billot (2013)
Sorghum Ma5 and Ma6 maturity genes
J. A. Brady (2009)
10.1105/tpc.109.068437
Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design
S. Myles (2009)
Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L
H Kebede (2001)
10.1101/GR.737703
Genomic gene clustering analysis of pathways in eukaryotes.
J. M. Lee (2003)
10.1073/pnas.0700643104
Plant domestication, a unique opportunity to identify the genetic basis of adaptation
J. Ross-Ibarra (2007)
10.1038/nature08494
Finding the missing heritability of complex diseases
T. Manolio (2009)
10.1534/genetics.107.074518
Meta-analysis of Polyploid Cotton QTL Shows Unequal Contributions of Subgenomes to a Complex Network of Genes and Gene Clusters Implicated in Lint Fiber Development
J. Rong (2007)
10.1371/journal.pgen.1003281
Ehd4 Encodes a Novel and Oryza-Genus-Specific Regulator of Photoperiodic Flowering in Rice
H. Gao (2013)
Resolution of quantitative traits into Mendelian factors by using a complete RFLP linkage map
AH Paterson (1988)
10.1016/j.cell.2006.12.006
The Molecular Genetics of Crop Domestication
J. Doebley (2006)
10.2135/CROPSCI1972.0011183X001200030037X
Inheritance and Genetic Relationships of Six Endosperm Types in Sorghum 1
D. Gorbet (1972)
Food and feed crops of the United States
Magness (2006)
10.1073/pnas.1106212108
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
R. L. Murphy (2011)
10.1007/978-1-4939-6658-5_15
CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses.
Dong Zhang (2017)
10.2135/CROPSCI2007.02.0080
Community Resources and Strategies for Association Mapping in Sorghum
A. M. Casa (2008)
10.1007/s001220100582
Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters
G. Hart (2001)
Food and feed crops of the United States. Interregional Research Project IR-4, IR Bul. 1 (Bul
JR Magness (1971)
Gene analysis and Linkage in Biology of Rice
T. Kinoshita (1984)
10.1038/SCIENTIFICAMERICAN0108-42A
The Wellcome Trust Case Control Consortium, U.K.
K. Mossman (2008)
10.1007/s11032-008-9182-6
Identification of QTL for sugar-related traits in a sweet × grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population
Kimberley B. Ritter (2008)
10.1126/SCIENCE.1086072
Loss of an MDR Transporter in Compact Stalks of Maize br2 and Sorghum dw3 Mutants
D. Multani (2003)
Genome duplication in soybean (Glycine subgenus soja).
R. Shoemaker (1996)
10.2135/CROPSCI1965.0011183X000500060032X
Inheritance of beta-carotene in grain sorghum hybrids
W. W. Worzella (1965)
Sorghum, 2nd edition
H. Doggett (1988)
10.1038/ng.2289
One gene's shattering effects
K. Olsen (2012)
10.1534/genetics.107.074245
Genetic Design and Statistical Power of Nested Association Mapping in Maize
J. Yu (2008)
10.1038/90135
Dwarf8 polymorphisms associate with variation in flowering time
J. Thornsberry (2001)
10.1111/tpj.12268
Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response
K. Hori (2013)
SEED-COLOR INHERITANCE IN CERTAIN GRAIN-SORGHUM CROSSES
SORGHUM CROSSES (2010)
10.1038/ng.2281
Parallel domestication of the Shattering1 genes in cereals
Zhongwei Lin (2012)
Sorghum improvement and the genetics of growth
J. R. Quinby (1974)
10.1111/tpj.12411
The DROOPING LEAF and OsETTIN2 genes promote awn development in rice.
T. Toriba (2014)
10.1007/s00122-006-0352-9
Inheritance of inflorescence architecture in sorghum
P. Brown (2006)
10.1126/science.1174276
The Genetic Architecture of Maize Flowering Time
E. Buckler (2009)
10.1038/nature11798
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
A. Paterson (2012)
10.1038/nbt.2050
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes
X. Xu (2012)
UK: Longman
H Doggett (1988)
10.1007/s00122-009-0993-6
Identification of quantitative trait loci for agronomically important traits and their association with genic-microsatellite markers in sorghum
G. Srinivas (2009)
10.1006/PMPP.2002.0411
Excision of the Candystripe1 transposon from a hyper-mutable Y1-cs allele shows that the sorghumY1 gene controls the biosynthesis of both 3-deoxyanthocyanidin phytoalexins and phlobaphene pigments☆
S. Chopra (2002)
10.1073/pnas.1215985110
Population genomic and genome-wide association studies of agroclimatic traits in sorghum
G. Morris (2012)
10.1371/journal.pone.0110046
Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records
I. Matthies (2014)
10.2135/CROPSCI1999.0011183X0039000200016X
Genetic control of a photoperiod-sensitive response in Sorghum bicolor (L.) Moench
W. Rooney (1999)
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)
10.1073/PNAS.0307901101
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.
A. Paterson (2004)
10.1371/journal.pone.0033470
Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers
Sophie Bouchet (2012)
10.1038/ng.546
Mixed linear model approach adapted for genome-wide association studies
Zhiwu Zhang (2010)
Mapping of genes for awn in rice using Oryza meridionalis introgression lines
S Matsushita (2003)
10.1126/science.269.5231.1714
Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci
A. Paterson (1995)
10.1534/g3.112.004499
Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum
W. Kong (2013)
10.1104/pp.113.2.611
The Sorghum Photoperiod Sensitivity Gene, Ma3, Encodes a Phytochrome B
K. Childs (1997)
Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.
Y. R. Lin (1995)



This paper is referenced by
10.19103/as.2017.0015.06
Ensuring the genetic diversity of sorghum
H. Upadhyaya (2018)
10.1080/15592324.2016.1261232
Photoperiod response and floral transition in sorghum
Tezera W. Wolabu (2016)
10.1534/g3.118.200551
Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum
Marcus O. Olatoye (2018)
10.3389/fpls.2017.02213
Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice (Oryza sativa L.)
Q. Lu (2018)
10.1093/pcp/pcaa056
RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum Using a Japanese Landrace Takakibi NOG.
Hiromi Kajiya-Kanegae (2020)
10.1104/pp.18.00974
Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS1[OPEN]
Y. Zhou (2018)
10.3198/JPR2018.09.0058CRGS
Registration of BTx623dw5, a New Sorghum Dwarf Mutant
Junping Chen (2019)
10.1101/308478
Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection
W. Kong (2018)
10.1007/978-1-4939-6658-5_15
CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses.
Dong Zhang (2017)
10.1016/j.fcr.2019.107619
Linkage disequilibrium mapping of high-throughput image-derived descriptors of plant architecture traits under field conditions
Matthew W. Breitzman (2019)
10.1101/2020.06.03.132217
A Genomics Resource for Genetics, Physiology, and Breeding of West African Sorghum
J. Faye (2020)
10.1101/2021.01.03.425108
Elucidating biosynthetic pathway of piperine using comparative transcriptome analysis of leaves, root and spike in Piper longum L
Prem Kumar Dantu (2021)
10.1534/g3.118.200173
Genotyping by Sequencing of 393 Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection
W. Kong (2018)
10.1111/tpj.13440
The effects of becoming taller: direct and pleiotropic effects of artificial selection on plant height in Brassica rapa
Pengjuan Zu (2017)
10.1371/journal.pone.0225979
Genome-wide association mapping of total antioxidant capacity, phenols, tannins, and flavonoids in a panel of Sorghum bicolor and S. bicolor × S. halepense populations using multi-locus models
E. Habyarimana (2019)
10.1534/g3.120.401608
Genetic Analysis of Stem Diameter and Water Contents To Improve Sorghum Bioenergy Efficiency
W. Kong (2020)
10.1534/g3.119.400061
Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids (Cynodon dactylon x transvaalensis): Morphological Traits
S. Khanal (2019)
10.3835/plantgenome2015.06.0044
Genome‐Wide Association Study for Nine Plant Architecture Traits in Sorghum
Jing Zhao (2016)
10.1038/srep38081
Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L
Padma Nimmakayala (2016)
10.1371/journal.pone.0151346
Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria
Margarita Mauro-Herrera (2016)
10.1186/s12864-016-3475-7
Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement
H. Cuevas (2016)
10.1186/s12864-018-5055-5
Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought
J. E. Spindel (2018)
10.1002/agj2.20123
Combining ability of biomass sorghum in different crop years and sites for bioenergy generation
M. J. D. Silva (2020)
10.3835/plantgenome2016.09.0091
Genome‐Wide Association Study of Developing Leaves' Heat Tolerance during Vegetative Growth Stages in a Sorghum Association Panel
J. Chen (2017)
10.1371/journal.pone.0216886
Genetic diversity and population structure of Ethiopian Capsicum germplasms
Abate Mekonnen Solomon (2019)
10.1017/s1479262119000212
Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers
Gloria Afolayan (2019)
Quantitative genomic analysis of agroclimatic traits in sorghum
Olalere Marcus Olatoye (2017)
10.4172/2229-4473.1000405
Omics Technologies in Unraveling Plant Stress Responses; Using Sorghum as a Model Crop, How Far Have We Gone?
O. Ibraheem (2018)
10.1007/s00438-018-1486-6
Interspecific genetic maps in Miscanthus floridulus and M. sacchariflorus accelerate detection of QTLs associated with plant height and inflorescence
Chunxia Ge (2018)
Breakthrough Technologies A High-Throughput , Field-Based Phenotyping Technology for Tall Biomass Crops 1
M. Fernandez (2017)
10.1101/2020.10.27.355495
Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum
Ravi V. Mural (2020)
10.1534/genetics.116.198499
Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population
S. Bouchet (2017)
See more
Semantic Scholar Logo Some data provided by SemanticScholar