Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)
Abstract
Domestication 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. We 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 modernmore »
- Authors:
-
- Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab. and Inst. of Bioinformatics
- Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab. and Dept. of Crop and Soil Sciences
- Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab.
- Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab., Inst. of Bioinformatics, Dept. of Crop and Soil Sciences, Dept. of Plant Biology, Dept. of Genetics
- Publication Date:
- Research Org.:
- Univ. of Georgia, Athens, GA (United States). Plant Genome Mapping Lab.
- Sponsoring Org.:
- USDOE; USDOE-US Department of Agriculture Plant Feedstock Program
- OSTI Identifier:
- 1184791
- Alternate Identifier(s):
- OSTI ID: 1188764
- Grant/Contract Number:
- AI52-08NA28654; 2011-02786; 2012-03304 (DOE-USDA project grants)
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Plant Biology
- Additional Journal Information:
- Journal Volume: 15; Journal Issue: 1; Journal ID: ISSN 1471-2229
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; sorghum; GWAS; biparental QTL mapping; inflorescence; flowering time; plant height; domestication; genetic correspondence
Citation Formats
Zhang, Dong, Kong, Wenqian, Robertson, Jon, Goff, Valorie H, Epps, Ethan, Kerr, Alexandra, Mills, Gabriel, Cromwell, Jay, Lugin, Yelena, Phillips, Christine, and Paterson, Andrew H. Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae). United States: N. p., 2015.
Web. doi:10.1186/s12870-015-0477-6.
Zhang, Dong, Kong, Wenqian, Robertson, Jon, Goff, Valorie H, Epps, Ethan, Kerr, Alexandra, Mills, Gabriel, Cromwell, Jay, Lugin, Yelena, Phillips, Christine, & Paterson, Andrew H. Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae). United States. https://doi.org/10.1186/s12870-015-0477-6
Zhang, Dong, Kong, Wenqian, Robertson, Jon, Goff, Valorie H, Epps, Ethan, Kerr, Alexandra, Mills, Gabriel, Cromwell, Jay, Lugin, Yelena, Phillips, Christine, and Paterson, Andrew H. Tue .
"Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)". United States. https://doi.org/10.1186/s12870-015-0477-6. https://www.osti.gov/servlets/purl/1184791.
@article{osti_1184791,
title = {Genetic analysis of inflorescence and plant height components in sorghum (Panicoidae) and comparative genetics with rice (Oryzoidae)},
author = {Zhang, Dong and Kong, Wenqian and Robertson, Jon and Goff, Valorie H and Epps, Ethan and Kerr, Alexandra and Mills, Gabriel and Cromwell, Jay and Lugin, Yelena and Phillips, Christine and Paterson, Andrew H},
abstractNote = {Domestication 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. We 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. Intersections 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.},
doi = {10.1186/s12870-015-0477-6},
journal = {BMC Plant Biology},
number = 1,
volume = 15,
place = {United States},
year = {Tue Dec 01 00:00:00 EST 2015},
month = {Tue Dec 01 00:00:00 EST 2015}
}
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Figures / Tables:
Figure 1: Population structure of 502 worldwide sorghum accessions. 476 belong to the five main cultivated races and 26 are wild types. (a) PCA plots of the first three components for 265,487 SNPs. The five main cultivated races and the wild type are color-coded. (b) Neighbor-joining tree of 502 sorghummore »
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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
journal, June 2002
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Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations
journal, February 2006
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journal, July 2006
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Genetic mapping of QTLs for sugar-related traits in a RIL population of Sorghum bicolor L. Moench
journal, March 2010
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- Theoretical and Applied Genetics, Vol. 121, Issue 2
Quantitative trait loci influencing drought tolerance in grain sorghum (Sorghum bicolor L. Moench)
journal, August 2001
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- Theoretical and Applied Genetics, Vol. 103, Issue 2-3
Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters
journal, December 2001
- Hart, G. E.; Schertz, K. F.; Peng, Y.
- Theoretical and Applied Genetics, Vol. 103, Issue 8
Identification of QTL for sugar-related traits in a sweet × grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population
journal, April 2008
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journal, October 1988
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Dwarf8 polymorphisms associate with variation in flowering time
journal, July 2001
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Finding the missing heritability of complex diseases
journal, October 2009
- Manolio, Teri A.; Collins, Francis S.; Cox, Nancy J.
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A map of rice genome variation reveals the origin of cultivated rice
journal, October 2012
- Huang, Xuehui; Kurata, Nori; Wei, Xinghua
- Nature, Vol. 490, Issue 7421
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
journal, December 2012
- Paterson, Andrew H.; Wendel, Jonathan F.; Gundlach, Heidrun
- Nature, Vol. 492, Issue 7429
Parallel domestication of the Shattering1 genes in cereals
journal, May 2012
- Lin, Zhongwei; Li, Xianran; Shannon, Laura M.
- Nature Genetics, Vol. 44, Issue 6
Mixed linear model approach adapted for genome-wide association studies
journal, March 2010
- Zhang, Zhiwu; Ersoz, Elhan; Lai, Chao-Qiang
- Nature Genetics, Vol. 42, Issue 4
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
journal, December 2005
- Yu, Jianming; Pressoir, Gael; Briggs, William H.
- Nature Genetics, Vol. 38, Issue 2
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
journal, May 2004
- Paterson, A. H.; Bowers, J. E.; Chapman, B. A.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 26
Plant domestication, a unique opportunity to identify the genetic basis of adaptation
journal, May 2007
- Ross-Ibarra, J.; Morrell, P. L.; Gaut, B. S.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue Supplement 1
Presence of tannins in sorghum grains is conditioned by different natural alleles of Tannin1
journal, June 2012
- Wu, Y.; Li, X.; Xiang, W.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 26
TASSEL: software for association mapping of complex traits in diverse samples
journal, June 2007
- Bradbury, P. J.; Zhang, Z.; Kroon, D. E.
- Bioinformatics, Vol. 23, Issue 19
GAPIT: genome association and prediction integrated tool
journal, July 2012
- Lipka, Alexander E.; Tian, Feng; Wang, Qishan
- Bioinformatics, Vol. 28, Issue 18
Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.
journal, September 1995
- Lin, Y. R.; Schertz, K. F.; Paterson, A. H.
- Genetics, Vol. 141, Issue 1
Genome Duplication in Soybean ( Glycine subgenus soja )
journal, September 1996
- Shoemaker, R. C.; Polzin, K.; Labate, J.
- Genetics, Vol. 144, Issue 1
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
journal, September 2003
- Bowers, John E.; Abbey, Colette; Anderson, Sharon
- Genetics, Vol. 165, Issue 1
The Sorghum Photoperiod Sensitivity Gene, Ma3, Encodes a Phytochrome B
journal, February 1997
- Childs, K. L.; Miller, F. R.; Cordonnier-Pratt, M. M.
- Plant Physiology, Vol. 113, Issue 2
Caught Red-Handed: Rc Encodes a Basic Helix-Loop-Helix Protein Conditioning Red Pericarp in Rice
journal, January 2006
- Sweeney, Megan T.; Thomson, Michael J.; Pfeil, Bernard E.
- The Plant Cell, Vol. 18, Issue 2
Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design
journal, August 2009
- Myles, Sean; Peiffer, Jason; Brown, Patrick J.
- The Plant Cell, Vol. 21, Issue 8
H d16 , a gene for casein kinase I , is involved in the control of rice flowering time by modulating the day‐length response
journal, July 2013
- Hori, Kiyosumi; Ogiso‐Tanaka, Eri; Matsubara, Kazuki
- The Plant Journal, Vol. 76, Issue 1
The DROOPING LEAF and OsETTIN2 genes promote awn development in rice
journal, February 2014
- Toriba, Taiyo; Hirano, Hiro-Yuki
- The Plant Journal, Vol. 77, Issue 4
The Genetic Architecture of Maize Flowering Time
journal, August 2009
- Buckler, E. S.; Holland, J. B.; Bradbury, P. J.
- Science, Vol. 325, Issue 5941, p. 714-718
Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci
journal, September 1995
- Paterson, A. H.; Lin, Y. -R.; Li, Z.
- Science, Vol. 269, Issue 5231
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
journal, January 2013
- Kawahara, Yoshihiro; de la Bastide, Melissa; Hamilton, John P.
- Rice, Vol. 6, Issue 1
Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production
journal, June 2013
- Thurber, Carrie S.; Ma, Justin M.; Higgins, Race H.
- Genome Biology, Vol. 14, Issue 6
A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana
journal, July 2009
- Kover, Paula X.; Valdar, William; Trakalo, Joseph
- PLoS Genetics, Vol. 5, Issue 7
Ehd4 Encodes a Novel and Oryza-Genus-Specific Regulator of Photoperiodic Flowering in Rice
journal, February 2013
- Gao, He; Zheng, Xiao-Ming; Fei, Guilin
- PLoS Genetics, Vol. 9, Issue 2
Massive Sorghum Collection Genotyped with SSR Markers to Enhance Use of Global Genetic Resources
journal, April 2013
- Billot, Claire; Ramu, Punna; Bouchet, Sophie
- PLoS ONE, Vol. 8, Issue 4
Genome-Wide Association Mapping for Kernel and Malting Quality Traits Using Historical European Barley Records
journal, November 2014
- Matthies, Inge E.; Malosetti, Marcos; Röder, Marion S.
- PLoS ONE, Vol. 9, Issue 11
Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum
journal, January 2013
- Kong, Wenqian; Jin, Huizhe; Franks, Cleve D.
- G3: Genes|Genomes|Genetics, Vol. 3, Issue 1
Genetic Design and Statistical Power of Nested Association Mapping in Maize
journal, January 2008
- Yu, Jianming; Holland, James B.; McMullen, Michael D.
- Genetics, Vol. 178, Issue 1
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
journal, June 2007
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