1
|
Dai D, Mudunkothge JS, Galli M, Char SN, Davenport R, Zhou X, Gustin JL, Spielbauer G, Zhang J, Barbazuk WB, Yang B, Gallavotti A, Settles AM. Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize. Nat Commun 2022; 13:5366. [PMID: 36100609 PMCID: PMC9470594 DOI: 10.1038/s41467-022-33055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Historically, xenia effects were hypothesized to be unique genetic contributions of pollen to seed phenotype, but most examples represent standard complementation of Mendelian traits. We identified the imprinted dosage-effect defective1 (ded1) locus in maize (Zea mays) as a paternal regulator of seed size and development. Hypomorphic alleles show a 5–10% seed weight reduction when ded1 is transmitted through the male, while homozygous mutants are defective with a 70–90% seed weight reduction. Ded1 encodes an R2R3-MYB transcription factor expressed specifically during early endosperm development with paternal allele bias. DED1 directly activates early endosperm genes and endosperm adjacent to scutellum cell layer genes, while directly repressing late grain-fill genes. These results demonstrate xenia as originally defined: Imprinting of Ded1 causes the paternal allele to set the pace of endosperm development thereby influencing grain set and size. Xenia effects describe the genetic contribution of pollen to seed phenotypes. Here the authors show that paternal imprinting of Ded1 contributes to the xenia effect in maize by setting the pace of endosperm development.
Collapse
Affiliation(s)
- Dawei Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Janaki S Mudunkothge
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Galli
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruth Davenport
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jeffery L Gustin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,United States Department of Agriculture, Urbana, IL, 61801, USA
| | - Gertraud Spielbauer
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Junya Zhang
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. .,Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
| |
Collapse
|
2
|
Zhao M, Su B, Zhang X, Zhang X, Li R, Cheng P, Wang B, Li Q. Molecular Mapping of a Recessive Gene for Stripe Rust Resistance at the YrCf75 Locus Using Bulked Segregant Analysis Combined with Single Nucleotide Polymorphism Genotyping Arrays and Bulked Segregant RNA-Sequencing. PLANT DISEASE 2022; 106:2090-2096. [PMID: 35196106 DOI: 10.1094/pdis-11-21-2564-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases in wheat worldwide. Planting resistant varieties is the most economical, effective, and environment-friendly measure to control wheat stripe rust. Changfeng 75, a Chinese winter wheat variety, shows high stripe rust resistance in both seedling and adult-plant stages. The seedling tests of F1, F2, and F2:3 populations derived from Mingxian 169/Changfeng 75 inoculated with Chinese predominant Pst race CYR34 showed that the stripe rust resistance of Changfeng 75 was controlled by a single recessive gene. The locus was temporarily designated as YrCf75. Bulked segregant analysis (BSA) combined with the wheat 660K single-nucleotide polymorphism (SNP) array and bulked segregant RNA-sequencing indicated that the proportion of polymorphic SNPs on wheat chromosome 2A was the highest, which suggested that YrCf75 was likely located on chromosome 2A. Two hundred and twenty-five Kompetitive allele-specific PCR (KASP) and 75 simple sequence repeat (SSR) markers on chromosome 2A were used to map YrCf75 using the BSA approach. Linkage analysis indicated that 31 KASP markers and one SSR marker were linked to YrCf75, and the genetic distances of the two closest flanking KASP markers, AX-1110060462 and AX-111004763, were 1.2 and 2.7 cM, respectively. YrCf75 was located on wheat chromosome 2AL. The molecular detection, resistance specificity, and chromosome location showed that YrCf75 is likely a new gene that is different from the known stripe rust resistance genes (Yr1 and Yr32) on wheat chromosome 2AL.
Collapse
Affiliation(s)
- Minghui Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bei Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoxu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaomei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruobing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| |
Collapse
|
3
|
Julius BT, McCubbin TJ, Mertz RA, Baert N, Knoblauch J, Grant DG, Conner K, Bihmidine S, Chomet P, Wagner R, Woessner J, Grote K, Peevers J, Slewinski TL, McCann MC, Carpita NC, Knoblauch M, Braun DM. Maize Brittle Stalk2-Like3, encoding a COBRA protein, functions in cell wall formation and carbohydrate partitioning. THE PLANT CELL 2021; 33:3348-3366. [PMID: 34323976 PMCID: PMC8505866 DOI: 10.1093/plcell/koab193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/16/2021] [Indexed: 05/14/2023]
Abstract
Carbohydrate partitioning from leaves to sink tissues is essential for plant growth and development. The maize (Zea mays) recessive carbohydrate partitioning defective28 (cpd28) and cpd47 mutants exhibit leaf chlorosis and accumulation of starch and soluble sugars. Transport studies with 14C-sucrose (Suc) found drastically decreased export from mature leaves in cpd28 and cpd47 mutants relative to wild-type siblings. Consistent with decreased Suc export, cpd28 mutants exhibited decreased phloem pressure in mature leaves, and altered phloem cell wall ultrastructure in immature and mature leaves. We identified the causative mutations in the Brittle Stalk2-Like3 (Bk2L3) gene, a member of the COBRA family, which is involved in cell wall development across angiosperms. None of the previously characterized COBRA genes are reported to affect carbohydrate export. Consistent with other characterized COBRA members, the BK2L3 protein localized to the plasma membrane, and the mutants condition a dwarf phenotype in dark-grown shoots and primary roots, as well as the loss of anisotropic cell elongation in the root elongation zone. Likewise, both mutants exhibit a significant cellulose deficiency in mature leaves. Therefore, Bk2L3 functions in tissue growth and cell wall development, and this work elucidates a unique connection between cellulose deposition in the phloem and whole-plant carbohydrate partitioning.
Collapse
Affiliation(s)
- Benjamin T Julius
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Tyler J McCubbin
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Rachel A Mertz
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Present address: Inari Agriculture, West Lafayette, Indiana 47906, USA
| | - Nick Baert
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Jan Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - DeAna G Grant
- Electron Microscopy Core Facility, University of Missouri, Columbia, Missouri 65211, USA
| | - Kyle Conner
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Saadia Bihmidine
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Paul Chomet
- NRGene Inc., 8910 University Center Lane, San Diego, California 92122, USA
| | - Ruth Wagner
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Jeff Woessner
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | - Karen Grote
- Bayer Crop Science, Chesterfield, Missouri 63017, USA
| | | | | | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Nicholas C Carpita
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - David M Braun
- Divisions of Plant Science and Technology, Biological Sciences, Interdisciplinary Plant Group, and the Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
- Author for correspondence:
| |
Collapse
|
4
|
Tran TM, McCubbin TJ, Bihmidine S, Julius BT, Baker RF, Schauflinger M, Weil C, Springer N, Chomet P, Wagner R, Woessner J, Grote K, Peevers J, Slewinski TL, Braun DM. Maize Carbohydrate Partitioning Defective33 Encodes an MCTP Protein and Functions in Sucrose Export from Leaves. MOLECULAR PLANT 2019; 12:1278-1293. [PMID: 31102785 DOI: 10.1016/j.molp.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 05/29/2023]
Abstract
To sustain plant growth, development, and crop yield, sucrose must be transported from leaves to distant parts of the plant, such as seeds and roots. To identify genes that regulate sucrose accumulation and transport in maize (Zea mays), we isolated carbohydrate partitioning defective33 (cpd33), a recessive mutant that accumulated excess starch and soluble sugars in mature leaves. The cpd33 mutants also exhibited chlorosis in the leaf blades, greatly diminished plant growth, and reduced fertility. Cpd33 encodes a protein containing multiple C2 domains and transmembrane regions. Subcellular localization experiments showed the CPD33 protein localized to plasmodesmata (PD), the plasma membrane, and the endoplasmic reticulum. We also found that a loss-of-function mutant of the CPD33 homolog in Arabidopsis, QUIRKY, had a similar carbohydrate hyperaccumulation phenotype. Radioactively labeled sucrose transport assays showed that sucrose export was significantly lower in cpd33 mutant leaves relative to wild-type leaves. However, PD transport in the adaxial-abaxial direction was unaffected in cpd33 mutant leaves. Intriguingly, transmission electron microscopy revealed fewer PD at the companion cell-sieve element interface in mutant phloem tissue, providing a possible explanation for the reduced sucrose export in mutant leaves. Collectively, our results suggest that CPD33 functions to promote symplastic transport into sieve elements.
Collapse
Affiliation(s)
- Thu M Tran
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA; Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; National Key Laboratory for Plant Cell Technology, Agricultural Genetics Institute, Hanoi, Vietnam
| | - Tyler J McCubbin
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA; Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Saadia Bihmidine
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA
| | - Benjamin T Julius
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA
| | - R Frank Baker
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA
| | - Martin Schauflinger
- Electron Microscopy Core Facility, University of Missouri, Columbia, MO 65211, USA
| | - Clifford Weil
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Nathan Springer
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Paul Chomet
- NRGene Inc., 8910 University Center Lane, ∖r∖nSuite 400, San Diego, CA 92122, USA
| | - Ruth Wagner
- Bayer Crop Science, Chesterfield, MO 63017, USA
| | | | - Karen Grote
- Bayer Crop Science, Chesterfield, MO 63017, USA
| | | | | | - David M Braun
- Division of Biological Sciences, Interdisciplinary Plant Group, Missouri Maize Center, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
5
|
Yao H, Skirpan A, Wardell B, Matthes MS, Best NB, McCubbin T, Durbak A, Smith T, Malcomber S, McSteen P. The barren stalk2 Gene Is Required for Axillary Meristem Development in Maize. MOLECULAR PLANT 2019; 12:374-389. [PMID: 30690173 DOI: 10.1016/j.molp.2018.12.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/08/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
The diversity of plant architecture is determined by axillary meristems (AMs). AMs are produced from small groups of stem cells in the axils of leaf primordia and generate vegetative branches and reproductive inflorescences. Previous studies identified genes critical for AM development that function in auxin biosynthesis, transport, and signaling. barren stalk1 (ba1), a basic helix-loop-helix transcription factor, acts downstream of auxin to control AM formation. Here, we report the cloning and characterization of barren stalk2 (ba2), a mutant that fails to produce ears and has fewer branches and spikelets in the tassel, indicating that ba2 functions in reproductive AM development. Furthermore, the ba2 mutation suppresses tiller growth in the teosinte branched1 mutant, indicating that ba2 also plays an essential role in vegetative AM development. The ba2 gene encodes a protein that co-localizes and heterodimerizes with BA1 in the nucleus. Characterization of the genetic interaction between ba2 and ba1 demonstrates that ba1 shows a gene dosage effect in ba2 mutants, providing further evidence that BA1 and BA2 act together in the same pathway. Characterization of the molecular and genetic interaction between ba2 and additional genes required for the regulation of ba1 further supports this finding. The ba1 and ba2 genes are orthologs of rice genes, LAX PANICLE1 (LAX1) and LAX2, respectively, hence providing insights into pathways controlling AMs development in grasses.
Collapse
Affiliation(s)
- Hong Yao
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Andrea Skirpan
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Brian Wardell
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Michaela S Matthes
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Norman B Best
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Tyler McCubbin
- Division of Biological Sciences, Interdisciplinary Plant Group, Columbia, MO 65211, USA
| | - Amanda Durbak
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Taylor Smith
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Simon Malcomber
- Department of Biological Sciences, California State University, Long Beach, CA 90840, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
6
|
Bai F, Corll J, Shodja DN, Davenport R, Feng G, Mudunkothge J, Brigolin CJ, Martin F, Spielbauer G, Tseung CW, Siebert AE, Barbazuk WB, Lal S, Settles AM. RNA Binding Motif Protein 48 Is Required for U12 Splicing and Maize Endosperm Differentiation. THE PLANT CELL 2019; 31:715-733. [PMID: 30760564 PMCID: PMC6482629 DOI: 10.1105/tpc.18.00754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 05/19/2023]
Abstract
The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize (Zea mays) RNA binding motif protein 48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, zinc finger CCCH-type, RNA binding motif, and Ser/Arg rich 2/Rough endosperm 3 (RGH3). Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors required for intron recognition form complexes with RBM48. Human RBM48 interacts with armadillo repeat containing 7 (ARMC7). Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.
Collapse
Affiliation(s)
- Fang Bai
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Donya N Shodja
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Guanqiao Feng
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Janaki Mudunkothge
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Christian J Brigolin
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Federico Martin
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Gertraud Spielbauer
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Chi-Wah Tseung
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - A Mark Settles
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
7
|
Zheng J, He C, Qin Y, Lin G, Park WD, Sun M, Li J, Lu X, Zhang C, Yeh CT, Gunasekara CJ, Zeng E, Wei H, Schnable PS, Wang G, Liu S. Co-expression analysis aids in the identification of genes in the cuticular wax pathway in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:530-542. [PMID: 30375131 DOI: 10.1111/tpj.14140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/09/2018] [Accepted: 10/22/2018] [Indexed: 06/08/2023]
Abstract
Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. To elucidate the molecular functions of maize glossy mutants that reduce the accumulation of epicuticular waxes, eight non-allelic glossy mutants were subjected to transcriptomic comparisons with their respective wild-type siblings. Transcriptomic comparisons identified 2279 differentially expressed (DE) genes. Other glossy genes tended to be down-regulated in glossy mutants; by contrast stress-responsive pathways were induced in mutants. Gene co-expression network (GCN) analysis found that glossy genes were clustered, suggestive of co-regulation. Genes that potentially regulate the accumulation of glossy gene transcripts were identified via a pathway level co-expression analysis. Expression data from diverse organs showed that maize glossy genes are generally active in young leaves, silks, and tassels, while largely inactive in seeds and roots. Through reverse genetics, a DE gene homologous to Arabidopsis CER8 and co-expressed with known glossy genes was confirmed to participate in epicuticular wax accumulation. GCN data-informed forward genetics approach enabled cloning of the gl14 gene, which encodes a putative membrane-associated protein. Our results deepen understanding of the transcriptional regulation of the genes involved in the accumulation of epicuticular wax, and provide two maize glossy genes and a number of candidate genes for further characterization.
Collapse
Affiliation(s)
- Jun Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng He
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yang Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Woojun D Park
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Minghao Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Jian Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3605, USA
| | - Chathura J Gunasekara
- USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Hairong Wei
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3605, USA
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| |
Collapse
|
8
|
van der Linde K, Timofejeva L, Egger RL, Ilau B, Hammond R, Teng C, Meyers BC, Doehlemann G, Walbot V. Pathogen Trojan Horse Delivers Bioactive Host Protein to Alter Maize Anther Cell Behavior in Situ. THE PLANT CELL 2018; 30:528-542. [PMID: 29449414 PMCID: PMC5894838 DOI: 10.1105/tpc.17.00238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 01/16/2018] [Accepted: 02/13/2018] [Indexed: 05/21/2023]
Abstract
Small proteins are crucial signals during development, host defense, and physiology. The highly spatiotemporal restricted functions of signaling proteins remain challenging to study in planta. The several month span required to assess transgene expression, particularly in flowers, combined with the uncertainties from transgene position effects and ubiquitous or overexpression, makes monitoring of spatiotemporally restricted signaling proteins lengthy and difficult. This situation could be rectified with a transient assay in which protein deployment is tightly controlled spatially and temporally in planta to assess protein functions, timing, and cellular targets as well as to facilitate rapid mutagenesis to define functional protein domains. In maize (Zea mays), secreted ZmMAC1 (MULTIPLE ARCHESPORIAL CELLS1) was proposed to trigger somatic niche formation during anther development by participating in a ligand-receptor module. Inspired by Homer's Trojan horse myth, we engineered a protein delivery system that exploits the secretory capabilities of the maize smut fungus Ustilago maydis, to allow protein delivery to individual cells in certain cell layers at precise time points. Pathogen-supplied ZmMAC1 cell-autonomously corrected both somatic cell division and differentiation defects in mutant Zmmac1-1 anthers. These results suggest that exploiting host-pathogen interactions may become a generally useful method for targeting host proteins to cell and tissue types to clarify cellular autonomy and to analyze steps in cell responses.
Collapse
Affiliation(s)
| | - Ljudmilla Timofejeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rachel L Egger
- Department of Biology, Stanford University, Stanford, California 94305
| | - Birger Ilau
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Reza Hammond
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, 50674 Cologne, Germany
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, California 94305
| |
Collapse
|
9
|
Ott A, Liu S, Schnable JC, Yeh CT‘E, Wang KS, Schnable PS. tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci. Nucleic Acids Res 2017; 45:e178. [PMID: 29036322 PMCID: PMC5716196 DOI: 10.1093/nar/gkx853] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/09/2017] [Accepted: 09/13/2017] [Indexed: 12/20/2022] Open
Abstract
Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only double-digested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3'-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (>97-99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci.
Collapse
Affiliation(s)
- Alina Ott
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
| | - Sanzhen Liu
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | - James C. Schnable
- Data2Bio LLC, Ames, IA 50011-3650, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Cheng-Ting ‘Eddy’ Yeh
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| | | | - Patrick S. Schnable
- Department of Agronomy, Iowa State University, Ames, IA 50011-3650, USA
- Data2Bio LLC, Ames, IA 50011-3650, USA
| |
Collapse
|
10
|
Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
Collapse
|
11
|
Strable J, Wallace JG, Unger-Wallace E, Briggs S, Bradbury PJ, Buckler ES, Vollbrecht E. Maize YABBY Genes drooping leaf1 and drooping leaf2 Regulate Plant Architecture. THE PLANT CELL 2017; 29:1622-1641. [PMID: 28698237 PMCID: PMC5559738 DOI: 10.1105/tpc.16.00477] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 06/12/2017] [Accepted: 07/07/2017] [Indexed: 05/19/2023]
Abstract
Leaf architecture directly influences canopy structure, consequentially affecting yield. We discovered a maize (Zea mays) mutant with aberrant leaf architecture, which we named drooping leaf1 (drl1). Pleiotropic mutations in drl1 affect leaf length and width, leaf angle, and internode length and diameter. These phenotypes are enhanced by natural variation at the drl2 enhancer locus, including reduced expression of the drl2-Mo17 allele in the Mo17 inbred. A second drl2 allele, produced by transposon mutagenesis, interacted synergistically with drl1 mutants and reduced drl2 transcript levels. The drl genes are required for proper leaf patterning, development and cell proliferation of leaf support tissues, and for restricting auricle expansion at the midrib. The paralogous loci encode maize CRABS CLAW co-orthologs in the YABBY family of transcriptional regulators. The drl genes are coexpressed in incipient and emergent leaf primordia at the shoot apex, but not in the vegetative meristem or stem. Genome-wide association studies using maize NAM-RIL (nested association mapping-recombinant inbred line) populations indicated that the drl loci reside within quantitative trait locus regions for leaf angle, leaf width, and internode length and identified rare single nucleotide polymorphisms with large phenotypic effects for the latter two traits. This study demonstrates that drl genes control the development of key agronomic traits in maize.
Collapse
Affiliation(s)
- Josh Strable
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology, Iowa State University, Ames, Iowa 50011
| | - Jason G Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602
| | - Erica Unger-Wallace
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Sarah Briggs
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Peter J Bradbury
- U.S. Department of Agriculture-Agriculture Research Service, Ithaca, New York 14853
| | - Edward S Buckler
- U.S. Department of Agriculture-Agriculture Research Service, Ithaca, New York 14853
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Erik Vollbrecht
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Interdepartmental Plant Biology, Iowa State University, Ames, Iowa 50011
| |
Collapse
|
12
|
Bernardo R. Prospective Targeted Recombination and Genetic Gains for Quantitative Traits in Maize. THE PLANT GENOME 2017; 10. [PMID: 28724082 DOI: 10.3835/plantgenome2016.11.0118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Advances in clustered regularly interspaced short palindromic repeats (CRISPR) technology have allowed targeted recombination in specific DNA sequences in yeast (). My objective was to determine if the selection gains from targeted recombination are large enough to warrant the development of targeted recombination technology in plants. Genomewide marker effects for quantitative traits in two maize ( L.) experiments were used to identify targeted recombination points that would maximize the per-chromosome genetic gains in a given cross. With nontargeted recombination in the intermated B73 × Mo17 population, selecting the best out of 180 recombinant inbreds led to a 7.1% gain for testcross yield. Having one targeted recombination on each of the 10 maize chromosomes led to a predicted gain of 15.3% for yield. Targeted recombination therefore led to a predicted relative efficiency () of (0.153 ÷ 0.071) = 212% of targeted recombination compared with nontargeted recombination. For the five other traits in the intermated B73 × Mo17 population and for four traits in 45 other maize crosses, the values ranged from 105 to 600%. The targeted recombination points differed among traits and crosses. Predicted gains increased when the number of targeted recombinations per chromosome increased from one to two. Overall, the results suggested that targeted recombination could double the selection gains for quantitative traits in maize and that the development of targeted recombination technology is worthwhile. Empirical experiments with current marker-assisted breeding procedures are needed to validate the per-chromosome predicted gains.
Collapse
|
13
|
Liu S, Zheng J, Migeon P, Ren J, Hu Y, He C, Liu H, Fu J, White FF, Toomajian C, Wang G. Unbiased K-mer Analysis Reveals Changes in Copy Number of Highly Repetitive Sequences During Maize Domestication and Improvement. Sci Rep 2017; 7:42444. [PMID: 28186206 PMCID: PMC5301235 DOI: 10.1038/srep42444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2017] [Indexed: 12/15/2022] Open
Abstract
The major component of complex genomes is repetitive elements, which remain recalcitrant to characterization. Using maize as a model system, we analyzed whole genome shotgun (WGS) sequences for the two maize inbred lines B73 and Mo17 using k-mer analysis to quantify the differences between the two genomes. Significant differences were identified in highly repetitive sequences, including centromere, 45S ribosomal DNA (rDNA), knob, and telomere repeats. Genotype specific 45S rDNA sequences were discovered. The B73 and Mo17 polymorphic k-mers were used to examine allele-specific expression of 45S rDNA in the hybrids. Although Mo17 contains higher copy number than B73, equivalent levels of overall 45S rDNA expression indicates that transcriptional or post-transcriptional regulation mechanisms operate for the 45S rDNA in the hybrids. Using WGS sequences of B73xMo17 doubled haploids, genomic locations showing differential repetitive contents were genetically mapped, which displayed different organization of highly repetitive sequences in the two genomes. In an analysis of WGS sequences of HapMap2 lines, including maize wild progenitor, landraces, and improved lines, decreases and increases in abundance of additional sets of k-mers associated with centromere, 45S rDNA, knob, and retrotransposons were found among groups, revealing global evolutionary trends of genomic repeats during maize domestication and improvement.
Collapse
Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jie Ren
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Cheng He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian 271018, P.R. China.,College of Life Sciences, Shandong Agricultural University, Taian 271018, P.R. China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
| |
Collapse
|
14
|
Nan GL, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V. MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize. Development 2016; 144:163-172. [PMID: 27913638 DOI: 10.1242/dev.140673] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 11/21/2016] [Indexed: 11/20/2022]
Abstract
Successful male gametogenesis involves orchestration of sequential gene regulation for somatic differentiation in pre-meiotic anthers. We report here the cloning of Male Sterile23 (Ms23), encoding an anther-specific predicted basic helix-loop-helix (bHLH) transcription factor required for tapetal differentiation; transcripts localize initially to the precursor secondary parietal cells then predominantly to daughter tapetal cells. In knockout ms23-ref mutant anthers, five instead of the normal four wall layers are observed. Microarray transcript profiling demonstrates a more severe developmental disruption in ms23-ref than in ms32 anthers, which possess a different bHLH defect. RNA-seq and proteomics data together with yeast two-hybrid assays suggest that MS23 along with MS32, bHLH122 and bHLH51 act sequentially as either homo- or heterodimers to choreograph tapetal development. Among them, MS23 is the earliest-acting factor, upstream of bHLH51 and bHLH122, controlling tapetal specification and maturation. By contrast, MS32 is constitutive and independently regulated and is required later than MS23 in tapetal differentiation.
Collapse
Affiliation(s)
- Guo-Ling Nan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jixian Zhai
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA.,Department of Biology, South University of Science and Technology, Shenzhen 518055, China
| | - Siwaret Arikit
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Darren Morrow
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - John Fernandes
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Lan Mai
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nhi Nguyen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
15
|
Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
Collapse
Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
| |
Collapse
|
16
|
Abstract
Flowering plants, like placental mammals, have an extensive maternal contribution toward progeny development. Plants are distinguished from animals by a genetically active haploid phase of growth and development between meiosis and fertilization, called the gametophyte. Flowering plants are further distinguished by the process of double fertilization that produces sister progeny, the endosperm and the embryo, of the seed. Because of this, there is substantial gene expression in the female gametophyte that contributes to the regulation of growth and development of the seed. A primary function of the endosperm is to provide growth support to its sister embryo. Several mutations in Zea mays subsp. mays have been identified that affect the contribution of the mother gametophyte to the seed. The majority affect both the endosperm and the embryo, although some embryo-specific effects have been observed. Many alter the pattern of expression of a marker for the basal endosperm transfer layer, a tissue that transports nutrients from the mother plant to the developing seed. Many of them cause abnormal development of the female gametophyte prior to fertilization, revealing potential cellular mechanisms of maternal control of seed development. These effects include reduced central cell size, abnormal architecture of the central cell, abnormal numbers and morphology of the antipodal cells, and abnormal egg cell morphology. These mutants provide insight into the logic of seed development, including necessary features of the gametes and supporting cells prior to fertilization, and set up future studies on the mechanisms regulating maternal contributions to the seed.
Collapse
|
17
|
Parent-of-Origin-Effect rough endosperm Mutants in Maize. Genetics 2016; 204:221-31. [PMID: 27440865 DOI: 10.1534/genetics.116.191775] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/12/2016] [Indexed: 01/06/2023] Open
Abstract
Parent-of-origin-effect loci have non-Mendelian inheritance in which phenotypes are determined by either the maternal or paternal allele alone. In angiosperms, parent-of-origin effects can be caused by loci required for gametophyte development or by imprinted genes needed for seed development. Few parent-of-origin-effect loci have been identified in maize (Zea mays) even though there are a large number of imprinted genes known from transcriptomics. We screened rough endosperm (rgh) mutants for parent-of-origin effects using reciprocal crosses with inbred parents. Six maternal rough endosperm (mre) and three paternal rough endosperm (pre) mutants were identified with three mre loci mapped. When inherited from the female parent, mre/+ seeds reduce grain fill with a rough, etched, or pitted endosperm surface. Pollen transmission of pre mutants results in rgh endosperm as well as embryo lethality. Eight of the mutants had significant distortion from the expected one-to-one ratio for parent-of-origin effects. Linked markers for mre1, mre2, and mre3 indicated that the mutant alleles have no bias in transmission. Histological analysis of mre1, mre2, mre3, and pre*-949 showed altered timing of starch grain accumulation and basal endosperm transfer cell layer (BETL) development. The mre1 locus delays BETL and starchy endosperm development, while mre2 and pre*-949 cause ectopic starchy endosperm differentiation. We conclude that many parent-of-origin effects in maize have incomplete penetrance of kernel phenotypes and that there is a large diversity of endosperm developmental roles for parent-of-origin-effect loci.
Collapse
|
18
|
The first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers. J Genet 2016; 95:377-82. [PMID: 27350682 DOI: 10.1007/s12041-016-0650-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Primulina eburnea is a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flowers. An F₂ population of 189 individuals was established for the construction of first-generation linkage maps based on expressed sequence tags-derived single-nucleotide polymorphism markers using the massARRAY genotyping platform. Of the 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. The linkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage map provides a framework for identification of important genes in breeding programmes.
Collapse
|
19
|
Zhou Z, Zhang C, Zhou Y, Hao Z, Wang Z, Zeng X, Di H, Li M, Zhang D, Yong H, Zhang S, Weng J, Li X. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics 2016; 17:178. [PMID: 26940065 PMCID: PMC4778306 DOI: 10.1186/s12864-016-2555-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/29/2016] [Indexed: 11/21/2022] Open
Abstract
Background Plant architecture attributes, such as plant height, ear height, and internode number, have played an important role in the historical increases in grain yield, lodging resistance, and biomass in maize (Zea mays L.). Analyzing the genetic basis of variation in plant architecture using high density QTL mapping will be of benefit for the breeding of maize for many traits. However, the low density of molecular markers in existing genetic maps has limited the efficiency and accuracy of QTL mapping. Genotyping by sequencing (GBS) is an improved strategy for addressing a complex genome via next-generation sequencing technology. GBS has been a powerful tool for SNP discovery and high-density genetic map construction. The creation of ultra-high density genetic maps using large populations of advanced recombinant inbred lines (RILs) is an efficient way to identify QTL for complex agronomic traits. Results A set of 314 RILs derived from inbreds Ye478 and Qi319 were generated and subjected to GBS. A total of 137,699,000 reads with an average of 357,376 reads per individual RIL were generated, which is equivalent to approximately 0.07-fold coverage of the maize B73 RefGen_V3 genome for each individual RIL. A high-density genetic map was constructed using 4183 bin markers (100-Kb intervals with no recombination events). The total genetic distance covered by the linkage map was 1545.65 cM and the average distance between adjacent markers was 0.37 cM with a physical distance of about 0.51 Mb. Our results demonstrated a relatively high degree of collinearity between the genetic map and the B73 reference genome. The quality and accuracy of the bin map for QTL detection was verified by the mapping of a known gene, pericarp color 1 (P1), which controls the color of the cob, with a high LOD value of 80.78 on chromosome 1. Using this high-density bin map, 35 QTL affecting plant architecture, including 14 for plant height, 14 for ear height, and seven for internode number were detected across three environments. Interestingly, pQTL10, which influences all three of these traits, was stably detected in three environments on chromosome 10 within an interval of 14.6 Mb. Two MYB transcription factor genes, GRMZM2G325907 and GRMZM2G108892, which might regulate plant cell wall metabolism are the candidate genes for qPH10. Conclusions Here, an ultra-high density accurate linkage map for a set of maize RILs was constructed using a GBS strategy. This map will facilitate identification of genes and exploration of QTL for plant architecture in maize. It will also be helpful for further research into the mechanisms that control plant architecture while also providing a basis for marker-assisted selection. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2555-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Chaoshu Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Yu Zhou
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Xing Zeng
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Hong Di
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, Heilongjiang, 150030, China.
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Shihuang Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
| |
Collapse
|
20
|
Liu H, Niu Y, Gonzalez-Portilla PJ, Zhou H, Wang L, Zuo T, Qin C, Tai S, Jansen C, Shen Y, Lin H, Lee M, Ware D, Zhang Z, Lübberstedt T, Pan G. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. BMC Genomics 2015; 16:1078. [PMID: 26691201 PMCID: PMC4687334 DOI: 10.1186/s12864-015-2242-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/24/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus. RESULTS In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73 × Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http://data.maizecode.org/maize/qtl/syn10/ ). Moreover, in this population combined with the IBM Syn4 RIL population, we detected 135 QTLs for flowering time and plant height traits across the two populations. Eighteen known functional genes and twenty-five candidate genes for flowering time and plant height trait were fine-mapped into a 2.21-4.96 Mb interval. Map expansion and segregation distortion were also analyzed, and evidence for inadvertent selection of early flowering time in the process of mapping population development was observed. Furthermore, an updated integrated map with 1,151,856 high-quality SNPs, 2,916 traditional markers and 6,618 bin markers was constructed. The data were deposited into the iPlant Discovery Environment (DE), which provides a fundamental resource of genetic data for the maize genetic research community. CONCLUSIONS Our findings provide basic essential genetic data for the maize genetic research community. An updated IBM Syn10 population and a reliable, verified high-quality SNP set between Mo17 and B73 will aid in future molecular breeding efforts.
Collapse
Affiliation(s)
- Hongjun Liu
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| | | | | | | | - Liya Wang
- Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853, Ithaca, NY, USA.
| | - Tao Zuo
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, 50011, USA.
| | - Cheng Qin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| | | | - Constantin Jansen
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
| | - Yaou Shen
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| | - Haijian Lin
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| | - Michael Lee
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory and USDA: USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, 14853, Ithaca, NY, USA.
| | - Zhiming Zhang
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| | | | - Guangtang Pan
- Maize Research Institute of Sichuan Agricultural University/Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, 611130, Chengdu, China.
| |
Collapse
|
21
|
Yang J, Jiang H, Yeh CT, Yu J, Jeddeloh JA, Nettleton D, Schnable PS. Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:587-96. [PMID: 26386250 DOI: 10.1111/tpj.13029] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/17/2015] [Accepted: 09/08/2015] [Indexed: 05/03/2023]
Abstract
Although approaches for performing genome-wide association studies (GWAS) are well developed, conventional GWAS requires high-density genotyping of large numbers of individuals from a diversity panel. Here we report a method for performing GWAS that does not require genotyping of large numbers of individuals. Instead XP-GWAS (extreme-phenotype GWAS) relies on genotyping pools of individuals from a diversity panel that have extreme phenotypes. This analysis measures allele frequencies in the extreme pools, enabling discovery of associations between genetic variants and traits of interest. This method was evaluated in maize (Zea mays) using the well-characterized kernel row number trait, which was selected to enable comparisons between the results of XP-GWAS and conventional GWAS. An exome-sequencing strategy was used to focus sequencing resources on genes and their flanking regions. A total of 0.94 million variants were identified and served as evaluation markers; comparisons among pools showed that 145 of these variants were statistically associated with the kernel row number phenotype. These trait-associated variants were significantly enriched in regions identified by conventional GWAS. XP-GWAS was able to resolve several linked QTL and detect trait-associated variants within a single gene under a QTL peak. XP-GWAS is expected to be particularly valuable for detecting genes or alleles responsible for quantitative variation in species for which extensive genotyping resources are not available, such as wild progenitors of crops, orphan crops, and other poorly characterized species such as those of ecological interest.
Collapse
Affiliation(s)
- Jinliang Yang
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Haiying Jiang
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Cheng-Ting Yeh
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | | | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Center for Plant Genomics, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
22
|
Lee DH, Kao YH, Ku JC, Lin CY, Meeley R, Jan YS, Wang CJR. The Axial Element Protein DESYNAPTIC2 Mediates Meiotic Double-Strand Break Formation and Synaptonemal Complex Assembly in Maize. THE PLANT CELL 2015; 27:2516-29. [PMID: 26296964 PMCID: PMC4815100 DOI: 10.1105/tpc.15.00434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/14/2015] [Accepted: 07/29/2015] [Indexed: 05/18/2023]
Abstract
During meiosis, homologous chromosomes pair and recombine via repair of programmed DNA double-strand breaks (DSBs). DSBs are formed in the context of chromatin loops, which are anchored to the proteinaceous axial element (AE). The AE later serves as a framework to assemble the synaptonemal complex (SC) that provides a transient but tight connection between homologous chromosomes. Here, we showed that DESYNAPTIC2 (DSY2), a coiled-coil protein, mediates DSB formation and is directly involved in SC assembly in maize (Zea mays). The dsy2 mutant exhibits homologous pairing defects, leading to sterility. Analyses revealed that DSB formation and the number of RADIATION SENSITIVE51 (RAD51) foci are largely reduced, and synapsis is completely abolished in dsy2 meiocytes. Super-resolution structured illumination microscopy showed that DSY2 is located on the AE and forms a distinct alternating pattern with the HORMA-domain protein ASYNAPTIC1 (ASY1). In the dsy2 mutant, localization of ASY1 is affected, and loading of the central element ZIPPER1 (ZYP1) is disrupted. Yeast two-hybrid and bimolecular fluorescence complementation experiments further demonstrated that ZYP1 interacts with DSY2 but does not interact with ASY1. Therefore, DSY2, an AE protein, not only mediates DSB formation but also bridges the AE and central element of SC during meiosis.
Collapse
Affiliation(s)
- Ding Hua Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan National Chung-Hsing University, Taichung 40227, Taiwan Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Yu-Hsin Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jia-Chi Ku
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chien-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Robert Meeley
- Crop Genetics Research, Pioneer Hi-Bred-A DuPont Business, Johnston, Iowa 50131
| | - Ya-Shiun Jan
- Potzu Branch Station, Tainan District Agricultural Research and Extension Station, Chiayi 61359, Taiwan
| | - Chung-Ju Rachel Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan National Chung-Hsing University, Taichung 40227, Taiwan Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| |
Collapse
|
23
|
Yi G, Neelakandan AK, Gontarek BC, Vollbrecht E, Becraft PW. The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation. PLANT PHYSIOLOGY 2015; 167:443-56. [PMID: 25552497 PMCID: PMC4326753 DOI: 10.1104/pp.114.251413] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/30/2014] [Indexed: 05/18/2023]
Abstract
The aleurone is the outermost layer of cereal endosperm and functions to digest storage products accumulated in starchy endosperm cells as well as to confer important dietary health benefits. Whereas normal maize (Zea mays [Zm]) has a single aleurone layer, naked endosperm (nkd) mutants produce multiple outer cell layers of partially differentiated cells that show sporadic expression of aleurone identity markers such as a viviparous1 promoter-β-glucuronidase transgene. The 15:1 F2 segregation ratio suggested that two recessive genes were involved, and map-based cloning identified two homologous genes in duplicated regions of the genome. The nkd1 and nkd2 genes encode the INDETERMINATE1 domain (IDD) containing transcription factors ZmIDDveg9 and ZmIDD9 on chromosomes 2 and 10, respectively. Independent mutant alleles of nkd1 and nkd2, as well as nkd2-RNA interference lines in which both nkd genes were knocked down, also showed the nkd mutant phenotype, confirming the gene identities. In wild-type kernels, the nkd transcripts were most abundant around 11 to 16 d after pollination. The NKD proteins have putative nuclear localization signals, and green fluorescent protein fusion proteins showed nuclear localization. The mutant phenotype and gene identities suggest that NKD controls a gene regulatory network involved in aleurone cell fate specification and cell differentiation.
Collapse
Affiliation(s)
- Gibum Yi
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Anjanasree K Neelakandan
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Bryan C Gontarek
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Erik Vollbrecht
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| | - Philip W Becraft
- Genetics, Development, and Cell Biology Department (G.Y., A.K.N., B.C.G., E.V., P.W.B.), Interdepartmental Plant Biology Program (G.Y., B.C.G., E.V., P.W.B.), and Agronomy Department (P.W.B.), Iowa State University, Ames, Iowa 50011
| |
Collapse
|
24
|
Gallavotti A, Whipple CJ. Positional cloning in maize (Zea mays subsp. mays, Poaceae). APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400092. [PMID: 25606355 PMCID: PMC4298233 DOI: 10.3732/apps.1400092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/11/2014] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Positional (or map-based) cloning is a common approach to identify the molecular lesions causing mutant phenotypes. Despite its large and complex genome, positional cloning has been recently shown to be feasible in maize, opening up a diverse collection of mutants to molecular characterization. • METHODS AND RESULTS Here we outline a general protocol for positional cloning in maize. While the general strategy is similar to that used in other plant species, we focus on the unique resources and approaches that should be considered when applied to maize mutants. • CONCLUSIONS Positional cloning approaches are appropriate for maize mutants and quantitative traits, opening up to molecular characterization the large array of genetic diversity in this agronomically important species. The cloning approach described should be broadly applicable to other species as more plant genomes become available.
Collapse
Affiliation(s)
- Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020 USA
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901 USA
| | - Clinton J. Whipple
- Department of Biology, Brigham Young University, Provo, Utah 84602 USA
- Author for correspondence:
| |
Collapse
|
25
|
Nestler J, Liu S, Wen TJ, Paschold A, Marcon C, Tang HM, Li D, Li L, Meeley RB, Sakai H, Bruce W, Schnable PS, Hochholdinger F. Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:729-40. [PMID: 24902980 DOI: 10.1111/tpj.12578] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 05/19/2023]
Abstract
Root hairs are instrumental for nutrient uptake in monocot cereals. The maize (Zea mays L.) roothairless5 (rth5) mutant displays defects in root hair initiation and elongation manifested by a reduced density and length of root hairs. Map-based cloning revealed that the rth5 gene encodes a monocot-specific NADPH oxidase. RNA-Seq, in situ hybridization and qRT-PCR experiments demonstrated that the rth5 gene displays preferential expression in root hairs but also accumulates to low levels in other tissues. Immunolocalization detected RTH5 proteins in the epidermis of the elongation and differentiation zone of primary roots. Because superoxide and hydrogen peroxide levels are reduced in the tips of growing rth5 mutant root hairs as compared with wild-type, and Reactive oxygen species (ROS) is known to be involved in tip growth, we hypothesize that the RTH5 protein is responsible for establishing the high levels of ROS in the tips of growing root hairs required for elongation. Consistent with this hypothesis, a comparative RNA-Seq analysis of 6-day-old rth5 versus wild-type primary roots revealed significant over-representation of only two gene ontology (GO) classes related to the biological functions (i.e. oxidation/reduction and carbohydrate metabolism) among 893 differentially expressed genes (FDR <5%). Within these two classes the subgroups 'response to oxidative stress' and 'cellulose biosynthesis' were most prominently represented.
Collapse
Affiliation(s)
- Josefine Nestler
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
Collapse
Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| |
Collapse
|
27
|
Durbak AR, Phillips KA, Pike S, O'Neill MA, Mares J, Gallavotti A, Malcomber ST, Gassmann W, McSteen P. Transport of boron by the tassel-less1 aquaporin is critical for vegetative and reproductive development in maize. THE PLANT CELL 2014; 26:2978-95. [PMID: 25035406 PMCID: PMC4145126 DOI: 10.1105/tpc.114.125898] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/23/2014] [Indexed: 05/18/2023]
Abstract
The element boron (B) is an essential plant micronutrient, and B deficiency results in significant crop losses worldwide. The maize (Zea mays) tassel-less1 (tls1) mutant has defects in vegetative and inflorescence development, comparable to the effects of B deficiency. Positional cloning revealed that tls1 encodes a protein in the aquaporin family co-orthologous to known B channel proteins in other species. Transport assays show that the TLS1 protein facilitates the movement of B and water into Xenopus laevis oocytes. B content is reduced in tls1 mutants, and application of B rescues the mutant phenotype, indicating that the TLS1 protein facilitates the movement of B in planta. B is required to cross-link the pectic polysaccharide rhamnogalacturonan II (RG-II) in the cell wall, and the percentage of RG-II dimers is reduced in tls1 inflorescences, indicating that the defects may result from altered cell wall properties. Plants heterozygous for both tls1 and rotten ear (rte), the proposed B efflux transporter, exhibit a dosage-dependent defect in inflorescence development under B-limited conditions, indicating that both TLS1 and RTE function in the same biological processes. Together, our data provide evidence that TLS1 is a B transport facilitator in maize, highlighting the importance of B homeostasis in meristem function.
Collapse
Affiliation(s)
- Amanda R Durbak
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Kimberly A Phillips
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sharon Pike
- Division of Plant Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Malcolm A O'Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jonathan Mares
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Simon T Malcomber
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Walter Gassmann
- Division of Plant Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| |
Collapse
|
28
|
Chatterjee M, Tabi Z, Galli M, Malcomber S, Buck A, Muszynski M, Gallavotti A. The boron efflux transporter ROTTEN EAR is required for maize inflorescence development and fertility. THE PLANT CELL 2014; 26:2962-77. [PMID: 25035400 PMCID: PMC4145125 DOI: 10.1105/tpc.114.125963] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/02/2014] [Accepted: 06/23/2014] [Indexed: 05/18/2023]
Abstract
Although boron has a relatively low natural abundance, it is an essential plant micronutrient. Boron deficiencies cause major crop losses in several areas of the world, affecting reproduction and yield in diverse plant species. Despite the importance of boron in crop productivity, surprisingly little is known about its effects on developing reproductive organs. We isolated a maize (Zea mays) mutant, called rotten ear (rte), that shows distinct defects in vegetative and reproductive development, eventually causing widespread sterility in its inflorescences, the tassel and the ear. Positional cloning revealed that rte encodes a membrane-localized boron efflux transporter, co-orthologous to the Arabidopsis thaliana BOR1 protein. Depending on the availability of boron in the soil, rte plants show a wide range of phenotypic defects that can be fully rescued by supplementing the soil with exogenous boric acid, indicating that rte is crucial for boron transport into aerial tissues. rte is expressed in cells surrounding the xylem in both vegetative and reproductive tissues and is required for meristem activity and organ development. We show that low boron supply to the inflorescences results in widespread defects in cell and cell wall integrity, highlighting the structural importance of boron in the formation of fully fertile reproductive organs.
Collapse
Affiliation(s)
- Mithu Chatterjee
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Zara Tabi
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116
| | - Mary Galli
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854-8020
| | - Simon Malcomber
- Department of Biological Sciences, California State University Long Beach, Long Beach, California 90840 Division of Environmental Biology, National Science Foundation, Arlington, Virginia 22230
| | - Amy Buck
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116
| | - Michael Muszynski
- Department of Genetics, Development, and Cell Biology, Iowa State University, Iowa 50011-2156
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, New Jersey 08854-8020 Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901
| |
Collapse
|
29
|
Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track. G3-GENES GENOMES GENETICS 2014; 4:1143-5. [PMID: 24747759 PMCID: PMC4065257 DOI: 10.1534/g3.114.010454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion–deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize.
Collapse
|
30
|
Association of C(-106)T Polymorphism in Aldose Reductase Gene with Diabetic Retinopathy in Chinese Patients with Type 2 Diabetes Mellitus. ACTA ACUST UNITED AC 2014; 29:1-6. [DOI: 10.1016/s1001-9294(14)60016-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
31
|
Garcia AAF, Mollinari M, Marconi TG, Serang OR, Silva RR, Vieira MLC, Vicentini R, Costa EA, Mancini MC, Garcia MOS, Pastina MM, Gazaffi R, Martins ERF, Dahmer N, Sforça DA, Silva CBC, Bundock P, Henry RJ, Souza GM, van Sluys MA, Landell MGA, Carneiro MS, Vincentz MAG, Pinto LR, Vencovsky R, Souza AP. SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Sci Rep 2013; 3:3399. [PMID: 24292365 PMCID: PMC3844970 DOI: 10.1038/srep03399] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 11/15/2013] [Indexed: 12/12/2022] Open
Abstract
Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.
Collapse
Affiliation(s)
- Antonio A F Garcia
- 1] Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" Universidade de São Paulo, Brazil [2]
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Meng Q, Xiong Y, Lan R, Ye C, Wang T, Qi T, Wang Y, Wang H, Bai X, Bai X, Ji S, Jin D, Yuan X, Zhao A, Sun H, Jing H, Xu J. SNP genotyping of enterohemorrhagic Escherichia coli O157:H7 isolates from China and genomic identity of the 1999 Xuzhou outbreak. INFECTION GENETICS AND EVOLUTION 2013; 16:275-81. [DOI: 10.1016/j.meegid.2013.02.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 02/19/2013] [Accepted: 02/22/2013] [Indexed: 11/16/2022]
|
33
|
Pérez-de-Castro AM, Vilanova S, Cañizares J, Pascual L, Blanca JM, Díez MJ, Prohens J, Picó B. Application of genomic tools in plant breeding. Curr Genomics 2012; 13:179-95. [PMID: 23115520 PMCID: PMC3382273 DOI: 10.2174/138920212800543084] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/16/2011] [Accepted: 10/11/2011] [Indexed: 02/08/2023] Open
Abstract
Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.
Collapse
Affiliation(s)
- A M Pérez-de-Castro
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Zhang X, Facette M, Humphries JA, Shen Z, Park Y, Sutimantanapi D, Sylvester AW, Briggs SP, Smith LG. Identification of PAN2 by quantitative proteomics as a leucine-rich repeat-receptor-like kinase acting upstream of PAN1 to polarize cell division in maize. THE PLANT CELL 2012; 24:4577-89. [PMID: 23175742 PMCID: PMC3531853 DOI: 10.1105/tpc.112.104125] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/04/2012] [Accepted: 10/30/2012] [Indexed: 05/03/2023]
Abstract
Mechanisms governing the polarization of plant cell division are poorly understood. Previously, we identified pangloss1 (PAN1) as a leucine-rich repeat-receptor-like kinase (LRR-RLK) that promotes the polarization of subsidiary mother cell (SMC) divisions toward the adjacent guard mother cell (GMC) during stomatal development in maize (Zea mays). Here, we identify pangloss2 (PAN2) as a second LRR-RLK promoting SMC polarization. Quantitative proteomic analysis identified a PAN2 candidate by its depletion from membranes of pan2 single and pan1;pan2 double mutants. Genetic mapping and sequencing of mutant alleles confirmed the identity of this protein as PAN2. Like PAN1, PAN2 has a catalytically inactive kinase domain and accumulates in SMCs at sites of GMC contact before nuclear polarization. The timing of polarized PAN1 and PAN2 localization is very similar, but PAN2 acts upstream because it is required for polarized accumulation of PAN1 but is independent of PAN1 for its own localization. We find no evidence that PAN2 recruits PAN1 to the GMC contact site via a direct or indirect physical interaction, but PAN2 interacts with itself. Together, these results place PAN2 at the top of a cascade of events promoting the polarization of SMC divisions, potentially functioning to perceive or amplify GMC-derived polarizing cues.
Collapse
Affiliation(s)
- Xiaoguo Zhang
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Michelle Facette
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - John A. Humphries
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Yeri Park
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Dena Sutimantanapi
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Anne W. Sylvester
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071
| | - Steven P. Briggs
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| | - Laurie G. Smith
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, California 92093
| |
Collapse
|
35
|
Abstract
Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been previously identified. Because of the digital nature of next-generation sequencing (NGS) data, it is possible to conduct de novo SNP discovery and quantitatively genotype BSA samples by analyzing the same RNA-Seq data using an empirical Bayesian approach. In addition, analysis of the RNA-Seq data provides information on the effects of the mutant on global patterns of gene expression at no extra cost. In combination these results greatly simplify gene cloning experiments. To demonstrate the utility of this strategy BSR-Seq was used to clone the glossy3 (gl3) gene of maize. Mutants of the glossy loci exhibit altered accumulation of epicuticular waxes on juvenile leaves. By subjecting the reference allele of gl3 to BSR-Seq, we were able to map the gl3 locus to an ≈ 2 Mb interval. The single gene located in the ≈ 2 Mb mapping interval whose expression was down-regulated in the mutant pool was subsequently demonstrated to be the gl3 gene via the analysis of multiple independent transposon induced mutant alleles. The gl3 gene encodes a putative myb transcription factor, which directly or indirectly affects the expression of a number of genes involved in the biosynthesis of very-long-chain fatty acids.
Collapse
|
36
|
Gao Q, Yue G, Li W, Wang J, Xu J, Yin Y. Recent progress using high-throughput sequencing technologies in plant molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:215-27. [PMID: 22409591 DOI: 10.1111/j.1744-7909.2012.01115.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
High-throughput sequencing is a revolutionary technological innovation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi-faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.
Collapse
Affiliation(s)
- Qiang Gao
- Beijing Genomics Institute-Shenzhen, Shenzhen 518083, China
| | | | | | | | | | | |
Collapse
|
37
|
Trick M, Adamski NM, Mugford SG, Jiang CC, Febrer M, Uauy C. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC PLANT BIOLOGY 2012; 12:14. [PMID: 22280551 PMCID: PMC3296661 DOI: 10.1186/1471-2229-12-14] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/26/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) technologies are providing new ways to accelerate fine-mapping and gene isolation in many species. To date, the majority of these efforts have focused on diploid organisms with readily available whole genome sequence information. In this study, as a proof of concept, we tested the use of NGS for SNP discovery in tetraploid wheat lines differing for the previously cloned grain protein content (GPC) gene GPC-B1. Bulked segregant analysis (BSA) was used to define a subset of putative SNPs within the candidate gene region, which were then used to fine-map GPC-B1. RESULTS We used Illumina paired end technology to sequence mRNA (RNAseq) from near isogenic lines differing across a ~30-cM interval including the GPC-B1 locus. After discriminating for SNPs between the two homoeologous wheat genomes and additional quality filtering, we identified inter-varietal SNPs in wheat unigenes between the parental lines. The relative frequency of these SNPs was examined by RNAseq in two bulked samples made up of homozygous recombinant lines differing for their GPC phenotype. SNPs that were enriched at least 3-fold in the corresponding pool (6.5% of all SNPs) were further evaluated. Marker assays were designed for a subset of the enriched SNPs and mapped using DNA from individuals of each bulk. Thirty nine new SNP markers, corresponding to 67% of the validated SNPs, mapped across a 12.2-cM interval including GPC-B1. This translated to 1 SNP marker per 0.31 cM defining the GPC-B1 gene to within 13-18 genes in syntenic cereal genomes and to a 0.4 cM interval in wheat. CONCLUSIONS This study exemplifies the use of RNAseq for SNP discovery in polyploid species and supports the use of BSA as an effective way to target SNPs to specific genetic intervals to fine-map genes in unsequenced genomes.
Collapse
Affiliation(s)
- Martin Trick
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | | | - Sarah G Mugford
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Cong-Cong Jiang
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Melanie Febrer
- The Genome Analysis Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge CB3 0LE, UK
| |
Collapse
|
38
|
Makarevitch I, Thompson A, Muehlbauer GJ, Springer NM. Brd1 gene in maize encodes a brassinosteroid C-6 oxidase. PLoS One 2012; 7:e30798. [PMID: 22292043 PMCID: PMC3266906 DOI: 10.1371/journal.pone.0030798] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/29/2011] [Indexed: 11/18/2022] Open
Abstract
The role of brassinosteroids in plant growth and development has been well-characterized in a number of plant species. However, very little is known about the role of brassinosteroids in maize. Map-based cloning of a severe dwarf mutant in maize revealed a nonsense mutation in an ortholog of a brassinosteroid C-6 oxidase, termed brd1, the gene encoding the enzyme that catalyzes the final steps of brassinosteroid synthesis. Homozygous brd1–m1 maize plants have essentially no internode elongation and exhibit no etiolation response when germinated in the dark. These phenotypes could be rescued by exogenous application of brassinolide, confirming the molecular defect in the maize brd1-m1 mutant. The brd1-m1 mutant plants also display alterations in leaf and floral morphology. The meristem is not altered in size but there is evidence for differences in the cellular structure of several tissues. The isolation of a maize mutant defective in brassinosteroid synthesis will provide opportunities for the analysis of the role of brassinosteroids in this important crop system.
Collapse
Affiliation(s)
- Irina Makarevitch
- Department of Biology, Hamline University, Saint Paul, Minnesota, United States of America.
| | | | | | | |
Collapse
|
39
|
Makarevitch I, Kralich E. Mapping maize genes: a series of research-based laboratory exercises. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 39:375-383. [PMID: 21948509 DOI: 10.1002/bmb.20524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Open-ended, inquiry-based multiweek laboratory exercises are the key elements to increasing students' understanding and retention of the major biological concepts. Including original research into undergraduate teaching laboratories has also been shown to motivate students and improve their learning. Here, we present a series of original laboratory exercises on fine mapping novel maize mutations producing interesting phenotypes. In this 4-week lab series, students get involved in the whole process of identifying novel genes controlling specific phenotypes, from phenotype characterization and choosing appropriate molecular markers to calculating the genetic distance between the mutation and the marker and finding possible candidate genes using a complete genome sequence. We chose to use maize mutant lines produced by TILLING project. These lines have been partially mapped to a chromosomal bin by a high-throughput bulk segregant analysis; however, the exact map positions for these mutations have never been determined. Mapping these novel maize mutations provides students with the opportunity to conduct original research as a part of their classroom experience and to contribute to the field of maize genetics. The laboratory series was well received by the students, and the assessment results demonstrated an improvement of student learning of gene mapping, molecular marker analysis, and positional cloning concepts.
Collapse
Affiliation(s)
- Irina Makarevitch
- Biology Department, Hamline University, Saint Paul, Minnesota 55104, USA.
| | | |
Collapse
|
40
|
Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti MC, Massi A, van der Vossen EAG, Tuberosa R. High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:555-69. [PMID: 21611761 DOI: 10.1007/s00122-011-1607-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Accepted: 04/26/2011] [Indexed: 05/07/2023]
Abstract
We describe the application of complexity reduction of polymorphic sequences (CRoPS(®)) technology for the discovery of SNP markers in tetraploid durum wheat (Triticum durum Desf.). A next-generation sequencing experiment was carried out on reduced representation libraries obtained from four durum cultivars. SNP validation and minor allele frequency (MAF) estimate were carried out on a panel of 12 cultivars, and the feasibility of genotyping these SNPs in segregating populations was tested using the Illumina Golden Gate (GG) technology. A total of 2,659 SNPs were identified on 1,206 consensus sequences. Among the 768 SNPs that were chosen irrespective of their genomic repetitiveness level and assayed on the Illumina BeadExpress genotyping system, 275 (35.8%) SNPs matched the expected genotypes observed in the SNP discovery phase. MAF data indicated that the overall SNP informativeness was high: a total of 196 (71.3%) SNPs had MAF >0.2, of which 76 (27.6%) showed MAF >0.4. Of these SNPs, 157 were mapped in one of two mapping populations (Meridiano × Claudio and Colosseo × Lloyd) and integrated into a common genetic map. Despite the relatively low genotyping efficiency of the GG assay, the validated CRoPS-derived SNPs showed valuable features for genomics and breeding applications such as a uniform distribution across the wheat genome, a prevailing single-locus codominant nature and a high polymorphism. Here, we report a new set of 275 highly robust genome-wide Triticum SNPs that are readily available for breeding purposes.
Collapse
Affiliation(s)
- Daniele Trebbi
- Keygene NV, Applied Research, Agro Business Park 90, 6708, PW, Wageningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Eichten SR, Foerster JM, de Leon N, Kai Y, Yeh CT, Liu S, Jeddeloh JA, Schnable PS, Kaeppler SM, Springer NM. B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize. PLANT PHYSIOLOGY 2011; 156:1679-90. [PMID: 21705654 PMCID: PMC3149956 DOI: 10.1104/pp.111.174748] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recombinant inbred lines developed from the maize (Zea mays ssp. mays) inbreds B73 and Mo17 have been widely used to discover quantitative trait loci controlling a wide variety of phenotypic traits and as a resource to produce high-resolution genetic maps. These two parents were used to produce a set of near-isogenic lines (NILs) with small regions of introgression into both backgrounds. A novel array-based genotyping platform was used to score genotypes of over 7,000 loci in 100 NILs with B73 as the recurrent parent and 50 NILs with Mo17 as the recurrent parent. This population contains introgressions that cover the majority of the maize genome. The set of NILs displayed an excess of residual heterozygosity relative to the amount expected based on their pedigrees, and this excess residual heterozygosity is enriched in the low-recombination regions near the centromeres. The genotyping platform provided the ability to survey copy number variants that exist in more copies in Mo17 than in B73. The majority of these Mo17-specific duplications are located in unlinked positions throughout the genome. The utility of this population for the discovery and validation of quantitative trait loci was assessed through analysis of plant height variation.
Collapse
|
42
|
Yi G, Lauter AM, Scott MP, Becraft PW. The thick aleurone1 mutant defines a negative regulation of maize aleurone cell fate that functions downstream of defective kernel1. PLANT PHYSIOLOGY 2011; 156:1826-36. [PMID: 21617032 PMCID: PMC3149929 DOI: 10.1104/pp.111.177725] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 05/25/2011] [Indexed: 05/18/2023]
Abstract
The maize (Zea mays) aleurone layer occupies the single outermost layer of the endosperm. The defective kernel1 (dek1) gene is a central regulator required for aleurone cell fate specification. dek1 mutants have pleiotropic phenotypes including lack of aleurone cells, aborted embryos, carotenoid deficiency, and a soft, floury endosperm deficient in zeins. Here we describe the thick aleurone1 (thk1) mutant that defines a novel negative function in the regulation of aleurone differentiation. Mutants possess multiple layers of aleurone cells as well as aborted embryos. Clonal sectors of thk1 mutant tissue in otherwise normal endosperm showed localized expression of the phenotype with sharp boundaries, indicating a localized cellular function for the gene. Sectors in leaves showed expanded epidermal cell morphology but the mutant epidermis generally remained in a single cell layer. Double mutant analysis indicated that the thk1 mutant is epistatic to dek1 for several aspects of the pleiotropic dek1 phenotype. dek1 mutant endosperm that was mosaic for thk1 mutant sectors showed localized patches of multilayered aleurone. Localized sectors were surrounded by halos of carotenoid pigments and double mutant kernels had restored zein profiles. In sum, loss of thk1 function restored the ability of dek1 mutant endosperm to accumulate carotenoids and zeins and to differentiate aleurone. Therefore the thk1 mutation defines a negative regulator that functions downstream of dek1 in the signaling system that controls aleurone specification and other aspects of endosperm development. The thk1 mutation was found to be caused by a deletion of approximately 2 megabases.
Collapse
|
43
|
Li W, Zhang J, Mou Y, Geng J, McVetty PBE, Hu S, Li G. Integration of Solexa sequences on an ultradense genetic map in Brassica rapa L. BMC Genomics 2011; 12:249. [PMID: 21595929 PMCID: PMC3125265 DOI: 10.1186/1471-2164-12-249] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 05/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequence related amplified polymorphism (SRAP) is commonly used to construct high density genetic maps, map genes and QTL of important agronomic traits in crops and perform genetic diversity analysis without knowing sequence information. To combine next generation sequencing technology with SRAP, Illumina's Solexa sequencing was used to sequence tagged SRAP PCR products. RESULTS Three sets of SRAP primers and three sets of tagging primers were used in 77,568 SRAP PCR reactions and the same number of tagging PCR reactions respectively to produce a pooled sample for Illumina's Solexa sequencing. After sequencing, 1.28 GB of sequence with over 13 million paired-end sequences was obtained and used to match Solexa sequences with their corresponding SRAP markers and to integrate Solexa sequences on an ultradense genetic map. The ultradense genetic bin map with 465 bins was constructed using a recombinant inbred (RI) line mapping population in B. rapa. For this ultradense genetic bin map, 9,177 SRAP markers, 1,737 integrated unique Solexa paired-end sequences and 46 SSR markers representing 10,960 independent genetic loci were assembled and 141 unique Solexa paired-end sequences were matched with their corresponding SRAP markers. The genetic map in B. rapa was aligned with the previous ultradense genetic map in B. napus through common SRAP markers in these two species. Additionally, SSR markers were used to perform alignment of the current genetic map with other five genetic maps in B. rapa and B. napus. CONCLUSION We used SRAP to construct an ultradense genetic map with 10,960 independent genetic loci in B. rapa that is the most saturated genetic map ever constructed in this species. Using next generation sequencing, we integrated 1,878 Solexa sequences on the genetic map. These integrated sequences will be used to assemble the scaffolds in the B. rapa genome. Additionally, this genetic map may be used for gene cloning and marker development in B. rapa and B. napus.
Collapse
Affiliation(s)
- Wei Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | | | | | | | | | | | | |
Collapse
|
44
|
Bulk segregant analysis followed by high-throughput sequencing reveals the Neurospora cell cycle gene, ndc-1, to be allelic with the gene for ornithine decarboxylase, spe-1. EUKARYOTIC CELL 2011; 10:724-33. [PMID: 21515825 DOI: 10.1128/ec.00016-11] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
With the advent of high-throughput DNA sequencing, it is now straightforward and inexpensive to generate high-density small nucleotide polymorphism (SNP) maps. Here we combined high-throughput sequencing with bulk segregant analysis to expedite mutation mapping. The general map location of a mutation can be identified by a single backcross to a strain enriched in SNPs compared to a standard wild-type strain. Bulk segregant analysis simultaneously increases the likelihood of determining the precise nature of the mutation. We present here a high-density SNP map between Neurospora crassa Mauriceville-1-c (FGSC2225) and OR74A (FGSC2489), the strains most typically used by Neurospora researchers to carry out mapping crosses. We further have demonstrated the utility of the Mauriceville sequence and our approach by mapping the mutation responsible for the only existing temperature-sensitive (ts) cell cycle mutation in Neurospora, nuclear division cycle-1 (ndc-1). The single T-to-C point mutation maps to the gene encoding ornithine decarboxylase (ODC), spe-1 (NCU01271), and changes a Phe to a Ser residue within a highly conserved motif next to the catalytic site of the enzyme. By growth on spermidine and complementation with a wild-type spe-1 gene, we showed that the defect in spe-1 is responsible for the ts ndc-1 mutation. Based on our results, we propose changing ndc-1 to spe-1(ndc), which reflects that this mutation results in an ODC with a specific nuclear division defect.
Collapse
|
45
|
Abstract
Single nucleotide polymorphisms (SNPs) are single base differences between haplotypes. SNPs are abundant in many species and valuable as markers for genetic map construction, modern molecular breeding programs, and quantitative genetic studies. SNPs are readily mined from genomic DNA or cDNA sequence obtained from individuals having two or more distinct genotypes. While automated Sanger sequencing has become less expensive over time, it is still costly to acquire deep Sanger sequence from several genotypes. "Next-generation" DNA sequencing technologies that utilize new chemistries and massively parallel approaches have enabled DNA sequences to be acquired at extremely high depths of coverage faster and for less cost than traditional sequencing. One such method is represented by the Roche/454 Life Sciences GS-FLX Titanium Series, which currently uses pyrosequencing to produce up to 400-600 million bases of DNA sequence/run (>1 million reads, ~400 bp/read). This chapter discusses the use of high-throughput pyrosequencing for SNP discovery by focusing on 454 sequencing of maize cDNA, the development of a computational pipeline for polymorphism detection, and the subsequent identification of over 7,000 putative SNPs between Mo17 and B73 maize. In addition, alternative alignment and polymorphism detection strategies that implement Illumina short reads, data processing and visualization tools, and reduced representation techniques that reduce the sequencing of repeat DNA, thus enabling efficient analysis of genome sequence, are discussed.
Collapse
Affiliation(s)
- W Brad Barbazuk
- Department of Biology and the Genetics Institute, University of Florida, Gainesville, FL, USA.
| | | |
Collapse
|
46
|
Delseny M, Han B, Hsing YI. High throughput DNA sequencing: The new sequencing revolution. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2010; 179:407-22. [PMID: 21802600 DOI: 10.1016/j.plantsci.2010.07.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2010] [Revised: 07/23/2010] [Accepted: 07/26/2010] [Indexed: 05/02/2023]
Abstract
Improvements in technology have rapidly changed the field of DNA sequencing. These improvements are boosted by bio-medical research. Plant science has benefited from this breakthrough, and a number of plant genomes are now available, new biological questions can be approached and new breeding strategies can be designed. The first part of this review aims to briefly describe the principles of the new sequencing methods, many of which are already used in plant laboratories. The second part summarizes the state of plant genome sequencing and illustrates the achievements in the last few years. Although already impressive, these results represent only the beginning of a new genomic era in plant science. Finally we describe some of the exciting discoveries in the structure and evolution of plant genomes made possible by genome sequencing in terms of biodiversity, genome expression and epigenetic regulations. All of these findings have already influenced plant breeding and biodiversity protection. Finally we discuss current trends, challenges and perspectives.
Collapse
Affiliation(s)
- Michel Delseny
- Laboratoire Génome et Développement des Plantes, UMR5096 CNRS-IRD-UP, University of Perpignan, 58 av. Paul Alduy, 66860 Perpignan, France.
| | | | | |
Collapse
|
47
|
Martin F, Dailey S, Settles AM. Distributed simple sequence repeat markers for efficient mapping from maize public mutagenesis populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:697-704. [PMID: 20401644 DOI: 10.1007/s00122-010-1341-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/03/2010] [Indexed: 05/29/2023]
Abstract
The genome sequence of the B73 maize inbred enables map-based cloning of genetic variants underlying phenotypes. In parallel to sequencing efforts, multiple public mutagenesis resources are being developed predominantly in the W22 and B73 inbreds. Efficient platforms to map mutants in these genetic backgrounds would aid molecular genetic analysis of the public resources. We screened 505 simple sequence repeat markers for polymorphisms between the B73, Mo17, and W22 inbreds. Using common thermocycling conditions, 47.1% of the markers showed co-dominant polymorphisms in at least one pair of inbreds. Based on these results, we identified 85 distributed markers for mapping in all three inbred pairs. For each inbred pair, the distributed set has 64-71 polymorphic markers with a mean distance of 27-29 cM between markers. The distributed markers give nearly complete coverage of the genetic map for each inbred pair. We demonstrate the utility of the marker set for efficient placement of mutants on the maize genetic map with an example mapping experiment of a seed mutant from the UniformMu mutagenesis resource. We conclude that these distributed molecular markers enable rapid mapping of phenotypic variants from public mutagenesis populations.
Collapse
Affiliation(s)
- Federico Martin
- Horticultural Sciences Department, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611-0690, USA
| | | | | |
Collapse
|
48
|
Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 2009; 5:e1000733. [PMID: 19936291 PMCID: PMC2774946 DOI: 10.1371/journal.pgen.1000733] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 10/19/2009] [Indexed: 11/19/2022] Open
Abstract
The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination. Genomic insertion sites of Mu transposons were amplified and sequenced via next generation technology, revealing more than 40,000 non-redundant Mu insertion sites that are non-uniformly distributed across the maize genome and within genes. Along chromosomes, frequencies of Mu transposon insertions are strongly correlated with recombination rates. Although both Mu and recombination occur preferentially in genes, gene density does not fully explain these patterns. Instead, the finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.
Collapse
Affiliation(s)
- Sanzhen Liu
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Cheng-Ting Yeh
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Tieming Ji
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Haiyan Wu
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
| | - Ho Man Tang
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Yan Fu
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Center for Carbon Capturing Crops, Iowa State University, Ames, Iowa, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Patrick S. Schnable
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
- Center for Carbon Capturing Crops, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|