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Xu G, Zhang X, Chen W, Zhang R, Li Z, Wen W, Warburton ML, Li J, Li H, Yang X. Population genomics of Zea species identifies selection signatures during maize domestication and adaptation. BMC PLANT BIOLOGY 2022; 22:72. [PMID: 35180846 PMCID: PMC8855575 DOI: 10.1186/s12870-022-03427-w] [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] [Received: 08/03/2021] [Accepted: 01/05/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Maize (Zea mays L. ssp. mays) was domesticated from teosinte (Zea mays ssp. parviglumis) about 9000 years ago in southwestern Mexico and adapted to a range of environments worldwide. Researchers have depicted the maize domestication and adaptation processes over the past two decades, but efforts have been limited either in sample size or genetic diversity. To better understand these processes, we conducted a genome-wide survey of 982 maize inbred lines and 190 teosinte accessions using over 40,000 single-nucleotide polymorphism markers. RESULTS Population structure, principal component analysis, and phylogenetic trees all confirmed the evolutionary relationship between maize and teosinte, and determined the evolutionary lineage of all species within teosinte. Shared haplotype analysis showed similar levels of ancestral alleles from Zea mays ssp. parviglumis and Zea mays ssp. mexicana in maize. Scans for selection signatures identified 394 domestication sweeps by comparing wild and cultivated maize and 360 adaptation sweeps by comparing tropical and temperate maize. Permutation tests revealed that the public association signals for flowering time were highly enriched in the domestication and adaptation sweeps. Genome-wide association study identified 125 loci significantly associated with flowering-time traits, ten of which identified candidate genes that have undergone selection during maize adaptation. CONCLUSIONS In this study, we characterized the history of maize domestication and adaptation at the population genomic level and identified hundreds of domestication and adaptation sweeps. This study extends the molecular mechanism of maize domestication and adaptation, and provides resources for basic research and genetic improvement in maize.
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Affiliation(s)
- Gen Xu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Wenkang Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Renyu Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhi Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Marilyn L Warburton
- United States of Department of Agriculture, Agricultural Research Service, Corn Host Plant Resistance Research Unit, Box 9555, Mississippi, MS, 39762, USA
| | - Jiansheng Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, MOA Key Laboratory of Maize Biology, China Agricultural University, Beijing, 100193, China.
- Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Song GQ, Han X. K-Domain Technology: Constitutive Expression of a Blueberry Keratin-Like Domain Mimics Expression of Multiple MADS-Box Genes in Enhancing Maize Grain Yield. FRONTIERS IN PLANT SCIENCE 2021; 12:664983. [PMID: 34025703 PMCID: PMC8137907 DOI: 10.3389/fpls.2021.664983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/15/2021] [Indexed: 06/02/2023]
Abstract
MADS-box genes are considered as the foundation of all agronomic traits because they play essential roles in almost every aspect of plant reproductive development. Keratin-like (K) domain is a conserved protein domain of tens of MIKC-type MADS-box genes in plants. K-domain technology constitutively expresses a K-domain to mimic expression of the K-domains of other MADS-box genes simultaneously and thus to generate new opportunities for yield enhancement, because the increased K-domains can likely prevent MADS-domain proteins from binding to target DNA. In this study, we evaluated utilizing the K-domain technology to increase maize yield. The K-domain of a blueberry's SUPPRESSOR of CONSTITUTIVE EXPRESSION OF CONSTANS 1 (VcSOC1K) has similarities to five MADS-box genes in maize. Transgenic maize plants expressing the VcSOC1K showed 13-100% of more grain per plant than the nontransgenic plants in all five experiments conducted under different experimental conditions. Transcriptome comparisons revealed 982 differentially expressed genes (DEGs) in the leaves from 83-day old plants, supporting that the K-domain technology were powerful and multiple functional. The results demonstrated that constitutive expression of the VcSOC1K was very effective to enhance maize grain production. With the potential of mimicking the K-domains of multiple MADS-box genes, the K-domain technology opens a new approach to increase crop yield.
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Anderson JA, Herman RA, Carlson A, Mathesius C, Maxwell C, Mirsky H, Roper J, Smith B, Walker C, Wu J. Hypothesis-based food, feed, and environmental safety assessment of GM crops: A case study using maize event DP-202216-6. GM CROPS & FOOD 2021; 12:282-291. [PMID: 33472515 PMCID: PMC7833765 DOI: 10.1080/21645698.2020.1869492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Event DP-2Ø2216-6 (referred to as DP202216 maize) was genetically modified to increase and extend the expression of the introduced zmm28 gene relative to endogenous zmm28 gene expression, resulting in plants with enhanced grain yield potential. The zmm28 gene expresses the ZMM28 protein, a MADS-box transcription factor. The safety assessment of DP202216 maize included an assessment of the potential hazard of the ZMM28 protein, as well as an assessment of potential unintended effects of the genetic insertion on agronomics, composition, and nutrition. The history of safe use (HOSU) of the ZMM28 protein was evaluated and a bioinformatics approach was used to compare the deduced amino acid sequence of the ZMM28 protein to databases of known allergens and toxins. Based on HOSU and the bioinformatics assessment, the ZMM28 protein was determined to be unlikely to be either allergenic or toxic to humans. The composition of DP202216 maize forage and grain was comparable to non-modified forage and grain, with no unintended effects on nutrition or food and feed safety. Additionally, feeding studies with broiler chickens and rats demonstrated a low likelihood of unintentional alterations in nutrition and low potential for adverse effects. Furthermore, the agronomics observed for DP202216 maize and non-modified maize were comparable, indicating that the likelihood of increased weediness or invasiveness of DP202216 maize in the environment is low. This comprehensive review serves as a reference for regulatory agencies and decision-makers in countries where authorization of DP202216 maize will be pursued, and for others interested in food, feed, and environmental safety.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jingrui Wu
- Corteva Agriscience™, Johnston, Iowa, USA
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4
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Crop reproductive meristems in the genomic era: a brief overview. Biochem Soc Trans 2020; 48:853-865. [PMID: 32573650 DOI: 10.1042/bst20190441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/15/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
Modulation of traits beneficial for cultivation and yield is one of the main goals of crop improvement. One of the targets for enhancing productivity is changing the architecture of inflorescences since in many species it determines fruit and seed yield. Inflorescence shape and organization is genetically established during the early stages of reproductive development and depends on the number, arrangement, activities, and duration of meristems during the reproductive phase of the plant life cycle. Despite the variety of inflorescence architectures observable in nature, many key aspects of inflorescence development are conserved among different species. For instance, the genetic network in charge of specifying the identity of the different reproductive meristems, which can be indeterminate or determinate, seems to be similar among distantly related species. The availability of a large number of published transcriptomic datasets for plants with different inflorescence architectures, allowed us to identify transcription factor gene families that are differentially expressed in determinate and indeterminate reproductive meristems. The data that we review here for Arabidopsis, rice, barley, wheat, and maize, particularly deepens our knowledge of their involvement in meristem identity specification.
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5
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Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie WZ, Cheng Y, Zhang Y, Liu K, Yang QY, Chen LL, Guo L. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. NATURE PLANTS 2020; 6:34-45. [PMID: 31932676 PMCID: PMC6965005 DOI: 10.1038/s41477-019-0577-7] [Citation(s) in RCA: 346] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/29/2019] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2-149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhilin Guan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jianlin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Chaocheng Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Zhiquan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Dongxu Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Bo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuanfang Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yuting Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China.
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, People's Republic of China.
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6
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Wu J, Lawit SJ, Weers B, Sun J, Mongar N, Van Hemert J, Melo R, Meng X, Rupe M, Clapp J, Haug Collet K, Trecker L, Roesler K, Peddicord L, Thomas J, Hunt J, Zhou W, Hou Z, Wimmer M, Jantes J, Mo H, Liu L, Wang Y, Walker C, Danilevskaya O, Lafitte RH, Schussler JR, Shen B, Habben JE. Overexpression of zmm28 increases maize grain yield in the field. Proc Natl Acad Sci U S A 2019; 116:23850-23858. [PMID: 31685622 PMCID: PMC6876154 DOI: 10.1073/pnas.1902593116] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Increasing maize grain yield has been a major focus of both plant breeding and genetic engineering to meet the global demand for food, feed, and industrial uses. We report that increasing and extending expression of a maize MADS-box transcription factor gene, zmm28, under the control of a moderate-constitutive maize promoter, results in maize plants with increased plant growth, photosynthesis capacity, and nitrogen utilization. Molecular and biochemical characterization of zmm28 transgenic plants demonstrated that their enhanced agronomic traits are associated with elevated plant carbon assimilation, nitrogen utilization, and plant growth. Overall, these positive attributes are associated with a significant increase in grain yield relative to wild-type controls that is consistent across years, environments, and elite germplasm backgrounds.
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Affiliation(s)
- Jingrui Wu
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Shai J Lawit
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Ben Weers
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Jindong Sun
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Nick Mongar
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - John Van Hemert
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Rosana Melo
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Xin Meng
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Mary Rupe
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Joshua Clapp
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | | | - Libby Trecker
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Keith Roesler
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | | | - Jill Thomas
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Joanne Hunt
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Wengang Zhou
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Zhenglin Hou
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Matthew Wimmer
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Justin Jantes
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Hua Mo
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Lu Liu
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Yiwei Wang
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | - Carl Walker
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | | | - Renee H Lafitte
- Research & Development, Corteva Agriscience, Johnston, IA 50131
| | | | - Bo Shen
- Research & Development, Corteva Agriscience, Johnston, IA 50131
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7
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Chen Q, Yang CJ, York AM, Xue W, Daskalska LL, DeValk CA, Krueger KW, Lawton SB, Spiegelberg BG, Schnell JM, Neumeyer MA, Perry JS, Peterson AC, Kim B, Bergstrom L, Yang L, Barber IC, Tian F, Doebley JF. TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize. Genetics 2019; 213:1065-1078. [PMID: 31481533 PMCID: PMC6827374 DOI: 10.1534/genetics.119.302594] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 08/30/2019] [Indexed: 12/21/2022] Open
Abstract
Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.
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Affiliation(s)
- Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Alessandra M York
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Wei Xue
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Lora L Daskalska
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Craig A DeValk
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Kyle W Krueger
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Samuel B Lawton
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | | | - Jack M Schnell
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Michael A Neumeyer
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Joseph S Perry
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Aria C Peterson
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Brandon Kim
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Laura Bergstrom
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Liyan Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
- School of Life Science, Shanxi Normal University, Linfen, Shanxi 041004, China
| | - Isaac C Barber
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Feng Tian
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - John F Doebley
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
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8
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Wills DM, Fang Z, York AM, Holland JB, Doebley JF. Defining the Role of the MADS-Box Gene, Zea Agamous-like1, a Target of Selection During Maize Domestication. J Hered 2019; 109:333-338. [PMID: 28992108 DOI: 10.1093/jhered/esx073] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 09/02/2017] [Indexed: 11/12/2022] Open
Abstract
Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time. To determine the trait(s) controlled by zagl1 that was (were) the target(s) of selection during maize domestication, we created a set of recombinant chromosome isogenic lines that differ for the maize versus teosinte alleles of zagl1 and which carry cross-overs between zagl1 and its neighbor genes. These lines were grown in a randomized trial and scored for flowering time and domestication related traits. The results indicated that the maize versus teosinte alleles of zagl1 affect flowering time as expected, as well as multiple traits related to ear size with the maize allele conferring larger ears with more kernels. Our results suggest that zagl1 may have been under selection during domestication to increase the size of the maize ear.
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Affiliation(s)
- David M Wills
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI.,USDA-ARS Plant Genetics Research Unit, Columbia, MO
| | - Zhou Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC.,Bayer Corporation, Morrisville, NC
| | - Alessandra M York
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI
| | - James B Holland
- USDA-ARS Plant Science Research Unit, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC
| | - John F Doebley
- Laboratory of Genetics, The University of Wisconsin-Madison, Madison, WI
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9
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Natural Variation and Domestication Selection of ZmPGP1 Affects Plant Architecture and Yield-Related Traits in Maize. Genes (Basel) 2019; 10:genes10090664. [PMID: 31480272 PMCID: PMC6770335 DOI: 10.3390/genes10090664] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
ZmPGP1, involved in the polar auxin transport, has been shown to be associated with plant height, leaf angle, yield traits, and root development in maize. To explore natural variation and domestication selection of ZmPGP1, we re-sequenced the ZmPGP1 gene in 349 inbred lines, 68 landraces, and 32 teosintes. Sequence polymorphisms, nucleotide diversity, and neutral tests revealed that ZmPGP1 might be selected during domestication and improvement processes. Marker–trait association analysis in inbred lines identified 11 variants significantly associated with 4 plant architecture and 5 ear traits. SNP1473 was the most significant variant for kernel length and ear grain weight. The frequency of an increased allele T was 40.6% in teosintes, and it was enriched to 60.3% and 89.1% during maize domestication and improvement. This result revealed that ZmPGP1 may be selected in the domestication and improvement process, and significant variants could be used to develop functional markers to improve plant architecture and ear traits in maize.
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10
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Anderson JA, Brustkern S, Cong B, Deege L, Delaney B, Hong B, Lawit S, Mathesius C, Schmidt J, Wu J, Zhang J, Zimmermann C. Evaluation of the History of Safe Use of the Maize ZMM28 Protein. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7466-7474. [PMID: 31184886 DOI: 10.1021/acs.jafc.9b00391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The ZMM28 protein encoded by the zmm28 gene is endogenous to maize. DP202216 maize was genetically modified to increase and extend expression of the zmm28 gene relative to native zmm28 gene expression, resulting in plants with enhanced grain yield potential. Evaluation of the history of safe use (HOSU) is one component of the safety assessment framework for a newly expressed protein in a GM crop. The deduced amino acid sequence of the introduced ZMM28 protein in DP202216 maize is identical to the ZMM28 protein in nonmodified conventional maize. The ZMM28 protein has also been found in selected varieties of sweet corn kernels, and closely related proteins are found in other commonly consumed food crops. Concentrations of the ZMM28 protein in event DP202216 maize, conventional maize, and sweet corn are reported. This information supports, in part, the evaluation of HOSU, which can be leveraged in the safety assessment of the ZMM28 protein. Additional studies will be considered in the food and feed safety assessment of the DP202216 maize event.
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Affiliation(s)
- Jennifer A Anderson
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Sarah Brustkern
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bin Cong
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Lora Deege
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bryan Delaney
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Bonnie Hong
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Shai Lawit
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Carey Mathesius
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Jean Schmidt
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Jingrui Wu
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - John Zhang
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
| | - Cindi Zimmermann
- Corteva Agriscience , Agriculture Division of DowDuPont , Johnston , Iowa 50131 , United States
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Anderson JA, Hong B, Moellring E, TeRonde S, Walker C, Wang Y, Maxwell C. Composition of forage and grain from genetically modified DP202216 maize is equivalent to non-modified conventional maize ( Zea mays L.). GM CROPS & FOOD 2019; 10:77-89. [PMID: 31094289 PMCID: PMC6615539 DOI: 10.1080/21645698.2019.1609849] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DP202216 maize was genetically modified to increase and extend the expression of the zmm28 gene relative to native zmm28 gene expression, resulting in plants with enhanced grain yield potential. Standard nutritional and compositional parameters for maize grain and forage (e.g., proximates, fiber, minerals, amino acids, fatty acids, vitamins, anti-nutrients, secondary metabolites) from DP202216 maize were compared to grain and forage from non-modified near-isoline maize (control). Three amino acids (glycine, methionine, and serine) and two vitamins (vitamin B1 and vitamin B3) were statistically different between DP202216 and control maize grain but were not statistically different when adjusted using the false discovery rate method. These analyte values also fell within the ranges of natural variation of non-modified commercial maize varieties supporting that statistical differences were not biologically relevant. The composition of grain and forage from DP202216 maize is comparable to grain and forage from non-modified maize with a history of safe use.
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Affiliation(s)
- Jennifer A Anderson
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Bonnie Hong
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Emily Moellring
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Sarah TeRonde
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Carl Walker
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Yiwei Wang
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
| | - Carl Maxwell
- a Corteva Agriscience™ , Agriculture Division of DowDuPont , Johnston , IA USA
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Shen G, Yang CH, Shen CY, Huang KS. Origination and selection of ABCDE and AGL6 subfamily MADS-box genes in gymnosperms and angiosperms. Biol Res 2019; 52:25. [PMID: 31018872 PMCID: PMC6480507 DOI: 10.1186/s40659-019-0233-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The morphological diversity of flower organs is closely related to functional divergence within the MADS-box gene family. Bryophytes and seedless vascular plants have MADS-box genes but do not have ABCDE or AGAMOUS-LIKE6 (AGL6) genes. ABCDE and AGL6 genes belong to the subgroup of MADS-box genes. Previous works suggest that the B gene was the first ABCDE and AGL6 genes to emerge in plant but there are no mentions about the probable origin time of ACDE and AGL6 genes. Here, we collected ABCDE and AGL6 gene 381 protein sequences and 361 coding sequences from gymnosperms and angiosperms and reconstructed a complete Bayesian phylogeny of these genes. In this study, we want to clarify the probable origin time of ABCDE and AGL6 genes is a great help for understanding the role of the formation of the flower, which can decipher the forming order of MADS-box genes in the future. RESULTS These genes appeared to have been under purifying selection and their evolutionary rates are not significantly different from each other. Using the Bayesian evolutionary analysis by sampling trees (BEAST) tool, we estimated that: the mutation rate of the ABCDE and AGL6 genes was 2.617 × 10-3 substitutions/site/million years, and that B genes originated 339 million years ago (MYA), CD genes originated 322 MYA, and A genes shared the most recent common ancestor with E/AGL6 296 MYA, respectively. CONCLUSIONS The phylogeny of ABCDE and AGL6 genes subfamilies differed. The APETALA1 (AP1 or A gene) subfamily clustered into one group. The APETALA3/PISTILLATA (AP3/PI or B genes) subfamily clustered into two groups: the AP3 and PI clades. The AGAMOUS/SHATTERPROOF/SEEDSTICK (AG/SHP/STK or CD genes) subfamily clustered into a single group. The SEPALLATA (SEP or E gene) subfamily in angiosperms clustered into two groups: the SEP1/2/4 and SEP3 clades. The AGL6 subfamily clustered into a single group. Moreover, ABCDE and AGL6 genes appeared in the following order: AP3/PI → AG/SHP/STK → AGL6/SEP/AP1. In this study, we collected candidate sequences from gymnosperms and angiosperms. This study highlights important events in the evolutionary history of the ABCDE and AGL6 gene families and clarifies their evolutionary path.
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Affiliation(s)
- Gangxu Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Chih-Hui Yang
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Chi-Yen Shen
- Department of Electrical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Keng-Shiang Huang
- The School of Chinese Medicine for Post-Baccalaureate, I-Shou University, Kaohsiung, Taiwan
- College of Medicine, I-Shou University, Kaohsiung, Taiwan
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13
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Cao Y, Liang X, Yin P, Zhang M, Jiang C. A domestication-associated reduction in K + -preferring HKT transporter activity underlies maize shoot K + accumulation and salt tolerance. THE NEW PHYTOLOGIST 2019; 222:301-317. [PMID: 30461018 DOI: 10.1111/nph.15605] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/10/2018] [Indexed: 05/26/2023]
Abstract
Maize was domesticated from Balsas teosinte c. 10 000 yr ago. Previous studies have suggested that increased tolerance to environmental stress occurred during maize domestication. However, the underlying genetic basis remains largely unknown. We used a maize (W22)-teosinte recombinant inbred line (RIL) to investigate the salt wild-type tolerance aspects of maize domestication. We revealed that ZmHKT2 is a major QTL that regulates K+ homeostasis in saline soils. ZmHKT2 encodes a K+ -preferring HKT family transporter and probably reduces shoot K+ content by removing K+ ions from root-to-shoot flowing xylem sap, ZmHKT2 deficiency increases xylem sap and shoot K+ concentrations, and increases salt tolerance. A coding sequence polymorphism in the ZmHKT2W22 allele (SNP389-G) confers an amino acid variant ZmHKT2 that increases xylem sap K+ concentration, thereby increasing shoot K+ content and salt tolerance. Additional analyses showed that SNP389-G first existed in teosinte (allele frequency 56% in assayed accessions), then swept through the maize population (allele frequency 98%), and that SNP389-G probably underwent positive selection during maize domestication. We conclude that a domestication-associated reduction in K+ transport activity in ZmHKT2 underlies maize shoot K+ content and salt tolerance, and propose that CRISPR-based editing of ZmHKT2 might provide a feasible strategy for improving maize salt tolerance.
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Affiliation(s)
- Yibo Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Xiaoyan Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Pan Yin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Ming Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Caifu Jiang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100094, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100094, China
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14
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Stitzer MC, Ross-Ibarra J. Maize domestication and gene interaction. THE NEW PHYTOLOGIST 2018; 220:395-408. [PMID: 30035321 DOI: 10.1111/nph.15350] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/05/2018] [Indexed: 05/24/2023]
Abstract
Contents Summary 395 I. Introduction 395 II. The genetic basis of maize domestication 396 III. The tempo of maize domestication 401 IV. Genetic interactions and selection during maize domestication 401 V. Gene networks of maize domestication alleles 404 VI. Implications of gene interactions on evolution and selection404 VII. Conclusions 405 Acknowledgements 405 References 405 SUMMARY: Domestication is a tractable system for following evolutionary change. Under domestication, wild populations respond to shifting selective pressures, resulting in adaptation to the new ecological niche of cultivation. Owing to the important role of domesticated crops in human nutrition and agriculture, the ancestry and selection pressures transforming a wild plant into a domesticate have been extensively studied. In Zea mays, morphological, genetic and genomic studies have elucidated how a wild plant, the teosinte Z. mays subsp. parviglumis, was transformed into the domesticate Z. mays subsp. mays. Five major morphological differences distinguish these two subspecies, and careful genetic dissection has pinpointed the molecular changes responsible for several of these traits. But maize domestication was a consequence of more than just five genes, and regions throughout the genome contribute. The impacts of these additional regions are contingent on genetic background, both the interactions between alleles of a single gene and among alleles of the multiple genes that modulate phenotypes. Key genetic interactions include dominance relationships, epistatic interactions and pleiotropic constraint, including how these variants are connected in gene networks. Here, we review the role of gene interactions in generating the dramatic phenotypic evolution seen in the transition from teosinte to maize.
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Affiliation(s)
- Michelle C Stitzer
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
- Center for Population Biology, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
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Zhu C, Yang J, Box MS, Kellogg EA, Eveland AL. A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics. FRONTIERS IN PLANT SCIENCE 2018; 9:1309. [PMID: 30258452 PMCID: PMC6143762 DOI: 10.3389/fpls.2018.01309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/20/2018] [Indexed: 05/29/2023]
Abstract
The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.
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Anderson SL, Mahan AL, Murray SC, Klein PE. Four Parent Maize (FPM) Population: Effects of Mating Designs on Linkage Disequilibrium and Mapping Quantitative Traits. THE PLANT GENOME 2018; 11:170102. [PMID: 30025026 DOI: 10.3835/plantgenome2017.11.0102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Multiparent advanced generation inter-cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; L.) population implemented five different mating designs used in MAGIC and bi-parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years. Linkage disequilibrium (LD) analysis of subpopulations indicated MAGIC population designs should incorporate generations of intermating to overcome initial LD increase caused by population admixture in a non-intermated four parent population (4way0sib). A 3- to 4-fold increase in genetic resolution (<0.8) and a 2.5-fold decrease in the extent of LD decay (<0.2) compared to the biparental populations was found for the four parent cross at the third generation of intermating (4way3sib). Power of QTL detection was affected to a greater extent by sample size rather than by mating designs. The FPM power simulations indicated that MAGIC populations have the ability to meet or exceed the mapping power of nested association panels with fewer individuals and diversity inputs. Using association mapping software we identified 2, 5, 7, and 6 QTL for PH, EH, DTA, and DTS, respectively. The FPM population is a valuable resource for quantifying empirical improvements of parent number, intermating, and the number of progeny for QTL linkage mapping.
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17
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Laricchia KM, Johnson MG, Ragone D, Williams EW, Zerega NJC, Wickett NJ. A transcriptome screen for positive selection in domesticated breadfruit and its wild relatives (Artocarpus spp.). AMERICAN JOURNAL OF BOTANY 2018; 105:915-926. [PMID: 29882953 DOI: 10.1002/ajb2.1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Underutilized crops, such as breadfruit (Artocarpus altilis, Moraceae) have the potential to improve global food security. Humans have artificially selected many cultivars of breadfruit since its domestication began approximately 3500 years ago. The goal of this research was to identify transcriptomic signals of positive selection and to develop genomic resources that may facilitate the development of improved breadfruit cultivars in the future. METHODS A reference transcriptome of breadfruit was assembled de novo and annotated. Twenty-four transcriptomes of breadfruit and its wild relatives were generated and analyzed to reveal signals of positive selection that may have resulted from local adaptation or natural selection. Emphasis was placed on MADS-box genes, which are important because they often regulate fruiting timing and structures, and on carotenoid biosynthesis genes, which can impact the nutritional quality of the fruit. KEY RESULTS Over 1000 genes showed signals of positive selection, and these genes were enriched for localization to plastids. Nucleotide sites and individuals under positive selection were discovered in MADS-box genes and carotenoid biosynthesis genes, with several sites located in cofactor or DNA-binding domains. A McDonald-Kreitman test comparing wild to cultivated samples revealed selection in one of the carotenoid biosynthesis genes, abscisic acid 8'-hydroxylase 3. CONCLUSIONS This research highlights some of the many genes that may have been intentionally or unintentionally selected for during the human-mediated dispersal of breadfruit and stresses the importance of conserving a varied germplasm collection. It has revealed candidate genes for further study and produced new genomic resources for breadfruit.
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Affiliation(s)
- Kristen M Laricchia
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Matthew G Johnson
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI, 96741, USA
| | - Evelyn W Williams
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Nyree J C Zerega
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
| | - Norman J Wickett
- Program in Plant Biology and Conservation, Northwestern University, Evanston, IL, 60208, USA
- Department of Plant Science, Chicago Botanic Garden, Glencoe, IL, 60022, USA
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Callens C, Tucker MR, Zhang D, Wilson ZA. Dissecting the role of MADS-box genes in monocot floral development and diversity. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2435-2459. [PMID: 29718461 DOI: 10.1093/jxb/ery086] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/16/2018] [Indexed: 05/05/2023]
Abstract
Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum), and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers such ase lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species, with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 60 amino acid MADS-box motif. In plants, attention has been devoted to characterization of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less well characterized roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies.
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Affiliation(s)
- Cindy Callens
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, Australia
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
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Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1447-1469. [PMID: 29474735 DOI: 10.1093/jxb/erx479] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/10/2018] [Indexed: 05/25/2023]
Abstract
MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.
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Affiliation(s)
- Susanne Schilling
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Sirui Pan
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Alice Kennedy
- School of Biology and Environmental Science, University College Dublin, Irel
| | - Rainer Melzer
- School of Biology and Environmental Science, University College Dublin, Irel
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20
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Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture. Genetics 2017; 207:755-765. [PMID: 28754660 DOI: 10.1534/genetics.117.300071] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 01/11/2023] Open
Abstract
Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture. Additional genes, known from the literature, also act in this network. We observed that tb1 regulates both core cell cycle genes and another maize domestication gene, teosinte glume architecture1 (tga1). We show that several members of the MADS-box gene family are either directly or indirectly regulated by tb1 and/or tga1, and that tb1 sits atop a cascade of transcriptional regulators controlling both plant and inflorescence architecture. Multiple members of the tb1 network appear to have been the targets of selection during maize domestication. Knowledge of the regulatory hierarchies controlling traits is central to understanding how new morphologies evolve.
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Soyk S, Lemmon ZH, Oved M, Fisher J, Liberatore KL, Park SJ, Goren A, Jiang K, Ramos A, van der Knaap E, Van Eck J, Zamir D, Eshed Y, Lippman ZB. Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene. Cell 2017; 169:1142-1155.e12. [PMID: 28528644 DOI: 10.1016/j.cell.2017.04.032] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 02/03/2023]
Abstract
Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing "jointless" fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms. VIDEO ABSTRACT.
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Affiliation(s)
- Sebastian Soyk
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Zachary H Lemmon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Matan Oved
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Josef Fisher
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Katie L Liberatore
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Soon Ju Park
- Division of Biological Sciences and Research Institute for Basic Science, Wonkwang University, Iksan, Jeonbuk 54538, Rep. of Korea
| | - Anna Goren
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ke Jiang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexis Ramos
- Institute of Plant Breeding, Genetic & Genomics, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetic & Genomics, University of Georgia, Athens, GA 30602, USA
| | | | - Dani Zamir
- Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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Yang CJ, Kursel LE, Studer AJ, Bartlett ME, Whipple CJ, Doebley JF. A Gene for Genetic Background in Zea mays: Fine-Mapping enhancer of teosinte branched1.2 to a YABBY Class Transcription Factor. Genetics 2016; 204:1573-1585. [PMID: 27729422 PMCID: PMC5161286 DOI: 10.1534/genetics.116.194928] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023] Open
Abstract
The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (teosinte), an allelic substitution at teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear, which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression, with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, nonshattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication.
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Affiliation(s)
- Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Lisa E Kursel
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Anthony J Studer
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | | | | | - John F Doebley
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
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Unterseer S, Pophaly SD, Peis R, Westermeier P, Mayer M, Seidel MA, Haberer G, Mayer KFX, Ordas B, Pausch H, Tellier A, Bauer E, Schön CC. A comprehensive study of the genomic differentiation between temperate Dent and Flint maize. Genome Biol 2016; 17:137. [PMID: 27387028 PMCID: PMC4937532 DOI: 10.1186/s13059-016-1009-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/15/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Dent and Flint represent two major germplasm pools exploited in maize breeding. Several traits differentiate the two pools, like cold tolerance, early vigor, and flowering time. A comparative investigation of their genomic architecture relevant for quantitative trait expression has not been reported so far. Understanding the genomic differences between germplasm pools may contribute to a better understanding of the complementarity in heterotic patterns exploited in hybrid breeding and of mechanisms involved in adaptation to different environments. RESULTS We perform whole-genome screens for signatures of selection specific to temperate Dent and Flint maize by comparing high-density genotyping data of 70 American and European Dent and 66 European Flint inbred lines. We find 2.2 % and 1.4 % of the genes are under selective pressure, respectively, and identify candidate genes associated with agronomic traits known to differ between the two pools. Taking flowering time as an example for the differentiation between Dent and Flint, we investigate candidate genes involved in the flowering network by phenotypic analyses in a Dent-Flint introgression library and find that the Flint haplotypes of the candidates promote earlier flowering. Within the flowering network, the majority of Flint candidates are associated with endogenous pathways in contrast to Dent candidate genes, which are mainly involved in response to environmental factors like light and photoperiod. The diversity patterns of the candidates in a unique panel of more than 900 individuals from 38 European landraces indicate a major contribution of landraces from France, Germany, and Spain to the candidate gene diversity of the Flint elite lines. CONCLUSIONS In this study, we report the investigation of pool-specific differences between temperate Dent and Flint on a genome-wide scale. The identified candidate genes represent a promising source for the functional investigation of pool-specific haplotypes in different genetic backgrounds and for the evaluation of their potential for future crop improvement like the adaptation to specific environments.
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Affiliation(s)
- Sandra Unterseer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Saurabh D Pophaly
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Regina Peis
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Peter Westermeier
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.,Present Address: Institute for Crop Science and Plant Breeding, Bavarian State Research Center, 85354, Freising, Germany
| | - Manfred Mayer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Michael A Seidel
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Georg Haberer
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Bernardo Ordas
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), 36080, Pontevedra, Spain
| | - Hubert Pausch
- Animal Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Aurélien Tellier
- Section of Population Genetics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Eva Bauer
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Chris-Carolin Schön
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany.
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Lin CS, Hsu CT, Liao DC, Chang WJ, Chou ML, Huang YT, Chen JJW, Ko SS, Chan MT, Shih MC. Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:284-98. [PMID: 25917508 DOI: 10.1111/pbi.12383] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/05/2015] [Accepted: 03/18/2015] [Indexed: 05/04/2023]
Abstract
Orchids exhibit a range of unique flower shapes and are a valuable ornamental crop. MADS-box transcription factors are key regulatory components in flower initiation and development. Changing the flower shape and flowering time can increase the value of the orchid in the ornamental horticulture industry. In this study, 28 MADS-box genes were identified from the transcriptome database of the model orchid Erycina pusilla. The full-length genomic sequences of these MADS-box genes were obtained from BAC clones. Of these, 27 were MIKC-type EpMADS (two truncated forms) and one was a type I EpMADS. Eleven EpMADS genes contained introns longer than 10 kb. Phylogenetic analysis classified the 24 MIKC(c) genes into nine subfamilies. Three specific protein motifs, AG, FUL and SVP, were identified and used to classify three subfamilies. The expression profile of each EpMADS gene correlated with its putative function. The phylogenetic analysis was highly correlated with the protein domain identification and gene expression results. Spatial expression of EpMADS6, EpMADS12 and EpMADS15 was strongly detected in the inflorescence meristem, floral bud and seed via in situ hybridization. The subcellular localization of the 28 EpMADS proteins was also investigated. Although EpMADS27 lacks a complete MADS-box domain, EpMADS27-YFP was localized in the nucleus. This characterization of the orchid MADS-box family genes provides useful information for both orchid breeding and studies of flowering and evolution.
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Affiliation(s)
- Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - De-Chih Liao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Lun Chou
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-yi, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Swee-Suak Ko
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ming-Tsair Chan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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25
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Liu H, Wang X, Warburton ML, Wen W, Jin M, Deng M, Liu J, Tong H, Pan Q, Yang X, Yan J. Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding. MOLECULAR PLANT 2015; 8:871-84. [PMID: 25620769 DOI: 10.1016/j.molp.2015.01.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 05/25/2023]
Abstract
The temperate-tropical division of early maize germplasms to different agricultural environments was arguably the greatest adaptation process associated with the success and near ubiquitous importance of global maize production. Deciphering this history is challenging, but new insight has been gained from examining 558 529 single nucleotide polymorphisms, expression data of 28 769 genes, and 662 traits collected from 368 diverse temperate and tropical maize inbred lines in this study. This is a new attempt to systematically exploit the mechanisms of the adaptation process in maize. Our results indicate that divergence between tropical and temperate lines apparently occurred 3400-6700 years ago. Seven hundred and one genomic selection signals and transcriptomic variants including 2700 differentially expressed individual genes and 389 rewired co-expression network genes were identified. These candidate signals were found to be functionally related to stress responses, and most were associated with directionally selected traits, which may have been an advantage under widely varying environmental conditions faced by maize as it was migrated away from its domestication center. Our study also clearly indicates that such stress adaptation could involve evolution of protein-coding sequences as well as transcriptome-level regulatory changes. The latter process may be a more flexible and dynamic way for maize to adapt to environmental changes along its short evolutionary history.
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Affiliation(s)
- Haijun Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Marilyn L Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Box 9555, Mississippi State, MS 39762, USA
| | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Tong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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26
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Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR. Insights into the maize pan-genome and pan-transcriptome. THE PLANT CELL 2014; 26:121-35. [PMID: 24488960 PMCID: PMC3963563 DOI: 10.1105/tpc.113.119982] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 01/03/2014] [Accepted: 01/09/2014] [Indexed: 05/18/2023]
Abstract
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
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Affiliation(s)
- Candice N. Hirsch
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | | | - James M. Johnson
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | - Rajandeep S. Sekhon
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706
| | - German Muttoni
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | | | - Erika Lindquist
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Mary Ann Pedraza
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin 53706
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
- Address correspondence to
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27
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Wallace JG, Larsson SJ, Buckler ES. Entering the second century of maize quantitative genetics. Heredity (Edinb) 2014; 112:30-8. [PMID: 23462502 PMCID: PMC3860165 DOI: 10.1038/hdy.2013.6] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/27/2012] [Accepted: 01/14/2013] [Indexed: 12/14/2022] Open
Abstract
Maize is the most widely grown cereal in the world. In addition to its role in global agriculture, it has also long served as a model organism for genetic research. Maize stands at a genetic crossroads, as it has access to all the tools available for plant genetics but exhibits a genetic architecture more similar to other outcrossing organisms than to self-pollinating crops and model plants. In this review, we summarize recent advances in maize genetics, including the development of powerful populations for genetic mapping and genome-wide association studies (GWAS), and the insights these studies yield on the mechanisms underlying complex maize traits. Most maize traits are controlled by a large number of genes, and linkage analysis of several traits implicates a 'common gene, rare allele' model of genetic variation where some genes have many individually rare alleles contributing. Most natural alleles exhibit small effect sizes with little-to-no detectable pleiotropy or epistasis. Additionally, many of these genes are locked away in low-recombination regions that encourage the formation of multi-gene blocks that may underlie maize's strong heterotic effect. Domestication left strong marks on the maize genome, and some of the differences in trait architectures may be due to different selective pressures over time. Overall, maize's advantages as a model system make it highly desirable for studying the genetics of outcrossing species, and results from it can provide insight into other such species, including humans.
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Affiliation(s)
- J G Wallace
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
| | - S J Larsson
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - E S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
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28
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Ha J, Lestari P, Lee SH. Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0075-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci U S A 2012. [PMID: 22753482 DOI: 10.1073/pnas.1201961109/-/dcsupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1201961109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
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Affiliation(s)
- Ruth Swanson-Wagner
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA
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30
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Abstract
Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses.
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31
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Tranbarger TJ, Kluabmongkol W, Sangsrakru D, Morcillo F, Tregear JW, Tragoonrung S, Billotte N. SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis. BMC PLANT BIOLOGY 2012; 12:1. [PMID: 22214433 PMCID: PMC3282652 DOI: 10.1186/1471-2229-12-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 01/03/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm. RESULTS In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing vegetative and reproductive tissues were annotated and searched for simple sequence repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect polymorphisms in elite breeding parents and their crosses. 230 of these amplified PCR products, 88 of which were polymorphic within the breeding material tested. A detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms within the transcripts, and that the main functional category was related to transcription and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors in addition to other transcriptional regulatory proteins and several RNA interacting proteins. CONCLUSIONS The identification of new EST-SSRs that detect polymorphisms in elite breeding material provides tools for molecular breeding strategies. The identification of SSRs within transcripts, in particular those that encode proteins involved in transcriptional and post-transcriptional regulation, will allow insight into the functional roles of these proteins by studying the phenotypic traits that cosegregate with these markers. Finally, the oil palm EST-SSRs derived from vegetative and reproductive development will be useful for studies on the evolution of the functional diversity within the palm family.
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Affiliation(s)
- Timothy John Tranbarger
- IRD, UMR DIADE (IRD, UM2), 911 Avenue Agropolis BP 64501, 34394, Montpellier cedex 5, France
| | - Wanwisa Kluabmongkol
- Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Duangjai Sangsrakru
- Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | | | - James W Tregear
- IRD, UMR DIADE (IRD, UM2), 911 Avenue Agropolis BP 64501, 34394, Montpellier cedex 5, France
| | - Somvong Tragoonrung
- Genome Institute, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 2011; 43:1160-3. [PMID: 21946354 DOI: 10.1038/ng.942] [Citation(s) in RCA: 467] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 08/19/2011] [Indexed: 01/21/2023]
Abstract
Genetic diversity created by transposable elements is an important source of functional variation upon which selection acts during evolution. Transposable elements are associated with adaptation to temperate climates in Drosophila, a SINE element is associated with the domestication of small dog breeds from the gray wolf and there is evidence that transposable elements were targets of selection during human evolution. Although the list of examples of transposable elements associated with host gene function continues to grow, proof that transposable elements are causative and not just correlated with functional variation is limited. Here we show that a transposable element (Hopscotch) inserted in a regulatory region of the maize domestication gene, teosinte branched1 (tb1), acts as an enhancer of gene expression and partially explains the increased apical dominance in maize compared to its progenitor, teosinte. Molecular dating indicates that the Hopscotch insertion predates maize domestication by at least 10,000 years, indicating that selection acted on standing variation rather than new mutation.
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Affiliation(s)
- Anthony Studer
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
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