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Gao H, Wang Y, Li W, Gu Y, Lai Y, Bi Y, He C. Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5089-5104. [PMID: 30113693 PMCID: PMC6184420 DOI: 10.1093/jxb/ery291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/31/2018] [Indexed: 05/22/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 d after fertilization, G15). A module in which the co-expressed genes were significantly down-regulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy.
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Affiliation(s)
- Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongcai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yingdong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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Singh J, Zhao J, Vallejos CE. Differential transcriptome patterns associated with early seedling development in a wild and a domesticated common bean (Phaseolus vulgaris L.) accession. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:153-162. [PMID: 30080599 DOI: 10.1016/j.plantsci.2018.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/22/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Genes that control "Domestication Syndrome" traits were direct targets of selection, like those controlling increased seed size in the common bean. However, selection for this trait brought about unintentional selection on genes controlling seedling growth. We hypothesized that wild and domesticated plants have different early seedling growth patterns as an indirect consequence of selection for a larger seed size during domestication, and those differences resulted from changes in gene expression patterns of the wild ancestor. Large seeds pose a challenge to reserve remobilization during early heterotrophic growth, particularly during a transition towards more fertile alluvial soils. To address our hypothesis, we characterized the patterns of gene expression of cotyledon, root, and leaf tissues of 7-day old seedlings of a wild and a landrace accession of the common bean. Differential expression analyses detected genes with contrasting patterns of expression between the two genotypes in all three tissues. Some of the differentially expressed genes with contrasting genotypic patterns are known to have domestication-related signatures of selection. Among these genes were some transcription factors associated with key roles in development. These genes may represent targets of indirect selection and ultimately explain the growth phenotypic differences between wild and domesticated seedlings.
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Affiliation(s)
- Jugpreet Singh
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Jianxin Zhao
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
| | - C Eduardo Vallejos
- Department of Horticultural Sciences, University of Florida, Gainesville, FL 32611, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.
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Gaudin ACM, McClymont SA, Soliman SSM, Raizada MN. The effect of altered dosage of a mutant allele of Teosinte branched 1 (tb1-ref) on the root system of modern maize. BMC Genet 2014; 15:23. [PMID: 24524734 PMCID: PMC3930895 DOI: 10.1186/1471-2156-15-23] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There was ancient human selection on the wild progenitor of modern maize, Balsas teosinte, for decreased shoot branching (tillering), in order to allow more nutrients to be diverted to grain. Mechanistically, the decline in shoot tillering has been associated with selection for increased expression of the major domestication gene Teosinte Branched 1 (Tb1) in shoot primordia. Therefore, TB1 has been defined as a repressor of shoot branching. It is known that plants respond to changes in shoot size by compensatory changes in root growth and architecture. However, it has not been reported whether altered TB1 expression affects any plant traits below ground. Previously, changes in dosage of a well-studied mutant allele of Tb1 in modern maize, called tb1-ref, from one to two copies, was shown to increase tillering. As a result, plants with two copies of the tb1-ref allele have a larger shoot biomass than heterozygotes. Here we used aeroponics to phenotype the effects of tb1-ref copy number on maize roots at macro-, meso- and micro scales of development. RESULTS An increase in the tb1-ref copy number from one to two copies resulted in: (1) an increase in crown root number due to the cumulative initiation of crown roots from successive tillers; (2) higher density of first and second order lateral roots; and (3) reduced average lateral root length. The resulting increase in root system biomass in homozygous tb1-ref mutants balanced the increase in shoot biomass caused by enhanced tillering. These changes caused homozygous tb1-ref mutants of modern maize to more closely resemble its ancestor Balsas teosinte below ground. CONCLUSION We conclude that a decrease in TB1 function in maize results in a larger root system, due to an increase in the number of crown roots and lateral roots. Given that decreased TB1 expression results in a more highly branched and larger shoot, the impact of TB1 below ground may be direct or indirect. We discuss the potential implications of these findings for whole plant coordination of biomass accumulation and maize domestication.
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Affiliation(s)
| | | | | | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, Ontario N1G 2W1, Canada.
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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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Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, Qi XT, Guo XS, Zhang L, He WM, Chang RZ, Liang QS, Guo Y, Ye C, Wang XB, Tao Y, Guan RX, Wang JY, Liu YL, Jin LG, Zhang XQ, Liu ZX, Zhang LJ, Chen J, Wang KJ, Nielsen R, Li RQ, Chen PY, Li WB, Reif JC, Purugganan M, Wang J, Zhang MC, Wang J, Qiu LJ. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 2013; 14:579. [PMID: 23984715 PMCID: PMC3844514 DOI: 10.1186/1471-2164-14-579] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 07/04/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Artificial selection played an important role in the origin of modern Glycine max cultivars from the wild soybean Glycine soja. To elucidate the consequences of artificial selection accompanying the domestication and modern improvement of soybean, 25 new and 30 published whole-genome re-sequencing accessions, which represent wild, domesticated landrace, and Chinese elite soybean populations were analyzed. RESULTS A total of 5,102,244 single nucleotide polymorphisms (SNPs) and 707,969 insertion/deletions were identified. Among the SNPs detected, 25.5% were not described previously. We found that artificial selection during domestication led to more pronounced reduction in the genetic diversity of soybean than the switch from landraces to elite cultivars. Only a small proportion (2.99%) of the whole genomic regions appear to be affected by artificial selection for preferred agricultural traits. The selection regions were not distributed randomly or uniformly throughout the genome. Instead, clusters of selection hotspots in certain genomic regions were observed. Moreover, a set of candidate genes (4.38% of the total annotated genes) significantly affected by selection underlying soybean domestication and genetic improvement were identified. CONCLUSIONS Given the uniqueness of the soybean germplasm sequenced, this study drew a clear picture of human-mediated evolution of the soybean genomes. The genomic resources and information provided by this study would also facilitate the discovery of genes/loci underlying agronomically important traits.
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Affiliation(s)
- Ying-hui Li
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Shan-cen Zhao
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Jian-xin Ma
- Department of Agronomy, Purdue University, 47907, West Lafayette, IN, USA
| | - Dong Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Long Yan
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences / Shijiazhuang Branch Center of National Center for Soybean Improvement / the Key Laboratory of Crop Genetics and Breeding, 050031 Shijiazhuang, China
| | - Jun Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Xiao-tian Qi
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xiao-sen Guo
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Le Zhang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Wei-ming He
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Ru-zhen Chang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Qin-si Liang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Yong Guo
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Chen Ye
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Xiao-bo Wang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Yong Tao
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rong-xia Guan
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Jun-yi Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing, China
| | - Yu-lin Liu
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Long-guo Jin
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xiu-qing Zhang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Zhang-xiong Liu
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Li-juan Zhang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Jie Chen
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Ke-jing Wang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Rasmus Nielsen
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, 94820 Berkeley, CA, USA
| | - Rui-qiang Li
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Peng-yin Chen
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 72701 Fayetteville, Arkansas, USA
| | - Wen-bin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Northeast Agricultural University, 150030 Harbin, China
| | - Jochen C Reif
- State Plant Breeding Institute, University of Hohenheim, Hohenheim, Germany
| | - Michael Purugganan
- Department of Biology and Centre for Genomics and Systems Biology, 12 Waverly Place, New York University, 10003 New York, USA
| | - Jian Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
| | - Meng-chen Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences / Shijiazhuang Branch Center of National Center for Soybean Improvement / the Key Laboratory of Crop Genetics and Breeding, 050031 Shijiazhuang, China
| | - Jun Wang
- Shenzhen Key Laboratory of Transomics Biotechnologies, BGI-Shenzhen, 518083 Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Li-juan Qiu
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) / Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, 100081 Beijing, China
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Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN. Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci U S A 2013; 110:E2655-62. [PMID: 23803858 PMCID: PMC3710864 DOI: 10.1073/pnas.1309606110] [Citation(s) in RCA: 229] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
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Affiliation(s)
- Daniel Koenig
- Department of Plant Biology and
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Seisuke Kimura
- Department of Plant Biology and
- Department of Bioresource and Environmental Sciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | | | | | | | | | | | | | | | | | - Anthony Bolger
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
| | - Korbinian Schneeberger
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Stephan Ossowski
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Genes and Disease Program, Centre for Genomic Regulation, Barcelona 08003, Spain
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Guangyan Xiong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | | | - Siobhan M. Brady
- Department of Plant Biology and
- Genome Center, University of California, Davis, CA 95616
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Björn Usadel
- Department of Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, 14476 Golm, Germany
- Institute of Biology 1, Rheinisch-Westfaelische Technische Hochschule Aachen, 52056 Aachen, Germany; and
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | | | - Jie Peng
- Department of Statistics, University of California, Davis, CA 95616
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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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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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10
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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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Rhoné B, Brandenburg JT, Austerlitz F. Impact of selection on genes involved in regulatory network: a modelling study. J Evol Biol 2011; 24:2087-98. [PMID: 21682788 DOI: 10.1111/j.1420-9101.2011.02335.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Complex phenotypes are often controlled by many interacting genes. One question emerging from such organization is how selection, acting at the phenotypic level, shapes the evolution of genes involved in regulatory networks controlling the phenotypes. We studied this issue through a matrix model of such networks. In a population submitted to selection, we simulated the evolution of a quantitative trait controlled by a set of loci that regulate each other through positive or negative interactions. Investigating several levels of selection intensity on the trait, we studied the evolution of regulation intensity between the genes and the evolution of the genetic diversity of those genes as an indirect measure of the strength of selection acting on them. We show that an increasing intensity of selection on the phenotype leads to an increased level of regulation between the loci. Moreover, we found that the genes responding more strongly to selection within the network were those evolving towards stronger regulatory action on the other genes and/or those that are the less regulated by the other genes. This observation is strongest for an intermediate level of selection. This may explain why several experimental studies have shown evidence of selection on regulatory genes inside gene networks.
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Affiliation(s)
- B Rhoné
- Ecologie, Systématique et Evolution, UMR 8079 CNRS/Université Paris-Sud/AgroParisTech, Université Paris-Sud 11, Orsay Cedex, France
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Corbi J, Debieu M, Rousselet A, Montalent P, Le Guilloux M, Manicacci D, Tenaillon MI. Contrasted patterns of selection since maize domestication on duplicated genes encoding a starch pathway enzyme. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:705-22. [PMID: 21060986 DOI: 10.1007/s00122-010-1480-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 10/22/2010] [Indexed: 05/08/2023]
Abstract
Maize domestication from teosinte (Zea mays ssp. parviglumis) was accompanied by an increase of kernel size in landraces. Subsequent breeding has led to a diversification of kernel size and starch content among major groups of inbred lines. We aim at investigating the effect of domestication on duplicated genes encoding a key enzyme of the starch pathway, the ADP-glucose pyrophosphorylase (AGPase). Three pairs of paralogs encode the AGPase small (SSU) and large (LSU) subunits mainly expressed in the endosperm, the embryo and the leaf. We first validated the putative sequence of LSU(leaf) through a comparative expression assay of the six genes. Second, we investigated the patterns of molecular evolution on a 2 kb coding region homologous among the six genes in three panels: teosintes, landraces, and inbred lines. We corrected for demographic effects by relying on empirical distributions built from 580 previously sequenced ESTs. We found contrasted patterns of selection among duplicates: three genes exhibit patterns of directional selection during domestication (SSU(end), LSU(emb)) or breeding (LSU(leaf)), two exhibit patterns consistent with diversifying (SSU(leaf)) and balancing selection (SSU(emb)) accompanying maize breeding. While patterns of linkage disequilibrium did not reveal sign of coevolution between genes expressed in the same organ, we detected an excess of non-synonymous substitutions in the small subunit functional domains highlighting their role in AGPase evolution. Our results offer a different picture on AGPase evolution than the one depicted at the Angiosperm level and reveal how genetic redundancy can provide flexibility in the response to selection.
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Affiliation(s)
- J Corbi
- CNRS, UMR 0320/UMR 8120 Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
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13
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Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity (Edinb) 2010; 106:927-35. [PMID: 21081965 DOI: 10.1038/hdy.2010.139] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F(st) (θ) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, fresh-market and vintage germplasm by using an F(st)-outlier method based on the deviation from the expected distribution of F(st) and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.
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SIGMON BRANDI, VOLLBRECHT ERIK. Evidence of selection at theramosa1locus during maize domestication. Mol Ecol 2010; 19:1296-311. [DOI: 10.1111/j.1365-294x.2010.04562.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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15
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Fan L, Bao J, Wang Y, Yao J, Gui Y, Hu W, Zhu J, Zeng M, Li Y, Xu Y. Post-domestication selection in the maize starch pathway. PLoS One 2009; 4:e7612. [PMID: 19859548 PMCID: PMC2762603 DOI: 10.1371/journal.pone.0007612] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 10/08/2009] [Indexed: 11/18/2022] Open
Abstract
Modern crops have usually experienced domestication selection and subsequent genetic improvement (post-domestication selection). Chinese waxy maize, which originated from non-glutinous domesticated maize (Zea mays ssp. mays), provides a unique model for investigating the post-domestication selection of maize. In this study, the genetic diversity of six key genes in the starch pathway was investigated in a glutinous population that included 55 Chinese waxy accessions, and a selective bottleneck that resulted in apparent reductions in diversity in Chinese waxy maize was observed. Significant positive selection in waxy (wx) but not amylose extender1 (ae1) was detected in the glutinous population, in complete contrast to the findings in non-glutinous maize, which indicated a shift in the selection target from ae1 to wx during the improvement of Chinese waxy maize. Our results suggest that an agronomic trait can be quickly improved into a target trait with changes in the selection target among genes in a crop pathway.
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Affiliation(s)
- Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
- * E-mail:
| | - Jiandong Bao
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Yu Wang
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Jianqiang Yao
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
- Institute of Crop Science, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Yijie Gui
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Weiming Hu
- Institute of Crop Science and Institute of Bioinformatics, Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Jinqing Zhu
- Institute of Crop Science, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Mengqian Zeng
- Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CIMMYT), Mexico, D.F., Mexico
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