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Costa FM, Vidal R, de Almeida Silva NC, Veasey EA, de Oliveira Freitas F, Zucchi MI. Archaeological findings show the extent of primitive characteristics of maize in South America. SCIENCE ADVANCES 2024; 10:eadn1466. [PMID: 39231236 PMCID: PMC11373604 DOI: 10.1126/sciadv.adn1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 07/29/2024] [Indexed: 09/06/2024]
Abstract
Scientific research has suggested that maize spread from Mexico and arrived in lowland South America in a state of partial domestication. However, archaeological samples with primitive morphological characteristics that corroborate this finding have not been recorded in the region thus far. Unexpectedly, many samples were identified in the Peruaçu Valley with characteristics never previously observed in South America. These archaeological samples with primitive characteristics, which are the focus of this work, represent the furthest records from the center of origin of the species and the longest duration of the maintenance of such characteristics (between 1010 and 570 years before present). The findings of this study, including archaeological samples, native races, and samples of teosinte, attest to a long history of maize diversification in lowland South America.
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Affiliation(s)
- Flaviane Malaquias Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | - Rafael Vidal
- Universidad de la República, Facultad de Agronomía, Montevideo 12900, Uruguay
| | | | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP 13418-900, Brazil
| | | | - Maria Imaculada Zucchi
- Secretaria de Agricultura e Abastecimento do Estado de São Paulo, APTA-URPD, Piracicaba, SP, CEP 13400-900, Brazil
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2
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Li P, Zhang Z, Xiao G, Zhao Z, He K, Yang X, Pan Q, Mi G, Jia Z, Yan J, Chen F, Yuan L. Genomic basis determining root system architecture in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:102. [PMID: 38607439 DOI: 10.1007/s00122-024-04606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
KEY MESSAGE A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.
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Affiliation(s)
- Pengcheng Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhihai Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Gui Xiao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zheng Zhao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Kunhui He
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingchun Pan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanjun Chen
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Lixing Yuan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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3
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Cao S, Zhang H, Liu Y, Sun Y, Chen ZJ. Cytoplasmic genome contributions to domestication and improvement of modern maize. BMC Biol 2024; 22:64. [PMID: 38481288 PMCID: PMC10938767 DOI: 10.1186/s12915-024-01859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated. RESULTS Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes. CONCLUSIONS Our results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.
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Affiliation(s)
- Shuai Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Huanhuan Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yi Sun
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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4
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Acosta-Bayona J, León-Martínez G, Vielle-Calzada JP. Origin and diversification of maize: Two teosintes but different contributions. MOLECULAR PLANT 2024; 17:233-235. [PMID: 38168636 DOI: 10.1016/j.molp.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Jonathan Acosta-Bayona
- Grupo de Desarrollo Reproductivo y Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato Gto CP36825, México
| | - Gloria León-Martínez
- Grupo de Desarrollo Reproductivo y Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato Gto CP36825, México
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, UGA Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato Gto CP36825, México.
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5
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Shrestha A, Limay-Rios V, Brettingham DJL, Raizada MN. Maize pollen carry bacteria that suppress a fungal pathogen that enters through the male gamete fertilization route. FRONTIERS IN PLANT SCIENCE 2024; 14:1286199. [PMID: 38269134 PMCID: PMC10806238 DOI: 10.3389/fpls.2023.1286199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024]
Abstract
In flowering plants, after being released from pollen grains, the male gametes use the style channel to migrate towards the ovary where they fertilize awaiting eggs. Environmental pathogens exploit the style passage, resulting in diseased progeny seed. The belief is that pollen also transmits pathogens into the style. By contrast, we hypothesized that pollen carries beneficial microbes that suppress environmental pathogens on the style passage. No prior studies have reported pollen-associated bacterial functions in any plant species. Here, bacteria were cultured from maize (corn) pollen encompassing wild ancestors and farmer-selected landraces from across the Americas, grown in a common field in Canada for one season. In total, 298 bacterial isolates were cultured, spanning 45 genera, 103 species, and 88 OTUs, dominated by Pantoea, Bacillus, Pseudomonas, Erwinia, and Microbacterium. Full-length 16S DNA-based taxonomic profiling showed that 78% of bacterial taxa from the major wild ancestor of maize (Parviglumis teosinte) were present in at least one cultivated landrace. The species names of the bacterial isolates were used to search the pathogen literature systematically; this preliminary evidence predicted that the vast majority of the pollen-associated bacteria analyzed are not maize pathogens. The pollen-associated bacteria were tested in vitro against a style-invading Fusarium pathogen shown to cause Gibberella ear rot (GER): 14 isolates inhibited this pathogen. Genome mining showed that all the anti-Fusarium bacterial species encode phzF, associated with biosynthesis of the natural fungicide, phenazine. To mimic the male gamete migration route, three pollen-associated bacterial strains were sprayed onto styles (silks), followed by Fusarium inoculation; these bacteria reduced GER symptoms and mycotoxin accumulation in progeny seed. Confocal microscopy was used to search for direct evidence that pollen-associated bacteria can defend living silks against Fusarium graminearum (Fg); bacterial strain AS541 (Kluyvera intermedia), isolated from pollen of ancestral Parviglumis, was observed to colonize the susceptible style/silk entry points of Fg (silk epidermis, trichomes, wounds). Furthermore, on style/silk tissue, AS541 colonized/aggregated on Fg hyphae, and was associated with Fg hyphal breaks. These results suggest that pollen has the potential to carry bacteria that can defend the style/silk passage against an environmental pathogen - a novel observation.
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Affiliation(s)
- Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Victor Limay-Rios
- Department of Plant Agriculture, University of Guelph, Ridgetown, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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6
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Khalaf EM, Shrestha A, Reid M, McFadyen BJ, Raizada MN. Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq. Front Microbiol 2023; 14:1276241. [PMID: 38179444 PMCID: PMC10764481 DOI: 10.3389/fmicb.2023.1276241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/21/2023] [Indexed: 01/06/2024] Open
Abstract
Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.
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Affiliation(s)
- Eman M. Khalaf
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
| | - Anuja Shrestha
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Michelle Reid
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | | | - Manish N. Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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7
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Yang N, Wang Y, Liu X, Jin M, Vallebueno-Estrada M, Calfee E, Chen L, Dilkes BP, Gui S, Fan X, Harper TK, Kennett DJ, Li W, Lu Y, Ding J, Chen Z, Luo J, Mambakkam S, Menon M, Snodgrass S, Veller C, Wu S, Wu S, Zhuo L, Xiao Y, Yang X, Stitzer MC, Runcie D, Yan J, Ross-Ibarra J. Two teosintes made modern maize. Science 2023; 382:eadg8940. [PMID: 38033071 DOI: 10.1126/science.adg8940] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/02/2023] [Indexed: 12/02/2023]
Abstract
The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative, Zea mays ssp. mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize and Zea mays ssp. mexicana in the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas.
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Affiliation(s)
- Ning Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Yuebin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Miguel Vallebueno-Estrada
- Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV Irapuato, 36821 Guanajuato, México
| | - Erin Calfee
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Lu Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650200, China
| | - Thomas K Harper
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Wenqiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Junqiang Ding
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450046, China
| | - Ziqi Chen
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Sowmya Mambakkam
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Mitra Menon
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
| | - Samantha Snodgrass
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Carl Veller
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Shenshen Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Siying Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Zhuo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Michelle C Stitzer
- Institute for Genomic Diversity and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Daniel Runcie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Yazhouwan National Laboratory, Sanya 572024, China
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
- Center for Population Biology, University of California, Davis, CA 95616, USA
- Genome Center, University of California, Davis, CA 95616, USA
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8
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Berube B, Ernst E, Cahn J, Roche B, de Santis Alves C, Lynn J, Scheben A, Siepel A, Ross-Ibarra J, Kermicle J, Martienssen R. Teosinte Pollen Drive guides maize diversification and domestication by RNAi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548689. [PMID: 37503269 PMCID: PMC10370002 DOI: 10.1101/2023.07.12.548689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Meiotic drivers subvert Mendelian expectations by manipulating reproductive development to bias their own transmission. Chromosomal drive typically functions in asymmetric female meiosis, while gene drive is normally postmeiotic and typically found in males. Using single molecule and single-pollen genome sequencing, we describe Teosinte Pollen Drive, an instance of gene drive in hybrids between maize (Zea mays ssp. mays) and teosinte mexicana (Zea mays ssp. mexicana), that depends on RNA interference (RNAi). 22nt small RNAs from a non-coding RNA hairpin in mexicana depend on Dicer-Like 2 (Dcl2) and target Teosinte Drive Responder 1 (Tdr1), which encodes a lipase required for pollen viability. Dcl2, Tdr1, and the hairpin are in tight pseudolinkage on chromosome 5, but only when transmitted through the male. Introgression of mexicana into early cultivated maize is thought to have been critical to its geographical dispersal throughout the Americas, and a tightly linked inversion in mexicana spans a major domestication sweep in modern maize. A survey of maize landraces and sympatric populations of teosinte mexicana reveals correlated patterns of admixture among unlinked genes required for RNAi on at least 4 chromosomes that are also subject to gene drive in pollen from synthetic hybrids. Teosinte Pollen Drive likely played a major role in maize domestication and diversification, and offers an explanation for the widespread abundance of "self" small RNAs in the germlines of plants and animals.
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Affiliation(s)
- Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Evan Ernst
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Benjamin Roche
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | | | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
| | - Jeffrey Ross-Ibarra
- Dept. of Evolution & Ecology, Center for Population Biology and Genome Center, University of California, Davis CA
| | - Jerry Kermicle
- Laboratory of Genetics, University of Wisconsin, Madison WI
| | - Rob Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor NY11724
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9
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Rivera-Rodríguez DM, Mastretta-Yanes A, Wegier A, De la Cruz Larios L, Santacruz-Ruvalcaba F, Ruiz Corral JA, Hernández B, Sánchez González JDJ. Genomic diversity and population structure of teosinte (Zea spp.) and its conservation implications. PLoS One 2023; 18:e0291944. [PMID: 37819917 PMCID: PMC10566683 DOI: 10.1371/journal.pone.0291944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/09/2023] [Indexed: 10/13/2023] Open
Abstract
The wild species of the genus Zea commonly named teosintes, comprise nine different taxa, distributed from northern Mexico to Costa Rica. Although this genus of plants has been extensively studied from a morphological, ecogeographical and genetic point of view, most contributions have been limited to the study of a few populations and taxa. To understand the great variability that exists between and within teosinte species, it is necessary to include the vast majority of known populations. In this context, the objective of this work was to evaluate the diversity and genomic structure of 276 teosinte populations. Molecular analyzes were performed with 3,604 plants and with data from 33,929 SNPs. The levels of genetic diversity by taxonomic group show a marked difference between species, races and sections, where the highest values of genomic diversity was found in ssp. parviglumis and ssp. mexicana. The lower values were obtained for the Luxuriantes section as well as ssp. huehuetenagensis of the section Zea. The results of structure show that there is a great genetic differentiation in all the taxonomic groups considered. For ssp. parviglumis and mexicana, which are the taxa with the largest number of populations, a marked genomic differentiation was found that is consistent with their geographic distribution patterns. These results showed a loss of diversity in several teosinte populations, making a strong case for further collection, and ex situ and in situ conservation. Also, this study highlights the importance of integrating genomic diversity and structure for the applications of conservation and management.
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Affiliation(s)
- Diana María Rivera-Rodríguez
- Departamento de Ciencias Básicas, Tecnológico Nacional de México, Instituto Tecnológico de Tlajomulco, Tlajomulco de Zúñiga, Jalisco, México
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, Ciudad de México, Mexico
| | - Ana Wegier
- Laboratorio de Genética de la Conservación, Jardín Botánico, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Lino De la Cruz Larios
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Fernando Santacruz-Ruvalcaba
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - José Ariel Ruiz Corral
- Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Benjamín Hernández
- Departamento de Ciencias Básicas, Tecnológico Nacional de México, Instituto Tecnológico de Tlajomulco, Tlajomulco de Zúñiga, Jalisco, México
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10
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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11
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Dai F, Zhuo X, Luo G, Wang Z, Xu Y, Wang D, Zhong J, Lin S, Chen L, Li Z, Wang Y, Zhang D, Li Y, Zheng Q, Zheng T, Liu Z, Wang L, Zhang Z, Tang C. Genomic Resequencing Unravels the Genetic Basis of Domestication, Expansion, and Trait Improvement in Morus Atropurpurea. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300039. [PMID: 37339798 PMCID: PMC10460887 DOI: 10.1002/advs.202300039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/28/2023] [Indexed: 06/22/2023]
Abstract
Mulberry is an economically important plant in the sericulture industry and traditional medicine. However, the genetic and evolutionary history of mulberry remains largely unknown. Here, this work presents the chromosome-level genome assembly of Morus atropurpurea (M. atropurpurea), originating from south China. Population genomic analysis using 425 mulberry accessions reveal that cultivated mulberry is classified into two species, M. atropurpurea and M. alba, which may have originated from two different mulberry progenitors and have independent and parallel domestication in north and south China, respectively. Extensive gene flow is revealed between different mulberry populations, contributing to genetic diversity in modern hybrid cultivars. This work also identifies the genetic architecture of the flowering time and leaf size. In addition, the genomic structure and evolution of sex-determining regions are identified. This study significantly advances the understanding of the genetic basis and domestication history of mulberry in the north and south, and provides valuable molecular markers of desirable traits for mulberry breeding.
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Affiliation(s)
- Fanwei Dai
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
- Key Laboratory of Urban Agriculture in South ChinaMinistry of Agriculture and Rural AffairsGuangzhou510610P. R. China
| | - Xiaokang Zhuo
- College of HorticultureFujian Agriculture and Forestry UniversityFuzhou350002P. R. China
- National Engineering Research Center for FloricultureBeijing Forestry UniversityBeijing100083P. R. China
| | - Guoqing Luo
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
- Key Laboratory of Urban Agriculture in South ChinaMinistry of Agriculture and Rural AffairsGuangzhou510610P. R. China
| | - Zhenjiang Wang
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
- Key Laboratory of Urban Agriculture in South ChinaMinistry of Agriculture and Rural AffairsGuangzhou510610P. R. China
| | - Yujuan Xu
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Dan Wang
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Jianwu Zhong
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Sen Lin
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Lian Chen
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Zhiyi Li
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Yuan Wang
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhou350002P. R. China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhou350002P. R. China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhou350002P. R. China
| | - Tangchun Zheng
- National Engineering Research Center for FloricultureBeijing Forestry UniversityBeijing100083P. R. China
| | - Zhong‐Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape ArchitectureFujian Agriculture and Forestry UniversityFuzhou350002P. R. China
| | - Li Wang
- Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518120P. R. China
- Kunpeng Institute of Modern Agriculture at FoshanChinese Academy of Agricultural SciencesFoshan528225P. R. China
| | - Zhiyong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing University of AgricultureBeijing102206P. R. China
| | - Cuiming Tang
- Sericultural & Agri‐Food Research Institute Guangdong Academy of Agricultural Sciences/Key Laboratory of Functional FoodsMinistry of Agriculture and Rural Affairs/Guangdong Key Laboratory of Agricultural Products ProcessingGuangzhou510610P. R. China
- Key Laboratory of Urban Agriculture in South ChinaMinistry of Agriculture and Rural AffairsGuangzhou510610P. R. China
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12
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Adhikari S, Kumari J, Bhardwaj R, Jacob S, Langyan S, Sharma S, M. Singh A, Kumar A. Unlocking the potential of ancient hexaploid Indian dwarf wheat, Tritium sphaerococcum for grain quality improvement. PeerJ 2023; 11:e15334. [PMID: 37525662 PMCID: PMC10387235 DOI: 10.7717/peerj.15334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/11/2023] [Indexed: 08/02/2023] Open
Abstract
Wild and ancient wheat are considered to be a rich source of nutrients and better stress tolerant, hence being re-considered for mainstreaming its cultivation by the farmers and bringing it back to the food basket. In the present study, thirty-four diverse accessions of Indian dwarf wheat, Triticum sphaerococcum conserved in the Indian National Genebank were evaluated for thirteen-grain quality parameters namely thousand-grain weight (TGW), hectolitre weight (HW), sedimentation value (Sed), grain hardness index (HI), protein (Pro), albumin (Alb), globulin (Glo), gliadin (Gli), glutenin (Glu), gluten, lysine (Lys), Fe2+ and Zn2+ content, and four antioxidant enzymes activities. Substantial variations were recorded for studied traits. TGW, HW, Sed, HI, Pro, Alb, Glo, Gli, Glu, Gluten, Lys, Fe2+, and Zn2+ varied from 26.50-45.55 g, 70.50-86.00 kg/hl, 24.00-38.00 ml, 40.49-104.90, 15.34-19.35%, 17.60-40.31 mg/g, 10.75-16.56 mg/g, 26.35-44.94 mg/g, 24.47-39.56 mg/g, 55.33-75.06 mg/g, 0.04-0.29%, 42.72-90.72 ppm, and 11.45-25.70 ppm, respectively. Among antioxidants, peroxidase (POX), catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD) activity ranged from 0.06-0.60 unit/ml, 0.02-0.61 unit/ml, 0.11-2.26 unit/ml, and 0.14-0.97 unit/ml, respectively. Hardness Index was positively associated with Pro and Zn2+ content whereas Lys was negatively associated with gluten content. Likewise, gluten and Fe2+ content had a positive association with the major protein fraction i.e., Gli and Glu. Hierarchical cluster analysis grouped 34 accessions into four clusters and the major group had nine indigenous and eight exotic accessions. We also validated high GPC accessions and EC182958 (17.16%), EC187176 and EC182945 (16.16%), EC613057 (15.79%), IC634028 (15.72%) and IC533826 (15.01%) were confirmed with more than 15% GPC. Also, superior trait-specific accessions namely, EC187167, IC534021, EC613055, EC180066, and EC182959 for low gluten content and IC384530, EC313761, EC180063, IC397363, EC10494 for high iron content (>76.51) were identified that may be used in wheat quality improvement for nutritional security of mankind.
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Affiliation(s)
- Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Shimla, HP, India
| | - Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Sherry Jacob
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Sapna Langyan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Shivani Sharma
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
| | - Anju M. Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Ashok Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, Delhi, India
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13
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Yuan G, He D, Shi J, Li Y, Yang Y, Du J, Zou C, Ma L, Gao S, Pan G, Shen Y. Genome-Wide Association Study Discovers Novel Germplasm Resources and Genetic Loci with Resistance to Gibberella Ear Rot Caused by Fusarium graminearum. PHYTOPATHOLOGY 2023; 113:1317-1324. [PMID: 36721376 DOI: 10.1094/phyto-09-22-0336-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Gibberella ear rot (GER) in maize caused by Fusarium graminearum is one of the most devastating maize diseases reducing grain yield and quality worldwide. The genetic bases of maize GER resistance remain largely unknown. Using artificial inoculation across multiple environments, the GER severity of an association panel consisting of 316 diverse inbred lines was observed with wide phenotypic variation. In the association panel, a genome-wide association study using a general linear model identified 69 single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance at the threshold of 2.04 × 10-5, and the average phenotypic variation explained (PVE) of these SNPs was 5.09%. We also conducted a genome-wide association study analysis using a mixed linear model at a threshold of 1.0 × 10-4, and 16 significantly associated SNPs with an average PVE of 4.73% were detected. A combined general linear model and mixed linear model method obtained 10 co-localized significantly associated SNPs linked to GER resistance, including the most significant SNP (PZE-105079915) with the greatest PVE value, 9.07%, at bin 5.05 following 10 candidate genes. These findings are significant for the exploration of the complicated genetic variations in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the elite germplasm resources that can be used for breeding GER resistance in maize.
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Affiliation(s)
- Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaxin Shi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Youliang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Juan Du
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region of Ministry of Agriculture, Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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14
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Arca M, Gouesnard B, Mary-Huard T, Le Paslier MC, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1123-1139. [PMID: 36740649 DOI: 10.1111/pbi.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/18/2023] [Indexed: 05/27/2023]
Abstract
Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.
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Affiliation(s)
- Mariangela Arca
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
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15
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Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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16
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Liu J, Dawe RK. Large haplotypes highlight a complex age structure within the maize pan-genome. Genome Res 2023; 33:359-370. [PMID: 36854668 PMCID: PMC10078284 DOI: 10.1101/gr.276705.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023]
Abstract
The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA;
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
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17
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Grzybowski MW, Mural RV, Xu G, Turkus J, Yang J, Schnable JC. A common resequencing-based genetic marker data set for global maize diversity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1109-1121. [PMID: 36705476 DOI: 10.1111/tpj.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Maize (Zea mays ssp. mays) populations exhibit vast ranges of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole-genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here, we employ resequencing data from 1276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of approximately 366 million segregating variants and approximately 46 million high-confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering-time genes using previously published trait data sets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.
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Affiliation(s)
- Marcin W Grzybowski
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Plant Molecular Ecophysiology, Institute of Plant Experimental Biology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ravi V Mural
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Gen Xu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jonathan Turkus
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jinliang Yang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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18
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Sun X, Xiang Y, Dou N, Zhang H, Pei S, Franco AV, Menon M, Monier B, Ferebee T, Liu T, Liu S, Gao Y, Wang J, Terzaghi W, Yan J, Hearne S, Li L, Li F, Dai M. The role of transposon inverted repeats in balancing drought tolerance and yield-related traits in maize. Nat Biotechnol 2023; 41:120-127. [PMID: 36229611 DOI: 10.1038/s41587-022-01470-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/02/2022] [Indexed: 01/21/2023]
Abstract
The genomic basis underlying the selection for environmental adaptation and yield-related traits in maize remains poorly understood. Here we carried out genome-wide profiling of the small RNA (sRNA) transcriptome (sRNAome) and transcriptome landscapes of a global maize diversity panel under dry and wet conditions and uncover dozens of environment-specific regulatory hotspots. Transgenic and molecular studies of Drought-Related Environment-specific Super eQTL Hotspot on chromosome 8 (DRESH8) and ZmMYBR38, a target of DRESH8-derived small interfering RNAs, revealed a transposable element-mediated inverted repeats (TE-IR)-derived sRNA- and gene-regulatory network that balances plant drought tolerance with yield-related traits. A genome-wide scan revealed that TE-IRs associate with drought response and yield-related traits that were positively selected and expanded during maize domestication. These results indicate that TE-IR-mediated posttranscriptional regulation is a key molecular mechanism underlying the tradeoff between crop environmental adaptation and yield-related traits, providing potential genomic targets for the breeding of crops with greater stress tolerance but uncompromised yield.
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Affiliation(s)
- Xiaopeng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanli Xiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Nannan Dou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hui Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Surui Pei
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Arcadio Valdes Franco
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Mitra Menon
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, Davis, CA, USA
| | - Brandon Monier
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Taylor Ferebee
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Tao Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Sanyang Liu
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Yuchi Gao
- Annoroad Gene Tech (Beijing) Co., Ltd, Beijing, China
| | - Jubin Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | | | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Sarah Hearne
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, Texcoco, Mexico
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
| | - Feng Li
- Hubei Hongshan Laboratory, Wuhan, China.
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China.
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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19
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Rivas JG, Gutierrez AV, Defacio RA, Schimpf J, Vicario AL, Hopp HE, Paniego NB, Lia VV. Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes. PLoS One 2022; 17:e0271424. [PMID: 36542628 PMCID: PMC9770441 DOI: 10.1371/journal.pone.0271424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The North-Western Argentina (NWA) region constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the "Banco Activo de Germoplasma INTA Pergamino, Argentina" (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.
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Affiliation(s)
- Juan Gabriel Rivas
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Angela Veronica Gutierrez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Raquel Alicia Defacio
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Pergamino, Buenos Aires, Argentina
| | - Jorge Schimpf
- Facultad de Ciencias Agrarias, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Ana Laura Vicario
- Laboratorio de Marcadores Moleculares y Fitopatología, Instituto Nacional de Semillas, (INASE), Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Veronica Viviana Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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20
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Feng X, Jia L, Cai Y, Guan H, Zheng D, Zhang W, Xiong H, Zhou H, Wen Y, Hu Y, Zhang X, Wang Q, Wu F, Xu J, Lu Y. ABA-inducible DEEPER ROOTING 1 improves adaptation of maize to water deficiency. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2077-2088. [PMID: 35796628 PMCID: PMC9616520 DOI: 10.1111/pbi.13889] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/31/2022] [Accepted: 07/03/2022] [Indexed: 05/26/2023]
Abstract
Root architecture remodelling is critical for forage moisture in water-limited soil. DEEPER ROOTING 1 (DRO1) in Oryza, Arabidopsis, and Prunus has been reported to improve drought avoidance by promoting roots to grow downward and acquire water from deeper soil. In the present study, we found that ZmDRO1 responded more strongly to abscisic acid (ABA)/drought induction in Zea mays ssp. mexicana, an ancestral species of cultivated maize, than in B73. It was proposed that this is one of the reasons why Zea mays ssp. mexicana has a more noticeable change in the downward direction angle of the root and fewer biomass penalties under water-deficient conditions. Thus, a robust, synthetic ABA/drought-inducible promoter was used to control the expression of ZmDRO1B73 in Arabidopsis and cultivated maize for drought-resistant breeding. Interestingly, ABA-inducible ZmDRO1 promoted a larger downward root angle and improved grain yield by more than 40% under water-limited conditions. Collectively, these results revealed that different responses to ABA/drought induction of ZmDRO1 confer different drought avoidance abilities, and we demonstrated the application of ZmDRO1 via an ABA-inducible strategy to alter the root architecture of modern maize to improve drought adaptation in the field.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
- Maize Research Institute, Sichuan Agricultural UniversityWenjingChina
| | - Li Jia
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yunting Cai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Huarui Guan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Dan Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Weixiao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Hao Xiong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Hanmei Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Ying Wen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yue Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Xuemei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest ChinaWenjingChina
- Maize Research Institute, Sichuan Agricultural UniversityWenjingChina
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21
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Serna L. Maize stomatal responses against the climate change. FRONTIERS IN PLANT SCIENCE 2022; 13:952146. [PMID: 36204083 PMCID: PMC9531676 DOI: 10.3389/fpls.2022.952146] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Drought and heat, in the context of climate change, are expected to increase in many agricultural areas across the globe. Among current abiotic stresses, they are the most limiting factors that influence crop growth and productivity. Maize is one of most widely produced crops of the world, being the first in grain production with a yield that exceeded 1.1 billion tons in 2021. Despite its wide distribution in semi-arid regions, it is highly vulnerable to climate change, which triggers important losses in its productivity. This article explores how maize yield may persevere through climate change by focusing on the stomatal regulation of gas exchange. The emerging picture unravels that maize copes with drought stress by reducing stomatal size and stomatal pore area, and increasing stomatal density, which, in turn, reduces transpiration and photosynthetic rate. When drought and heat co-occur, heat enhances stomatal response to drought stress. To avoid plant heat damage, the decline in stomatal aperture could trigger the expansion of the distance of action, from the longitudinal leaf veins, of ZmSHR1, which might act to positively regulate ZmSPCHs/ZmICE1 heterodimers, increasing the stomatal density. Only when drought is not very severe, elevated CO2 levels reduce yield losses. The knowledge of the upcoming climate changes together with the prediction of the developmental and physiological stomatal responses will allow not only to anticipate maize yield in the next years, but also to contribute to the correct decision-making in the management of this important crop.
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Affiliation(s)
- Laura Serna
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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22
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Ubbens J, Feldmann MJ, Stavness I, Sharpe AG. Quantitative evaluation of nonlinear methods for population structure visualization and inference. G3 GENES|GENOMES|GENETICS 2022; 12:6651067. [PMID: 35900169 PMCID: PMC9434256 DOI: 10.1093/g3journal/jkac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/20/2022] [Indexed: 11/20/2022]
Abstract
Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations in a population as a result of nonrandom mating between individuals. It can be informative of genetic ancestry, and in the context of medical genetics, it is an important confounding variable in genome-wide association studies. Recently, many nonlinear dimensionality reduction techniques have been proposed for the population structure visualization task. However, an objective comparison of these techniques has so far been missing from the literature. In this article, we discuss the previously proposed nonlinear techniques and some of their potential weaknesses. We then propose a novel quantitative evaluation methodology for comparing these nonlinear techniques, based on populations for which pedigree is known a priori either through artificial selection or simulation. Based on this evaluation metric, we find graph-based algorithms such as t-SNE and UMAP to be superior to principal component analysis, while neural network-based methods fall behind.
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Affiliation(s)
- Jordan Ubbens
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California , Davis, CA95616, USA
| | - Ian Stavness
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
- Department of Computer Science, University of Saskatchewan , Saskatoon, SKS7N 0W9, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security (GIFS), University of Saskatchewan, Saskatoon, SKS7N 0W9, Canada
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23
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild-to-crop introgression during the domestication of scarlet runner bean ( Phaseolus coccineus L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small-scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open-pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single-nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSKS7N 5A2Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
- Environmental GenomicsMax Planck Institute for Evolutionary Biology24306PlönGermany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome CenterUniversity of California, DavisDavisCalifornia95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed AmbientaliUniversità Politecnica delle MarcheAncona60131Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de México04510México
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24
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Feng X, Xiong H, Zheng D, Xin X, Zhang X, Wang Q, Wu F, Xu J, Lu Y. Identification of Fusarium verticillioides Resistance Alleles in Three Maize Populations With Teosinte Gene Introgression. FRONTIERS IN PLANT SCIENCE 2022; 13:942397. [PMID: 35909731 PMCID: PMC9331921 DOI: 10.3389/fpls.2022.942397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Fusarium ear rot (FER) is a common fungal disease in maize (Zea mays L.) caused by Fusarium verticillioides. Resistant germplasm resources for FER are rare in cultivated maize; however, teosintes (Z. mays ssp. parviglumis and Z. mays ssp. diploperennis), which are wild-type species of maize, have the potential to offer a novel source of resistance alleles to enhance pathogen resistance in modern maize. Therefore, the aim of this study was to identify favorable alleles that confer significant levels of resistance toward FER. Three populations of BC2F8 recombinant inbred lines (RILs) were developed by crossing two different teosintes, Z. diploperennis and Z. parviglumis, with maize inbred lines B73 and Zheng58, and were screened for FER resistance. We found that Z. diploperennis and Z. parviglumis had higher resistance toward F. verticillioides in the leaves than B73 and Zheng58. However, the resistance toward F. verticillioides in the leaf and ear was unrelated among RILs. FER resistance was positively correlated with grain yield in the B73 × diploperennis (BD) and Zheng58 × parviglumis (ZP) populations, partly because the quantitative trait loci (QTLs) of FER resistance and yield traits were located close together. Four coincident QTLs (qFERbd5.177, qFERbd10.140, qFERzp4.066, and qFERzp5.116) and two highly reliable resistance-yield synergistic QTLs (qFERbd10.140 and qFERzp4.066) were identified in the BD and ZP populations, opening up the possibility of breeding for FER resistance without reducing yield.
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Affiliation(s)
- Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hao Xiong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dan Zheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaobing Xin
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuemei Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
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25
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Mohammed S, Alsafadi K, Enaruvbe GO, Bashir B, Elbeltagi A, Széles A, Alsalman A, Harsanyi E. Assessing the impacts of agricultural drought (SPI/SPEI) on maize and wheat yields across Hungary. Sci Rep 2022; 12:8838. [PMID: 35614172 PMCID: PMC9132936 DOI: 10.1038/s41598-022-12799-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
This study examined the physical properties of agricultural drought (i.e., intensity, duration, and severity) in Hungary from 1961 to 2010 based on the Standardized Precipitation Index (SPI) and the Standardized Precipitation Evapotranspiration Index (SPEI). The study analyzed the interaction between drought and crop yield for maize and wheat using standardized yield residual series (SYRS), and the crop-drought resilient factor (CDRF). The results of both SPI and SPEI (-3, -6) showed that the western part of Hungary has significantly more prone to agricultural drought than the eastern part of the country. Drought frequency analysis reveals that the eastern, northern, and central parts of Hungary were the most affected regions. Drought analysis also showed that drought was particularly severe in Hungary during 1970–1973, 1990–1995, 2000–2003, and 2007. The yield of maize was more adversely affected than wheat especially in the western and southern regions of Hungary (1961–2010). In general, maize and wheat yields were severely non-resilient (CDRF < 0.8) in the central and western part of the country. The results suggest that drought events are a threat to the attainment of the second Sustainable Development Goals (SDG-2). Therefore, to ensure food security in Hungary and in other parts of the world, drought resistant crop varieties need to be developed to mitigate the adverse effects of climate change on agricultural production.
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Affiliation(s)
- Safwan Mohammed
- Institute of Land Use, Engineering and Precision Farming Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary. .,Institutes for Agricultural Research and Educational Farm, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary.
| | - Karam Alsafadi
- School of Geographical Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Glory O Enaruvbe
- African Regional Institute for Geospatial Information Science and Technology, Obafemi Awolowo University, Ile-Ife, 220282, Nigeria
| | - Bashar Bashir
- Department of Civil Engineering, College of Engineering, King Saud University, P.O. Box 800, Riyadh, 11421, Saudi Arabia
| | - Ahmed Elbeltagi
- Agricultural Engineering Dept., Faculty of Agriculture, Mansoura University, Mansoura, 35516, Egypt
| | - Adrienn Széles
- Institute of Land Use, Engineering and Precision Farming Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary
| | - Abdullah Alsalman
- Department of Civil Engineering, College of Engineering, King Saud University, P.O. Box 800, Riyadh, 11421, Saudi Arabia
| | - Endre Harsanyi
- Institute of Land Use, Engineering and Precision Farming Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary.,Institutes for Agricultural Research and Educational Farm, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary
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26
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Costa FM, Silva NCDA, Vidal R, Clement CR, Freitas FDO, Alves-Pereira A, Petroli CD, Zucchi MI, Veasey EA. Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America. ANNALS OF BOTANY 2022; 129:737-751. [PMID: 35390119 PMCID: PMC9113157 DOI: 10.1093/aob/mcac049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 03/31/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND AND AIMS The lowlands of South America appear to be remarkably important in the evolutionary history of maize, due to new evidence that suggests that maize dispersed from Mexico and arrived in this region in a state of partial domestication. This study aimed to identify dispersal patterns of maize genetic diversity in this part of the continent. METHODS A total of 170 maize accessions were characterized with 4398 single nucleotide polymorphisms (SNPs) and analysed to determine if maize dispersal was associated with types of endosperm and indigenous language families. KEY RESULTS Four genetic groups were identified in the discriminant analysis of principal components and five groups in the cluster analysis (neighbour-joining method). The groups were structured according to the predominance of endosperm types (popcorn, floury, flint/semi-flint). Spatial principal component analysis of genetic variation suggests different dispersal patterns for each endosperm type and can be associated with hypotheses of expansions of different indigenous groups. CONCLUSIONS From a possible origin in Southwestern Amazonia, different maize dispersal routes emerged: (1) towards Northern Amazonia, which continued towards the Caatinga and south-eastern Atlantic Forest (Floury); (2) towards Southern Brazil, passing through the Cerrado and Southern Atlantic Forest reaching the Pampa region (Floury); and (3) along the Atlantic Coast, following Tupi movements originating from two separate expansions: one (Tupinamba) from north to south, and the other (Guarani) in the opposite direction, from south to north (flint, floury and popcorn).
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Affiliation(s)
- Flaviane Malaquias Costa
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, 13418-900, Brazil
| | | | - Rafael Vidal
- Facultad de Agronomía, Universidad de la República, Montevideo, 12900, Uruguay
| | | | | | | | | | - Maria Imaculada Zucchi
- Secretaria de Agricultura e Abastecimento do Estado de São Paulo, Piracicaba, SP, 13400-900, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, 13418-900, Brazil
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27
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Janzen GM, Aguilar‐Rangel MR, Cíntora‐Martínez C, Blöcher‐Juárez KA, González‐Segovia E, Studer AJ, Runcie DE, Flint‐Garcia SA, Rellán‐Álvarez R, Sawers RJH, Hufford MB. Demonstration of local adaptation in maize landraces by reciprocal transplantation. Evol Appl 2022; 15:817-837. [PMID: 35603032 PMCID: PMC9108319 DOI: 10.1111/eva.13372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 11/28/2022] Open
Abstract
Populations are locally adapted when they exhibit higher fitness than foreign populations in their native habitat. Maize landrace adaptations to highland and lowland conditions are of interest to researchers and breeders. To determine the prevalence and strength of local adaptation in maize landraces, we performed a reciprocal transplant experiment across an elevational gradient in Mexico. We grew 120 landraces, grouped into four populations (Mexican Highland, Mexican Lowland, South American Highland, South American Lowland), in Mexican highland and lowland common gardens and collected phenotypes relevant to fitness and known highland-adaptive traits such as anthocyanin pigmentation and macrohair density. 67k DArTseq markers were generated from field specimens to allow comparisons between phenotypic patterns and population genetic structure. We found phenotypic patterns consistent with local adaptation, though these patterns differ between the Mexican and South American populations. Quantitative trait differentiation (Q ST) was greater than neutral allele frequency differentiation (F ST) for many traits, signaling directional selection between pairs of populations. All populations exhibited higher fitness metric values when grown at their native elevation, and Mexican landraces had higher fitness than South American landraces when grown in these Mexican sites. As environmental distance between landraces' native collection sites and common garden sites increased, fitness values dropped, suggesting landraces are adapted to environmental conditions at their natal sites. Correlations between fitness and anthocyanin pigmentation and macrohair traits were stronger in the highland site than the lowland site, supporting their status as highland-adaptive. These results give substance to the long-held presumption of local adaptation of New World maize landraces to elevation and other environmental variables across North and South America.
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Affiliation(s)
- Garrett M. Janzen
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
- Present address:
Department of Plant BiologyUniversity of GeorgiaAthensGeorgia30602USA
| | | | | | | | | | - Anthony J. Studer
- Department of Crop SciencesUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Daniel E. Runcie
- Department of Plant SciencesUniversity of California‐DavisBerkeleyCaliforniaUSA
| | - Sherry A. Flint‐Garcia
- Agricultural Research ServiceUnited States Department of AgricultureColumbiaMissouriUSA
- University of MissouriColumbiaMissouriUSA
| | - Rubén Rellán‐Álvarez
- LangebioIrapuato, GuanajuatoMexico
- Present address:
Molecular and Structural BiochemistryNorth Carolina State University128 Polk HallRaleighNorth Carolina27695‐7622USA
| | - Ruairidh J. H. Sawers
- LangebioIrapuato, GuanajuatoMexico
- Present address:
Department of Plant SciencePennsylvania State UniversityUniversity ParkPennsylvania16802USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
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The effect of different solvents and acidifying reagents on the anthocyanin profiles and antioxidant capacity of purple corn. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Filyushin MA, Khatefov EB, Kochieva EZ, Shchennikova AV. Comparative Analysis of Transcription Factor Genes liguleless1 and liguleless1-like in Teosinte and Modern Maize Accessions. RUSS J GENET+ 2022. [DOI: 10.1134/s102279542203005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Badaeva ED, Konovalov FA, Knüpffer H, Fricano A, Ruban AS, Kehel Z, Zoshchuk SA, Surzhikov SA, Neumann K, Graner A, Hammer K, Filatenko A, Bogaard A, Jones G, Özkan H, Kilian B. Genetic diversity, distribution and domestication history of the neglected GGA tA t genepool of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:755-776. [PMID: 34283259 PMCID: PMC8942905 DOI: 10.1007/s00122-021-03912-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 05/03/2023]
Abstract
We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.
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Affiliation(s)
- Ekaterina D Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Fedor A Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Agostino Fricano
- Council for Agricultural Research and Economics - Research Centre for Genomics & Bioinformatics, Fiorenzuola d'Arda (PC), Italy
| | - Alevtina S Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Zakaria Kehel
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Karl Hammer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anna Filatenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Independent Researcher, St. Petersburg, Russia
| | | | - Glynis Jones
- Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Global Crop Diversity Trust, Bonn, Germany
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Zhao S, Li X, Song J, Li H, Zhao X, Zhang P, Li Z, Tian Z, Lv M, Deng C, Ai T, Chen G, Zhang H, Hu J, Xu Z, Chen J, Ding J, Song W, Chang Y. Genetic dissection of maize plant architecture using a novel nested association mapping population. THE PLANT GENOME 2022; 15:e20179. [PMID: 34859966 DOI: 10.1002/tpg2.20179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
The leaf angle (LA), plant height (PH), and ear height (EH) are key plant architectural traits influencing maize (Zea mays L.) yield. However, their genetic determinants have not yet been well-characterized. Here, we developed a maize advanced backcross-nested association mapping population in Henan Agricultural University (HNAU-NAM1) comprised of 1,625 BC1 F4 /BC2 F4 lines. These were obtained by crossing a diverse set of 12 representative inbred lines with the common GEMS41 line, which were then genotyped using the MaizeSNP9.4K array. Genetic diversity and phenotypic distribution analyses showed considerable levels of genetic variation. We obtained 18-88 quantitative trait loci (QTLs) associated with LA, PH, and EH by using three complementary mapping methods, named as separate linkage mapping, joint linkage mapping, and genome-wide association studies. Our analyses enabled the identification of ten QTL hot-spot regions associated with the three traits, which were distributed on nine different chromosomes. We further selected 13 major QTLs that were simultaneously detected by three methods and deduced the candidate genes, of which eight were not reported before. The newly constructed HNAU-NAM1 population in this study will further broaden our insights into understanding of genetic regulation of plant architecture, thus will help to improve maize yield and provide an invaluable resource for maize functional genomics and breeding research.
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Affiliation(s)
- Sheng Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xueying Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Junfeng Song
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural Univ., Beijing, 100193, China
| | - Huimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Xiaodi Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Peng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Life Science and Technology, Guangxi Univ., Nanning, 530004, China
| | - Zhimin Li
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Zhiqiang Tian
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Meng Lv
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Ce Deng
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Tangshun Ai
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Gengshen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural Univ., Wuhan, 430070, China
| | - Hui Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jianlin Hu
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Zhijun Xu
- Zhanjiang Experiment Station, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524013, China
| | - Jiafa Chen
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Junqiang Ding
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural Univ., Zhengzhou, 450002, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural Univ., Beijing, 100193, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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Kazemi-Shahandashti SS, Mann L, El-nagish A, Harpke D, Nemati Z, Usadel B, Heitkam T. Ancient Artworks and Crocus Genetics Both Support Saffron's Origin in Early Greece. FRONTIERS IN PLANT SCIENCE 2022; 13:834416. [PMID: 35283878 PMCID: PMC8913524 DOI: 10.3389/fpls.2022.834416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Saffron crocus (Crocus sativus) is a male-sterile, triploid flower crop, and source of the spice and colorant saffron. For over three millennia, it was cultivated across the Mediterranean, including ancient Greece, Persia, and other cultures, later spreading all over the world. Despite saffron crocus' early omnipresence, its origin has been the matter of a century-old debate, in terms of area and time as well as parental species contribution. While remnants of the ancient arts, crafts, and texts still provide hints on its origin, modern genetics has the potential to efficiently follow these leads, thus shedding light on new possible lines of descent. In this review, we follow ancient arts and recent genetics to trace the evolutionary origin of saffron crocus. We focus on the place and time of saffron domestication and cultivation, and address its presumed autopolyploid origin involving cytotypes of wild Crocus cartwrightianus. Both ancient arts from Greece, Iran, and Mesopotamia as well as recent cytogenetic and comparative next-generation sequencing approaches point to saffron's emergence and domestication in ancient Greece, showing how both disciplines converge in tracing its origin.
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Affiliation(s)
- Seyyedeh-Sanam Kazemi-Shahandashti
- Institute of Biological Data Science, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany
| | - Ludwig Mann
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Abdullah El-nagish
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, Egypt
| | - Dörte Harpke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Zahra Nemati
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Björn Usadel
- Institute of Biological Data Science, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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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: 4] [Impact Index Per Article: 2.0] [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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Proteomic analysis reveals the metabolic versatility of Amycolatopsis sp. BX17: A strain native from milpa agroecosystem soil. J Proteomics 2021; 253:104461. [PMID: 34922014 DOI: 10.1016/j.jprot.2021.104461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/02/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022]
Abstract
Amycolatopsis sp. BX17 is an actinobacterium isolated from milpa soils, which antagonizes the phytopathogenic fungus Fusarium graminearum. Metabolites secreted by the actinobacterium cultured in glucose-free medium inhibited 100% of the mycelial growth of F. graminearum RH1, while the inhibition rate was 65% in medium supplemented with 20 g/L glucose. With the aim of studying how the metabolism of strain BX17 is modulated by glucose as the main carbon source, media with 0 and 20 g/L glucose were selected to analyze the intracellular proteins by quantitative label-free proteomic analysis. Data are available via ProteomeXchange with identifier PXD028644. Proteins identified in bacteria cultured in medium without glucose were involved in glutamate metabolism, the Krebs cycle and the shikimate pathway, suggesting that amino acids are metabolized to synthesize antifungal compounds. In glucose-containing medium, carbon flux was directed mainly toward the synthesis of energy and cell growth. This study shows the metabolic versatility of Amycolatopsis BX17, and strengthens its potential use in designing biotechnological strategies for phytopathogen control. SIGNIFICANCE: Amycolatopsis BX17 is a bacterium isolated from milpa agroecosystems that antagonizes the phytopathogenic fungus Fusarium graminearum. Currently, there is scarce information about the metabolism involved in the biosynthesis of antifungal agents by this genus. We used a label-free proteomic approach to identify the differences in metabolic routes for antifungal biosynthesis in Amycolatopsis BX17 grown in media with 0 and 20 g/L glucose. Taken together the results suggest that the BX17 strain could be synthesizing the antifungal metabolite(s) from the Shikimate pathway through the synthesis and degradation of the amino acid tyrosine, which is a known precursor of glycopeptides with antibiotic and antifungal activity. While the lower antifungal activity of the metabolites secreted by Amycolatopsis BX17 when grown in a medium with glucose as the main carbon source, may be correlated with a lower synthesis of antifungal compounds, due to the directing of carbon flux toward metabolic pathways involved with energy synthesis and cell growth. Likewise, it is possible that the bacteria synthesize other compounds with biological activity, such as glycopeptides with antibiotic activity. These findings are relevant because they represent the first stage to understand the metabolic regulation involved in the biosynthesis of antifungal metabolites by the genus Amycolatopsis. Finally, improving our understanding of the metabolic regulation involved in the biosynthesis of antifungal metabolites is essential to design of strategies in agricultural biotechnology for phytopathogen control.
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Oliveira GCX, Vieira ICG, Tremblay RL. Editorial: Gene Flow Among Wild and Domesticated Plant Species in the Neotropical Region. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.799071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Wang L, Josephs EB, Lee KM, Roberts LM, Rellán-Álvarez R, Ross-Ibarra J, Hufford MB. Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces. Mol Biol Evol 2021; 38:3567-3580. [PMID: 33905497 PMCID: PMC8382895 DOI: 10.1093/molbev/msab119] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.
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Affiliation(s)
- Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - Emily B Josephs
- The Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kristin M Lee
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
| | - Lucas M Roberts
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Rubén Rellán-Álvarez
- Langebio, Irapuato, Gto., Mexico
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Genome Center and Center for Population Biology, University of California, Davis, Davis, CA, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
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Huang Y, Huang W, Meng Z, Braz GT, Li Y, Wang K, Wang H, Lai J, Jiang J, Dong Z, Jin W. Megabase-scale presence-absence variation with Tripsacum origin was under selection during maize domestication and adaptation. Genome Biol 2021; 22:237. [PMID: 34416918 PMCID: PMC8377971 DOI: 10.1186/s13059-021-02448-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. RESULTS In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. CONCLUSIONS These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
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Affiliation(s)
- Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Zhuang Meng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Guilherme Tomaz Braz
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yunfei Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (MOE), Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Hai Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), Joint International Research Laboratory of Crop Molecular Breeding (MOE), China Agricultural University, Beijing, 100193, China.
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Advances in Genomics Approaches Shed Light on Crop Domestication. PLANTS 2021; 10:plants10081571. [PMID: 34451616 PMCID: PMC8401213 DOI: 10.3390/plants10081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 11/18/2022]
Abstract
Crop domestication occurred ~10,000–12,000 years ago when humans shifted from a hunter–gatherer to an agrarian society. Crops were domesticated by selecting the traits in wild plant species that were suitable for human use. Research is crucial to elucidate the mechanisms and processes involved in modern crop improvement and breeding. Recent advances in genomics have revolutionized our understanding of crop domestication. In this review, we summarized cutting-edge crop domestication research by presenting its (1) methodologies, (2) current status, (3) applications, and (4) perspectives. Advanced genomics approaches have clarified crop domestication processes and mechanisms, and supported crop improvement.
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Matus-Acuña V, Caballero-Flores G, Martínez-Romero E. The influence of maize genotype on the rhizosphere eukaryotic community. FEMS Microbiol Ecol 2021; 97:6261178. [PMID: 33930111 DOI: 10.1093/femsec/fiab066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/28/2021] [Indexed: 01/04/2023] Open
Abstract
The microbiota colonizing the rhizosphere contributes to plant growth, productivity, carbon sequestration and phytoremediation. Several studies address plant-associated bacteria; however, few studies analyze the effect of plant genotype on the eukaryotic community. Here, we analyzed the eukaryotic composition of maize rhizosphere from three different plant landraces and one inbred line grown in the same soil (common garden approach). This experimental design, coupled with 18S rDNA gene amplicon sequencing, allowed us to test the influence of maize and its genotype on the rhizosphere's eukaryotic community. We found that plant growth modified the eukaryotic community in soil, as diversity comparisons between maize rhizosphere and unplanted soil revealed significantly different eukaryotic composition. Various genera of nematodes and fungi, predominantly bacterial feeding nematodes and mycorrhizal fungi among other taxa, were increased in the rhizosphere samples. We also observed that maize genotype differentially shaped the relative abundance of the following fungal families in the rhizosphere: Acaulosporaceae, Aspergillaceae, Chaetomiaceae, Claroideoglomeraceae, Corticiaceae, Mortierellaceae, Trichocomaceae and Trichomeriaceae. Thus, plant genotype has a selective influence on establishing fungal communities in the rhizosphere. This study emphasizes the importance of an integrated consideration of plant genetics for future agricultural applications of microbes to crops.
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Affiliation(s)
- Violeta Matus-Acuña
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Gustavo Caballero-Flores
- Department of Pathology and Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Esperanza Martínez-Romero
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
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41
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Li Z, Han L, Luo Z, Li L. Single-molecule long-read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis). Mol Ecol Resour 2021; 22:272-282. [PMID: 34157795 DOI: 10.1111/1755-0998.13454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/27/2022]
Abstract
Teosinte (Zea mays ssp. parviglumis), the wild progenitor of maize (Zea mays L.), is an important germplasm resource for improvement of modern maize lines. However, we have limited genetic and genomic information about teosinte and lack state-of-the-art tools to annotate transcriptomes assembled by single-molecule long-read sequencing without a reference genome. Here, we employed single-molecule long-read sequencing of cDNA libraries from five tissues of the teosinte inbred line TIL11 and identified 70,044 nonredundant transcript isoforms. We devised a state-of-the-art, machine learning-based bioinformatics pipeline DenovoAS_Finder to annotate the TIL11 transcriptome without a complete reference genome with an accuracy of up to 91%, providing a robust gene classifier of complex genomes. Additionally, we constructed a draft TIL11 genome with 16,633 high-quality contigs and a N50 of 112 kb by Nanopore sequencing. Genes from families that expanded from teosinte to maize were significantly enriched in the gene ontology (GO) term "RNA modification pathway" and had more transcript isoforms in TIL11 than in the maize inbred line B73. Genes showed collinearity between TIL11 and B73, and intergenic regions were extensively altered by transposable elements. Our study furthers the understanding of maize domestication and provides a resource for the utilization of wild germplasm in maize breeding.
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Affiliation(s)
- Zhao Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zi Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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42
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Joint analysis of days to flowering reveals independent temperate adaptations in maize. Heredity (Edinb) 2021; 126:929-941. [PMID: 33888874 PMCID: PMC8178344 DOI: 10.1038/s41437-021-00422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 02/07/2021] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.
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43
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Zhang X, Lu M, Xia A, Xu T, Cui Z, Zhang R, Liu W, He Y. Genetic analysis of three maize husk traits by QTL mapping in a maize-teosinte population. BMC Genomics 2021; 22:386. [PMID: 34034669 PMCID: PMC8152318 DOI: 10.1186/s12864-021-07723-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The maize husk consists of numerous leafy layers and plays vital roles in protecting the ear from pathogen infection and dehydration. Teosinte, the wild ancestor of maize, has about three layers of small husk outer covering the ear. Although several quantitative trait loci (QTL) underlying husk morphology variation have been reported, the genetic basis of husk traits between teosinte and maize remains unclear. RESULTS A linkage population including 191 BC2F8 inbred lines generated from the maize line Mo17 and the teosinte line X26-4 was used to identify QTL associated with three husk traits: i.e., husk length (HL), husk width (HW) and the number of husk layers (HN). The best linear unbiased predictor (BLUP) depicted wide phenotypic variation and high heritability of all three traits. The HL exhibited greater correlation with HW than HN. A total of 4 QTLs were identified including 1, 1, 2, which are associated with HL, HW and HN, respectively. The proportion of phenotypic variation explained by these QTLs was 9.6, 8.9 and 8.1% for HL, HN and HW, respectively. CONCLUSIONS The QTLs identified in this study will pave a path to explore candidate genes regulating husk growth and development, and benefit the molecular breeding program based on molecular marker-assisted selection to cultivate maize varieties with an ideal husk morphology.
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Affiliation(s)
- Xiaolei Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China
| | - Aiai Xia
- Sanya institute of China Agricultural University, Sanya, 572025, China
| | - Tao Xu
- Tieling Academy of Agricultural Sciences, Tieling, 112000, China
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Ruiying Zhang
- Quality and Safety Institute of Agricultural Products, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Wenguo Liu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, 136100, China.
| | - Yan He
- Sanya institute of China Agricultural University, Sanya, 572025, China.
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Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, Aquino C, Nishimura K, Kobayashi F, Murata K, Kuo T, Delorean E, Poland J, Haberer G, Spannagl M, Mayer KFX, Gutierrez-Gonzalez J, Muehlbauer GJ, Monat C, Himmelbach A, Padmarasu S, Mascher M, Walkowiak S, Nakazaki T, Ban T, Kawaura K, Tsuji H, Pozniak C, Stein N, Sese J, Nasuda S, Handa H. De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes. PLANT & CELL PHYSIOLOGY 2021; 62:8-27. [PMID: 33244607 PMCID: PMC7991897 DOI: 10.1093/pcp/pcaa152] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 05/08/2023]
Abstract
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.
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Affiliation(s)
- Kentaro K Shimizu
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Dario Copetti
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Environmental Systems Science, Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Moeko Okada
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Toshiaki Tameshige
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Biology, Faculty of Science, Niigata University, Niigata, Japan
| | - Masaomi Hatakeyama
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Functional Genomics Center Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | | | - Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Fuminori Kobayashi
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
| | - Kazuki Murata
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tony Kuo
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- University of Guelph, Centre for Biodiversity Genomics, Guelph, ON, Canada
| | - Emily Delorean
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Georg Haberer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Manuel Spannagl
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München—Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Weihenstephan, Germany
| | | | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA
| | - Cecile Monat
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Sean Walkowiak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
- Canadian Grain Commission, Grain Research Laboratory, Winnipeg, MB, Canada
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, Kizugawa, Japan
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
- Department of Crop Science, Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Jun Sese
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Humanome Lab, Inc, Tokyo, Japan
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hirokazu Handa
- Division of Basic Research, Institute of Crop Science, NARO, Tsukuba, Japan
- Laboratoty of Plant Breeding, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
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Yang Y, Sang Z, Du Q, Guo Z, Li Z, Kong X, Xu Y, Zou C. Flowering time regulation model revisited by pooled sequencing of mass selection populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110797. [PMID: 33568296 DOI: 10.1016/j.plantsci.2020.110797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Maize is one of the most broadly cultivated crops throughout the world, and flowering time is a major adaptive trait for its diffusion. The biggest challenge in understanding maize flowering genetic architecture is that the trait is confounded with population structure. To eliminate the effect, we revisited the flower time genetic network by using a tropical maize population Pop32, which was under mass selection for adaptation to early flowering time in China for six generations from tropical to temperate regions. The days to anthesis (DTA) of the initial (Pop32C0), intermedia (Pop32C3), and final population (Pop32C5) was 90.77, 84.63, and 79.72 days on average, respectively. To examine the genetic mechanism and identify the genetic loci underlying this rapid change in flowering time of Pop32, we bulked 30 individuals from C0, C3, and C5 to conduct the whole genome sequencing. And we finally identified 4,973,810 high-quality single nucleotide polymorphisms (SNPs) and 6,517 genes with allele frequency significantly changed during the artificial improvement process. We speculate that these genes might participate in the adaptive improvement process and control flowering time. To identify the candidate genes for flowering time from the gene set with allele frequency changed, we carried out weighted gene co-expression network analysis (WGCNA), and identified four co-expression modules that highly associated with the flowering time development, as well as constructed the co-expression network of key flowering time genes. Gene Ontology (GO) enrichment analysis revealed that the GO terms photosynthesis/light reaction, carbohydrate binding, auxin mediated signaling pathway, response to temperature stimulus that are closely connected with flowering time. Furthermore, targeted GWAS revealed the genes are significantly connected with the flowering time. qRT-PCR of four candidate genes GRMZM2G019879, GRMZM2G055905, GRMZM2G058158, and GRMZM2G171365 showed that their expression level is similar to the flowering time genes, which playing a key role in maize flowering time transition. This study revealed that the changes of flowering time in mass selection process may be strongly associated with the variations of allele frequency changes, and we identified some important candidate genes for flowering time, which will provide a new insight for the rapid improvement of maize important agronomic traits and promote the gene cloning of maize flowering time.
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Affiliation(s)
- Yuxin Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhiqin Sang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China.
| | - Qingguo Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zifeng Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhiwei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xiuying Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Yunbi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; International Maize and Wheat Improvement Center (CIMMYT), El Batán 56130, Texcoco, Mexico.
| | - Cheng Zou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Arca M, Mary-Huard T, Gouesnard B, Bérard A, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array. FRONTIERS IN PLANT SCIENCE 2021; 11:568699. [PMID: 33488638 PMCID: PMC7817617 DOI: 10.3389/fpls.2020.568699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/12/2020] [Indexed: 05/13/2023]
Abstract
Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger's genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.
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Affiliation(s)
- Mariangela Arca
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélie Bérard
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux, Evry-Courcouronnes, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
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Archaeological Central American maize genomes suggest ancient gene flow from South America. Proc Natl Acad Sci U S A 2020; 117:33124-33129. [PMID: 33318213 PMCID: PMC7777085 DOI: 10.1073/pnas.2015560117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Maize is a global food staple with great economic and cultural importance. Archaeogenomic studies have revealed a process of protracted maize domestication and multiple waves of human-mediated dispersal in the Americas. Maize first arrived in South America as a partial domesticate, where the domestication syndrome became independently fixed and improved varieties developed away from the influence of wild gene flow. We demonstrate that hybrids of some of these improved varieties were likely reintroduced back to Central America. We hypothesize that this backflow of South American genetic material may have contributed to the development of a more productive staple, which was related to the growth and aggregation of human populations, and the formation of more complex social and political structures regionally. Maize (Zea mays ssp. mays) domestication began in southwestern Mexico ∼9,000 calendar years before present (cal. BP) and humans dispersed this important grain to South America by at least 7,000 cal. BP as a partial domesticate. South America served as a secondary improvement center where the domestication syndrome became fixed and new lineages emerged in parallel with similar processes in Mesoamerica. Later, Indigenous cultivators carried a second major wave of maize southward from Mesoamerica, but it has been unclear until now whether the deeply divergent maize lineages underwent any subsequent gene flow between these regions. Here we report ancient maize genomes (2,300–1,900 cal. BP) from El Gigante rock shelter, Honduras, that are closely related to ancient and modern maize from South America. Our findings suggest that the second wave of maize brought into South America hybridized with long-established landraces from the first wave, and that some of the resulting newly admixed lineages were then reintroduced to Central America. Direct radiocarbon dates and cob morphological data from the rock shelter suggest that more productive maize varieties developed between 4,300 and 2,500 cal. BP. We hypothesize that the influx of maize from South America into Central America may have been an important source of genetic diversity as maize was becoming a staple grain in Central and Mesoamerica.
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Crow T, Ta J, Nojoomi S, Aguilar-Rangel MR, Torres Rodríguez JV, Gates D, Rellán-Álvarez R, Sawers R, Runcie D. Gene regulatory effects of a large chromosomal inversion in highland maize. PLoS Genet 2020; 16:e1009213. [PMID: 33270639 PMCID: PMC7752097 DOI: 10.1371/journal.pgen.1009213] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 12/21/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms underlying an inversion's role in adaptation. In this study, we used large-scale transcriptomic data to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m was introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. However, the specific genetic variants and traits that underlie this adaptation are not known. We created two families segregating for the standard and inverted haplotypes of Inv4m in a common genetic background and measured gene expression effects associated with the inversion across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m across the 9 tissues, including a strong effect on the expression of genes involved in photosynthesis and chloroplast physiology. Although we could not confidently identify the causal alleles within Inv4m, this research accelerates progress towards understanding this inversion and will guide future research on these important genomic features.
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Affiliation(s)
- Taylor Crow
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - James Ta
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - Saghi Nojoomi
- Department of Plant Sciences/University of California, Davis, California, United States of America
| | - M. Rocío Aguilar-Rangel
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Corteva Agriscience, Agriculture Division of DowDuPont, Tlajomulco, Jalisco, Mexico
| | - Jorge Vladimir Torres Rodríguez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
| | - Daniel Gates
- Department of Evolution and Ecology/University of California, Davis, California, United States of America
| | - Rubén Rellán-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ruairidh Sawers
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV- IPN), Irapuato CP 36821, Guanajuato, Mexico
- Department of Plant Science, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Daniel Runcie
- Department of Plant Sciences/University of California, Davis, California, United States of America
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A Tale of Maize, Palm, and Pine: Changing Socio-Ecological Interactions from Pre-Classic Maya to the Present Day in Belize. QUATERNARY 2020. [DOI: 10.3390/quat3040030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The environmental impact of the ancient Maya, and subsequent ecological recovery following the Terminal Classic decline, have been the key foci of research into socio-ecological interactions in the Yucatán peninsula. These foci, however, belie the complex pattern of resource exploitation and agriculture associated with post-Classic Maya societies and European colonisation. We present a high-resolution, 1200-year record of pollen and charcoal data from a 52-cm short core extracted from New River Lagoon, near to the European settlement of Indian Church, northern Belize. This study complements and extends a previous 3500-year reconstruction of past environmental change, located 1-km north of the new record and adjacent to the ancient Maya site of Lamanai. This current study shows a mixed crop production and palm agroforestry management strategy of the ancient Maya, which corroborates previous evidence at Lamanai. Comparison of the two records suggests that core agricultural and agroforestry activities shifted southwards, away from the centre of Lamanai, beginning at the post-Classic period. The new record also demonstrates that significant changes in land-use were not associated with drought at the Terminal Classic (ca. CE 1000) or the European Encounter (ca. CE 1500), but instead resulted from social and cultural change in the post-Classic period (CE 1200) and new economies associated with the British timber trade (CE 1680). The changes in land-use documented in two adjacent records from the New River Lagoon underline the need to reconstruct human–environment interactions using multiple, spatially, and temporally diverse records.
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Abstract
AbstractLegume genotype (GL) x rhizobium genotype (GR) interaction in chickpea was studied using a genetically diverse set of accessions and rhizobium strains in modified Leonard Jars. A subset of effective GL x GR combinations was subsequently evaluated in a pot experiment to identify combinations of chickpea genotypes and rhizobium strains with stable and superior symbiotic performance. A linear mixed model was employed to analyse the occurrence of GL x GR interaction and an additive main effects and multiplicative interaction (AMMI) model was used to study patterns in the performance of genotype-strain combinations. We found statistically significant interaction in jars in terms of symbiotic effectiveness that was entirely due to the inclusion of one of the genotypes, ICC6263. No interaction was found in a subsequent pot experiment. The presence of two genetic groups (Kabuli and Desi genepools) did not affect interaction with Mesorhizobium strains. With the exception of a negative interaction with genotype ICC6263 in the jar experiment, the type strain Mesorhizobium ciceri LMG 14989 outperformed or equalled other strains on all chickpea genotypes in both jar and pot experiments. Similar to earlier reports in common bean, our results suggest that efforts to find more effective strains may be more rewarding than aiming for identification of superior combinations of strains and genotypes.
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