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Satomura K. Tribe Paniceae Cereals with Different Ploidy Levels: Setaria italica, Panicum miliaceum, and Echinochloa esculenta. Genes (Basel) 2025; 16:426. [PMID: 40282385 PMCID: PMC12026846 DOI: 10.3390/genes16040426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/29/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025] Open
Abstract
Plants have repeatedly undergone whole-genome duplication during their evolutionary history. Even in modern plants, there is diversity in ploidy within and between species, providing a snapshot of the evolutionary turnover of ploidy. Here, I will review the diversity of ploidy and the evolution of the genome constitution, focusing on the millet species Setaria italica, Panicum miliaceum, and Echinochloa esculenta. These are all historically important cereal crops that have been domesticated in East Asia. They all display a basic chromosome set of nine, but they are diploid, tetraploid, and hexaploid, respectively. The timing of ploidy is different among the millet species, as is the extent of gene family expansion and gene loss. There also exists complex subgenomic evolution in the wild species within each genus. These three millet species and their related wild species are suitable models for elucidating the molecular evolution and diversity of genome duplication by comparative genomic analysis.
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Affiliation(s)
- Kazuhiro Satomura
- Department of BioScience, Nagahama Institute of Bio-Science and Technology, Shiga 526-0829, Japan
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2
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Kasule F, Diack O, Mbaye M, Kakeeto R, Econopouly BF. Genomic resources, opportunities, and prospects for accelerated improvement of millets. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:273. [PMID: 39565376 PMCID: PMC11579216 DOI: 10.1007/s00122-024-04777-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 10/28/2024] [Indexed: 11/21/2024]
Abstract
KEY MESSAGE Genomic resources, alongside the tools and expertise required to leverage them, are essential for the effective improvement of globally significant millet crop species. Millets are essential for global food security and nutrition, particularly in sub-Saharan Africa and South Asia. They are crucial in promoting nutrition, climate resilience, economic development, and cultural heritage. Despite their critical role, millets have historically received less investment in developing genomic resources than major cereals like wheat, maize, and rice. However, recent advancements in genomics, particularly next-generation sequencing technologies, offer unprecedented opportunities for rapid improvement in millet crops. This review paper provides an overview of the status of genomic resources in millets and in harnessing the recent opportunities in artificial intelligence to address challenges in millet crop improvement to boost productivity, nutrition, and end quality. It emphasizes the significance of genomics in tackling global food security issues and underscores the necessity for innovative breeding strategies to translate genomics and AI into effective breeding strategies for millets.
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Affiliation(s)
- Faizo Kasule
- Interdepartmental Genetics and Genomics (IGG), Iowa State University, Ames, IA, 50011, USA
| | - Oumar Diack
- Centre National de Recherches Agronomiques de Bambey (CNRA), Institut Sénégalais de Recherches Agricoles (ISRA), BP 53, Bambey, Sénégal
| | - Modou Mbaye
- Centre d'Etude Régional Pour L'Amélioration de L'Adaptation À La Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, BP 3320, Thiès, Sénégal
| | - Ronald Kakeeto
- National Agricultural Research Organization (NARO), National Semi-Arid Resources Research Institute (NaSARRI), P.O. Box 56, Soroti, Uganda
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3
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Liu Y, Cheng Z, Chen W, Wu C, Chen J, Sui Y. Establishment of genome-editing system and assembly of a near-complete genome in broomcorn millet. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1688-1702. [PMID: 38695644 DOI: 10.1111/jipb.13664] [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: 01/18/2024] [Accepted: 03/29/2024] [Indexed: 08/17/2024]
Abstract
The ancient crop broomcorn millet (Panicum miliaceum L.) is an indispensable orphan crop in semi-arid regions due to its short life cycle and excellent abiotic stress tolerance. These advantages make it an important alternative crop to increase food security and achieve the goal of zero hunger, particularly in light of the uncertainty of global climate change. However, functional genomic and biotechnological research in broomcorn millet has been hampered due to a lack of genetic tools such as transformation and genome-editing techniques. Here, we successfully performed genome editing of broomcorn millet. We identified an elite variety, Hongmi, that produces embryogenic callus and has high shoot regeneration ability in in vitro culture. We established an Agrobacterium tumefaciens-mediated genetic transformation protocol and a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated genome-editing system for Hongmi. Using these techniques, we produced herbicide-resistant transgenic plants and edited phytoene desaturase (PmPDS), which is involved in chlorophyll biosynthesis. To facilitate the rapid adoption of Hongmi as a model line for broomcorn millet research, we assembled a near-complete genome sequence of Hongmi and comprehensively annotated its genome. Together, our results open the door to improving broomcorn millet using biotechnology.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Zixiang Cheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weiyao Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chuanyin Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi Sui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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4
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Wang H, Wang J, Chen C, Chen L, Li M, Qin H, Tian X, Hou S, Yang X, Jian J, Gao P, Wang L, Qiao Z, Mu Z. A complete reference genome of broomcorn millet. Sci Data 2024; 11:657. [PMID: 38906866 PMCID: PMC11192726 DOI: 10.1038/s41597-024-03489-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
Broomcorn millet (Panicum miliaceum L.), known for its traits of drought resistance, adaptability to poor soil, short growth period, and high photosynthetic efficiency as a C4 plant, represents one of the earliest domesticated crops globally. This study reports the telomere-to-telomere (T2T) gap-free reference genome for broomcorn millet (AJ8) using PacBio high-fidelity (HiFi) long reads, Oxford Nanopore long-read technologies and high-throughput chromosome conformation capture (Hi-C) sequencing data. The size of AJ8 genome was approximately 834.7 Mb, anchored onto 18 pseudo-chromosomes. Notably, 18 centromeres and 36 telomeres were obtained. The assembled genome showed high quality in terms of completeness (BUSCO score: 99.6%, QV: 61.7, LAI value: 20.4). In addition, 63,678 protein-coding genes and 433.8 Mb (~52.0%) repetitive sequences were identified. The complete reference genome for broomcorn millet provides a valuable resource for genetic studies and breeding of this important cereal crop.
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Affiliation(s)
- Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
| | - Junjie Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | | | - Ling Chen
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Meng Li
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Huibin Qin
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Xiang Tian
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | - Sen Hou
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China
| | | | | | | | - Lun Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
| | - Zhixin Mu
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan, 030031, China.
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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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6
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Goldberg JK, Allan CW, Copetti D, Matzkin LM, Bronstein J. A pooled-sample draft genome assembly provides insights into host plant-specific transcriptional responses of a Solanaceae-specializing pest, Tupiocoris notatus (Hemiptera: Miridae). Ecol Evol 2024; 14:e10979. [PMID: 38476697 PMCID: PMC10928254 DOI: 10.1002/ece3.10979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 03/14/2024] Open
Abstract
The assembly of genomes from pooled samples of genetically heterogenous samples of conspecifics remains challenging. In this study, we show that high-quality genome assemblies can be produced from samples of multiple wild-caught individuals. We sequenced DNA extracted from a pooled sample of conspecific herbivorous insects (Hemiptera: Miridae: Tupiocoris notatus) acquired from a greenhouse infestation in Tucson, Arizona (in the range of 30-100 individuals; 0.5 mL tissue by volume) using PacBio highly accurate long reads (HiFi). The initial assembly contained multiple haplotigs (>85% BUSCOs duplicated), but duplicate contigs could be easily purged to reveal a highly complete assembly (95.6% BUSCO, 4.4% duplicated) that is highly contiguous by short-read assembly standards (N 50 = 675 kb; Largest contig = 4.3 Mb). We then used our assembly as the basis for a genome-guided differential expression study of host plant-specific transcriptional responses. We found thousands of genes (N = 4982) to be differentially expressed between our new data from individuals feeding on Datura wrightii (Solanaceae) and existing RNA-seq data from Nicotiana attenuata (Solanaceae)-fed individuals. We identified many of these genes as previously documented detoxification genes such as glutathione-S-transferases, cytochrome P450s, and UDP-glucosyltransferases. Together our results show that long-read sequencing of pooled samples can provide a cost-effective genome assembly option for small insects and can provide insights into the genetic mechanisms underlying interactions between plants and herbivorous pests.
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Affiliation(s)
- Jay K. Goldberg
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of Cellular and Developmental BiologyJohn Innes CentreNorwichNorfolkUK
| | - Carson W. Allan
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
| | - Dario Copetti
- Arizona Genomics InstituteUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
| | - Luciano M. Matzkin
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
| | - Judith Bronstein
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
- Department of EntomologyUniversity of ArizonaTucsonArizonaUSA
- BIO5 InstituteUniversity of ArizonaTucsonArizonaUSA
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7
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Liang Y, Han Y. Pan-genome brings opportunities to revitalize the ancient crop foxtail millet. PLANT COMMUNICATIONS 2024; 5:100735. [PMID: 37864332 PMCID: PMC10811366 DOI: 10.1016/j.xplc.2023.100735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/14/2023] [Accepted: 10/18/2023] [Indexed: 10/22/2023]
Affiliation(s)
- Yinpei Liang
- College of Agriculture, Shanxi Agricultural University, Taigu 030810, China; Joint Key Laboratory of Sustainable Dryland Agriculture of MOARA (with Shanxi Province), Shanxi Agricultural University, Taigu 030810, China.
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu 030810, China; Joint Key Laboratory of Sustainable Dryland Agriculture of MOARA (with Shanxi Province), Shanxi Agricultural University, Taigu 030810, China; Houji Laboratory, Shanxi Agricultural University, Taiyuan 030810, China.
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