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Wright H, Devos KM. Finger millet: a hero in the making to combat food insecurity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:139. [PMID: 38771345 PMCID: PMC11108925 DOI: 10.1007/s00122-024-04637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
Climate change and population growth pose challenges to food security. Major crops such as maize, wheat, and rice are expected to face yield reductions due to warming in the coming years, highlighting the need for incorporating climate-resilient crops in agricultural production systems. Finger millet (Eleusine coracana (L.) Gaertn) is a nutritious cereal crop adapted to arid regions that could serve as an alternative crop for sustaining the food supply in low rainfall environments where other crops routinely fail. Despite finger millet's nutritional qualities and climate resilience, it is deemed an "orphan crop," neglected by researchers compared to major crops, which has hampered breeding efforts. However, in recent years, finger millet has entered the genomics era. Next-generation sequencing resources, including a chromosome-scale genome assembly, have been developed to support trait characterization. This review discusses the current genetic and genomic resources available for finger millet while addressing the gaps in knowledge and tools that are still needed to aid breeders in bringing finger millet to its full production potential.
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Affiliation(s)
- Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Devos KM, Qi P, Bahri BA, Gimode DM, Jenike K, Manthi SJ, Lule D, Lux T, Martinez-Bello L, Pendergast TH, Plott C, Saha D, Sidhu GS, Sreedasyam A, Wang X, Wang H, Wright H, Zhao J, Deshpande S, de Villiers S, Dida MM, Grimwood J, Jenkins J, Lovell J, Mayer KFX, Mneney EE, Ojulong HF, Schatz MC, Schmutz J, Song B, Tesfaye K, Odeny DA. Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet. Nat Commun 2023; 14:3694. [PMID: 37344528 DOI: 10.1038/s41467-023-38915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/19/2023] [Indexed: 06/23/2023] Open
Abstract
Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a 'poor man's crop', finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.
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Affiliation(s)
- Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Bochra A Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Pathology, University of Georgia, Griffin, GA, 30223, USA
| | - Davis M Gimode
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
| | - Katharine Jenike
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Samuel J Manthi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Dagnachew Lule
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
- Ethiopian Agricultural Transformation Agency, Addis Ababa, Bole, Ethiopia
| | - Thomas Lux
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- UR Ventures, University of Rochester, Rochester, NY, 14627, USA
| | - Thomas H Pendergast
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Dipnarayan Saha
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- ICAR-Central Research Institute for Jute and Allied Fibers, Kolkata, West Bengal, 700120, India
| | - Gurjot S Sidhu
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hao Wang
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Jianxin Zhao
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Santosh Deshpande
- ICRISAT, Patancheru, 502 324, T.S., India
- Hytech Seed India Pvt. Ltd., Ravalkol Village, Medcahl-Malkajgiri Dist-, 501 401, Hubballi, T.S, India
| | - Santie de Villiers
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, 80108, Kenya
- Pwani University Biosciences Research Center (PUBReC), Kilifi, 80108, Kenya
| | - Mathews M Dida
- Department of Crop and Soil Science, Maseno University, P.O. 333, Maseno, Kenya
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - John Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, 85764, Neuherberg, Germany
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Emmarold E Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar Es Salaam, Tanzania
- Biotechnology Society of Tanzania, P.O. Box 10257, Dar es Salaam, Tanzania
| | - Henry F Ojulong
- ICRISAT, Matopos Research Station, P.O. Box 776, Bulawayo, Zimbabwe
| | - Michael C Schatz
- Departments of Computer Science, Biology and Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bo Song
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, P.O. Box 39063-00623, Nairobi, Kenya
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Pendergast TH, Qi P, Odeny DA, Dida MM, Devos KM. A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits. THE PLANT GENOME 2022; 15:e20175. [PMID: 34904374 DOI: 10.1002/tpg2.20175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/08/2021] [Indexed: 06/14/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.
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Affiliation(s)
- Thomas H Pendergast
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Peng Qi
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
| | - Damaris Achieng Odeny
- The International Crops Research Institute for the Semi-Arid Tropics-Eastern and Southern Africa, Nairobi, Kenya
| | - Mathews M Dida
- Dep. of Applied Sciences, Maseno Univ., Private Bag-40105, Maseno, Kenya
| | - Katrien M Devos
- Dep. of Plant Biology, Univ. of Georgia, Athens, GA, 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, Univ. of Georgia, Athens, GA, 30602, USA
- Dep. of Crop and Soil Sciences, Univ. of Georgia, Athens, GA, 30602, USA
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Zhang H, Hall N, Goertzen LR, Chen CY, Peatman E, Patel J, McElroy JS. Transcriptome Analysis Reveals Unique Relationships Among Eleusine Species and Heritage of Eleusine coracana. G3 (BETHESDA, MD.) 2019; 9:2029-2036. [PMID: 31010823 PMCID: PMC6553535 DOI: 10.1534/g3.119.400214] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/19/2019] [Indexed: 01/02/2023]
Abstract
Relationships in the genus Eleusine were obtained through transcriptome analysis. Eleusine coracana (E. coracana ssp. coracana), also known as finger millet, is an allotetraploid minor crop primarily grown in East Africa and India. Domesticated E. coracana evolved from wild E. africana (E. coracana ssp. africana) with the maternal genome donor largely supported to be E. indica; however, the paternal genome donor remains elusive. We developed transcriptomes for six Eleusine species from fully developed seedlings using Illumina technology and three de novo assemblers (Trinity, Velvet, and SOAPdenovo2) with the redundancy-reducing EvidentialGene pipeline. Mapping E. coracana reads to the chloroplast genes of all Eleusine species detected fewer variants between E. coracana and E. indica compared to all other species. Phylogenetic analysis further supports E. indica as the maternal parent of E. coracana and E. africana, in addition to a close relationship between E. indica and E. tristachya, and between E. floccifolia and E. multiflora, and E. intermedia as a separate group. A close relationship between E. floccifolia and E. multiflora was unexpected considering they are reported to have distinct nuclear genomes, BB and CC, respectively. Further, it was expected that E. intermedia and E. floccifolia would have a closer relationship considering they have similar nuclear genomes, AB and BB, respectively. A rethinking of the labeling of ancestral genomes of E. floccifolia, E. multiflora, and E. intermedia is maybe needed based on this data.
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Affiliation(s)
- Hui Zhang
- Department of Crop, Soil and Environmental Science
| | - Nathan Hall
- Department of Crop, Soil and Environmental Science
| | | | | | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849
| | - Jinesh Patel
- Department of Crop, Soil and Environmental Science
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Qi P, Gimode D, Saha D, Schröder S, Chakraborty D, Wang X, Dida MM, Malmberg RL, Devos KM. UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study. BMC PLANT BIOLOGY 2018; 18:117. [PMID: 29902967 PMCID: PMC6003085 DOI: 10.1186/s12870-018-1316-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/23/2018] [Indexed: 05/28/2023]
Abstract
BACKGROUND Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals. Furthermore, bioinformatics pipelines often lack the flexibility to deal with paired-end reads or to be applied in polyploid species. RESULTS UGbS-Flex combines publicly available software with in-house python and perl scripts to efficiently call SNPs from genotyping-by-sequencing reads irrespective of the species' ploidy level, breeding system and availability of a reference genome. Noteworthy features of the UGbS-Flex pipeline are an ability to use paired-end reads as input, an effective approach to cluster reads across samples with enhanced outputs, and maximization of SNP calling. We demonstrate use of the pipeline for the identification of several thousand high-confidence SNPs with high representation across samples in an F3-derived F2 population in the allotetraploid finger millet. Robust high-density genetic maps were constructed using the time-tested mapping program MAPMAKER which we upgraded to run efficiently and in a semi-automated manner in a Windows Command Prompt Environment. We exploited comparative GBS with one of the diploid ancestors of finger millet to assign linkage groups to subgenomes and demonstrate the presence of chromosomal rearrangements. CONCLUSIONS The paper combines GBS protocol modifications, a novel flexible GBS analysis pipeline, UGbS-Flex, recommendations to maximize SNP identification, updated genetic mapping software, and the first high-density maps of finger millet. The modules used in the UGbS-Flex pipeline and for genetic mapping were applied to finger millet, an allotetraploid selfing species without a reference genome, as a case study. The UGbS-Flex modules, which can be run independently, are easily transferable to species with other breeding systems or ploidy levels.
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Affiliation(s)
- Peng Qi
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA 30602 USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
| | - Davis Gimode
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA 30602 USA
- ICRISAT-Nairobi, P.O. Box 39063-00623, Nairobi, Kenya
- Present address: Institute of Plant Breeding, Genetics and Genomics (Department of Horticulture), Tifton, GA 31793 USA
| | - Dipnarayan Saha
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA 30602 USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
- Present address: ICAR-Central Research Institute for Jute and Allied Fibres, Kolkata, India
| | - Stephan Schröder
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA 30602 USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
- Present address: Department of Plant Sciences, North Dakota State University, Fargo, ND 58108 USA
| | | | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Mathews M. Dida
- Department of Applied Plant Sciences, Maseno University, Maseno, Kenya
| | | | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), University of Georgia, Athens, GA 30602 USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602 USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602 USA
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Prabhu KS, Das AB, Dikshit N. Assessment of genetic diversity in ragi [Eleusine coracana (L.) Gaertn] using morphological, RAPD and SSR markers. Z NATURFORSCH C 2018; 73:165-176. [PMID: 29654693 DOI: 10.1515/znc-2017-0182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 02/28/2018] [Indexed: 11/15/2022]
Abstract
Finger millet (Eleusine coracana L. Gaertn., 2n=36) is one of the most important minor crops, commonly known as 'ragi' and used as a staple food grain in more than 25 countries including Africa and south Asia. Twenty-seven accessions of ragi were collected from different parts of India and were evaluated for morpho-genetic diversity studies. Simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers were used for assessment of genetic diversity among 27 genotypes of E. coracana. High degree of similarity (90%) was obtained between 'IC49979A' and 'IC49974B' genotypes, whereas low level of similarity (9.09%) was found between 'IC204141' and 'IC49985' as evident in morphological and DNA markers. A total of 64 SSR and 301 RAPD amplicons were produced, out of which 87.50% and 77.20% DNA fragments showed polymorphism, respectively. The clustering pattern obtained among the genotypes corresponded well with their morphological and cytological data with a monophyletic origin of this species which was further supported by high bootstrap values and principal component analysis. Cluster analysis showed that ragi accessions were categorised into three distinct groups. Genotypes IC344761, IC340116, IC340127, IC49965 and IC49985 found accession specific in RAPD and SSR markers. The variation among ragi accessions might be used as potential source of germplasm for crop improvement.
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Affiliation(s)
- Kalapad Santosh Prabhu
- Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Orissa, India
| | - Anath Bandhu Das
- Department of Agricultural Biotechnology, College of Agriculture, Orissa University of Agriculture and Technology, Bhubaneswar-751003, Orissa, India.,Post Graduate Department of Botany, Utkal University, Vani Vihar, Bhubaneswar 751004, Odisha, India
| | - Nilamani Dikshit
- NBPGR Regional Station, Dr. PDKV Campus, Akola 444104, Maharastra, India
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Zhang H, Hall N, McElroy JS, Lowe EK, Goertzen LR. Complete plastid genome sequence of goosegrass (Eleusine indica) and comparison with other Poaceae. Gene 2016; 600:36-43. [PMID: 27899326 DOI: 10.1016/j.gene.2016.11.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/12/2016] [Accepted: 11/24/2016] [Indexed: 11/18/2022]
Abstract
Eleusine indica, also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively. The plastome of goosegrass has 38.19% GC content and includes 108 unique genes, of which 76 are protein-coding, 28 are transfer RNA, and 4 are ribosomal RNA. The goosegrass plastome sequence was compared to eight other species of Poaceae. Although generally conserved with respect to Poaceae, this genomic resource will be useful for evolutionary studies within this weed species and the genus Eleusine.
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Affiliation(s)
- Hui Zhang
- Department of Crop, Soil and Environmental Science, Auburn University, AL 36849, USA
| | - Nathan Hall
- Department of Biological Sciences, Auburn University, AL 36849, USA
| | - J Scott McElroy
- Department of Crop, Soil and Environmental Science, Auburn University, AL 36849, USA.
| | - Elijah K Lowe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
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Chandra D, Chandra S, Pallavi, Sharma A. Review of Finger millet (Eleusine coracana (L.) Gaertn): A power house of health benefiting nutrients. FOOD SCIENCE AND HUMAN WELLNESS 2016. [DOI: 10.1016/j.fshw.2016.05.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Agrawal R, Agrawal N, Tandon R, Raina SN. Chloroplast genes as genetic markers for inferring patterns of change, maternal ancestry and phylogenetic relationships among Eleusine species. AOB PLANTS 2014; 6:plt056. [PMID: 24790119 PMCID: PMC3924058 DOI: 10.1093/aobpla/plt056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
Assessment of phylogenetic relationships is an important component of any successful crop improvement programme, as wild relatives of the crop species often carry agronomically beneficial traits. Since its domestication in East Africa, Eleusine coracana (2n = 4x = 36), a species belonging to the genus Eleusine (x = 8, 9, 10), has held a prominent place in the semi-arid regions of India, Nepal and Africa. The patterns of variation between the cultivated and wild species reported so far and the interpretations based upon them have been considered primarily in terms of nuclear events. We analysed, for the first time, the phylogenetic relationship between finger millet (E. coracana) and its wild relatives by species-specific chloroplast deoxyribonucleic acid (cpDNA) polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and chloroplast simple sequence repeat (cpSSR) markers/sequences. Restriction fragment length polymorphism of the seven amplified chloroplast genes/intergenic spacers (trnK, psbD, psaA, trnH-trnK, trnL-trnF, 16S and trnS-psbC), nucleotide sequencing of the chloroplast trnK gene and chloroplast microsatellite polymorphism were analysed in all nine known species of Eleusine. The RFLP of all seven amplified chloroplast genes/intergenic spacers and trnK gene sequences in the diploid (2n = 16, 18, 20) and allotetraploid (2n = 36, 38) species resulted in well-resolved phylogenetic trees with high bootstrap values. Eleusine coracana, E. africana, E. tristachya, E. indica and E. kigeziensis did not show even a single change in restriction site. Eleusine intermedia and E. floccifolia were also shown to have identical cpDNA fragment patterns. The cpDNA diversity in Eleusine multiflora was found to be more extensive than that of the other eight species. The trnK gene sequence data complemented the results obtained by PCR-RFLP. The maternal lineage of all three allotetraploid species (AABB, AADD) was the same, with E. indica being the maternal diploid progenitor species. The markers specific to certain species were also identified.
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Affiliation(s)
- Renuka Agrawal
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110007, India
| | - Nitin Agrawal
- Cluster Innovation Centre, University of Delhi, Delhi 110007, India
| | - Rajesh Tandon
- Laboratory of Cellular and Molecular Cytogenetics, Department of Botany, University of Delhi, Delhi 110007, India
| | - Soom Nath Raina
- Present address: Amity Institute of Biotechnology, Amity University, Sector 125, Noida 201303, Uttar Pradesh, India
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Dida MM, Ramakrishnan S, Bennetzen JL, Gale MD, Devos KM. The genetic map of finger millet, Eleusine coracana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:321-32. [PMID: 17103137 DOI: 10.1007/s00122-006-0435-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Accepted: 10/12/2006] [Indexed: 05/12/2023]
Abstract
Restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), expressed-sequenced tag (EST), and simple sequence repeat (SSR) markers were used to generate a genetic map of the tetraploid finger millet (Eleusine coracana subsp. coracana) genome (2n = 4x = 36). Because levels of variation in finger millet are low, the map was generated in an inter-subspecific F(2) population from a cross between E. coracana subsp. coracana cv. Okhale-1 and its wild progenitor E. coracana subsp. africana acc. MD-20. Duplicated loci were used to identify homoeologous groups. Assignment of linkage groups to the A and B genome was done by comparing the hybridization patterns of probes in Okhale-1, MD-20, and Eleusine indica acc. MD-36. E. indica is the A genome donor to E. coracana. The maps span 721 cM on the A genome and 787 cM on the B genome and cover all 18 finger millet chromosomes, at least partially. To facilitate the use of marker-assisted selection in finger millet, a first set of 82 SSR markers was developed. The SSRs were identified in small-insert genomic libraries generated using methylation-sensitive restriction enzymes. Thirty-one of the SSRs were mapped. Application of the maps and markers in hybridization-based breeding programs will expedite the improvement of finger millet.
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Affiliation(s)
- Mathews M Dida
- John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
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Neves SS, Swire-Clark G, Hilu KW, Baird WV. Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT–trnF sequences. Mol Phylogenet Evol 2005; 35:395-419. [PMID: 15804411 DOI: 10.1016/j.ympev.2004.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 12/03/2004] [Accepted: 12/06/2004] [Indexed: 10/25/2022]
Abstract
Phylogenetic relationships in the genus Eleusine (Poaceae: Chloridoideae) were investigated using nuclear ITS and plastid trnT-trnF sequences. Separate and combined data sets were analyzed using parsimony, distance, and likelihood based methods, including Bayesian. Data congruence was examined using character and topological measures. Significant data heterogeneity was detected, but there was little conflict in the topological substructure measures for triplets and quartets, and resolution and clade support increased in the combined analysis. Data incongruence may be a result of noise and insufficient information in the slower evolving trnT-trnF. Monophyly of Eleusine is strongly supported in all analyses, but basal relationships in the genus remain uncertain. There is good support for a CAIK clade (E. coracana subsp. coracana and africana, E. indica, and E. kigeziensis), with E. tristachya as its sister group. Two putative ITS homeologues (A and B loci) were identified in the allotetraploid E. coracana; the 'B' locus sequence type was not found in the remaining species. Eleusine coracana and its putative 'A' genome donor, the diploid E. indica, are confirmed close allies, but sequence data contradicts the hypothesis that E. floccifolia is its second genome donor. The 'B' genome donor remains unidentified and may be extinct.
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Affiliation(s)
- Susana S Neves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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Salimath SS, Hiremath SC, Murthy HN. Genome Differentiation Patterns in Diploid Species of Elemine (Poaceae). Hereditas 2004. [DOI: 10.1111/j.1601-5223.1995.00189.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Salimath SS, de Oliveira AC, Godwin ID, Bennetzen JL. Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers. Genome 1995; 38:757-63. [PMID: 7672607 DOI: 10.1139/g95-096] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe--3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.
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Affiliation(s)
- S S Salimath
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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Abstract
Finger millet (Eleusine coracana ssp. coracana) is an annual tetraploid member of a predominantly African genus. The crop is believed to have been domesticated from the tetraploid E. coracana ssp. africana. Cytogenetic and isozyme data point to the allopolyploid nature of the species and molecular information has shown E. indica to be one of the genomic donors. A recent isozyme study questioned the proposed phylogenetic relationship between finger millet and its direct ancestor subspecies africana. An approach using random amplified polymorphic DNA (RAPD) was employed in this study to examine genetic diversity and to evaluate hypotheses concerning the evolution of domesticated and wild annual species of Eleusine. Unlike previous molecular approaches, the RAPD study revealed genetic diversity in the crop. The pattern of genetic variation was loosely correlated to geographic distribution. The allotetraploid nature of the crop was confirmed and molecular markers that can possibly identify the other genomic donor were proposed. Genotypes of subspecies africana did not group closely with those of the crop but showed higher affinities to E. indica, reflecting the pattern of similarity revealed by the isozyme study. The multiple origin of subspecies africana could explain the discrepancy between the isozyme-RAPD evidence and previous information. The RAPD study showed the close genetic affinity of E. tristachya to the E. coracana--E. indica group and understood the distinctness of E. multiflora.
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Affiliation(s)
- K W Hilu
- Department of Biology, Virginia Polytechnic Institute, Blacksburg, USA
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Murthy HN, Hiremath SC, Salimath SS. Origin, evolution and genome differentiation in Guizotia abyssinica and its wild species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1993; 87:587-592. [PMID: 24190353 DOI: 10.1007/bf00221882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/1993] [Accepted: 05/17/1993] [Indexed: 06/02/2023]
Abstract
Guizotia abyssinica, G. schimperi and G. scabra are diploid species (2n=2x=30) characterised by 15 bivalents during prophase-I/metaphase-I of meiosis. The former species is cultivated whereas the latter two are wild. Interspecific hybrids between these three species were generated and the F1 hybrids were analysed to assess cytogenetic relationships and crop evolution within the genus Guizotia. Meiotic chromosome configurations at diakenesis/metaphase-I in the pollen mother cells of hybrids averaged 0.25I + 14.60II + 0.15IV for G. abyssinica x G. schimperi, 0.05I + 13.6II + 0.14III + 0.58IV for G. abyssinica x G. scabra, and 0.8I + 12.7II + 0.08III + 0.88IV for G. schimperi x G. scabra. Based upon the results of our investigations we conclude that the genomes of G. abyssinica and G. schimperi are similar and homologous, whereas the G. scabra genome is only partially homologous to that of G. abyssinica/G. schimperi. Furthermore, the crop species G. abyssinica might have originated from G. schimperi through selection and cultivation; chromosome translocations appear to have played a significant role in the divergence and differentiation of these three species.
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Affiliation(s)
- H N Murthy
- Department of Botany, Karnatak University, 580003, Dharwad, India
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