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Zhang J, Chai MF, Shabala S, Wang KH, Zhang JL. Editorial: Adaptation mechanisms of grass and forage plants to stressful environments. FRONTIERS IN PLANT SCIENCE 2023; 14:1132198. [PMID: 36824208 PMCID: PMC9942521 DOI: 10.3389/fpls.2023.1132198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Jing Zhang
- College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Mao-Feng Chai
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ke-Hua Wang
- Department of Turfgrass Science and Engineering, College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Jin-Lin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Phylogenomics and Systematics of Overlooked Mesoamerican and South American Polyploid Broad-Leaved Festuca Grasses Differentiate F. sects. Glabricarpae and Ruprechtia and F. subgen. Asperifolia, Erosiflorae, Mallopetalon and Coironhuecu (subgen. nov.). PLANTS 2022; 11:plants11172303. [PMID: 36079685 PMCID: PMC9460391 DOI: 10.3390/plants11172303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Allopolyploidy is considered a driver of diversity in subtribe Loliinae. We investigate the evolution and systematics of the poorly studied Mesoamerican and South American polyploid broad-leaved Festuca L. species of uncertain origin and unclear taxonomy. A taxonomic study of seven diagnostic morphological traits was conducted on a representation of 22 species. Phylogenomic analyses were performed on a representation of these supraspecific taxa and all other Loliinae lineages using separate data from the entire plastome, nuclear rDNA 45S and 5S genes, and repetitive DNA elements. F. subgen. Mallopetalon falls within the fine-leaved (FL) Loliinae clade, whereas the remaining taxa are nested within the broad-leaved (BL) Loliinae clade forming two separate Mexico–Central–South American (MCSAI, MCSAII) lineages. MCSAI includes representatives of F. sect. Glabricarpae and F. subgen. Asperifolia plus F. superba, and MCSAII of F. subgen. Erosiflorae and F. sect. Ruprechtia plus F. argentina. MCSAII likely had a BL Leucopoa paternal ancestor, MCSAI and MCSAII a BL Meso-South American maternal ancestor, and Mallopetalon FL, American I–II ancestors. Plastome vs. nuclear topological discordances corroborated the hybrid allopolyploid origins of these taxa, some of which probably originated from Northern Hemisphere ancestors. The observed data indicate rapid reticulate radiations in the Central–South American subcontinent. Our systematic study supports the reclassification of some studied taxa in different supraspecific Festuca ranks.
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Moreno-Aguilar MF, Inda LA, Sánchez-Rodríguez A, Arnelas I, Catalán P. Evolutionary Dynamics of the Repeatome Explains Contrasting Differences in Genome Sizes and Hybrid and Polyploid Origins of Grass Loliinae Lineages. FRONTIERS IN PLANT SCIENCE 2022; 13:901733. [PMID: 35845705 PMCID: PMC9284676 DOI: 10.3389/fpls.2022.901733] [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: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
The repeatome is composed of diverse families of repetitive DNA that keep signatures on the historical events that shaped the evolution of their hosting species. The cold seasonal Loliinae subtribe includes worldwide distributed taxa, some of which are the most important forage and lawn species (fescues and ray-grasses). The Loliinae are prone to hybridization and polyploidization. It has been observed a striking two-fold difference in genome size between the broad-leaved (BL) and fine-leaved (FL) Loliinae diploids and a general trend of genome reduction of some high polyploids. We have used genome skimming data to uncover the composition, abundance, and potential phylogenetic signal of repetitive elements across 47 representatives of the main Loliinae lineages. Independent and comparative analyses of repetitive sequences and of 5S rDNA loci were performed for all taxa under study and for four evolutionary Loliinae groups [Loliinae, Broad-leaved (BL), Fine-leaved (FL), and Schedonorus lineages]. Our data showed that the proportion of the genome covered by the repeatome in the Loliinae species was relatively high (average ∼ 51.8%), ranging from high percentages in some diploids (68.7%) to low percentages in some high-polyploids (30.7%), and that changes in their genome sizes were likely caused by gains or losses in their repeat elements. Ty3-gypsy Retand and Ty1-copia Angela retrotransposons were the most frequent repeat families in the Loliinae although the relatively more conservative Angela repeats presented the highest correlation of repeat content with genome size variation and the highest phylogenetic signal of the whole repeatome. By contrast, Athila retrotransposons presented evidence of recent proliferations almost exclusively in the Lolium clade. The repeatome evolutionary networks showed an overall topological congruence with the nuclear 35S rDNA phylogeny and a geographic-based structure for some lineages. The evolution of the Loliinae repeatome suggests a plausible scenario of recurrent allopolyploidizations followed by diploidizations that generated the large genome sizes of BL diploids as well as large genomic rearrangements in highly hybridogenous lineages that caused massive repeatome and genome contractions in the Schedonorus and Aulaxyper polyploids. Our study has contributed to disentangling the impact of the repeatome dynamics on the genome diversification and evolution of the Loliinae grasses.
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Affiliation(s)
| | - Luis A. Inda
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Instituto Agroalimentario de Aragón, Universidad de Zaragoza, Centro de Investigación y Tecnología Agroalimentaria, Zaragoza, Spain
| | - Aminael Sánchez-Rodríguez
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Itziar Arnelas
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional, Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Unidad Asociada al CSIC, Zaragoza, Spain
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Talukder SK, Saha MC. Toward Genomics-Based Breeding in C3 Cool-Season Perennial Grasses. FRONTIERS IN PLANT SCIENCE 2017; 8:1317. [PMID: 28798766 PMCID: PMC5526908 DOI: 10.3389/fpls.2017.01317] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/12/2017] [Indexed: 05/13/2023]
Abstract
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind. In this review, we discuss the currently available genomics tools and approaches useful for C3 cool-season perennial grass breeding. Along with a general review, we emphasize the discussion focusing on forage grasses that were considered orphan and have little or no genetic information available. Transcriptome sequencing and genotype-by-sequencing technology for genome-wide marker detection using next-generation sequencing (NGS) are very promising as genomics tools. Most C3 cool-season perennial grass members have no prior genetic information; thus NGS technology will enhance collinear study with other C3 model grasses like Brachypodium and rice. Transcriptomics data can be used for identification of functional genes and molecular markers, i.e., polymorphism markers and simple sequence repeats (SSRs). Genome-wide association study with NGS-based markers will facilitate marker identification for marker-assisted selection. With limited genetic information, genomic selection holds great promise to breeders for attaining maximum genetic gain of the cool-season C3 perennial grasses. Application of all these tools can ensure better genetic gains, reduce length of selection cycles, and facilitate cultivar development to meet the future demand for food and fodder.
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Majka J, Książczyk T, Kiełbowicz-Matuk A, Kopecký D, Kosmala A. Exploiting repetitive sequences and BAC clones in Festuca pratensis karyotyping. PLoS One 2017; 12:e0179043. [PMID: 28591168 PMCID: PMC5462415 DOI: 10.1371/journal.pone.0179043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Festuca genus is thought to be the most numerous genus of the Poaceae family. One of the most agronomically important forage grasses, Festuca pratensis Huds. is treated as a model plant to study the molecular mechanisms associated with tolerance to winter stresses, including frost. However, the precise mapping of the genes governing stress tolerance in this species is difficult as its karyotype remains unrecognized. Only two F. pratensis chromosomes with 35S and 5S rDNA sequences can be easily identified, but its remaining chromosomes have not been distinguished to date. Here, two libraries derived from F. pratensis nuclear DNA with various contents of repetitive DNA sequences were used as sources of molecular probes for fluorescent in situ hybridisation (FISH), a BAC library and a library representing sequences most frequently present in the F. pratensis genome. Using FISH, six groups of DNA sequences were revealed in chromosomes on the basis of their signal position, including dispersed-like sequences, chromosome painting-like sequences, centromeric-like sequences, knob-like sequences, a group without hybridization signals, and single locus-like sequences. The last group was exploited to develop cytogenetic maps of diploid and tetraploid F. pratensis, which are presented here for the first time and provide a remarkable progress in karyotype characterization.
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Affiliation(s)
- Joanna Majka
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- * E-mail:
| | - Tomasz Książczyk
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | | | - David Kopecký
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Arkadiusz Kosmala
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Thorogood D, Yates S, Manzanares C, Skot L, Hegarty M, Blackmore T, Barth S, Studer B. A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae) Population. FRONTIERS IN PLANT SCIENCE 2017; 8:1331. [PMID: 28824669 PMCID: PMC5539123 DOI: 10.3389/fpls.2017.01331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 07/17/2017] [Indexed: 05/18/2023]
Abstract
Self-incompatibility (SI) is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L.) possesses a well-documented two locus (S and Z) gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3). These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs) 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with marker sequences on Lolium LGs 3 and 6 were also identified. We therefore demonstrate the power of a novel association genetics approach to identify the genes controlling multi-locus gametophytic SI systems and to identify novel loci potentially involved in already established SI systems.
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Affiliation(s)
- Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
- *Correspondence: Daniel Thorogood
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
| | - Leif Skot
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Matthew Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Tina Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, United Kingdom
| | - Susanne Barth
- Teagasc Crops Environment and Land Use Programme, Oak Park Research CentreCarlow, Ireland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH ZurichZurich, Switzerland
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Ansari HA, Ellison NW, Bassett SA, Hussain SW, Bryan GT, Williams WM. Fluorescence chromosome banding and FISH mapping in perennial ryegrass, Lolium perenne L. BMC Genomics 2016; 17:977. [PMID: 27887567 PMCID: PMC5124321 DOI: 10.1186/s12864-016-3231-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 11/01/2016] [Indexed: 11/29/2022] Open
Abstract
Background The unambiguous identification of individual chromosomes is a key part of the genomic characterization of any species. In this respect, the development and application of chromosome banding techniques has revolutionised mammalian and especially, human genomics. However, partly because of the traditional use of chromosome squash preparations, consistent fluorescence banding has rarely been achieved in plants. Here, successful fluorescence chromosome banding has been achieved for the first time in perennial ryegrass (Lolium perenne), a forage and turf grass with a large genome and a symmetrical karyotype with chromosomes that are difficult to distinguish. Results Based on flame-dried chromosome preparations instead of squashes, a simple fluorescence Q-banding technique using quinacrine mustard, unambiguously identified each chromosome and enabled the development of a banded karyotype and ideogram of the species. This Q-banding technique was also shown to be compatible with sequential FISH mapping enabling labelled genes and molecular markers to be precisely assigned to specific cytogenetic bands. A technique for DAPI-banding, which gave a similar pattern to Q-banding, was also introduced. This was compatible with FISH mapping and was used to anchor a single copy gene from an earlier mapped linkage group of L. perenne, thus providing a step towards integration of the genetic and cytogenetic maps. Conclusions By enabling the allocation of genes mapped by other methods to physically identified chromosome positions, this work will contribute to a better understanding of genomic structures and functions in grasses.
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Affiliation(s)
- Helal A Ansari
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand.
| | - Nicholas W Ellison
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand.,, Present address: 16 Moerangi St., Palmerston North, 4410, New Zealand
| | - Shalome A Bassett
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Syed W Hussain
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Gregory T Bryan
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Warren M Williams
- AgResearch Ltd, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North, 4442, New Zealand
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Wingler A, Hennessy D. Limitation of Grassland Productivity by Low Temperature and Seasonality of Growth. FRONTIERS IN PLANT SCIENCE 2016; 7:1130. [PMID: 27512406 PMCID: PMC4962554 DOI: 10.3389/fpls.2016.01130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/15/2016] [Indexed: 06/01/2023]
Abstract
The productivity of temperate grassland is limited by the response of plants to low temperature, affecting winter persistence and seasonal growth rates. During the winter, the growth of perennial grasses is restricted by a combination of low temperature and the lack of available light, but during early spring low ground temperature is the main limiting factor. Once temperature increases, growth is stimulated, resulting in a peak in growth in spring before growth rates decline later in the season. Growth is not primarily limited by the ability to photosynthesize, but controlled by active regulatory processes that, e.g., enable plants to restrict growth and conserve resources for cold acclimation and winter survival. An insufficient ability to cold acclimate can affect winter persistence, thereby also reducing grassland productivity. While some mechanistic knowledge is available that explains how low temperature limits plant growth, the seasonal mechanisms that promote growth in response to increasing spring temperatures but restrict growth later in the season are only partially understood. Here, we assess the available knowledge of the physiological and signaling processes that determine growth, including hormonal effects, on cellular growth and on carbohydrate metabolism. Using data for grass growth in Ireland, we identify environmental factors that limit growth at different times of the year. Ideas are proposed how developmental factors, e.g., epigenetic changes, can lead to seasonality of the growth response to temperature. We also discuss perspectives for modeling grass growth and breeding to improve grassland productivity in a changing climate.
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Affiliation(s)
- Astrid Wingler
- School of Biological, Earth and Environmental Sciences, University College Cork, CorkIreland
| | - Deirdre Hennessy
- Teagasc-The Agriculture and Food Development Authority, Moorepark Animal & Grassland Research and Innovation CentreFermoy, Ireland
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Manzanares C, Yates S, Ruckle M, Nay M, Studer B. TILLING in forage grasses for gene discovery and breeding improvement. N Biotechnol 2016; 33:594-603. [PMID: 26924175 DOI: 10.1016/j.nbt.2016.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/09/2016] [Accepted: 02/12/2016] [Indexed: 01/04/2023]
Abstract
Mutation breeding has a long-standing history and in some major crop species, many of the most important cultivars have their origin in germplasm generated by mutation induction. For almost two decades, methods for TILLING (Targeting Induced Local Lesions IN Genomes) have been established in model plant species such as Arabidopsis (Arabidopsis thaliana L.), enabling the functional analysis of genes. Recent advances in mutation detection by second generation sequencing technology have brought its utility to major crop species. However, it has remained difficult to apply similar approaches in forage and turf grasses, mainly due to their outbreeding nature maintained by an efficient self-incompatibility system. Starting with a description of the extent to which traditional mutagenesis methods have contributed to crop yield increase in the past, this review focuses on technological approaches to implement TILLING-based strategies for the improvement of forage grass breeding through forward and reverse genetics. We present first results from TILLING in allogamous forage grasses for traits such as stress tolerance and evaluate prospects for rapid implementation of beneficial alleles to forage grass breeding. In conclusion, large-scale induced mutation resources, used for forward genetic screens, constitute a valuable tool to increase the genetic diversity for breeding and can be generated with relatively small investments in forage grasses. Furthermore, large libraries of sequenced mutations can be readily established, providing enhanced opportunities to discover mutations in genes controlling traits of agricultural importance and to study gene functions by reverse genetics.
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Affiliation(s)
- Chloe Manzanares
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Steven Yates
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michael Ruckle
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Michelle Nay
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland.
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Fiedler JD, Lanzatella C, Okada M, Jenkins J, Schmutz J, Tobias CM. High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing. THE PLANT GENOME 2015; 8:eplantgenome2014.10.0065. [PMID: 33228324 DOI: 10.3835/plantgenome2014.10.0065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 03/05/2015] [Indexed: 06/11/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced-representation sequencing approach by genotyping 231 F1 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.
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Affiliation(s)
- Jason D Fiedler
- USDA-ARS, Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710
| | | | - Miki Okada
- Univ. of California-Davis, 1 Shields Ave., Davis, CA, 95616
| | - Jerry Jenkins
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 358206
- Dep. of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598
| | - Jeremy Schmutz
- HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 358206
- Dep. of Energy, Joint Genome Institute, 2800 Mitchell Dr., Walnut Creek, CA, 94598
| | - Christian M Tobias
- USDA-ARS, Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710
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Rocher S, Jean M, Castonguay Y, Belzile F. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing. PLoS One 2015; 10:e0131918. [PMID: 26115486 PMCID: PMC4482585 DOI: 10.1371/journal.pone.0131918] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/08/2015] [Indexed: 02/04/2023] Open
Abstract
Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids.
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Affiliation(s)
- Solen Rocher
- Centre de Recherche et de Développement sur les Sols et les Grandes Cultures, Agriculture et agroalimentaire Canada, Quebec City (QC), Canada
| | - Martine Jean
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City (QC), Canada
| | - Yves Castonguay
- Centre de Recherche et de Développement sur les Sols et les Grandes Cultures, Agriculture et agroalimentaire Canada, Quebec City (QC), Canada
- * E-mail:
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City (QC), Canada
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Li C, Waldbieser G, Bosworth B, Beck BH, Thongda W, Peatman E. SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Mol Ecol Resour 2014; 14:1261-70. [PMID: 24797164 DOI: 10.1111/1755-0998.12272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 11/28/2022]
Abstract
Blue catfish, Ictalurus furcatus, are valued in the United States as a trophy fishery for their capacity to reach large sizes, sometimes exceeding 45 kg. Additionally, blue catfish × channel catfish (I. punctatus) hybrid food fish production has recently increased the demand for blue catfish broodstock. However, there has been little study of the genetic impacts and interaction of farmed, introduced and stocked populations of blue catfish. We utilized genotyping-by-sequencing (GBS) to capture and genotype SNP markers on 190 individuals from five wild and domesticated populations (Mississippi River, Missouri, D&B, Rio Grande and Texas). Stringent filtering of SNP-calling parameters resulted in 4275 SNP loci represented across all five populations. Population genetics and structure analyses revealed potential shared ancestry and admixture between populations. We utilized the Sequenom MassARRAY to validate two multiplex panels of SNPs selected from the GBS data. Selection criteria included SNPs shared between populations, SNPs specific to populations, number of reads per individual and number of individuals genotyped by GBS. Putative SNPs were validated in the discovery population and in two additional populations not used in the GBS analysis. A total of 64 SNPs were genotyped successfully in 191 individuals from nine populations. Our results should guide the development of highly informative, flexible genotyping multiplexes for blue catfish from the larger GBS SNP set as well as provide an example of a rapid, low-cost approach to generate and genotype informative marker loci in aquatic species with minimal previous genetic information.
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Affiliation(s)
- Chao Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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