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Betekhtin A, Hus K, Rojek-Jelonek M, Kurczynska E, Nibau C, Doonan JH, Hasterok R. In Vitro Tissue Culture in Brachypodium: Applications and Challenges. Int J Mol Sci 2020; 21:E1037. [PMID: 32033195 PMCID: PMC7037373 DOI: 10.3390/ijms21031037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 01/29/2023] Open
Abstract
Brachypodium distachyon has become an excellent model for plant breeding and bioenergy grasses that permits many fundamental questions in grass biology to be addressed. One of the constraints to performing research in many grasses has been the difficulty with which they can be genetically transformed and the generally low frequency of such transformations. In this review, we discuss the contribution that transformation techniques have made in Brachypodium biology as well as how Brachypodium could be used to determine the factors that might contribute to transformation efficiency. In particular, we highlight the latest research on the mechanisms that govern the gradual loss of embryogenic potential in a tissue culture and propose using B. distachyon as a model for other recalcitrant monocots.
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Affiliation(s)
- Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Karolina Hus
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Magdalena Rojek-Jelonek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Ewa Kurczynska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
| | - Candida Nibau
- National Plant Phenomics Centre, IBERS, Aberystwyth University, Aberystwyth SY23 3EE, UK; (C.N.); (J.H.D.)
| | - John H. Doonan
- National Plant Phenomics Centre, IBERS, Aberystwyth University, Aberystwyth SY23 3EE, UK; (C.N.); (J.H.D.)
| | - Robert Hasterok
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 28 Jagiellonska Street, 40-032 Katowice, Poland; (K.H.); (M.R.-J.); (E.K.); (R.H.)
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Čerenak A, Kolenc Z, Sehur P, Whittock SP, Koutoulis A, Beatson R, Buck E, Javornik B, Škof S, Jakše J. New Male Specific Markers for Hop and Application in Breeding Program. Sci Rep 2019; 9:14223. [PMID: 31578340 PMCID: PMC6775077 DOI: 10.1038/s41598-019-50400-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 09/06/2019] [Indexed: 11/26/2022] Open
Abstract
Male specific DNA sequences were selected from a Diversity Arrays Technology (DArT) mapping study to evaluate their suitability for determination of the sex phenotype among young seedlings in a hop (Humulus lupulus L.) breeding program. Ten male specific DArT markers showed complete linkage with male sex phenotype in three crossing families. Following optimization, four were successfully converted into PCR markers and a multiplex PCR approach for their use was developed. Among 197 plants (97 from the world collection; 100 from three segregating families), 94-100% positive correlation with sex phenotypic data was achieved for the single PCR amplification, whereas the multiplex approach showed 100% correlation. To develop a fast and low-cost method, crude sample multiplex PCR was evaluated in 253 progenies from 14 segregating populations without losing accuracy. The study describes, for the first time, the routine application of molecular markers linked to male sex in an intensive Slovenian hop breeding program. The methods described could be employed for screening of sex at the seedling stage in other hop programs worldwide, thereby saving resources for desirable female plants.
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Affiliation(s)
- Andreja Čerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia.
| | - Zala Kolenc
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia
| | - Petra Sehur
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, 3310, Žalec, Slovenia
| | - Simon P Whittock
- Hop Products Australia, 446 Elizabeth Street Hobart, Tasmania & School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, Australia
| | - Anthony Koutoulis
- University of Tasmania, School of Natural Sciences, Private Bag 55, Hobart, TAS, 7001, Australia
| | - Ron Beatson
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Emily Buck
- The New Zealand Institute for Plant & Food Research Limited, Palmerston North Research Centre, Private Bag 11600, Palmerston North, 4442, New Zealand
| | - Branka Javornik
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Suzana Škof
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Agronomy Department, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
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Velmurugan J, Milbourne D, Connolly V, Heslop-Harrison JS, Anhalt UCM, Lynch MB, Barth S. An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping. FRONTIERS IN PLANT SCIENCE 2018; 9:717. [PMID: 29904390 PMCID: PMC5991167 DOI: 10.3389/fpls.2018.00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.
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Affiliation(s)
- Janaki Velmurugan
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Dan Milbourne
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
| | - Vincent Connolly
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
| | - J. S. Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ulrike C. M. Anhalt
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - M. B. Lynch
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Susanne Barth
- Crops Environment and Land Use Programme, Oak Park Research Centre, Teagasc – The Irish Agriculture and Food Development Authority, Carlow, Ireland
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Harper J, Phillips D, Thomas A, Gasior D, Evans C, Powell W, King J, King I, Jenkins G, Armstead I. B chromosomes are associated with redistribution of genetic recombination towards lower recombination chromosomal regions in perennial ryegrass. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1861-1871. [PMID: 29635481 PMCID: PMC6019035 DOI: 10.1093/jxb/ery052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/10/2018] [Indexed: 05/26/2023]
Abstract
Supernumerary 'B' chromosomes are non-essential components of the genome present in a range of plant and animal species-including many grasses. Within diploid and polyploid ryegrass and fescue species, including the forage grass perennial ryegrass (Lolium perenne L.), the presence of B chromosomes has been reported as influencing both chromosome pairing and chiasma frequencies. In this study, the effects of the presence/absence of B chromosomes on genetic recombination has been investigated through generating DArT (Diversity Arrays Technology) marker genetic maps for six perennial ryegrass diploid populations, the pollen parents of which contained either two B or zero B chromosomes. Through genetic and cytological analyses of these progeny and their parents, we have identified that, while overall cytological estimates of chiasma frequencies were significantly lower in pollen mother cells with two B chromosomes as compared with zero B chromosomes, the recombination frequencies within some marker intervals were actually increased, particularly for marker intervals in lower recombination regions of chromosomes, namely pericentromeric regions. Thus, in perennial ryegrass, the presence of two B chromosomes redistributed patterns of meiotic recombination in pollen mother cells in ways which could increase the range of allelic variation available to plant breeders.
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Affiliation(s)
- John Harper
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dylan Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ann Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Dagmara Gasior
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Caron Evans
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Julie King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Ian King
- School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Glyn Jenkins
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Ian Armstead
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
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DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling. BMC Genet 2018; 19:10. [PMID: 29357832 PMCID: PMC5778656 DOI: 10.1186/s12863-017-0589-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/19/2017] [Indexed: 01/28/2023] Open
Abstract
Background Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank. Due to the heterogeneous nature of Lolium accessions, bulk samples were used. Apart from germplasm set I, additional set II and set III was used to determine the reproducibility of marker system and judge the feasibility of bulk strategy in this study. Results By assessing different bulk sizes, 24 individuals per sample were shown to be a representative number of plants to discriminate different accessions. Among the 297 accessions, all marker types revealed a high polymorphism rate; 1.99, 2.00 and 8.19 alleles, were obtained per locus on average using DArTs, SNPs and SSRs, respectively. The Jaccard distance for DArT markers ranged from 0.00 to 0.73, the Modified Roger’s distance (MRD) for SNP markers ranged from 0.03 to 0.52, and for SSR markers from 0.26 to 0.76. Gene diversity for dominant DArT and co-dominant SNP and SSR markers was found to be 0.26, 0.32 and 0.45, respectively. DArT markers showed the highest consistency and reproducibility. Conclusion The resulting data were evaluated using a number of different classification methods, but none of the methods showed a clear differentiation into distinct genetic pools. With regard to hybrid breeding, this will possibly impede substantial progress towards increased biomass yields of L. perenne by utilising heterosis. Electronic supplementary material The online version of this article (10.1186/s12863-017-0589-0) contains supplementary material, which is available to authorized users.
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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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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Li F, Zhou C, Weng Q, Li M, Yu X, Guo Y, Wang Y, Zhang X, Gan S. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus. PLoS One 2015; 10:e0145144. [PMID: 26695430 PMCID: PMC4687840 DOI: 10.1371/journal.pone.0145144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/01/2015] [Indexed: 02/06/2023] Open
Abstract
Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.
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Affiliation(s)
- Fagen Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Changpin Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Qijie Weng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Mei Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaoli Yu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yong Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Yu Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Xiaohong Zhang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
| | - Siming Gan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China
- * E-mail:
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Kopecký D, Studer B. Emerging technologies advancing forage and turf grass genomics. Biotechnol Adv 2013; 32:190-9. [PMID: 24309540 DOI: 10.1016/j.biotechadv.2013.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 11/18/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
Grassland is of major importance for agricultural production and provides valuable ecosystem services. Its impact is likely to rise in changing socio-economic and climatic environments. High yielding forage grass species are major components of sustainable grassland production. Understanding the genome structure and function of grassland species provides opportunities to accelerate crop improvement and thus to mitigate the future challenges of increased feed and food demand, scarcity of natural resources such as water and nutrients, and high product qualities. In this review, we will discuss a selection of technological developments that served as main drivers to generate new insights into the structure and function of nuclear genomes. Many of these technologies were originally developed in human or animal science and are now increasingly applied in plant genomics. Our main goal is to highlight the benefits of using these technologies for forage and turf grass genome research, to discuss their potentials and limitations as well as their relevance for future applications.
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Affiliation(s)
- David Kopecký
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany, Šlechtitelů 31, CZ-78371, Olomouc-Holice, Czech Republic
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, Universitaetsstrasse 2, 8092 Zurich, Switzerland.
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