Wheat-Thinopyrum bessarabicum recombinant lines with intercalary translocations

Introgressed Chromosome Segments in Wheat-Thinopyrum lines

Introgressed chromosome segments in Wheat-Thinopyrum lines

318. Patokar C, Sepsi A, Schwarzacher T, Kishii M, Heslop-Harrison JS. 2015. Molecular cytogenetic characterization of novel wheat-Thinopyrum bessarabicum recombinant lines carrying intercalary translocations. Chromosoma In press July 2015. 10.1007/s00412-015-0537-6 Publisher website. Version from Wheat-Thinopyrum introgression and chromosomal recombinants.

Thinopyrum bessarabicum (2n=2x=14, JJ or EbEb) is a valuable source of genes for bread wheat (2n = 6x=42) improvement because of its salinity tolerance and disease resistance. Development of wheat–Th. bessarabicum translocation lines by backcrossing the amphiploid in the absence of the Ph1 gene (allowing intergenomic recombination) can assist its utilization in wheat improvement. In this study, six novel wheat–Th. bessarabicum translocation lines involving different chromosome segments (T4BS.4BL-4JL, T6BS.6BL-6JL, T5AS.5AL-5JL, T5DL.5DS-5JS, T2BS.2BL-2JL, and the whole arm translocation T1JS.1AL) were identified and characterized using genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH). No background translocations between wheat genomes were observed. The involvement of 5 of the 7 chromosomes, and small terminal segments of Th. bessarabicum chromosome arm were important, contributing to both reduced linkage drag of the derived lines by minimizing agronomically deleterious genes from the alien species, and high stability including transmission of the alien segment. All three wheat genomes were involved in the translocations with the alien chromosome, and GISH showed the Th. bessarabicum genome was more closely related to the D genome in wheat. All the introgression lines were disomic, stable and with good morphological characters.

Keyword: FISH, cytogenetics, wheat/alien introgression, background translocation, recombinant chromosome, linkage drag, salt tolerance.

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Diversity and relationships of Crocus sativus and its relatives analysed by IRAPs

Saffron Crocus: molecular work in Leicester

Saffron Crocus: molecular work in Leicester

315. Alsayied N, Fernández JA, Schwarzacher T, Heslop-Harrison JS. 2015. Diversity and relationships of Crocus sativus and its relatives analysed by Inter Retroelement Amplified Polymorphism (IRAP). Annals of Botany In press June 2015 doi:10.1093/aob/mcv103

Crocus IRAP Diversity Nouf AlSayied Ann Bot Author VersionoufAnnBotAuthorVersion

Background and Aims: Saffron (Crocus sativus L.) is a sterile triploid (2n=3x=24) cultivated species, of unknown origin from other diploid and polyploid species in the genus Crocus (Iridaceae). Species in the genus have high morphological diversity, with no clear phylogenetic patterns below the level of section Crocus, series Crocus. Using DNA markers, we aimed to examine diversity and relationships within and between Crocus series Crocus species.

Methods: We used a total of 11 Inter-Retroelement Amplified Polymorphisms (IRAPs) primers in 63 different combinations with 35 single-plant accessions of C. sativus and related Crocus species.

Key Results: A total of 4521 distinct polymorphic bands from 100bp to ~4kb were amplified; no fragment specific to all accessions of a single species was amplified. The polymorphic information content (PIC) values varied from ~0.37 to ~0.05 (average 0.17±0.1) and the major allele frequency averaged 0.87. High levels of polymorphism were identified between accessions of the six Crocus series Crocus species related to C. sativus, with further variation between the species. In contrast, no polymorphisms were seen among 17 C. sativus accessions obtained from across the world from Kashmir through Iran to Spain.

Conclusion: In contrast to the intraspecific variability seen in other Crocus species, C. sativus has minimal genetic variation, and we conclude that the triploid hybrid species has most likely arisen only once. Our data show that saffron is an allotriploid species, with the IRAP analysis indicating that the most likely ancestors are 30 C. cartwrightianus and C. pallasii subsp. pallasii (or close relatives). The results may facilitate resynthesizing saffron with improved characteristics and show the need for conservation and collection of wild Crocus.

Keywords: Crocus, Saffron, IRAP, Retrotransposons, Markers, Crops, Polyploidy, spices, selection, crops, triploid, domestication.

Crocus IRAP Diversity Nouf AlSayied Ann Bot Author Version

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Identification and evolutionary genomics of novel LTR retrotransposons in Brassica

Brassica Copia retrotransposon motifs. Nouroz et al. 2015

Brassica Copia retrotransposon motifs. Nouroz et al. 2015

315. Nouroz F, Noreen S, Heslop-Harrison JS. 2015. Identification and evolutionary genomics of Novel LTR retrotransposons in Brassica. Turkish Journal of Biology. in press May 2015 DOI: 10.3906/biy-1501-77 (This number will become active after the manuscript has been selected for inclusion in an issue.)

Link to manuscript PDF download http://online.journals.tubitak.gov.tr/openAcceptedDocument.htm?fileID=537667&no=140181 at publisher site

Retrotransposons (REs) are the most abundant and diverse elements identified from eukaryotic genomes. Using computational and molecular methods, 262 intact LTR retrotransposons were identified from Brassica genomes by dot plot analysis and data mining. The Copia superfamily was dominant (206 elements) over Gypsy (56) with estimated intact copies of ~1596 Copia and 540 Gypsy and ~7540 Copia and 780 Gypsy from Brassica rapa and Brassica oleracea whole genome respectively. Canonical Copia and Gypsy gag-pol polyprotein organizations were observed in most elements with few displaying 1-3 additional or internally deleted domains. The PBS and PPT motifs were identified with tRNA complementary to tRNAMet, or rarely other tRNA types. PCR amplification of RT regions revealed their abundance and distribution among A, B and C-genome Brassicas indicating their origin from a common ancestor. The evolutionary relationship of Brassica REs resolved them into superfamily (Copia/Gypsy) specific lineages. The phylogenetic analysis of 130 Brassica Copia clustered them into 2 clades, 10 sub-clades of 18 families, while Gypsy elements clustered into 2 clades. The results enabled the identification and understanding of the structure and nature of full length REs and their derivatives in Brassica. The markers derived here will be useful for examining chromosome and genome evolution in Brassica.

Key words: LTR retrotransposons, Brassica, Copia, Gypsy, evolutionary relationship, RTAP markers

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Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica

Active MITEs in Brassica giving genomic diversity. Nouroz et al. 2015

Active MITEs in Brassica giving genomic diversity. Nouroz et al. 2015

317. Nouroz F, Noreen S, Heslop-Harrison JS. 2015. Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica. Molecular Genetics and Genomics (MGG) in press June 2015. DOI: 10.1007/s00438-015-1076-9

Brassica MITEs Author Version MGG download

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of  which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

 Key words: Biodiversity, Brassica, Genome evolution, Genomics, MITEs, transposable elements.

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Genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization

In situ location on chromosomes of Primula S-locus-related gene loci. Li et al. New Phyt 2015.

In situ location on chromosomes of Primula S-locus-related genes. Li et al. New Phyt 2015.

314. Li J, Webster MA, Wright J, Cocker JM, Smith MC, Badakshi F, Heslop‐Harrison P, Gilmartin PM. 2015. Integration of genetic and physical maps of the Primula vulgaris S locus and localization by chromosome in situ hybridization. New Phytologist http://onlinelibrary.wiley.com/doi/10.1111/nph.13373/full. dx.doi.org/10.1111/nph.13373

  • Heteromorphic flower development in Primula is controlled by the S locus. The S locus genes, which control anther position, pistil length and pollen size in pin and thrum flowers, have not yet been characterized. We have integrated S-linked genes, marker sequences and mutant phenotypes to create a map of the P. vulgaris S locus region that will facilitate the identification of key S locus genes. We have generated, sequenced and annotated BAC sequences spanning the S locus, and identified its chromosomal location.
  • We have employed a combination of classical genetics and three-point crosses with molecular genetic analysis of recombinants to generate the map. We have characterized this region by Illumina sequencing and bioinformatic analysis, together with chromosomein situ hybridization.
  • We present an integrated genetic and physical map across the P. vulgaris S locus flanked by phenotypic and DNA sequence markers. BAC contigs encompass a 1.5-Mb genomic region with 1 Mb of sequence containing 82 S-linked genes anchored to overlapping BACs. The S locus is located close to the centromere of the largest metacentric chromosome pair.
  • These data will facilitate the identification of the genes that orchestrate heterostyly in Primula and enable evolutionary analyses of the S locus.
    • chromosome in situ;
    • genetic map;
    • heterostyly;
    • Primula vulgaris ;
    • S locus
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Agriculture and Climate Change in Southeast Asia and the Middle East: Breeding, Climate Change Adaptation, Agronomy, and Water Security

Challenges of Climate Change that plant breeders need to address: efficient use of water promoted by terracing to avoid erosion and invasion of undesirable plants

Challenges of Climate Change that plant breeders need to address: efficient use of water promoted by terracing to avoid erosion and invasion of undesirable plants

313. Noorka IR, Heslop-Harrison JS  2014. Agriculture and Climate Change in Southeast Asia and the Middle East: Breeding, Climate Change Adaptation, Agronomy, and Water Security. In: Handbook of Climate Change Adaptation, Ed Leal Filho W. 1-8.  Springer Berlin Heidelberg http://dx.doi.org/10.1007/978-3-642-40455-9_74-1

Link to NoorkaHeslopHarrisonBreedingClimateChangeAuthorVersion with colour figures.

Link to typeset first page of publication.

The agriculture of Southeast Asia and the Middle East is under threat due to vagaries of abiotic stress including climate change and water-related factors. With a particular focus on the challenges facing non-industrialized and developing countries, this paper attempts to create a framework for policy makers and planning commissions as well as increasing national and regional water stress awareness. The study elaborates the agriculture eminence, water provision, conventional water usage, and adverse consequences of water status under the changing climatic conditions and urban or industrial development. The study addresses the nature of problems, regional issues, current barriers, farmer’s perceptions, and concrete efforts to save regional agriculture for sustainable food security. The consequences of climate change, water stress, and salinity have affected huge areas of developing countries from an economic and resource security perspective that leads to disaster and unstable law and order issues. Long-term planning over timescales beyond the human lifespan and anticipation of threats and opportunities is required. Consequently, an emergency plan is also needed for international, national, and regional footprints including procedures for climate change mitigation and to implement inclusive plans to combat prevailing poverty, social changes, and allied anticipated risks. It elaborates the attempts to provide a framework for policy makers and political understanding to check the hidden but viable issues relating risks of climate change in local and global scenario. It is concluded that a viable charter of climate proofing and domestication is the way to success from on-farm-to-lab and lab-to-field outreach to mitigate declining food issues. The regional and international collaborative efforts are focused to modernizing crop genetics, agronomy, field-to-fork scrutiny, and adaptation training to increase quantity and quality of food with sustainable use of water.

Publisher site link: http://link.springer.com/referenceworkentry/10.1007/978-3-642-40455-9_74-1

Link to NoorkaHeslopHarrisonBreedingClimateChangeAuthorVersionwith colour figures.

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Plant Virus Evolution and Pararetroviruses in Petunia

Plant Pararetrovirus insertions on chromosomes seen on the cover of "Plant Virus Evolution" book

Plant Pararetrovirus insertions on chromosomes seen on the cover of “Plant Virus Evolution” book

TS. Hohn T, Richert-Pöggeler KR, Staginnus C, Harper G, Schwarzacher T, Teo CH, Teycheney P-Y, Iskra-Caruana M-L, Hull R. 2008. Evolution of Integrated Plant Viruses. Chapter 4 pp 53-81. In: Plant Virus Evolution Ed Roossinck MJ. Springer: Berlin

Link to Publisher homepage about the book with links to downloadable copies of the whole book or the chapter.

(Freely downloadable direct links do not seem to work except via the page above: PRV Pararetrovirus chapter or as the whole book”Plant Virus Evolution” 4Mb.)

This volume has just become free on-line. Despite being 7 years old, it had enough genomic information that the pararetrovirus (EPRV Endogenous Para Retro Virus) chapter is still current in 2015. It also foreshadowed the Journal papers linked via Google Scholar at the bottom of this page.

Plant pararetroviruses replicate their genome via a transcription–reverse transcription cycle like retroviruses, but unlike them their genomes do not obligatorily integrate into the host chromatin. Nevertheless, one can find complete or fragmented pararetrovirus PRV EPRV genomes, as well as those from geminiviruses and even RNA viruses incorporated into the genomes of nearly all plants analysed. Integration events are thought to be rare and even rarer are those that find their way into the germ line. Normally, these integrated viral sequences are incomplete, rearranged and mutated and cannot easily escape as active viruses. However, in some cases apparently more recently acquired and therefore less initiated integrates can escape by direct transcription from tandem insertions or by recombination. This can lead to severe outbreaks in crop and ornamental plants. In anticipation of such events, methods have been developed for the detection and characterization of integrated virus sequences in plant genomes.

See more recent journal articles on PRVs EPRVs relating to the work overviewed in this chapter

[HTML] Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species

…, MLC Machado, M Matzke, T Schwarzacher – BMC plant …, 2007 – biomedcentral.com
How Teo 4 , Eduviges Glenda Borroto-Fernández 5 , Margit Laimer da Câmara Machado 5 , Although EPRVs are being detected in an increasing number of plant species, the detailed structure of individual EPRV integrants and
 

Fluorescent in situ hybridization to detect transgene integration into plant genomes

T Schwarzacher – Transgenic Wheat, Barley and Oats, 2009 – Springer
Wild Petunia metaphase chromosomes (2 n = 14) after FISH with an endogenous pararetrovirus, EPRV probe (labelled with biotin d-UTP and detected with streptavidin conju- gated to Alexa594, red fluorescence under green excitation (for probe description ..
 

Impact of Retroelements in Shaping the Petunia Genome

KR Richert-Pöggeler, T Schwarzacher – Petunia, 2009 – Springer .. Evidence accumulated so far indicates that integration of EPRV into the plant genome does not occur actively but as a by  form higher-order repetitive DNA structures that are amplified by mechanisms of repetitive sequence amplification
 

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