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 Noorka Heslop-Harrison Breeding for Climate Change Author Version 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 Noorka Heslop-Harrison Breeding for Climate Change Author Version with colour figures.

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  6. Fischer G, Shah M, van Velthuizen H (2002) Climate change and agricultural vulnerability. In: International institute for applied systems analysis. Report prepared under UN Institutional Contract Agreement 1113 for World Summit on Sustainable Development, Luxemburg
  7. Hampel J (2006) Different concepts of risk – a challenge for risk communication. Int J Med Microbiol 296:5–10 CrossRef
  8. Heslop-Harrison JS, Schwarzacher T (2012) Genetics and genomics of crop domestication (archive preprint). (Published version). In: Altman A (ed) Plant biotechnology and agriculture: prospects for the 21st century. Paul Michael Hasegawa, pp 3–18. http://dx.doi.org/10.1016/B978-0-12-381466-1.00001-8
  9. IPCC (2007) Summary for policymakers: C. Current knowledge about future impacts. In: Parry ML et al (eds) Climate change 2007: impacts, adaptation and vulnerability. Contribution of working group II to the fourth assessment report of the intergovernmental panel on climate change. Cambridge University Press, New York
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  18. Noorka IR, Batool A, AlSultan S, Tabasum S, Ali A (2013a) Water stress tolerance, its relationship to assimilate partitioning and potence ratio in spring wheat. Am J Plant Sci 4(2):231–237. doi:10.4236/ajps.2013.42030 CrossRef
  19. Noorka IR, Tabassum S, Afzal M (2013b) Detection of genotypic variation in response to water stress at seedling stage in escalating selection intensity for rapid evaluation of drought tolerance in wheat breeding. Pak J Bot 45(1):99–104
  20. O’Brien K, Sygna L, Leichenko R, Adger WN, Barnett J, Mitchell T, Schipper L, Tanner T, Vogel C, Mortreux C (2008) Disaster risk reduction, climate change adaptation and human security, a commissioned report for the Norwegian Ministry of Foreign Affairs. GECHS Report 2008, 3
  21. One world Sustainable Investments (2008) A climate change strategy and action plan for the Western Cape, Report commissioned by the Provincial Government of the Western Cape. Department of Environmental Affairs and Development Planning, Western Cape
  22. Pahl-Whost C (2007) Transition towards adaptive management of water facing climate and global change. Water Res Manag 21:49–62 CrossRef
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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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Descriptors for Crocus (Crocus spp.)

Descriptors for Crocus species morphology

Descriptors for Crocus species morphology

312. Molina RV, Guardiola JL, García-Luis D, Renau-Morata B, Sanchis E, González-Nebauer S, de los Mozos M, Rodríguez-Conde MF, Santana O, Pastor-Férriz MT, Fernández JA, Santaella M, Roldán M, Tsimidou M, Polissiou M, Heslop-Harrison JS, Branca F, Mathew B. 2015. Descriptors for Crocus (Crocus spp.). 74pp. Bioversity International, Rome. ISBN-13: 978-92-9043-999-8

Full document:

http://www.bioversityinternational.org/uploads/tx_news/Descriptors_for_Crocus_1872_01.pdf

Abstract and summary:

http://www.bioversityinternational.org/e-library/publications/detail/descriptors-for-crocus-emcrocus-emsppemememem/

Conservation of saffron and allies is particularly concerning because of the shrinking of their populations both in the wild and in cultivated areas. In this regard, the descriptors developed for these species represent a valuable instrument for a better comprehension of these dwindling resources in support of their enhanced conservation and use and following the international agreed protocol of Bioversity International. A list of descriptors based on evaluation studies carried out on saffron and Crocus accessions and taking into account taxonomic criteria for this genus have been developed within the framework of the EU funded Programme AGRI GEN RES, (Action 018, www.crocusbank.org), coordinated by the Universidad de Castilla-La Mancha (Spain). One of the main achievements of this Programme has been the creation of the World Saffron and Crocus Collection, maintained by the Bank of Plant Germplasm of Cuenca, which belongs to the Junta de Comunidades de Castilla – La Mancha (Spain).

The Crocus genus is part of the Iridaceae family and consists of more than 88 corm-bearing perennial species distributed from Central and Southern Europe, to North Africa, Southwest Asia and Western China, with the centre of species diversity located in Asia Minor and the Balkan Peninsula (Mathew 1982; Goldblatt et al., 2008; Petersen et al., 2008; Harpke et al., 2013). Many Crocus species are highly appreciated as garden plants for their colourful flowers, but the genus is mainly known for the species C. sativus, commercially cultivated for the production of saffron, the world’s most expensive spice (Fernández 2004). Saffron has been widely known since the pre-Hellenic and Hellenic periods.

Download full book from:

http://www.bioversityinternational.org/uploads/tx_news/Descriptors_for_Crocus_1872_01.pdf

Download webpage with abstract, background and summary with link to full book:

http://www.bioversityinternational.org/e-library/publications/detail/descriptors-for-crocus-emcrocus-emsppemememem/

Local copy of book: Descriptors for Crocus species morphology

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Diversity and characters in Ethiopian linseed Linum #PAGXXIII Negash Worku

Worku looking at linseed Linum trails in Ethiopia

Worku looking at linseed Linum trails in Ethiopia

Many people have talked about Orphan crops – those where there has been little genetic or other research – and the characterization, evaluation and exploitation of germplasm at the #PAGXXIII Plant and Animal Genome Conference this week. Today, I am talking about work by Negash Worku on the Diversity and Characters in Ethiopian Linseed Accessions. SLIDES BELOW!

Ethiopia is a centre of diversity for linseed, where it is valued for cultural reasons as well as use as food and for export. Limited amounts of the crop are grown widely in Ethiopia, which includes the unique climatic conditions of the tropical highlands (3-15°N, >2000m). A range of some 200 accessions were evaluated for diverse quality, agronomic and morphological traits. They were also genotyped with IRAP (InterRetroelement Amplified Polymorphisms). It is probable that the genetic diversity in this area has not been exploited in breeding programmes. The results show a range of characters which can be exploited, some appropriate for smallholder and commercial farmers in Ethiopia, producing a sustainable, secure, high-value crop meeting agricultural, economic and cultural needs. Analysis of sequence data is likely to allow identification of probes suitable for chromosome identification and potentially tracking chromosomes in breeding programmes.
http://www.slideshare.net/PatHeslopHarrison/slideshelf

The slides are on Slideshare, http://www.slideshare.net/PatHeslopHarrison/linseed-linum-or-flax-morphological-molecular-diversity-in-ethiopia-pagxxiii-talk-worku-heslopharrison

Linked here on Molcyt.org there is a preprint of the first paper reporting this work.

Our work with Ethiopian germplasm and the farmer-led trials is overviewed here.

A related post on food security, our interests and needs in water usage and drought is here.

 

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Transposable Elements in the Musa and Banana Genome: PAGXXIII conference talk

There has been a lot of talk about transposable elements during the Plant and Animal Genome #PAGXXIII meeting this week. As half or more – often 75% – of all the DNA in a plant or animal genome is typically made of class I retrotransposons and class II DNA transposons, this widespread interest is right! My own talk at the Banana genomics session, now live on Slideshare, was one of many of the transposon talks. I focussed on a class of DNA elements, the hAT transposons, where the abundance, diversity and chromosomal localization has not been studied in detail in many species where the hAT elements and their derived MITEs with the major gene deleted. The talk is here: http://www.slideshare.net/PatHeslopHarrison/banana-transposable-elements-the-hat-dna-element-story-pagxxiii

It overviews our work on transposable elements in the Musa or banana genome, using genomic sequence, bioinformatics, diversity panels and in situ hybridization approaches.

References to the work are given at the end of the slideshare.

 

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2014 in review: Molecular cytogenetics website activity

The WordPress.com stats helper monkeys prepared a 2014 annual report for this blog. Obviously, my New Year’s Resolution must be to put more of the things I do onto the Molcyt.com website, and not have such long gaps. Of course, half-a-dozen posts of more general interest was also put onto AoBBlog.com and I’ll be planning to post more there as well!

Here’s an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 9,500 times in 2014. If it were a concert at Sydney Opera House, it would take about 4 sold-out performances for that many people to see it.

Click here to see the complete report.

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