School of Biosciences

NEWSLETTER OCTOBER 2016

News and Events From the Editor…… This month we welcome 10 new Masters students on the Plant Genetic Manipulation and Crop Improvement Masters courses as well as 35 undergraduate project students in and about the Division. Kevin

A WARM WELCOME TO NEW MEMBERS OF THE PLANT AND CROP SCIENCE DIVISION.

Gunjan Sharma is a new post doc in Mike Holdsworth’s group.

The forests of Honduras, Central America, recently visited by James Pickering, a 2nd year plant science undergraduate student. Read his report on Operation Wallacea inside. Professor David Salt, our new Professor of Genome Enabled Biology.

Ojha S, Fainberg HP, Wilson V, Pelella G,

Castellanos M, May ST, Lo]o AA, Sacks H,

Symonds ME, Budge H (2016) Gene pathway development in human epicardial adipose 9ssue during early life. JCI Insight Volume: 1, Issue: 13

DOI:10.1172/jci.insight.87460

Poretska O, Yang S, Pitorre D, Rozhon W, Zwerger

K, Castellanos Uribe M, May ST, McCourt P, Poppenberger B, Sieberer T (2016) The small molecule hyperphyllin enhances leaf forma9on rate and mimics shoot meristem integrity defects associated with AMP1 deficiency. Plant Physiology 05/2016; DOI:10.1104/pp.15.01633. Ma]a C, Lewis R, Barre]-Jolley R, Labeed FH, Hughes MP, Uribe MC, May S, Miosge N, Mobsheri A. (2016) Ion channel expression and func9on in a chondrogenic progenitor cell line derived from osteoarthri9c car9lage. Osteoarthri9s and Car9lage 04/2016; 24:S141. DOI:10.1016. Bonthala VS, Mayes K, Moreton J, Blythe M, Wright V, May ST, et al. (2016) Iden9fica9on of gene modules associated with low temperatures response in bambara groundnut by networkbased analysis. PLoS ONE 11: e0148771. doi: 10.1371/journal.pone.0148771.

SOME RECENT PUBLICATIONS FROM PLANT AND CROP SCIENCES STAFF (in no particular order) Aliyu, S ; Massawe, F; Mayes, S (2016) Gene9c diversity and popula9on structure of Bambara groundnut (Vigna subterranea (L.) Verdc.): synopsis of the past two decades of analysis and implica9ons for crop improvement programmes. Gene9c Resources and Crop Evolu9on 63: 925-943. Ahmad, NS; Redjeki, ES; Ho, WK; Aliyu, S; Mayes, K; Massawe, F; Kilian, A ; Mayes, S (2016) Construc9on of a gene9c linkage map and QTL analysis in bambara groundnut. Genome 59: 459-472.

May ST, (Feb 2016) The walking dead of Pride and Prejudice and Zombies. UoN Blog. h]p://blogs.noingham.ac.uk/popularculture/ 2016/02/17/1972/ Barberon, M; Vermeer, JEM; De Bellis, D; Wang, P; Naseer, S; Andersen, TG; Humbel, BM; Nawrath, C; Takano, J; Salt, DE, Geldner N (2016) Adapta9on of root func9on by nutrient-induced plas9city of endodermal differen9a9on. Cell 164: 447-459. Passot, S; Gnacko, F; Moukouanga, D; Lucas, M; Guyomarc'h, S; Ortega, BM; Atkinson, JA; Belko, MN; Benne], MJ; Gantet, P; Wells, DM; Guedon, Y; Vigouroux, Y; Verdeil, JL; Muller, B; Laplaze, L (2016) Characteriza9on of pearl millet root architecture and anatomy reveals three types of lateral roots. Fron9ers in Plant Science Volume: 7; Ar9cle Number 829.

Plant phenotyping by machine As recently published by Pound, MP; French, AP; Fozard, JA; Murchie, EH; Pridmore, TP (2016) A patchbased approach to 3D plant shoot phenotyping. Machine Vision and Applications 27: 767-779 Special Issue: SI

Mairhofer, S; Johnson, J; Sturrock, CJ; Bennett, MJ; Mooney, SJ; Pridmore, TP (2016) Visual tracking for the recovery of multiple interacting plant root systems from X-ray CT images. Machine Vision and Applications 27: 721-734 Special Issue: S.I Cormier, F; Foulkes, J; Hirel, B; Gouache, D; Moenne-Loccoz, Y; Le Gouis, J (2016) Breeding for increased nitrogen-use efficiency: a review for wheat (T. aestivum L.). Plant Breeding 135: 255-278. adaptation. Molecular Plant 9:787-797 Arnold, BJ; Lahner, B; DaCosta, JM; Weisman, CM; Hollister, JD; Salt, DE; Bomblies, K; Yant, L (2016) Borrowed alleles and convergence in serpentine adaptation. Proceedings of the National Academy of Sciences of The United States Of America 113:8320-8325. Huang, XY; Deng, FL; Yamaji, N; Pinson, SRM; Fujii-Kashino, M; Danku, J; Douglas, A; Guerinot, ML; Salt, DE; Ma, JF (2016) A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain. Nature Communications 7 Article Number: 12138. DOI: 10.1038/ncomms12138. Published: JUL 2016 Huang X-Y, Salt DE (2016), Plant Ionomics: from elemental profiling to environmental. Molecular Plant 9:787-797.

Mustafa, MA; Ali, A; Seymour, G; Tucker, G (2016) Enhancing the antioxidant content of carambola (Averrhoa carambola) during cold storage and methyl jasmonate treatment. Postharvest Biology and Technology 118:79-86. Gallusci, P; Hodgman, C ; Teyssier, E ; Seymour, GB (2016) DNA methylation and chromatin regulation during fleshy fruit development and ripening. Frontiers in Plant Science 7 Article Number: 807, Scharr, H; Dee, H; French, AP; Tsalaris, SA (2016) Special issue on computer vision and image analysis in plant phenotyping. Machine Vision and Applica9ons 27:607-609 Special Issue: SI

NEW STUDENTS ON THE PLANT GENETICMANIPULATION OF PLANTS MASTERS COURSE

Bshayer Bedaiwi

Cristovao De Jesus Vieira Teixeira,

Eunsun Lee,

Philippa Oakden,

Shanjida Rahman

Xin Zhang

NEW STUDENTS ON THE CROP IMPROVEMENT MASTERS COURSE

Macarena Arellano Sepulveda,

Xuting Peng

Diana Carolina Garzon Obando

Samantha Yun Kai Poon,

Jack Wood Ian Taylor

THE SEQUENCED PETUNIA GENOME The first Petunia genome sequences have recently been reported in a collaborative project involving 32 labs (including my own) from 10 countries. Two species of Petunia now have draft genome sequences, Petunia axillaris and Petunia inflata. Cultivated Petunia hybrida arose from hybridisation of these two species and selection for a wide variety of colours and patterns of floral pigmentation. Petunia is the highest value ornamental bedding plant in the USA but its economic value is not the main reason for this large research effort. Rather, it is increasingly being used as a model system to study diverse aspects of plant biology, evolution and ecology. Examples that are explored in 10 supplementary papers appended to the main manuscript include: the role of miRNAs during development; the biochemistry of floral scent and anthocyanin pathways; root symbiosis with mycorrhiza and self-incompatibility. The genomes of both parental species are estimated to be 1.4 Gbp which is approximately 1.5x the genome size of tomato. One of the most interesting classes of repetitive DNA identified in the study are the numerous transposable elements, many of which are active in Petunia hybrida. The parental species have relatively low copy numbers of the well-studied dTph1 element compared to the most active lines of Petunia hybrida. This has allowed dTph1 to become an effective tool in both forward and reverse genetics. Combined with the relative ease of Agrobacterium-mediated transformation, these developments should further strengthen the contribution of Petunia as a model asterid. The genome sequences of both parental species are available on the Sol Genomics Network and can be searched using Blast or JBrowse tools.

Tim Robbins

OPERATION WALLACEA CUSUCO NATIONAL PARK, HONDURAS. Last summer James Pickering, a 2nd Year Plant Science undergraduate student went with Operation Wallacea to Honduras As you will have realised by now making the most of your time at university ultimately means doing more than just turning up to lectures. It’s about making things happen for yourself, learning how to network with researchers around the world and setting yourself up with unique skills that will ultimately set you apart from your peers. Earlier this summer I made use of Nottingham’s reputation as Britain’s ‘truly global university’ by travelling to Honduras to aid the collection of much needed carbon data. After finally arriving in Honduras after ten hours over the Atlantic and a final hop from Miami over the Caribbean, I set foot in the industrial lowland city of San Pedro Sula. Here began my real journey; never before have I seen the vegetation change so starkly before my eyes. As we left behind the open fields of the Sula Valley, dominated by large palms, our jeep was quickly consumed by the claustrophobic tangle of the humid forest that clung from the ever growing slopes. It was here that we entered the Cusuco National Park; a 23,400ha area of protected forest in the Merendon mountains of northwest Honduras. The park ranges from just above sea level in its western reaches near San Pedro Sula, to 2425m in the centre. The road trans-versed narrow ridges, the abyssal drops either side thankfully obscured by thick cloud, offering only fleeting glimpses of the agricultural landscape we had left behind. Above us branches of great trees, weighed down by the sheer volume of epiphytes, hung in the mist as the flowers of various orchids and tillandsias clung from every available space. As we climbed the temperature dropped from a balmy 37 to a more comfortable 20, although the humidity never relented. As we neared the first and lowest camp at around 1300m the vegetation changed again as conifers formed a loose canopy over a mid-story of elegant tree ferns. Cusuco encompasses several major habit types including semi-arid pine forest, moist pine forest, moist broadleaf forest and my favourite, the dwarf forest (bosque enaño) at elevations above 2000m. It is therefore rich in endemic plant species that have evolved to live on these isolated sky-islands, many of which have yet to be formally described: placing it in the top 50 most irreplaceable forest sites in the world. The park is largely funded by the ‘Carbon Credit’ scheme, which allows industrial corporations to offset their CO2 emissions by paying to protect an area of forest, which acts as a carbon sink by absorbing atmospheric CO2 and storing the carbon as polymers such as cellulose. Cusuco represents such an incredible wealth of biodiversity that carbon credits here are worth around eight times more than usual. My role in this scheme, and the whole point of making this 16,780km round trip, was to assist researchers from the UK and USA in the ongoing survey of flora and fauna of the park. Operation Wallacea have been collecting data in the park along the same transects over many years, with the aim of building baseline data about several taxa so that the effects of future climate change can be more easily validated. Furthermore, detailed analysis of the ecosystem as a whole allows the park to gain maximum funding from the carbon credits scheme. Indeed, the collection of carbon data and ecosystem surveying was possibly the most important of the tasks undertaken during our stay, as it provides an insight into the overall health of the forest and therefore its ability to both store carbon and continue to support high species richness.

My time in Cusuco was divided into two week long courses that will supplement my undergraduate studies as a Plant Scientist at The University of Nottingham. The first week comprised a series of seven lectures taught at the DNA laboratory at base camp, with associated practical exercises conducted in the surrounding cloud forest. The course provided me with a comprehensive knowledge base covering the ecology of tropical cloud forest ecosystems as well as conservation biology and biodiversity monitoring techniques for the globally important, extremely rare and unique cloud forest flora. The lecture series delivered ‘live’ results from the various teams that have been working in Cusuco National Park, and DNA samples I collected were added to the growing database. Lecture topics including species distributional modelling; using commonly used techniques such as MAXENT, population genetics, using stable isotopes to determine trophic ecology of species and estimating species richness by using genetic bar coding to describe new species. The latter is of particular importance, as without thorough identification, the vast array of floral diversity in this incredible ecosystem could well be lost before we fully understand its complexity and potential. If you are an undergraduate with an interest in conservation biology and found my article inspiring, Operation Wallacea may have just what you need! Please do not hesitate to drop me an email at [email protected] - if you would like to see more information on any of the projects available for undergrad research assistants and dissertation students please visit the website at http://opwall.com/ where you will find the full list of destinations. James Pickering

An amazing ‘stink-thorn’ type fungus.

Oncidum sp. (Orchidaceae).

Another highly poisonous member of the Solanaceae family.

The huge and beautiful flowers of Sobralia xantholeuca only last a few days, so I was overjoyed with this find!

A photo showing the incredible vegetation of the dwarf forest, particularly rich in members of Orchidaceae (orchid) and Ericaceae (blueberry) families. The vibrant red flowers belong to a species of neo-tropical blueberry that was a favourite food plant of the local wine-throated hummingbirds!

MASTERS GRADUATE

Back in September, students from the Plant Genetic Manipulation Masters, the Crop Improvement Masters and the Crop Biotechnology and Entrepreneurship Masters graduated after their success. Here they are on the day! (Back row Left to right) Paul, Tainxu, Badar, Tarik, Hua, Mohamed, Kit, Azad, Luis, Chris, Patricio (Front row Left to right) Tim, Yaser, Yang, Zinnia, Jessica, Rumiana, Findimila, Nancy, Andina, Dimitra

This Newsle]er was edited en9rely by Kevin Pyke, so any mistakes are Kevin’s fault. It is available online on the Plant and Crop Sciences web page at www.noingham.ac.uk/biosciences/subject-areas/ plantcrop/index.aspx Contribu9ons for the next issue by November 21st 2016 to be published November 22nd 2016.