Tag Archives: genetics

A new day dawning: Hemerocallis as a model organism

Hemerocallis Genetic model organisms have revolutionized science, and today, with the rapid advances in technology, there is significant potential to launch many more plant species towards model status. However, these new model organisms have to be carefully selected.

Hemerocallis (the daylily) satisfies multiple criteria for selection and deserves serious consideration as a subject of intensive biological investigation. Several attributes of the genus are of great biological interest. These include the strict control of flower opening and, within a short period, the precisely regulated floral death by a programmed cell death system. The self-incompatibility system in Hemerocallis is also noteworthy and deserves more attention. Importantly, the genus is widely cultivated for food, medicinal value and ornamental interest. Hemerocallis has considerable potential as a ‘nutraceutical’ food plant and the source of new compounds with biomedical activity. The genus has also been embraced by ornamental plant breeders and the extraordinary morphological diversity of hybrid cultivars, produced within a relatively short time by amateur enthusiasts, is an exceptional resource for botanical and genetic studies.

This paper in AoB PLANTS explores these points in detail, explaining the reasons why this genus has considerable value – both academic and socio-economic – and deserves new resources devoted to its exploration as a model. Its impact as a future model will be enhanced by its amenability to cultivation in laboratory and field conditions. In addition, established methods for various tissue and cell culture systems as well as transformation will permit maximum exploitation of this genus by science.

Rodriguez-Enriquez, M.J., and Grant-Downton, R.T. (2012) A new day dawning: Hemerocallis (daylily) as a future model organism. AoB Plants 5: pls055 doi: 10.1093/aobpla/pls055

Proteaceae, Banksia, Macadamia nuts and the Annals of Botany Cover

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Leucospermum flowers in the family Proteaceae on the cover of Annals of Botany

Our videoblog discusses plants in the family Proteaceae, a well-known Southern hemisphere family with many beautiful and well-known representatives in Africa and Australia. The striking red flowers of the genus Leucospermum, from South Africa feature on the cover of the Annals of Botany for this year. Banksia is a well-known Australian genus, the bottle brush flowers, with attractive flowers and remarkable cone-like fruits. Protea, the type genus for the family, is from South Africa; the name of both genus and family is apposite, being named after the Greek God Proteus who was very variable in his form. Interestingly, there are no important food crops originating from Australia, despite its large area and range of climatic zones, and the now world-wide importance of Eucalyptus as a tree for construction timbers and paper-making fibre. In the family Proteaceae, Macadamia is the most internationally-significant food plant of any Australian native species; it’s very fat-rich nuts (75%) are widely available and much appreciated.



The videoblog is on YouTube:

Feeling sleepy

Medicago truncatula Like most animals, plants also sleep at night. At least, many do, but not, unfortunately, Arabidopsis, and our scientific over-reliance on this one species has hampered understanding of nyctinasty, sleeping movements of leaves. A new commentrary in PNAS discusses the genetic basis for sleepy plants, and is well worth a read:

Genetic basis of the “sleeping leaves” revealed. PNAS USA 6 July 2012, doi: 10.1073/pnas.1209532109

See also:

Conserved genetic determinant of motor organ identity in Medicago truncatula and related legumes. PNAS USA, 11 June 2012, doi: 10.1073/pnas.1204566109

Not so green as they’re cabbage looking

Not so mellow yellow There have been some very interesting papers published recently on how plants withstand diseases. Plants seeingly lack the sophisticated immune system of mamals, so discoveries of how they use the genes they have is noteworthy.


The fact that single immune receptors conferring multiple resistances to taxonomically unrelated pathogens may not be exceptional gives plant breeders a strong incentive to identify and to use common virulence targets as leads to discover broad-specificity resistance genes:
Dual disease resistance mediated by the immune receptor Cf-2 in tomato requires a common virulence target of a fungus and a nematode. PNAS USA 06 June 2012 doi: 10.1073/pnas.1202867109 Plants lack the seemingly unlimited receptor diversity of a somatic adaptive immune system as found in vertebrates and rely on only a relatively small set of innate immune receptors to resist a myriad of pathogens. Here, we show that disease-resistant tomato plants use an efficient mechanism to leverage the limited nonself recognition capacity of their innate immune system. We found that the extracellular plant immune receptor protein Cf-2 of the red currant tomato (Solanum pimpinellifolium) has acquired dual resistance specificity by sensing perturbations in a common virulence target of two independently evolved effectors of a fungus and a nematode. The Cf-2 protein, originally identified as a monospecific immune receptor for the leaf mold fungus Cladosporium fulvum, also mediates disease resistance to the root parasitic nematode Globodera rostochiensis pathotype Ro1-Mierenbos. The Cf-2–mediated dual resistance is triggered by effector-induced perturbations of the apoplastic Rcr3pim protein of S. pimpinellifolium. Binding of the venom allergen-like effector protein Gr-VAP1 of G. rostochiensis to Rcr3pim perturbs the active site of this papain-like cysteine protease. In the absence of the Cf-2 receptor, Rcr3pim increases the susceptibility of tomato plants to G. rostochiensis, thus showing its role as a virulence target of these nematodes. Furthermore, both nematode infection and transient expression of Gr-VAP1 in tomato plants harboring Cf-2 and Rcr3pim trigger a defense-related programmed cell death in plant cells. Our data demonstrate that monitoring host proteins targeted by multiple pathogens broadens the spectrum of disease resistances mediated by single plant immune receptors.

And there is also the recent work showing that plants can pass acquired defenses against pests and pathogens on to their offspring: Memory Tools for Plants – how plants pass defenses to offspring through a complex molecular network


Plants are clearly a lot smarter than many people give them credit for. The question is, are we smart enough to use these new discoveries to help feed ourselves in the future?

Free paper — Genome size in Anthurium evaluated in the context of karyotypes and phenotypes

Little is known about the genome of Anthurium other than chromosome observations, which frequently indicate supernumerary (“B”) chromosomes. New genome size estimates for 34 species and nine cultivars presented here  provide insights into genome organization and evolution in this very large genus.

AoB PLANTS Handling Editor involved in an exciting commercial paw paw breeding programme

A recent report places AoB PLANTS Handling Editor Kermit Ritland at the center of a commercial breeding programme of paw paw. “This guy Si Brown is so interesting” Kermit comments; “[He] made a cold call to me one day, that is the way venture capitalists work. Si got a degree in Plant Ecology from McGill University but ended up in business, and does all these high-end business deals [...] Botany and business can work together.”

Free paper — Identification of Stylosanthes guianensis varieties using molecular genetic analysis

Molecular genetic diversity and population structure analysis were used to clarify the controversial botanical classification of Stylosanthes guianensis.  In this paper, the accessions were clustered in nine groups, each of which was mainly composed of only one of the four botanical varieties.

Phenomics – technologies to relieve the phenotyping bottleneck

It's wheat Jim, but not as we know it Global agriculture is facing major challenges to ensure global food security, such as the need to breed high-yielding crops adapted to future climates and the identification of dedicated feedstock crops for biofuel production (biofuel feedstocks). Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses. This will enable breeders to develop new agricultural germplasm to support future agricultural production. This review presents plant physiology in an ‘omics’ perspective, covers some of the new high-throughput and high-resolution phenotyping tools and discuss their application to plant biology, functional genomics and crop breeding.

Phenomics – technologies to relieve the phenotyping bottleneck. Trends Plant Sci. Nov 8 2011

Italian Genetics Societies in Assisi: staple foods and orphan crops via epigenomics and systems biology

Joint meeting of the Italian Genetics Societies Assisi

Joint meeting of the Italian Genetics Societies Assisi

Italian genetic research is in good health: this week I’m at a meeting held in the Cittadella in Assisi with about 500 people and 300 posters. The conferees reflect my own research interest with respect to species: about 80% of the work was on plants, and 80% of that work on crops, making a good start. The posters were all in English, as were the slides, but almost all the talks were in Italian, proving an unusual challenge. Nevertheless, my command of Italian is improving, and I am now fluent with Italian phrases such as “loss of function mutanti” and “next generation sequencing risultati”.

The three Genetics Societies in Italy – AGI, SIBV and SIGA  – put together a programme that nicely flagged the research going on in the country with strong international-level programmes. It was great that many of the top geneticists took part in the meeting, including Roberto Tuberosa, Michele Morgante, Antonio Blanco, Giovanni Giuliano, Roberto Papa or Mariano Rocci, to name just a few from my area. Even better, many only played a supporting role to key laboratory members who showed their own dedication and hard work in their results! This was much appreciated by the strong student representation, many of whom presented their first work at this meeting with its informal and supportive ethos. Not least because of my general familiarity with the work presented and its background (making the language of presentation less of a problem for me), it was particularly valuable to hear the Italian students and post-docs focusing on their contributions to major European and international projects, whether in whole genome sequencing, annotation and functional analysis, or in crop physiology, or animal genetics. The Organizers juggled the difficulty of breadth of coverage with keeping the meeting short and focussed nicely, with plenary and mostly only two parallel sessions. Major sessions were on topical issues such as epigenetics and epigenomics, then genome plasticity, moving on to systems biology. Sadly though, despite coverage of so many crops of special importance in Italy and the involvement of the agricultural genetics society, I failed to notice substantial contributions to discussions or presentations from breeders or seed organizations, the end users of so much of the research discussed.

Thunderstoms, here approaching Assisi, kept us in the conference centre

Thunderstoms, here approaching Assisi, kept us in the conference centre

At a couple of recent conferences, I have helped writing a slightly more balanced report of many talks through Twitter. I’m not going to give any overview of the meeting here – the abstracts are of course helpful – but I can just point to a few pieces of work which I will certainly be discussing with my lab. Next week. It was very exciting to hear and consider the consequences of modern genetic work for the crops of particular importance in Italy: a systematic analysis of transcriptomics through three wine vintages in three different regions, all with same grape variety, Corvina, demonstrated how modern biology is addressing long-standing questions about genotype x environment interactions, agronomy and food production (Dal Santo et al.). Genes involved in transcriptome plasticity can be assigned to vineyards with different agronomic classes and plastic transcriptional drifts impacted metabolic rearrangements depending on microenvironment and growing conditions.

Pre-breakfast viewing avoids the crowds at the posters

Pre-breakfast viewing avoids the crowds at the posters

Several posters addressed the genetics and diversity of Tuber magnatum, the white truffle, and one was even using mitochondrial DNA fingerprinting to identify the oils in paints used by the Renaissance artists of Italy. The next area of genetics research – integrating systems – was well-covered, with A Vigilante showing network analysis approaches for identifying gene associations or functions, and understanding consequences of genome duplication.

I was really pleased to have been part of this meeting, and to have so many valuable discussions. I have a substantial list of people where I want to continue discussions – ranging from needs for cytogenetic textbooks, to systems biology, to alien gene transfer. I hope some of the discussions we had will lead to visits to my lab for periods of joint research too. Of course, the beautiful environment of the Cittadella in Assisi was ideal for the meeting. We could mediate on the impact of genetics in the shadow of St Francis and world’s finest renaissance frescoes, in a small enough venue (the conference represented nearly 15% of the total population of the town) that demanding meditation (translating words of the Cittadella website) was in the framework of informal discussions of molecular genetics.

Back to reality: 77 hours without e-mails and 248 new ones!

Back to reality: 77 hours without e-mails and 248 new ones!