The Week in Botany

The Week in Botany 6

The Week in Botany is our new weekly email newsletter covering what makes the news on Twitter. This issue came out last Monday. If you'd like get the newsletter on a Monday morning, then you can subscribe on our email page.

Monday, 17 July 2017

Welcome to The Week in Botany,  the first we’re expecting to release to the public. If you’re wondering why the first is labelled as edition six, then it turns out there are quite a few ways to send out a weekly email incorrectly. The email is in three parts: AoBBlog covers the posts from the blog. As output increases, we might tweet stories from the blog a little less, so it’ll be more easy to miss articles. The News also covers any links that Twitter’s botanists found interesting. Some of that might be commentary on life in Science. Finally, Scientific Papers is a selection of the most popular papers shared on Twitter and also some advance releases from the AoB journals. There are no prizes for reading it all so I won’t be offended if you just read the part that interests you – which is why we have the links to the different sections at the top.

From AoBBlog

Mapping wheat genes for root hair length in aneuploid lines of bread wheat
Long root hairs enable the efficient uptake of poorly mobile nutrients such as phosphorus. Mapping the chromosomal locations of genes that control root hair length can help exploit the natural variation within crops to develop improved cultivars. Liu et al. used genetic stocks of the wheat (Triticum aestivum) cultivar ‘Chinese Spring’ to map genes controlling root hair length.

The Secret Larder of Ancient America
The next big thing on your dinner plate could be plants that were first domesticated five thousand years ago then forgotten about for centuries.

Botany really rocks!
For a plant life on the edge, like on a cliff face, should be peaceful. But Nigel Chaffey discovers one species has a real talent for annoying others.

Different types of rice tiller responses to nitrogen
Tillering is an important agronomic trait for rice population quality and grain production. In a recent study published in AoB PLANTS, Wang et al. found that nitrogen fertilizer application increased the number of rice tillers, but not every tiller contributed equally to the overall yield.

Intra-specific variation in Arabidopsis functional strategies
Using a range of Arabidopsis (Arabidopsis thaliana) accessions from different geographic origins, May et al.test whether competitor, stress-tolerator, ruderal (CSR) theory can be applied to characterise intra-specific variation.

3 Ways to Tackle Plant Blindness
Plant conservation gets a fraction of the funding that animal conservation gets. A recent paper in Conservation Biology blames Plant Blindness. Is there a solution?

Illuminating work on bean domestication
What can you do with a light 10 billion times brighter than the sun? One thing you can do is examine 4000 year old seed coatings.

Carbon stores support efficient nitrate use during regrowth of perennial ryegrass
Plant regrowth in response to defoliation relies on efficient nitrogen use. Roche et al. find that remobilisation of water soluble carbohydrate stores in leaves of perennial ryegrass (Lolium perenne) is coordinated with nitrogen availability to support efficient N assimilation into amino acids in leaf and sheath tissues.

Introducing The Week in Botany
Apparently there’s an email list called The Week in Botany from AoBBlog.

Developing Sustainable Bioenergy Crops for Future Climates 24-27th September 2017

You are welcome to join us at Bioenergy 2017. This meeting will bring together researchers, breeders, growers and policy makers who are concerned with the development of new bioenergy crops for future climates.


Hot, Dry Madrid Aims For A Cooler, Greener Future
Tourists flood the area of Madrid’s “Museum Mile” — a stretch of the huge, eight-lane Paseo del Prado thoroughfare that’s home to Spain’s most renowned art museums. It’s smoggy and crowded with all the traffic. At the CaixaForum, an arts foundation, people pause. It’s what’s on the outside of this museum, rather than what’s inside, that’s halted them: a giant vertical garden with more than 15,000 plants from 300 native species — begonias, yucca plants, ferns — coating an entire outer wall stretching the length of a city block.

Scientifically Speaking, Your PowerPoint Sucks
A study from Harvard’s Decision Science Laboratory uses brain science to explain why we prefer certain types of presentations over others.

Why are we still debating GMOs?
A new film has reignited the controversy over what we eat.

Spanish fears for ‘liquid gold’ olive oil as destructive bacterium hits groves hard
After destroying entire olive groves in Italy and last year appearing in the Balearic Islands, the first case of the destructive bacterium Xylella fastidiosa has been confirmed on mainland Spain, making farmers worry in the land where olive oil is liquid gold.

Massive database of 182,000 leaves is helping predict plants’ family trees
The story of a plant is etched in its leaves. A tree growing in a cold environment with plenty of water is more likely to have large leaves with many serrated teeth around the edges. But if the same species lives in a warm, dry region, its leaves are likely to be smaller and smoother. Now, an atlas that traces the shapes of 182,000 leaves from 141 plant families and 75 locations around the world shows promise for refining scientists’ ability to read that story.

Biology’s Roiling Debate Over Publishing Research Early
Five years ago, Daniel MacArthur set out to build a massive library of human gene sequencesone of the biggest ever. The 60,706 raw sequences, collected from colleagues all over the globe, took up a petabyte of memory. It was the kind of flashy, blockbuster project that would secure MacArthur a coveted spot in one of science’s top three journals, launching his new lab at the Broad Institute into the scientific spotlight. But before all that happened, he did something that counted as an act of radicalism in the world of biology: He put it on the internet.

The day I broke some twitter feeds: insights into sexism in academia, Part 2
This is the follow up to Gina Baucom’s guest post last week on her experience asking on twitter about sexist comments made about women in academia. In that post, she summarized (and categorized) the variety of sexist comments that occur regularly in academia. The responses to her initial tweet were overwhelming, and her original post generated quite a lot of discussion (some of it, unfortunately, sexist). In this post, Gina has thoughts on how to move forward (with some additions from me at the end).

Are We as Doomed as That New York Magazine Article Says?
Why it’s so hard to talk about the worst problem in the world

Roaming the Desert, in Search of Rare Plants
Q&A with Janel Johnson, a botanist with the Nevada Natural Heritage Program in Carson City, Nev.

The Mother of All Apples Is Disappearing
In the wilds of Kazakhstan, there’s an unassuming tree that bears an unassuming fruit. Like many plant species, development encroaches on its usual territory while climate change makes it harder for the tree to thrive and bear healthy yields of fruit.

Plants turn caterpillars into cannibals
Chemical produced by tomato plants in response to pest attack can change insect behaviour.

Storing and restoring priceless maize
Natural disasters can have a dramatic impact on crop genetic diversity, threatening local and global food security. When Hurricane Stan swept through Guatemala in 2005, leading to 1,500 deaths, many farmers lost entire crops. Some indigenous communities were unable to harvest seed from their traditional maize varieties, known as landraces.

Connecting with trees
Thoughts on The Songs of Trees, a new book by David George Haskell

Meet The Powder Gun Moss
A moss that doesn’t expect the wind to disperse its offspring.

Newly established, a national park in Australia unveils a new plant species
A team of botanists from the US has named a new bush tomato species, based on collections made by their Australian colleagues, during government-funded surveys in a brand new national park.

Archives, Herbarium and the Arctic: Biodiversity Preservation at RBGE
On Monday June 26, Emily and I teamed up again and went back to the RBGE, this time to meet one of the staff members responsible for digitisation. We had previously sent her a list of those archival materials we have identified for our project in order to determine which digitisation equipment we would need to use.

DIY Plant Pressing
How does a plant specimen get turned into an herbarium sheet, ready for a Museum collection? In order for plants to be carefully cataloged and preserved so that they can be studied well into the future, they first have to be dried and pressed. You can do something similar at home—this DIY project is sort of like making a layer cake (or lasagna, depending on your tastes)

Field working, the horror of having to do science outside!
I don’t get out much – both socially, and from a research perspective. The first one is mostly due to the ridiculous hours required by the second one. But either way, I spend more time inside basking in the glow of fluorescent tubes (or tubes of fancy, expensive energy saving LEDS) than I do with the strange green stuff on the floor and the big light in the sky you can’t turn off.

Introducing learnr
We’re pleased to introduce the learnr package, now available on CRAN. The learnr package makes it easy to turn any R Markdown document into an interactive tutorial. Tutorials consist of content along with interactive components for checking and reinforcing understanding.

Brisbane researchers discover native Australian plant can kill Zika virus
QUT researchers in collaboration with Health Focus Products Australia (HFPA) have discovered a group of naturally occurring compounds in an Australian native plant that effectively kill the Zika virus.

Environmental defenders being killed in record numbers globally, new research reveals
Activists, wildlife rangers and indigenous leaders are dying violently at the rate of about four a week, with a growing sense around the world that ‘anyone can kill environmental defenders without repercussions’

Edward Bulkley and the Du Bois Herbarium
In the lead-up (or is it a wind-down?) to retirement I must clear my office, including four herbarium cabinets full of specimens laid aside from time to time pending further research. One such is a group of 52 Indian sheets mainly collected at Fort St George, the present day Chennai in South India, between 1700 and 1712, which are among the oldest specimens in the RBGE herbarium.

Organising a plant stem
Microscopy and computational techniques reveal how cells are arranged in the stems of some plants.

The most effective individual steps to tackle climate change aren’t being discussed
Governments and schools are not communicating the most effective ways for individuals to reduce their carbon footprints, according to new research.

Arks of the Apocalypse
All around the world, scientists are building repositories of everything from seeds to ice to mammal milk — racing to preserve a natural order that is fast disappearing.

Call for Papers: Special issue on the Ecology and Evolution of Plant Reproduction

Botanists have long been fascinated by the extraordinary diversity in flowering plant reproductive patterns and have sought to understand the ecological processes and genetic mechanisms influencing plant mating. Over the last five years, research progress in this discipline has rapidly accelerated. Important new insights in this field often combine elegant theoretical models with innovative field and laboratory experiments. Annals of Botany will release a Special Issue on the Ecology and Evolution of Plant Reproduction in January 2019, and it will highlight papers from 3 symposia at the XIX International Botanical Congress in Shenzhen, China. See the full call for papers for more information.

Scientific Papers

Sex-specific morphological and physiological differences in the moss Ceratodon purpureus (Dicranales)
In this study, fine-scale sex-specific cell and leaf morphological traits are correlated with sex-specific physiology and population sex ratios were assessed to determine how they vary across three populations within one moss species and whether fine-scale morphological traits scale up to physiological and sex ratio characteristics. Annals of Botany

A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana
Establishing homozygous transgenic lines is time-consuming and laborious, and using antibiotics or herbicides to select transformed plants may adversely affect the growth of some transgenic plants. Here we describe a novel technology, which we have named FAST (fluorescence-accumulating seed technology), that overcomes these difficulties. Although this technology was designed for use in Arabidopsis thaliana, it may be adapted for use in other plants. The Plant Journal

Evolution of the wheat blast fungus through functional losses in a host specificity determinant
In the 1980s, wheat crops began to fall to the fungal pathogen that causes blast disease. First seen in Brazil, wheat blast last year caused devastating crop losses in Bangladesh. Inoue et al. tracked down the shifting genetics that have allowed the emergence of this potentially global threat to wheat crops (see the Perspective by Maekawa and Schulze-Lefert). Wheat varieties with a disabled resistance gene were susceptible to pathogen strains that affected oat and ryegrass crops. Subsequent genetic changes in the pathogen amped up the virulence in wheat. Science

The potential for co-evolution of CO2-concentrating mechanisms and Rubisco in diatoms
This review explores our current understanding of the diatom CO2-concentrating mechanisms (CCMs) and highlights the diversity of both the CCM and Rubisco kinetics. We will suggest possible environmental, physiological, and evolutionary drivers for the co-evolution of the CCM and Rubisco in diatoms. JXB

Inhibition of RNA polymerase II allows controlled mobilisation of retrotransposons for plant breeding
Here we show that plants defective in Pol II activity lose DNA methylation at repeat sequences and produce more extrachromosomal retrotransposon DNA upon stress in Arabidopsis and rice. We demonstrate that combined inhibition of both DNA methylation and Pol II activity leads to a strong stress-dependent mobilization of the heat responsive ONSEN retrotransposon in Arabidopsis seedlings. Genome Biology

Speed breeding: a powerful tool to accelerate crop research and breeding
Here we present a method called ‘speed breeding’, which greatly shortens generation time and accelerates breeding and research programs. Speed breeding can be used to achieve up to 6 generations per year for spring wheat (Triticum aestivum), durum wheat (T. durum), barley (Hordeum vulgare), chickpea (Cicer arietinum), and pea (Pisum sativum) and 4 generations for canola (Brassica napus), instead of 2-3 under normal glasshouse conditions. bioRxiv

Potassium, not lepidimoide, is the principal ‘allelochemical’ of cress-seed exudate that promotes amaranth hypocotyl elongation (Open Access)
Imbibed cress (Lepidium sativum L.) seeds exude ‘allelochemicals’ that promote excessive hypocotyl elongation and inhibit root growth in neighbouring competitors, e.g. amaranth (Amaranthus caudatus L.) seedlings. The major hypocotyl promoter has recently been shown not to be the previously suggested acidic disaccharide, lepidimoic acid (LMA), a fragment of the pectic polysaccharide domain rhamnogalacturonan-I. The nature of the hypocotyl promoter has now been re-assessed. Annals of Botany

Pavement cells and the topology puzzle
We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. bioRxiv

Whole-genome analysis of candidate genes associated with seed size and weight in Sorghum bicolor reveals signatures of artificial selection and insights into parallel domestication in cereal crops
This study identified sorghum orthologues of genes with proven effects on seed size and weight in other plant species and searched for evidence of selection during domestication by utilizing resequencing data from a diversity panel. In total, 114 seed size candidate genes were identified in sorghum, 63 of which exhibited signals of purifying selection during domestication. frontiers in Plant Science

Herbarium specimens as exaptations: New uses for old collections
The conventional functions of herbaria remain essential to botanical research: new species continue to be described, systematic relationships are always subject to revision, nomenclature is routinely updated, and the documentation and study of biodiversity is increasingly important as we enter an anthropogenic era of mass extinction. However, emerging research also utilizes specimens in nontraditional, unanticipated ways. AmJBot

Point of View: Nomad scientists and the ones left behind
To improve the diversity of the scientific workforce, we should not penalize researchers who are unable to move abroad for long periods. eLife

Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum
The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage. Plant Methods

A role for LAX2 in regulating xylem development and lateral-vein symmetry in the leaf
Studying transgenic Arabidopsis plants ectopically expressing the sunflower transcription factor HaHB4, it was observed that there was a significant lateral-vein asymmetry in leaves and in xylem formation compared to wild type plants. To unravel the molecular mechanisms behind this phenotype, genes differentially expressed in these plants and related to auxin influx were investigated. Annals of Botany

…and that closes The Week in Botany for this week. If you’ve decided this is all a bit much and you’d rather not see it in your inbox then you can click to unsubscribe. Otherwise the next edition is scheduled to be with you next Monday. If you’ve got this far, thanks for reading.

About the author

Alun Salt

When he's not the web developer for AoB Blog, Alun Salt researches something that could be mistaken for the archaeology of science. His current research is about whether there's such a thing as scientific heritage and if there is how would you recognise it?