A new global study reveals the extent to which high-yielding rice varieties favored in the decades since the “Green Revolution” have a propensity to go feral, turning a staple food crop into a weedy scourge.
Many genetic and breeding studies have shown that point mutations and indels (insertions and deletions) can alter elite traits in crop plants. Although nuclease-initiated homology-directed repair (HDR) can generate such changes, it is limited by its low efficiency. Base editors are robust tools for creating base transitions, but not transversions, insertions or deletions. Thus, there is a pressing need for new genome engineering approaches in plants.
A team of researcher examined how 14 rice diverse varieties photosynthesize—the process by which all crops convert sunlight energy into sugars that ultimately become our food. Looking at a little-studied attribute of photosynthesis, they found small differences in photosynthetic efficiency under constant conditions, but a 117 percent difference in fluctuating light, suggesting a new trait for rice breeder selection.
Reading the Basmati Genome Provides Clues for Growing Drought-Tolerant and Bacteria-Resistant Rice. Using an innovative genome sequencing technology, researchers assembled the complete genetic blueprint of two basmati rice varieties, including one that is drought-tolerant and resistant to bacterial disease.
Researchers have discovered a new gene that improves the yield and fertilizer use efficiency of rice.
Research combining future climate conditions and arsenic-induced soil stresses predicts rice yields could decline about 40 percent by 2100, a loss that would impact about 2 billion people dependent on the global crop.
Rice is the No. 1 staple food for the world’s poorest and most undernourished people. More than half of the world’s population eats rice every day. In sub-Saharan Africa, rice is the fastest-growing food source, providing more food calories than any other crop. One dangerous threat to food security is the rice disease bacterial blight, caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The annual losses caused by bacterial blight are estimated at U.S. $3.6 billion in India alone. Xoo can destroy a smallholder’s entire annual harvest, putting their food supply, income and land ownership at risk.
This week’s post was written by Jonathan Ingram, Senior Commissioning Editor / Science Writer for the Journal of Experimental Botany. Jonathan moved from lab research into publishing and communications with the launch of Trends in Plant Science in 1995, then going on to New Phytologist and, in the third sector, Age UK and Mind.
In this week of the XIXth International Botanical Congress (IBC) in Shenzhen, it seems appropriate to highlight outstanding research from labs in China. More than a third of the current issue of Journal of Experimental Botany is devoted to papers from labs across this powerhouse of early 21st century plant science.
Collaborations are key, and this was a theme that came up time again at the congress. The work by Yongzhe Gu et al. is a fine example, involving scientists at four institutions studying a WRKY gene in wild and cultivated soybean: in Beijing, the State Key Laboratory of Systematic and Evolutionary Botany at the Institute of Botany in the Chinese Academy of Sciences, and the University of the Chinese Academy of Sciences; and in Harbin (Heilongjiang), the Crop Tillage and Cultivation Institute at Heilongjiang Academy of Agricultural Sciences, and the College of Agriculture at Northeast Agricultural University. Interest here centers on the changes which led to the increased seed size in cultivated soybean with possible practical application in cultivation and genetic improvement of such a vital crop.
Botanic gardens are also part of the picture. In another paper in the same issue, Yang Li et al. from the Key Laboratory of Tropical Plant Resources and Sustainable Use at Xishuangbanna Tropical Botanical Garden in Kunming (Yunnan) and the University of the Chinese Academy of Sciences in Beijing present research on DELLA-interacting proteins in Arabidopsis. Here the authors show that bHLH48 and bHLH60 are transcription factors involved in GA-mediated control of flowering under long-day conditions.
Naturally, research on rice is important. Wei Jiang et al. from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University (Wuhan) describe their research on WOX11 and the control of crown root development in the nation’s grain of choice, which will be important for breeders looking to increase crop yields and resilience.
The other work featured is either in Arabidopsis or plants of economic importance: Fangfang Zheng et al. (Qingdao Agricultural University, also with collaborators in Maryland) and Xiuli Han et al. (Beijing); Yun-Song Lai et al. (Beijing/Chengdu – cucumber), Wenkong Yao et al. (Yangling, Shaanxi – Chinese grapevine, Vitis pseudoreticulata), and Xiao-Juan Liu et al. (Tai-an, Shandong – apple).
Shenzehn has grown rapidly and is now highly significant for life science as home to the China National GeneBank (CNGB) project led by BGI Genomics. The vision as set out by Huan-Ming Yang, chairman of BGI-Shenzhen, is profound – from sequencing what’s already here, often in numbers per species, to innovative synthetic biology.
Shenzehn is also home to another significant institution, the beautiful and scientifically important Fairy Lake Botanic Garden. At the IBC, the importance of biodiversity conservation for effective, economically focused plant science, but also for so many other reasons to do with our intimate relationship with plants and continued co-existence on the planet, was a central theme.
The research highlighted in Journal of Experimental Botany is part of the wider, positive growth of plant science (and, indeed, botany) not just in China, but worldwide. The Shenzehn Declaration on Plant Sciences with its seven priorities for strategic action, launched at the congress, will be a guide for the right development in coming years.
Following on from last week’s post, Now That’s What I Call Plant Science 2015, we bring you a year in Plant Science!
Image credit: Jean Weber. Used under license CC BY 2.0.
The year began with a surprising paper that turned our understanding of the phytohormone auxin on its head. Researchers in China and the USA created Arabidopsis knockout mutants of AUXIN BINDING PROTEIN 1 (ABP1), expecting them to fail to respond to auxin and have developmental defects, as previously seen in the abp1-1 knockdown mutant. Instead, these plants were indistinguishable from wild type plants, leading the authors to conclude that ABP1 is not required for auxin signaling or Arabidopsis development as previously believed.
Read the paper in PNAS: Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development.
A paper later in the year from the same authors found that the embryonic lethality of the abp1-1 mutant is actually caused by the off-target linked deletion of the adjacent BSM gene.
Read this paper in Nature Plants: Embryonic lethality of Arabidopsis abp1-1 is caused by deletion of the adjacent BSM gene.
The tale of ABP1 was examined in more detail on the GARNet blog, Weeding the Gems, which concluded: “In many ways this story is an excellent example of how science should work, where claims are independently tested to ensure that earlier experiments have been conducted or interpreted correctly.” Click here to read more.
A clever experiment from Germany led to a significant breakthrough in crop protection from insect pests.
When double-stranded RNA (dsRNA) is present within a eukaryotic cell, it is cleaved by the Dicer enzyme to form short interfering RNAs. These can bind to complementary RNA within a cell to target it for destruction, thus silencing the corresponding gene expression. This process is known as RNA interference (RNAi).
RNAi has previously been used to tackle insect herbivory by expressing insect-specific dsRNA in plants; however the protection has previously been incomplete. In this new study, published in Science, researchers produced dsRNA within chloroplasts, which do not have RNAi machinery. When dsRNA is expressed in the cytoplasm, the plant’s own Dicer enzyme breaks most of it down. When expressed in the chloroplasts, the dsRNA remained intact when eaten by insects, which proved much more effective at killing these pests.
Read the paper here: Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids.
Another crop protection study followed in March, when researchers in China cloned the genetic locus in rice that confers broad-spectrum resistance to planthoppers – insect pests that cause the loss of billions of dollars of crops per year. Three lectin receptor kinase genes were found in rice cultivars from the Philippines, which enable plants to survive an infestation of insects. When cloned into a susceptible rice cultivar, these genes conferred resistance to two different planthopper species.
Understanding the genetic basis of resistance is very important as marker-assisted breeding and selection could be used to develop resistant rice varieties, and potentially utilized in other species of cereal.
Read the paper in Nature Biotechnology: A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice
A European collaboration led to the development of 3DCellAtlas, a computational approach that semi-automatically identifies cell types in a developing 3D organ without the need for transgenic lineage markers. This program will enable the interpretation of dynamic organ growth and the spatial and temporal context of developmental cell divisions that produce the resultant plant. It could be integrated with growth in different conditions or with developmental mutants to examine exactly how these processes affect growth in 3D.
Image credit: Montenegro-Johnson et al., 2015. Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas. The Plant Cell, vol. 27 no. 4, 1018–1033.
A special issue of the Plant Biotechnology Journal was published in May, focusing on the amazing advances in molecular farming. While the entire issue is worth delving into, we were particularly intrigued by the review on moss-made pharmaceuticals, which outlines the rapid progress made in the field.
The model moss Physcomitrella patens has rapidly become one of the organisms of choice in biotechnology, with a fully sequenced genome and an outstanding toolbox for genome-engineering. The authors describe how moss-made pharmaceuticals can easily be produced while remaining remarkably more stable from batch to batch than cultured animal cells. The system is easily scalable, making their production highly cost effective, and safe. The first moss-made pharmaceuticals are currently in clinical trials, so keep an eye out for much more from this field over the next few years.
Read the review: Moss-made pharmaceuticals: from bench to bedside.
In June, US researchers discovered a new role for chloroplast stromules, protrusions that extend from the surface of all plastid types. The function of stromules has been difficult to determine, but this research, published in Developmental Cell, suggests that they may provide a mechanism by which plastid signals are conveyed to the nucleus. The paper shows that chloroplast stromules are induced by defense responses such as programmed cell death signaling, and that the stromules extend to form dynamic connections with the nucleus. The stromules may therefore aid in the amplification and/or transport of immune response signals into the nucleus.
Read the paper: Chloroplast Stromules Function during Innate Immunity.
Image credit: Veresoglou et al., 2015. Self-DNA: a blessing in disguise? New Phytologist, vol. 207, no. 3, 488–490.
In late 2014 and early 2015, Italian researchers published a set of articles showing that extracellular self-DNA, DNA from conspecifics, could inhibit the growth of organisms from a wide range of taxa, including plants, bacteria, fungi and animals. Conversely, these organisms were not affected by extracellular DNA from other unrelated species.
In July, New Phytologist published a letter offering an interpretation of the data as it relates to plants. Plants could interpret extracellular self-DNA as an indicator of intraspecific competition (which seeds could use as a cue to remain dormant) or of a hostile environment that has already caused the death of conspecifics, signaling them to ramp up their pre-emptive immune response to increase survival after neighbors have been damaged or killed. There are still a lot of mechanisms and ecological effects to be investigated in this new field, but this letter suggests several interesting avenues to investigate.
Read the article: Self-DNA: a blessing in disguise?
Original research papers in New Phytologist:
Inhibitory effects of extracellular self-DNA: a general biological process?
A US study in August revealed a surprising degree of conservation in gene expression patterns across a wide range of plant taxa during root development. This was particularly interesting because the spikemoss Selaginella was shown to use many of the same genes as the evolutionarily distant angiosperms, despite the fossil record suggesting that roots evolved independently in these two lineages. Perhaps roots in these two groups evolved by independently recruiting the same developmental program, or perhaps by elaborating on a previously unknown proto-root that existed in the common ancestor of vascular plants.
Read the paper in The Plant Cell: Conserved Gene Expression Programs in Developing Roots from Diverse Plants.
Salt stress can significantly reduce the growth and yield of plants. Researchers in Germany identified two components of the cellulose synthase complex that directly interact with the microtubules and promote their dynamics, which interestingly were highly produced during salt stress conditions. During salt stress, cellulose microtubules depolymerize, however the newly discovered compounds, known as Companions of Cellulose Synthase, promote the reassembly of the microtubule to allow cellulose synthesis to continue.
Read the paper in Cell: A Mechanism for Sustained Cellulose Synthesis during Salt Stress
Throughout the year the GM debate in Europe reached several important milestones. In January the European Union (EU) changed its rules, giving individual countries more flexibility to decide for themselves whether or not to plant GM crops. In February, the UK Science and Technology Committee report stated that EU regulations preventing GM crops are not fit for purpose, and that they should be replaced with a trait-based system.
In October, EU member states revealed their stances on GM crops, with over half of Europe opting out of growing GM crops. Germany was the largest country to opt out of growing GM. The full list can be viewed here: Restrictions of geographical scope of GMO.
Read the news articles here:
EU changes rules on GM crop cultivation – January 2015
EU regulation on GM Organisms not ‘fit for purpose’ – February 2015
Half of Europe opts out of new GM crop scheme – October 2015
Image credit: University of Warwick, UK.
A collaboration between South African and UK scientists revealed how plants can use their circadian clock to pre-emptively boost their immune resistance at dawn, when fungal infection is most likely. Plants tend to decrease in susceptibility at dawn, but those with dysfunctional circadian clocks remained highly susceptible throughout the day. The research also showed that jasmonate signaling plays a crucial role in the circadian timing of resistance.
Read the article in The Plant Journal: Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea.
Image credit: Guo & Liu., 2015. A single-nucleotide exon found in Arabidopsis. Scientific Reports, 5:18087.
Researchers in China published the surprising finding that a single-nucleotide exon exists in the APC11 gene in Arabidopsis. This is the smallest exon ever to be discovered before. The team used an elegant set of APC11-GFP constructs to show that intron splicing around the single-nucleotide exon is effective in both Arabidopsis and rice. This finding has implications for future genome annotations, which might reveal many more single-nucleotide exons.
Read the paper in Scientific Reports: A single-nucleotide exon found in Arabidopsis.
What a wonderful year of science! What new knowledge will 2016 bring?
With another year nearly over we recently put out a call for nominations for the Most Influential Plant Science Research of 2015. Suggestions flooded in, and we also trawled through our social media feeds to see which stories inspired the most discussion and engagement. It was fantastic to read about so much amazing research from around the world. Below are our top five, selected based on impact for the plant science research community, engagement on social media, and importance for both policy and potential end product/application.
Choosing the most inspiring stories was not an easy job. If you think we’ve missed something, please let us know in the comments below, or via Twitter! In the coming weeks we’ll be posting a 2015 Plant Science Round Up, which will include other exciting research that didn’t quite make the top five, so watch this space!
Sweet potato contains genes from bacteria making it a naturally occurring GM crop. Image from Mike Licht used under creative commons license 2.0
Scientists at the International Potato Center in Lima, Peru, found that 291 varieties of sweet potato actually contain bacterial genes. This technically means that sweet potato is a naturally occurring genetically modified crop! Alongside all the general discussion about GM regulations, particularly in parts of Europe where regulations about growing GM crops have been decentralized from Brussels to individual EU Member States, this story caused much discussion on social media when it was published in March of this year.
It is thought that ancestors of the modern sweet potato were genetically modified by bacteria in the soil some 8000 years ago. Scientists hypothesize that it was this modification that made consumption and domestication of the crop possible. Unlike the potato, sweet potato is not a tuber but a mere root. The bacteria genes are thought to be responsible for root swelling, giving it the fleshy appearance we recognize today.
This story is incredibly important, firstly because sweet potato is the world’s seventh most important food crop, so knowledge of its genetics and development are essential for future food supply. Secondly, Agrobacterium is frequently used by scientists to artificially genetically modify plants. Evidence that this process occurs in nature opens up the conversation about GM, the methods used in this technology, and the safety of these products for human consumption.
Read the original paper in PNAS here.
Our number two on the list also relates to genetic modification, this time focusing on methods. Regardless of whether or not we want to have genetically modified crops in our food supply, GM is a valuable tool used by researchers to advance knowledge of gene function at the genetic and phenotypic level. Therefore, systems of modification that make the process faster, cheaper, and more accurate provide fantastic opportunities for the plant science community to progress its understanding.
The Cas9 system is a method of genome editing that can make precise changes at specific locations in the genome relatively cheaply. This novel system uses small non-coding RNA to direct Cas9 nuclease to the DNA target site. This type of RNA is small and easy to program, providing a flexible and easily accessible system for genome editing.
Barley in the field. Image by Moldova_field used under creative commons license 2.0
Inheritance of genome modifications using Cas9 has previously been shown in the model plants, Arabidopsis and rice. However, the efficiency of this inheritance, and therefore potential application in crop plants has been questionable.
The breakthrough study published in November by researchers at The Sainsbury Laboratory and John Innes Centre both in Norwich, UK, demonstrated the mutation of two commercial crop plants, Barley and Brassica oleracea, using the Cas9 system and subsequent inheritance mutations.
This is an incredibly exciting development in the plant sciences and opens up many options in the future in terms of genome editing and plant science research.
Read the full paper in Genome Biology here.
Striga is a parasitic plant that mainly affects parts of Africa. It is a major threat to food crops such as rice and corn, leading to yield losses worth over 10 billion US dollars, and affecting over 100 million people.
Striga infects the host crop plant through its roots, depriving them of their nutrients and water. The plant hormone strigolactone, which is released by host plants, is known to induce Striga germination when host plants are nearby.
In a study published in August of this year the Striga receptors for this hormone, and the proteins responsible for striga germination were identified.
Striga plants are known to wither and die if they cannot find a host plant upon germination. Induction of early germination using synthetic hormones could therefore remove Striga populations before crops are planted. This work is vital in terms of regulating Striga populations in areas where they are hugely damaging to crop plants and people’s livelihoods.
Read the full study in Science here.
Striga, a parasitic plant. Also known as Witchweed. Image from the International Institute of Tropical Agriculture used under creative commons license 2.0
Resurrection plants are a unique group of flora that can survive extreme water shortages for months or even years. There are more than 130 varieties in the world, and many researchers believe that unlocking the genetic codes of drought-tolerant plants could help farmers working in increasingly hot and dry conditions.
During a drought, the plant acts like a seed, becoming so dry that it appears dead. But as soon as the rains come, the shriveled plant bursts ‘back to life’, turning green and robust in just a few hours.
In November, researchers from the Donald Danforth Plant Science Centre in Missouri, US, published the complete draft genome of Oropetium thomaeum, a resurrection grass species.
O. thomaeum is a small C4 grass species found in Africa and India. It is closely related to major food feed and bioenergy crops. Therefore this work represents a significant step in terms of understanding novel drought tolerance mechanisms that could be used in agriculture.
Read the full paper in Nature here.
Currently, one of the greatest challenges for ecologists is to quantify plant diversity and understand how this affects plant survival. For the last 500 years independent research groups around the world have collected this diversity data, which has made organization and collaboration difficult in the past.
Over the last 500 years, independent research groups have collected a wealth of diversity data. The Botanical Information and Ecology Network (BIEN) are collecting and collating these data together for the Americas using high performance computing (HPC) and data resources, via the iPlant Collaborative and the Texas Advanced Computing Center (TACC). This will allow researchers to draw on data right from the earliest plant collections up to the modern day to understand plant diversity.
There are approximately 120,000 plant species in North and South America, but mapping and determining the hotspots of species richness requires computationally intensive geographic range estimates. With supercomputing the BIEN group could generate and store geographic range estimates for plant species in the Americas.
It also gives ecologists the ability to document continental scale patterns of species diversity, which show where any species of plant might be found. These novel maps could prove a fantastic resource for ecologists working on diversity and conservation.
Read more about this story on the TACC website, here.
