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Can someone identify this species from the pea family?

Can someone identify this species from the pea family?



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Can someone identify this species from the pea family? The plant was photographed in Morocco in spring. The location is south of Marrakesh at the foot of the high Atlas, in a dry riverbed.


The plant appears to be Medicago arborea. Common names include moon trefoil, shrub medick, alfalfa arborea, and tree medick. It is a member of the pea family Fabiaceae. The species is characterized by the woody stems, the leaves (three), and compressed, coiled seed pods. See further description in the links below. It is a native of the Mediterranean basin and apparently becoming rare in nature.

http://botanyphoto.botanicalgarden.ubc.ca/2015/09/medicago-arborea/

https://en.wikipedia.org/wiki/Medicago_arborea


Pisum sativum

Research studies

In our studies, we have examined one EU crop, Pisum sativum (pea). Peas are susceptible to a wide range of viruses including Pea enation mosaic virus, Pea early browning virus, and a range of viruses from the Potato virus Y group (Potyviridae). Within this last group, Bean yellow mosaic virus, Bean common mosaic virus, Pea mosaic virus and Pea seed borne mosaic virus (PSbMV) are all important pathogens. In particular, we have studied PSbMV for which all commercial cultivars of peas are susceptible. This susceptibility is compounded by the fact that this virus is not only transmitted from plant to plant by its aphid vector but is also transmitted vertically from generation to generation in the seed. This property has resulted in serious contamination of pea germplasm collections and provides a very effective means to give early and widespread infection of crops soon after seed germination. Consider that a seed transmission efficiency of only 0.1% would result in 10,000 infections after sowing seeds at 10 7 /hectare, and the importance of seed transmission becomes apparent. At present, this problem is countered by efficient post-harvest testing of seed samples by immunodetection of the virus coat protein, and rejection of contaminated seed lots. As an alternative, and since seed transmission in a range of pea cultivars varies from 0 to 100%, we have investigated whether resistance to seed transmission could be bred into improved pea lines. In test crosses and backcrosses between lines showing no transmission or 60-80% transmission, resistance behaved as a dominant character, although in the F2 and BC2 generations it did not segregate as a Mendelian trait. The quantitative nature of the phenotype suggested that seed transmission would be difficult to include as a resistance trait in a conventional breeding programme.

Natural resistance to PSbMV has been identified in pea accessions from North Africa and Asia [ 3, 4 ] although, so far, these recessive genes have not been introgressed into commercial lines. Genetic analysis has shown that these genes are clustered with other recessive genes with differing poty virus specificities at two locations on the pea genome. Genes sbm-1, sbm-3, and sbm-4, conferring resistance to PSbMV pathotypes PI, L-l and P4, respectively, are located on chromosome 6, while sbm-2 also conferring resistance to pathotype L-l is located on chromosome 2 [ 5 ]. Although this organisation is suggestive of local gene conversion and translocation between chromosomes 2 and 6, other evidence suggests that the two gene clusters may have distinct origin and function. Using recombinant hybrid viruses made between different pathotypes the virus avirulence determinant has been defined as the virus genomelinked protein (VPg) for sbm-1 [ 6 ]. A structural and functional analysis of the sbm-1 gene is the topic of an EC-Biotechnology project # BI04-CT97-2356 ( www.dias.kvl.dk/eupsbmv ) involving research groups and industry from Denmark, Finland, Spain and the UK.

Characterisation of the sbm-1 gene will provide particular intellectual and practical rewards. Since, approximately 20% of all virus resistance genes [ 7 ] and approximately 40% of genes conferring resistance to potyviruses are recessive [ 8 ], understanding how sbm-1 works and what controls the specificity of the adjacent sbm- and other potyvirus resistance genes will be important for a wide range of diseases. However, the sbm- project also has technical challenges, not least in having to deal with the size and redundancy within the pea genome. The pea genome is approximately 5 x 10 9 base pairs per haploid genome, some 50 times larger than that from Arabidopsis thaliana. Map-based cloning of genes in pea has not been achieved and large insert libraries are not yet available. However, there is the potential in sbm-1 to identify a new class of resistance genes. Resistance genes cloned so far from other species fall into two classes. The dominant resistance genes which function against specific viruses, fungi and bacteria fall broadly into the “NBS-LRR” class [ 9 ] and mediate a hypersensitive resistance to infection. The only recessive gene to be cloned (mlo) mediates a non-race specific resistance to powdery mildew in barley and is also associated with localisation of the pathogen in dead cells. Functionally, Mlo acts as a negative regulator of constitutive resistance [ 10 ]. In contrast, sbm-1 is race (or pathotype) specific and is not associated with cell death. From these comparisons, several functional mechanisms for sbm-1 seem possible. First, we can view Sbm-1 as a dominant susceptibility factor, required to assist virus replication. This would fit with the probable involvement of the VPg in viral RNA replication and the observation that protoplasts from resistant plants show no detectable virus replication [ 11 ]. Second, like Mlo, Sbm-1 could act as a negative regulator of resistance although the specificity differences from mlo would place sbm-1 in a distinct class of resistance genes. Third, sbm-1 could be a dominant but dose-dependent weak resistance allele. We favour the first option as the most direct and simple interpretation.

For our component in the EC-Biotechnology project we have opted to use genetic approaches to identify the sbm-1 resistance gene product. After identifying suitable pea lines (a BC4 pair of lines carrying homozygous resistance and susceptibility alleles) a cDNA-AFLP strategy has been used to identify expressed genes coming from the introgressed region. So far, ten polymorphic cDNAs have been identified. These are being mapped using recombinant inbred families to confirm their genomic origin. Our alternative strategy is to ‘fish’ for the sbm-1 gene product by using the yeast two-hybrid system with the PSbMV VPg as the bait protein. Two strong candidate cDNAs and eight other cDNAs encoding interactor proteins have been identified from a pea cDNA library made from a susceptible pea line. These cDNAs are also being sequenced and mapped.

As part of a previous EC-AIR project (# CT94-1171) involving academic and industrial partners in Denmark, France and the UK, we have also explored the potential for developing PDR to PSbMV in transgenic peas. Since in other systems the viral replicase gene had commonly been used to give PDR by triggering the process of post-transcriptional gene silencing (PTGS), we used the PSbMV replicase cistron (NIb) for transgenic expression in peas [ 12 ]. From 35 pea lines, transformed with Agrobacterium tumefaciens T- DNA carrying a 35S promoter -Nib - 35S terminator construct, and the bar gene as a selectable marker for transformed tissue in the presence of the herbicide Bialophos, three lines were shown to be resistant to PSbMV. Two of these lines carried a direct repeat of the 3’ end of the Nib gene (NIbIb) since there was some evidence [ 13 ] that complex transgene arrangements had more potential to initiate PTGS. All of these lines exhibited a type of PDR termed “recovery” where challenge inoculation results in an initial infection but the plants rapidly recover and show no more symptoms or virus accumulation. The recovered tissues are then resistant to further challenge with the homologous or closely related virus isolates. To assess the significance of this in the field where the plants may be challenged with a population of related viruses, the ability of different isolates of PSbMV to trigger PTGS and to be targeted by induced PTGS was assessed. This showed that viruses with ca. 89% or more identity in the NIb cistron could induce the resistance although the specificity requirements for a second challenge virus to be seen as a target may be higher. For reference, the two most divergent sequenced PSbMV isolates differ by 89% in the Nib region. This distinction in specificity requirements for triggering and targeting in PTGS will be an important consideration for the application of the technology to commercial crops. The relatively broad resistance to PSbMV isolates in Nib transgenic peas contrasts with the extreme pathotype specificity seen for the natural sbm-resistance genes where only one or a few changes in the virus avirulence determinant is enough change a PSbMV isolate from avirulent to virulent [ 6 ].

Despite the short period of initial infection, the transgenic pea plants showed good growth and seed set after challenge inoculation to give yields under glasshouse conditions equivalent to those seen for uninfected transgenic or non-transgenic lines. We believe that, subject to licensing agreements covering the use of the bar gene for selecting transformed plants, these plants could be useful additions to the panel of pathogen resistance genes to be used in developing new improved pea lines.

The transgenic pea plants represent the first legumes displaying PDR against potyviruses and some of the first experimental examples in the Leguminosae of plants showing PTGS. It was valuable, therefore, to establish that the principles governing PTGS and resistance in this system supported those characterised with more commonly used experimental plants (e.g. Nicotiana spp.). As expected for PTGS, induced virus resistance was associated with the degradation of transgene RNA and PSbMV RNA [ 12 ]. We also showed that PTGS was mediated in these plants by a systemic signal generated during the initial phase of virus infection, and that this signal had the potential to mediate the spread of PTGS by inducing methylation in the transcribed region of the NIb transgene [ 14 ].

In conclusion, we have recognised that the agricultural industry would benefit from having stable and effective resistance to PSbMV in peas. The least contentious route to achieve this would be through the incorporation of naturally occurring resistances (either to seed transmission or to virus replication) using conventional breeding strategies. Our relatively poor understanding of the genetic complexity of PSbMV seed transmission means that this is unlikely to be useful in the short term. The sbm- genes are more promising although the lack of closely linked genetic markers and the recessive nature of the resistance create some difficulties. Alternatively, we have demonstrated the potential for creating resistance through the application of transgenic technology although the issues of biosafety and public acceptability will need to be addressed. In addition to these applied considerations, the research has and is generating materials and knowledge that will influence how related approaches can be used in other crop plants. In particular, understanding the mechanisms of action of a new class of virus resistance genes will be important.


Taxonomy Chart 101 - Definition, Classifications & Examples

A taxonomy chart is the organized graphic practice and representation of things and concepts. Usually, the taxonomy chart is used in biology to classify all living things. In the 18th century, Carolus Linnaeus suggested a classification process, and this taxonomy system is still used today.

In a chart, taxonomy is an abstract rank or level. Taxonomy is the branch of biological systematics that is concerned with the naming of organisms (according to a set of rules developed for the process), identification (referring specimens to previously named taxa), and classification (ordering taxa into a hierarchy based on perceived characters).

For example, succulents in a plant taxonomy chart collect many plants that are very similar in appearance, including size and sharpness. With the development of the understanding of things and objectives people have, taxonomy is an evolving process using different categories.

Therefore, the taxonomy chart aims to display logic and hierarchical constructs based on different purposes in a mathematical way, such as bar, linear, and pie charts.

The Classifications in Taxonomy Charts

In the biological aspect, taxonomy classification, namely taxonomic rank, is a group of organisms related to commonalities of each other in a taxonomic ordered structure. Major taxonomic categories include seven topics: kingdom, phylum, class, order, family, genus, and species.

Image source: https://en.wikipedia.org/wiki/Taxonomic_rank

The red fox represents an inverted hierarchical triangle of each taxonomic dimension. The top of this triangle means the maximum range, and the bottom is the minimal classification for red fox.

From this graph, it is clear to see each level and classification rank and effectively build the taxonomy chart according to the subjects' or the living creatures' features. This red fox taxonomy chart is one of animal taxonomy.

Moreover, there are specific classification terms in different fields, and each taxonomic category can divide more levels and tiers. For example, the International Code of Zoological Nomenclature defines the nine taxonomic ranks in zoology: superfamily, family, subfamily, tribe, subtribe, genus, subgenus, species, and subspecies.

Overall, all living things can be classified based on their differences from the top of the taxonomic graph, there are huge differences among living creatures. At the bottom, their differences become smaller.

Image source: https://en.wikipedia.org/wiki/Taxonomic_rank#Examples

From this graph, Eukarya in Kingdom covers fruit fly, human being, pea, and fly agaric, while E.coli belongs to Bacteria. Biology domains refer to three groups: the Archaea domain, Bacteria domain, and Eukarya domain. This means all of the living creatures belong to one of these three top levels.

The picture below tells us that all living creatures' ancestors are from these three domains, and differences exist within each ancestors' classification. The second-largest taxonomic rank in biology is the kingdom, below domain. Commonly, kingdoms are divided into five aspects: Animalia, Plantae, Fungi, Protista, and Monera.

There are also many different classification methods within the three domains according to researchers' purposes. In summary, the differences in taxonomy charts depend on the users' purpose or the usages and classification situations. In different fields, there are fixed classification approaches and terms.

Image source: https://simple.wikipedia.org/wiki/Domain_(biology)

Various Taxonomy Chart Examples

With the classification process from top to the bottom, the context will be more specific and more minute. Besides the mentioned taxonomy charts, there are various classification examples with pictures.

Human Taxonomy Chart

Image source: pinterest

There are 8 classified levels for human beings. From the largest to the smallest communities, the domain of human beings is Eukarya, one of the three largest communities globally as part of this domain, humans are part of the Animalia kingdom.

Simplified, kingdom Animalia is the largest of the five existing kingdoms on Earth. From this taxonomy chart, human beings, fruit fly, pteropod, and gynoecium belong to the same domain and kingdom, which means that these members all have membrane-bound organelles.

Moreover, Eukarya can be divided into five kingdoms: Plantae, Protista, Animalia, Chromista, and Fungi. It means each kingdom includes a set of organisms that share similar characteristics, and these organisms in each kingdom are considered biologically distinct from the others.

Next, the smaller division after Kingdom is Phylum, and a human being is chordate of Phylum. The more you go down, the more minute the classification is. This kind of taxonomy table could effectively show the commonalities and differences among different living communities and contract living things orderly and logically.

The Classification of Class Insecta

Image source: https://forestrypedia.com/classification-of-class-insecta-insects/

This graph represents the class classification in insects. The insects are divided into two groups according to insects' wings: winged and wingless groups. Next to the order taxonomy, there are four wingless insect groups in order level.

In contrast, in winged insect groups, the order lever continues to separate into two more parts: Endopterygota and Exopterygota. Also, each order-level contains more than eight smaller groups. This linear graph shows readers a clear map of each division, and the reader can quickly locate specific groups.

The Classification of Kingdom Animalia

Image source: https://www.slideshare.net/ncarrejo/basic-entomology-2013-01-29

In this kingdom Animalia taxonomy chart, there are three types of Phylum: Arthropoda, Nematode, and Mollusca, but this graph emphasizes in class and order of Phylum Arthropoda.

Moreover, Arthropoda Phylum contains Insecta (as mentioned before), Arachnida, Crustacea, and other classes. Class Insecta also could be separated into seven smaller groups based on characteristics of wings: Coleoptera, Hymenoptera, Diptera, Orthoptera, Lepidoptera, Hemiptera, and Homoptera.

This is a part of the kingdom classification, but it gives users a way to explore the combination of lines and taxonomy approaches. Readers could follow the lines to find the destinations of each sub-division and separate from other sub-divisions.

Pomacanthidae Tree

Image source: http://bioweb.uwlax.edu/bio203/s2009/brocker_jord/Classification.htm

This graph starts at the level of Family in the order of taxonomy approach. Each branch is created from a distinctive feature that separates each level from others.

The first branch in the tree is the Family of this species. The middle of this tree highlights this species' path throughout the tree concerning each classification level. It is that each Genus has a branch to show the Species level.

This type of taxonomy chart offers readers a clear and concise map, which means readers could roughly see the overall classification at first glance. Readers can quickly know the classification number of each classified rank.

Overall, a taxonomy chart facilitates search and discovery and is knowledge-based. This relates to knowledge and personal preference. Specifically, throughout classifying the living creatures on the planet by features and commonalities, people could gain an in-depth understanding of them and analyze them from different angles.

Moreover, taxonomy is also limited to living things and other unliving subjects such as stationery and school supplies. The final goal of the taxonomy chart aims to the development of discovery and analysis abilities. During the classification process, the users' logic and expression also will be practiced.

Uses of Taxonomy Charts in Our Life

Usually, a biological taxonomic chart is composed of eight categories based on a hierarchical ranking system. The highest rank is always the most general classification, and the lower the rank goes, the more specific the classification becomes.

Steps to Taxonomy charts

There are a few simple steps to get access to taxonomy charts:

  • Browsing and Researching
  • Identification
  • Define your taxonomy chart model
  • Drawing a rough classification map

Before drawing your taxonomy chart, please make sure your research materials are sufficient and understand your classification reason. This means you have to know how to classify your materials, such as subjects' differences and commonalities.

Also, a simple and rough draw is a good way to establish your formal taxonomy chart, which could help you to map your materials and thoughts. Moreover, different chart models could bring different emphases and functions. Taking a few times on the chart model choice or searching a similar topic taxonomy chart could make you more effective in finishing your projects.

After identifying or labeling the characteristic you choose, you can quickly start your taxonomy chat. Mark how many levels and sublevels you need and then create them.

3. Reviewing and re-editing

After creating taxonomy charts based on your purposes, reviewing thought your chart and editing again could make you chart better, which means your chart would be more precise. After that, sharing with your friends and getting suggestions is also a great way to modify your taxonomy chart.

Why EdrawMax

EdrawMax is an all-in-one diagramming tool easily to create your personalized taxonomy charts with strong chart model supplement and function support.


Major species

Several acacia species are important economically. Gum acacia ( Acacia senegal), native to the Sudan region in Africa, yields true gum arabic, a substance used in adhesives, pharmaceuticals, inks, confections, and other products. The bark of most acacias is rich in tannin, which is used in tanning and in dyes, inks, pharmaceuticals, and other products. Several Australian acacias are valuable sources of tannin, among them the golden wattle (A. pycnantha), the green wattle (A. decurrens), and the silver wattle (A. dealbata). A few species produce valuable timber, among them the Australian blackwood (A. melanoxylon) the yarran (A. omalophylla), also of Australia and A. koa of Hawaii. Many of the Australian acacia species have been widely introduced elsewhere as cultivated small trees valued for their spectacular floral displays.

Once the second largest genus in the pea family with over 1,000 species, Acacia has undergone a number of major taxonomic revisions to better reflect its phylogeny (evolutionary history) many former species are now placed in the genera Vachellia and Senegalia. The babul tree (Vachellia nilotica, formerly A. arabica), of tropical Africa and across Asia, yields both an inferior type of gum arabic and a tannin that is extensively used in India. Sweet acacia (V. farnesiana, formerly A. farnesiana) is native to the southwestern United States.


Scientists Sequence Genome of Common Pea

A basket of peas (Pisum sativum) in pods in Vinnytsia district, Ukraine. Image credit: George Chernilevsky.

Pea was domesticated around 10,000 years ago by Neolithic farmers of the Fertile Crescent, along with cereals and other grain legumes.

This plant belongs to the Leguminosae (or Fabaceae) family, which includes cool season grain legumes such as pea, lentil, chickpea, faba bean, and tropical grain legumes such as common bean, cowpea, mungbean.

It is a valuable source of dietary proteins, mineral nutrients, complex starch and fibers with demonstrated health benefits. Its symbiosis with nitrogen-fixing soil bacteria reduces the need for applied fertilizers so mitigating greenhouse gas emissions.

“The high-quality, annotated pea genome sequence will facilitate the characterization of its many known mutants, enhance pea improvement and allow more efficient use of the wide genetic diversity present in the genus,” said team leader Dr. Judith Burstin from the Université Bourgogne Franche-Comté and colleagues.

Dr. Burstin’s team sequenced the genome of the pea cultivar ‘Caméor,’ released by the French breeding company Seminor in 1973 and characterized by its protein-rich seeds.

“The pea has a much larger and more complex genome compared to other legumes,” noted team member Professor David Edwards, from the University of Western Australia.

“Its genome assembly spans about 4.45 billion letters. But it’s only with relatively recent technological innovations that we’ve been able to sequence and assemble such large genomes.”

“The research built on pioneering concepts of inheritance developed by Gregor Mendel, a 19th century monk,” added team member Professor Jacqueline Batley, also from the University of Western Australia.

“With the pea genome sequenced, we can now start to understand the basis for the variation which has evolved.”

“Mendel analyzed the inheritance of different pea traits such as wrinkled peas, and he demonstrated that these traits were passed on from one generation to the next, a foundation for Darwin’s later discoveries in evolution.”

“More than 150 years later, we’ve now assembled the pea genome and can start to understand the DNA basis of the inheritance observed by Mendel.”

The results were published in the journal Nature Genetics.

Jonathan Kreplak et al. 2019. A reference genome for pea provides insight into legume genome evolution. Nature Genetics 51: 1411-1422 doi: 10.1038/s41588-019-0480-1


Can someone identify this species from the pea family? - Biology

The Father of Genetics

"Pea hybrids form germinal and pollen cells that in their composition correspond in equal numbers to all the constant forms resulting from the combination of traits united through fertilization."

Gregor Johann Mendel was born o n July 22, 1822 to peasant parents in a small agrarian town in Czechoslovakia. During his childhood he worked as a gardener, and as a young man attended the Olmutz Philosophical Institute. In 1843 he entered an Augustinian monastery in Brunn, Czechoslovakia. Soon afterward, his natural interest in science and specifically hereditary science led him to start experiments with the pea plant. Mendel's attraction for scientific research was based on his love of nature in general. He was not only interested in plants, but also in meteorology and theories of evolution. However, it is his work with the pea plant that changed the world of science forever.

His beautifully designed experiments with pea plants were the first to focus on the numerical relationships among traits appearing in the progeny of hybrids. His interpretation for this phenomenon was that material and unchanging hereditary elements undergo segregation and independent assortment. These elements are then passed on unchanged (except in arrangement) to offspring thus yielding a very large, but finite number of possible variations.

Mendel often wondered how plants obtained atypical characteristics. On one of his frequent walks around the monastery, he found an atypical variety of an ornamental plant. He took it and planted it next to the typical variety. He grew their progeny side by side to see if there would be any approximation of the traits passed on to the next generation. This experiment was designed to support or to illustrate Lamarck's views concerning the influence of environment upon plants. He found that the plants' respective offspring retained the essential traits of the parents, and therefore were not influenced by the environment. This simple test gave birth to the idea of heredity.

Overshadowing the creative brilliance of Mendel's work is the fact that it was virtually ignored for 34 years. Only after the dramatic rediscovery of Mendel's work in 1900 (16 years after Mendel's death) was he rightfully recognized as the founder of genetics. 1

Mendel was well aware that there were certain preconditions that had to be carefully established before commencing investigations into the inheritance of characteristics. The parental plants must be known to possess constant and differentiating characteristics. To establish this condition, Mendel took an entire year to test "true breeding" (non-hybrid) family lines, each having constant characteristics. The experimental plants also needed to produce flowers that would be easy to protect against foreign pollen. The special shape of the flower of the Leguminosae family, with their enclosed styles, drew his attention. On trying several from this family, he finally selected the garden pea plant (Pisum sativum) as being most ideal for his needs. M endel also picked the common garden pea plant because it can be grown in large numbers and its reproduction can be manipulated. As with many other flowering plants, pea plants have both male and female reproductive organs. As a result, they can either self-pollinate themselves or cross-pollinate with other plants. In his experiments, Mendel was able to selectively cross-pollinate purebred plants with particular traits and observe the outcome over many generations. This was the basis for his conclusions about the nature of genetic inheritance. 3

Mendel observed seven pea plant traits that are easily recognized in one of two forms:

1. Flower color: purple or white

2. Flower position: axial or terminal

3. Stem length: long or short

4. Seed shape: round or wrinkled

5. Seed color: yellow or green

6. Pod shape: inflated or constricted

7. Pod color: green or yellow

Mendel's Law of Segregation

Mendel's hypothesis essentially has four parts. The first part or "law" states that, "Alternative versions of genes account for variations in inherited characters." In a nutshell, this is the concept of alleles. Alleles are different versions of genes that impart the same characteristic. For example, each pea plant has two genes that control pea texture. There are also two possible textures (smooth and wrinkled) and thus two different genes for texture.
The second law states that, "For each character trait (ie: height, color, texture etc.) an organism inherits two genes, one from each parent." This statement alludes to the fact that when somatic cells are produced from two gametes, one allele comes from the mother, one from the father. These alleles may be the same (true-breeding organisms), or different (hybrids).

The third law, in relation to the second, declares that, "If the two alleles differ, then one, the dominant allele, is fully expressed in the organism's appearance the other, the recessive allele, has no noticeable effect on the organism's appearance."

The fourth law states that, "The two genes for each character segregate during gamete production." This is the last part of Mendel's generalization. This references meiosis when the chromosome count is changed from the diploid number to the haploid number. The genes are sorted into separate gametes, ensuring variation. This sorting process depends on genetic "recombination." During this time, genes mix and match in a random and yet very specific way. Genes for each trait only trade with genes of the same trait on the opposing strand of DNA so that all the traits are covered in the resulting offspring. For example, color genes do not trade off with genes for texture. Color genes only trade off with color genes from the opposing allelic sight as do texture genes and all other genes. The result is that each gamete that is produced by the parent is uniquely different as far as the traits that it codes for from every other gamete that is produced. For many creatures, this available statistical variation is so huge that in all probability, no two identical offspring will ever be produced even given trillions of years of time.

So, since a pea plant carries two genes, it can have both of its genes be the same. Both genes could be "smooth" genes or they could both be "wrinkled" genes. If both genes are the same, the resulting pea will of course be consistent. However, what if the genes are different or "hybrid"? One gene will then have "dominance" over the other "recessive" gene. The dominant trait will then be expressed. For example, if the smooth gene (A) is the dominant gene and the wrinkle gene (a) is the recessive gene, a plant with the "Aa" genotype will produce smooth peas. Only an "aa" plant will produce wrinkled peas. For instance, the pea flowers are either purple or white. Intermediate colors do not appear in the offspring of these cross-pollinated plants.

T he observation that there are inheritable traits that do not show up in intermediate forms was critically important because the leading theory in biology at the time was that inherited traits blend from generation to generation (Charles Darwin and most other cutting-edge scientists in the 19th century accepted this "blending theory."). Of course there are exceptions to this general rule. Some genes are now known to be "incompletely dominant." In this situation, the "dominant" gene has incomplete expression in the resulting phenotype causing a "mixed" phenotype. For example, some plants have "incomplete dominant" color genes such as white and red flower genes. A hybrid of this type of plant will produce pink flowers. Other genes are known to be "co-dominant" were both alleles are equally expressed in the phenotype. An example of co-dominant alleles is human blood typing. If a person has both "A" and "B" genes, they will have an "AB" blood type. Some traits are inherited through the combination of many genes acting together to produce a certain effect. This type of inheritance is called "polygenetic." Examples of polygenetic inheritance are human height, skin color, and body form. In all of these cases however, the genes (alleles) themselves remain unchanged. They are transmitted from parent to offspring through a process of random genetic recombination that can be calculated statistically. For example, the odds of a dominant trait being expressed over a recessive trait in a two-gene allelic system where both parents are hybrids are 3:1. If only one parent is a hybrid and the other parent has both dominant alleles, then 100% of the offspring will express the dominant trait. If one parent has both recessive alleles and the other parent is a hybrid, then the offspring will have a phenotypic ratio of 1:1.

Mendel's Law of Independent Assortment

The most important principle of Mendel's Law of Independent Assortment is that the emergence of one trait will not affect the emergence of another. For example, a pea plant's inheritance of the ability to produce purple flowers instead of white ones does not make it more likely that it would also inherit the ability to produce yellow peas in contrast to green ones. Mendel's findings allowed other scientists to simplify the emergence of traits to mathematical probability (While mixing one trait always resulted in a 3:1 ratio between dominant and recessive phenotypes, his experiments with two traits showed 9:3:3:1 ratios).

Mendel was so successful largely thanks to his careful and nonpassionate use of the scientific method. Also, his choice of peas as a subject for his experiments was quite fortunate. Peas have a relatively simple genetic structure and Mendel could always be in control of the plants' breeding. When Mendel wanted to cross-pollinate a pea plant he needed only to remove the immature stamens of the plant. In this way he was always sure of each plants' parents. Mendel made certain to start his experiments only with true breeding plants. He also only measured absolute characteristics such as color, shape, and texture of the offspring. His data was expressed numerically and subjected to statistical analysis. This method of data reporting and the large sampling size he used gave credibility to his data. He also had the foresight to look through several successive generations of his pea plants and record their variations. Without his careful attention to procedure and detail, Mendel's work could not have had the same impact that is has made on the world of genetics.

I n cross-pollinating plants that either produce yellow or green peas exclusively, Mendel found that the first offspring generation (f1) always has yellow peas. However, the following generation (f2) consistently has a 3:1 ratio of yellow to green.

This 3:1 ratio occurs in later generations as well. Mendel realized that this is the key to understanding the basic mechanisms of inheritance.

I t is important to realize that in this experiment, the parent plants were homozygous for pea color. That is to say, they each had two identical forms (or alleles) of the gene for this trait--2 yellows or 2 greens. The plants in the f1 generation were all heterozygous. In other words, they each had inherited two different alleles--one from each parent plant. It becomes clearer when we look at the actual genetic makeup, or genotype, of the pea plants instead of only the phenotype, or observable physical characteristics.

Note that each of the f1 generation plants (shown above) inherited a Y allele from one parent and a G allele from the other. When the f1 plants breed, each has an equal chance of passing on either Y or G alleles to each offspring.

W ith all of the seven pea plant traits that Mendel examined, one form appeared dominant over the other. Which is to say, it masked the presence of the other allele. For example, when the genotype for pea color is YG (heterozygous), the phenotype is yellow. However, the dominant yellow allele does not alter the recessive green one in any way. Both alleles can be passed on to the next generation unchanged.

M endel's observations from these experiments can be summarized in two principles:

The Principle of Segregation

The Principle of Independent Assortment

Mendel came to four important conclusions from these experimental results:

1. The inheritance of each trait is determined by "units" or "factors" (now called genes) that are passed on to descendents unchanged.

2. An individual inherits one such unit from each parent for each trait.

3. A trait may not show up in an individual but can still be passed on to the next generation.

4. The genes for each trait segregate themselves during gamete production.

While Mendel knew of Darwin's work (though Darwin was evidently not aware of Mendel's work), Mendel's ideas on heredity and evolution were fundamentally opposed, in certain key ways, to those of Darwin. 2,5

"In a letter to William Bateson written in 1902 by Mendel's nephew, Ferdinand Schindler, stated, "He [Mendel] read with great interest Darwin's work in German translation, and admired his genius, though he did not agree with all of the principles of this immortal natural philosopher" (Orel, 1996, p. 188). Bateson (1913, p. 329) wrote, "With the views of Darwin which at that time were coming into prominence Mendel did not find himself in full agreement." 5

Now, this isn't to say that there isn't a great deal of controversy in this regard. Arguably most past and present authors and scientists view or viewed Mendel as a supporter of Darwinism. By contrast, Olby (1979, 1985) studied the historical context of evolutionary thought during Mendel's day and determined that Darwin's "'views on the role of hybridization in evolution were very far removed from Mendel's'". 5

"The extreme disagreement among scholars about Mendel's view of Darwin's writings is probably because Mendel wrote very little about Darwin, and thus most claims are suppositions about what Mendel must have thought about Darwin. In his surviving writings, Mendel's overtly referred to Darwin only four times, all in 1870, four years after the publication of "Versuche" One reference is in Mendel's (1870) Hieracium paper and three are in his eighth and ninth letters to Nageli (Stern and Sherwood, 1966). All four references are brief and reveal neither strong support of nor opposition to Darwin's theories." 5

However, in Mendel's copy of Origins, he did make occasional marks and margin notations. Mendel marked one passage where Darwin discusses the uniformity of hybrids in the F1 generation and the variability of their F2 offspring. Darwin's explanation for this was that there was some alteration in the reproductive system, some mutational effect. This explanation differs substantially from Mendel's explanation of independent assortment of independent traits or alleles. Also, Mendel directly contradicted Darwin's claim in Origin that changing conditions of life were the cause of variation in domesticated species. 5

In short, Darwin believed in the inheritance of acquired characters. This led him to his famous theory of continuous evolution. Mendel, in contrast, rejected both the idea of inheritance of acquired characters (mutations) as well as the concept of continuous evolution. The laws discovered by him were understood to be the laws of constant elements for a great but finite variation, not only for cultured varieties but also for species in the wild. 3 In his short treatise, Experiments in Plant Hybridization, Mendel incessantly speaks of "constant characters", "constant offspring", "constant combinations", "constant forms", "constant law", "a constant species" etc. (in such combinations the adjective "constant" occurs 67 times in his original paper). He was convinced that the laws of heredity he had discovered corroborated Gärtner's conclusion "that species are fixed with limits beyond which they cannot change". And as Dobzhansky aptly put it, "It is. not a paradox to say that if someone should succeed in inventing a universally applicable, static definition of species, he would cast serious doubts on the validity of the theory of evolution."

As the Darwinians won the battle for the minds in the 19th century, no space was left in the next decades for the acceptance of the true scientific laws of heredity discovered by Mendel. Further work in genetics was continued mainly by Darwin's critics. In agreement with de Vries, Tschermak-Seysenegg, Johannsen, Nilsson, et al., Bateson stated:

"With the triumph of the evolutionary idea, curiosity as to the significance of specific differences was satisfied. The Origin was published in 1859. During the following decade, while the new views were on trial, the experimental breeders continued their work, but before 1870 the field was practically abandoned. In all that concerns the species the next thirty years are marked by the apathy characteristic of an age of faith. Evolution became the exercising-ground of essayists. The number indeed of naturalists increased tenfold, but their activities were directed elsewhere. Darwin's achievement so far exceeded anything that was thought possible before, that what should have been hailed as a long-expected beginning was taken for the completed work. I well remember receiving from one of the most earnest of my seniors the friendly warning that it was waste of time to study variation, for 'Darwin had swept the field.'" 4

The general acceptance of Darwin's theory of evolution and his ideas regarding variation and the inheritance of acquired characters are, in fact, the main reasons for the neglect of Mendel's work, which (in clear opposition to Darwin) pointed to an entirely different understanding of the questions involved. 1

Callender, L. A., Gregor Mendel: An opponent of descent with modification. History of Science 26: 41-75. 1988.

Mendel, Gregor. Experiments in Plant Hybridization. 1865.

Bateson, W. Mendel's Principles of Heredity. Cambridge: Cambridge University Press, 1909.

Daniel J. Fairbanks and Bryce Rytting, Mendelian Controversies: A Botanical and Historical Review, Invited Special Paper, American Journal of Botany 88(5): 737 752. 2001.


Golden Pea

This showy, yellow-flowered plant is most often found in damp or wet soils in hills and mountains. It can withstand drought and trampling. It is not a very palatable food for livestock or other animals.

Description

This plant attains a height of one to four feet, terminating in a long raceme of golden-yellow flowers, each flower being 1/2 to 3/4 inch long. These plants usually occur in patches, since they spread via undergound stems. The leaves are compound and trifoliate with leaflets mainly oval and one to three inches long. At the base of each leaf are found two large leaflike stipules.

People often confuse this Golden Pea or False Lupine with true lupines in the genus Lupinus. However, it can easily be distinguished since there are three leaflets instead of five or more. False Lupine also has all stamens distinct, instead of united together as in true lupines.

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Written by Rob Nelson

Rob is an ecologist from the University of Hawaii. He is the co-creator and director of Untamed Science. His goal is to create videos and content that are entertaining, accurate, and educational. When he's not making science content, he races whitewater kayaks and works on Stone Age Man.


Discussion

Methodology

Genome-wide sequencing can detect mutations in mutant populations and so identify candidate genes in forward genetic screens (Tsai et al., 2011 ), but this depends on the availability of a reference genome sequence (Hwang et al., 2015 Campbell et al., 2016 ) which is not yet available for pea. Insertion mutagenesis can also tag genes facilitating their isolation (Schauser et al., 1999 Tadege et al., 2008 Urbański et al., 2012 ), but in pea insertion mutagenesis is not available. Here we investigated an alternative approach in pea and demonstrated that restriction site associated (RAD) sequencing can identify sequences deleted from Fast Neutron (FN) mutants.

The nature of mutations induced by ionizing radiation depends on several factors, including the type and energy of the radiation and the cellular response to the free radical-induced damage. These factors need to be taken into account when considering FN mutagenesis as a methodology for gene identification. The studies of Belfield et al. ( 2012 ) and Li et al. ( 2016a ) describe sequence variation associated with FN mutagenesis in Arabidopsis and rice, respectively. Both studies attribute many types of mutation to FN mutagenesis, of which 36% were deletion mutations and 50–60% were single base substitutions. In Arabidopsis the deletions were small with only one greater than 55 bp, whereas in rice 10% of the deletions were greater than 1 kb and two (out of 873) were greater than 1 Mb. These results contrast with our observations in pea, where no FN-induced allele (of 28 alleles distributed over 10 loci Domoney et al., 2013 McAdam et al., 2017 ), was a single base change, suggesting that single base changes were relatively rarer in pea than in rice or Arabidopsis. It is notable that in these three examples the proportion and size of deletions increases with increasing genome size. The number of ways in which a deletion of x bp can occur, such that it that disrupts fewer than y genes, is a combinatorial function of intergenic distance, so it is perhaps not surprising that in pea, with a large genome and low gene density, large deletions are more common.

The successful detection of the presence/absence of Stipules reduced (St) depended on the large size of the FN-generated deletion. Previous studies in this population had shown that large deletions were common (Sainsbury et al., 2006 Wang et al., 2008 Hofer et al., 2009 Hellens et al., 2010 Moreau et al., 2012 Chen et al., 2012 Couzigou et al., 2012 Domoney et al., 2013 ). The absence of at least two adjacent genes in FN2122/2 suggests that a single large deletion has occurred in this line in the region encompassing both the Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rca) and St loci. Precedent for such a scale of deletion induced by FN in pea is the joint deletion of alae keel-like (k) and Convicilin (Cvc) (Domoney et al., 2013 ).

Our approach depended on reliable detection of a tag corresponding to a PstI site when it was actually present, so that any tag missing in a mutant would warrant further investigation. The variation in read depth of single copy sequences was very high and we found that a cut-off value of 150 reads was an adequate compromise between sensitivity and reliability. In JI2822, the St tags had read depths of 432 and 323 (Notes S2), whereas the Rca tags were 327 and 693 (Notes S1) consistent with the expected read depth of single copy genes (Fig. S3).

RNA-seq is an alternative approach (McAdam et al., 2017 ) which may be advantageous for large genome species such as pea, where many of the RAD-seq reads are effectively wasted because they derive from repetitive sequences not represented in the transcriptome. However, genes involved in developmental patterning may be expressed in very few cells and therefore would be unusually rare in the transcriptome, so for these types of gene, the advantage of RNA-seq may fail to materialize. Furthermore, low abundance sequences would be most susceptible to stochastic loss.

The current lack of a genome sequence for JI2822 (the mutagenized line) hindered the identification of paired RAD tags flanking the same PstI site. For this reason, M. truncatula, the closest relative to pea for which genome sequence is available, was used in conjunction with pea transcriptome sequence data. The sequences of many of the RAD tags presumed missing from FN2122/2 corresponded to sequences distributed throughout the medicago genome (Fig. S5), as would be expected of tags missing by chance.

It has been estimated that each M2 from this FN population has, on average, seven independent deletions (Domoney et al., 2013 ), suggesting that the BC4S1 individual studied here would not carry more than one deletion.

Publicly available transcriptome data were available for pea (Franssen et al., 2011 Kaur et al., 2012 and the USDA database at https://www.coolseasonfoodlegume.org/sativum_unigene_v2) but the work of Alves-Carvalho et al. ( 2015 ) was not available at the time that this analysis was initially performed. Alignment of the RAD tags to the transcriptome sequences from the USDA database enabled the identification of paired sequences corresponding to the two sides of a PstI site, providing independent evidence for a deletion of the PstI site. This permitted the identification of a C2H2 zinc finger sequence as a candidate for the St gene, which was confirmed by the sequence analysis of independently obtained mutant alleles.

Analysis of soybean FN mutant populations has highlighted the advantages of other genome-wide approaches such as resequencing or array hybridization when a reference genome sequence is available (Hwang et al., 2015 Campbell et al., 2016 ) these two studies also emphasize that in some cases simple deletions may not be the most frequent type of mutation. In both of these cases genomic rearrangements rather than deletions were detected. It may be that the larger genome of pea, with interspersed repetitive elements, permits large deletions that are nonlethal. The approach we took, in this and previous studies (Chen et al., 2012 Hofer et al., 2009 ), screened for loss of PstI sites, so we may have missed rearrangements. Although our results demonstrate that a complete genome sequence of the target species is not required for this method of gene identification, RAD-based deletion screens would be easier if extensive sequence were available.

The role of Stipules reduced in the pea compound leaf

St is required for stipule enlargement (Meicenheimer et al., 1983 Sinjushin et al., 2011 ) rather than stipule identity, consistent with St being required for the elaboration of the basal frilled mantle. The reduced vascularization of the st stipule may be a consequence of reduced stipule elaboration (Fig. 5) reminiscent of the reduced petal phenotype of the rabbit ears (rbe) mutant in A. thaliana (Takeda et al., 2004 ), RBE being the most closely related Arabidopsis sequence to St (over the whole length of the predicted amino acid sequence). In the st mutant there is no difference in cell size in the medial vs lateral position of the stipule, whereas there is a significant difference in the wild-type (Table 1, Fig. S9), showing that differences in cell expansion between zones of the stipule is dependent on St. Within the stipule, these St-dependent cell sizes may reflect medial vs lateral identity.

The st bs mutant phenotype is weaker than the other st mutants (Fig. 1, Fig. S8) and results from a mis-sense (D234N) mutation within the C terminal EAR domain rather than non-sense mutation. The L235P substitution in JI3530 also occurs in the EAR domain, but the phenotype of this mutant is more severe than st bs (Fig. 1) suggesting that this transcriptional repressor domain (Ohta et al., 2001 ) is required for St function. Like rbe (Huang et al., 2012 Huang & Irish, 2015 Li et al., 2016b ), all of the st alleles examined have reduced lamina growth at the proximal position of an organ.

St transcripts appear to be confined to stipules and bracts in pea but are not found in flowers, consistent with the lack of alterations to floral morphology in the st mutant. There has been no previous comment in the literature on an altered bract morphology in st mutants this would be hard to detect because bracts are variable in size and frequency of appearance in pea. However, it has been noted previously that bracts are altered in cochleata (coch) mutants (Couzigou et al., 2012 ), so Coch is likely to be expressed in bract primordia, where it could upregulate St expression and so determine the final size of bracts. A high level of St expression in the developing stipule (and bract) appears to be dependent on Coch (Figs 6, 7).

The st mutation in combination with unifoliata, but neither mutant alone, completely abolishes stipule formation at upper nodes (Hofer et al., 2001 Kumar et al., 2009 , 2013 ). The precise evolutionary relationship between the Arabidopsis C1–1iG family C2H2 zinc finger domain proteins and St is not clear, due to sequence duplications in Arabidopsis and possible recent diversifying selection acting on St (Fig. 4). RBE, through its regulation of TCP5 and microRNA164 (Huang & Irish, 2015 ), appears to be involved in regulating the switch between cell division and differentiation. Uni in pea leaves is responsible for a ‘transient phase of indeterminacy’ (Hofer et al., 1997 ) which is manifest as continued meristematic activity in the leaf primordium, whereas the st mutant has reduced stipule marginal meristem activity (Meicenheimer et al., 1983 ), and thus St promotes this marginal meristem activity. The complete loss of stipules, late in shoot development of the st uni double mutant, may reflect the roles of Uni in promoting primordial growth and St in promoting marginal growth.

The more distantly related Arabidopsis protein JAGGED (C1-1iA group, Englbrecht et al., 2004 ), like St, regulates cell growth and division (Dinneny et al., 2003 ) and is involved in both bract and petal development. St regulates cell division to a greater extent than cell size, similar to JAGGED (Dinneny et al., 2003 ) and to RBE (Huang & Irish, 2015 ) more generally.

The very low level of St transcript in the coch mutant predicts that the coch st double mutant would be indistinguishable from coch. Yaxley et al. ( 2001 ) reported that coch st and coch were indistinguishable, in disagreement with Blixt ( 1967 ), Marx ( 1987 ), Gourlay et al. ( 2000 ) and Kumar et al. ( 2009 , 2013 ). Our transcript abundance results seem to be consistent with Yaxley et al. ( 2001 ), unless the small amount of St expression in the coch mutant can, under some circumstances, have consequences different from the null st mutant. The upstream open reading frame (uORF) may be relevant to these observations if it mediates post-transcriptional regulation (Laing et al., 2015 ), so the lower amount of St transcript in the coch mutant vs Coch (Fig. 6) may not necessarily result in a difference in the amount of St protein. Such regulation may be dependent on additional genetic or environmental factors and therefore explain the differences in the reported phenotypes of the coch st double mutant.

The in situ hybridization and quantitative polymerase chain reaction (qPCR) results are in agreement. The in situ analysis additionally shows that the St transcript is limited to stipules and bracts, and is absent from floral meristems and other parts of the leaf primordium. The weak expression of St in the coch mutant is not associated with mis-location or mis-timing. It therefore appears that Coch is epistatic to St, consistent with Coch determining stipule identity. However, we cannot completely rule out a role for St in determining stipule identity in certain genetic backgrounds because a leaf-like stipule structure was reported in an af tl st triple mutant (Gourlay et al., 2000 ), notwithstanding that this phenotype was noted to occur sporadically and only in the triple mutant. There is no evidence from the qPCR result of a feedback between St and Coch whereby St would maintain Coch expression and indirectly stipule identity.

Stipules reduced in legume species

Coding sequence and structural differences between St and corresponding sequences in medicago and other legumes raises the possibility that St may have diverged in Pisum, in association with the occurrence of large stipules. Although Lathyrus aphaca and L. odoratus differ in stipule size – the L. aphaca stipules being notably large –sequence alignment (Notes S2) does not support a closer relationship between Pisum and L. aphaca St genes than Pisum and L. odoratus St genes. Nevertheless, one position (A199 see Notes S2) distinguishes the L. aphaca and P. sativum sequences from all the other sequences that were aligned in Fig. 3 and this could be targeted in future functional studies. Whether there is any association between stipule size and variation in the St gene more broadly in these taxa remains to be determined.

If St has undergone neo-functionalization this may explain the elaboration of the pea stipule. There are strong signals of purifying selection acting on parts of the gene, yet in comparison to Medtr3g068095, some regions of St have an excess of amino acid substitutions given the nucleotide divergence (Fig. 4), suggestive of diversification (in one or other or both sequences). It should be noted that the vascularization of the stipules of these two Lathyrus taxa is different from each other and from pea (Kupicha, 1975 ), so these may represent three different consequences of St gene variants, or, stipule development in Lathyrus taxa may be independent of St.


Nitrogen-fixing bacteria

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Nitrogen-fixing bacteria, microorganisms capable of transforming atmospheric nitrogen into fixed nitrogen (inorganic compounds usable by plants). More than 90 percent of all nitrogen fixation is effected by these organisms, which thus play an important role in the nitrogen cycle.

What are nitrogen-fixing bacteria?

Nitrogen-fixing bacteria are prokaryotic microorganisms that are capable of transforming nitrogen gas from the atmosphere into “fixed nitrogen” compounds, such as ammonia, that are usable by plants.

Why are nitrogen-fixing bacteria important?

Nitrogen is a component of proteins and nucleic acids and is essential to life on Earth. Although nitrogen is abundant in the atmosphere, most organisms cannot use it in that form. Nitrogen-fixing bacteria accomplish more than 90 percent of all nitrogen fixation and thus play an important role in the nitrogen cycle. Because of these bacteria, legumes have the nitrogen necessary to make lots of proteins, which, in turn, is why beans are such a good source of dietary protein for humans and other animals. Additionally, legumes and certain cereal grasses are often grown as green manures and for crop rotation on farms as an organic source of nitrogen for other crops.

Where do nitrogen-fixing bacteria live?

There are two main types of nitrogen-fixing bacteria. Symbiotic, or mutualistic, species live in root nodules of certain plants. Plants of the pea family, known as legumes, are some of the most important hosts for nitrogen-fixing bacteria, but a number of other plants can also harbour these helpful bacteria. Other nitrogen-fixing bacteria are free-living and do not require a host. They are commonly found in soil or in aquatic environments.

What are some examples of nitrogen-fixing bacteria?

Examples of symbiotic nitrogen-fixing bacteria include Rhizobium, which is associated with plants in the pea family, and various Azospirillum species, which are associated with cereal grasses. Free-living nitrogen-fixers include the cyanobacteria Anabaena and Nostoc and genera such as Azotobacter, Beijerinckia, and Clostridium.


Extinct species rediscovered in Winterhoek mountains, South Africa, after 200 years

Last seen in 1804, Psoralea cataracta was rediscovered by Brian du Preez, a Ph.D. student in botany at the University of Cape Town, when he accidentally stumbled upon a population on a narrow track close to a river on a farm near Tulbagh in the Western Cape. Credit: Wiida Fourie, Stellenbosch University

One of the first recorded species to have been lost to forestry and agriculture in the Western Cape in the 1800s, a type of fountain bush from the pea family that used to grow next to mountain streams in the Tulbagh region, have been rediscovered.

Psoralea cataracta was discovered by Brian du Preez, a Ph.D. student in botany at the University of Cape Town, when he accidently stumbled upon a population on a narrow track close to a river on a farm near Tulbagh on Oct. 24, 2019.

Until now, P. cataracta was only known from a single specimen collected from "Tulbagh waterfall" in 1804, and in 2008, after many fruitless searches, it was officially declared extinct on the Red Data List of South African Plants.

From previous search efforts as a volunteer with the Custodians of Rare and Endangered Wildflowers (CREW) around the Tulbagh waterfall, he instantly knew what a find this was: "As soon as I saw those delicate thread-like flower stalks, I knew it was Psoralea cataracta."

Prof Charles Stirton, an internationally recognised specialist on the genus Psoralea based in the United Kingdom, and his co-supervisor, has since confirmed that it is indeed the long lost species rediscovered, last seen in 1804.

"For me the definitive characteristics are the remarkable stipules, very long filiform pedicels, and the unique flower colour. This is a very important find as it shows how the Cape is still relatively unexplored in many mountainous areas. Given than many of the Cape Flora only come up briefly after fires, fading quickly, and that sometimes these fires are irregular, the chances of being in an area at the right time is slim. Well done to Brian for a wonderful find," he writes in an e-mail from the UK.

The delicate flower and thread-like flower stalks of Psoralea cataracta, a type of fountain bush which only occur close to mountain streams in the Tulbagh region of the Western Cape, last observed in 1804. Credit: Brian du Preez

Mr Ismail Ebrahim, project manager at CREW, agrees that it is an extraordinary finding: "It is really uncommon to find a properly extinct species, something that hasn't been seen for ages. And with Cape Flora it is even harder, because most species are restricted to a really small patch and it is easy to miss them if you don't go off the beaten path.

"It also just shows you the value of proper field botany, like they did it in the old days," he adds.

Thus far, the 26-year old student is building up quite a reputation for finding long lost species. As a BSc Hons-student in botany at Stellenbosch University (SU) in 2016, he rediscovered two presumed extinct species in the pea family, Polhillia ignota and Aspalathus cordicarpa, last seen in 1928 and the 1950s respectively, and subsequently completed an MSc on Polhillia in 2017, also at SU.

This year he collected a new species of Aspalathus growing on sand dunes on the banks of the Riet River in the Swartruggens Mountains north of Ceres. He is now in a rush to get the species described, as this part of the Riet River is earmarked for orchard expansion.

"We can only conserve what we have described. Only species that have been formally described can receive a Red Data List status, which by law then protect it from development, depending on its conservation status," he warns.

For this reason, Brian has decided to tackle a revision of the genus Indigofera in the Greater Cape Floristic Region (GCFR) for his Ph.D. This diverse genus comprises over 100 species in the region, with at least 30 new species to be formally described.

He has been covering thousands of kilometres in his Nissan bakkie—from the Richtersveld through into the Eastern Cape, and everything in between for the past six months, and has already collected over 60 Indigofera species.


Acknowledgments

We thank Servane Penvern, Wolfgang Weisser, and Brigitte Pélisson for their contribution and logistical support in field sampling. Nancy Moran, James Mallet, Douglas Bailey, Thomas Baldwin, and 2 anonymous referees provided valuable comments on the manuscript. We also thank Lucie Mieuzet and Solène Coedel for their support in genotyping and Maurice Hullé and Guillaume Evanno for helping with the analysis of performance data. Part of this work was carried out by using the resources of the Computational Biology Service Unit from Cornell University, which is partially funded by Microsoft Corporation. This work was funded by program ECOGER, “Écologie pour la gestion des écosystèmes et de leurs ressources”.