Questions Flashcards

1
Q

Why finger millet, and not a different opportunity crop?

A

In my opinion, finger millet is an opportunity crop that is just beginning to gain traction. As opposed to more commonly known opportunity crops such as sorghum, the research delineating its opportunities and challenges is far more current, and therefore has intrinsic interest.

I also personally have a great interest in Southern Asia, where finger millet is a staple food crop. I aim to do a postgraduate project at the Kerala Agricultural University.

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2
Q

Is finger millet a more promising opportunity crop than sorghum, for example?

A

I would say that the purpose of opportunity crops is not necessarily to outcompete each other. This is a very “intensified” way of thinking. Instead, we should aim to think about the different qualities that opportunity crops can provide in an integrated system.

So for example, here I have covered the advantages for finger millet in phenolic compounds for anti-diabetic aims, resilience to increased soil salinity and in its yield potential.

However, sorghum for example has advantages in a high quantity of slow release starch, resilence to heat stress and also in its use as a biofuel.

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3
Q

How do opportunity crops fit into a highly intensified agricultural system?

A

I am not saying we should do away with megacrops. I’m also not saying that we should stop investing in megacrop research.

What I am saying is that megacrops have left us in this Anthropocene, with a variety of symptoms: poor health, instability to changing conditions and yield gaps. In this way opportunity crops can provide a local solution to a global problem. They can tackle these localised health problems, changes that are arising due to climate change, and location-specific yield gaps.

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4
Q

How are opportunity crops superior to megacrops?

A

For example, maize, wheat and rice are all lower in phenolic content than finger millet.

Maize, wheat and rice are also intolerant of salinity to varying degrees, and in different ways. So for example: maize is particularly liable to have its seed germination interfered with, wheat is particularly susceptible to stunted growth and rice can have its photosynthetic capacity inhibited.

And finally, the yield gaps – so the amount of yield between requirmeents and productions that these megacrops leave are also location specific. Maize yield gap is localised to Eastern Central America, Southern Africa, Eastern Europe and Southeastern Asia. Wheat’s yiled gap is centralised in Europe and South Asia; and rice’s is also to South Asia and West Africa.

Clearly, these global problems require local solutions, and believe that opportunity crops could be part of this.

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5
Q

How do opportunity crops fit into land use?

A

And I’m not even necessarily saying that these opportunity crops have to take away from the land use that has been set aside for the megacrops. Clearly, in this Anthropocentric agricultural context we have set aside a vast amount of land, and the majority of this is allocated to megacrops: wheat, and then maize and then rice.

However, a study by Gururani in the Uttarakhand Hills of the Himalayas utilised a generations old Barahnaja intercropping system between wheat, rice and finger millet. This improved soil fertility, therefore reducing the need for inputs and decreasing this cost to both farmers and the environment.

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6
Q

Are there any other crucial characteristics for an opportunity crop to have?

A

Yes! One crucial characteristic of an opportunity crop that I unfortunately did not have time to mention is “cultural significance”. I believe cultural significance is important because, for a lot of populations, interactions with plant species is a huge factor of their culture; and crop intensification threatens this generational relationship.

One example in which I think finger millet satisfies this characteristic is in its use in making Chibwantu – a fermented probiotic drink that is traditional at several ceremonies such as weddings. The probiotic potential of these also ties into the health benefits of finger millet, as probiotics have been shown to help strengthen the immune system; as well as helping the synthesis of various nutrients such as B12.

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7
Q

How did the phenol analysis work?

A

Fractionation of polyphenols extracted by high performance liquid chromatography compared to a reference.

Ambali made and consumed. FRAP evaluates the ability of plasma antioxidants to reduce ferric ion into ferrous ion, which forms a blue colored complex when binding to 2,4,6-tripyridyl-s-triazine (or, for the sake of everyone’s time and convenience TPTZ), that you can measure using spectrophotometry; absorbance at this wavelength is an indicator of the antioxidant capacity.

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8
Q

Describe the FRAP in this case

A

In this specific case, Kumari et al took 30 μL of plasma and added to 1 mL of Fe(III)-TPTZ reagent. Antioxidants in the plasma then reduce Fe(III) to Fe(II). The reaction takes place for 4 minutes at 37°C and after 4 minutes, the reaction is considered complete, and the measurement is taken. The absorbance of the resulting colored solution is measured at 593 nm using a spectrophotometer. The greater the reduction of Fe(III) to Fe(II), the higher the antioxidant power of the plasma sample.

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9
Q

Standard curve

A

To calculate the antioxidant capacity of the plasma, a standard curve is prepared using a known concentration of a standard antioxidant solution.
To do this, they used a stock solution of FeSO4.7H2O (Iron (II) sulfate heptahydrate), which is then diluted to create a series of standards with known concentrations, ranging from 0.1 to 1 mM/L. The standard curve correlates the known concentrations of antioxidants (using FeSO4) with the absorbance readings at 593 nm. The curve allows the conversion of the plasma’s absorbance into a value for its antioxidant capacity.

Results are ultimately expressed in terms of μmol/L of antioxidant power.

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10
Q

How do phenolic compounds work?

A

Phenolic compounds are iron chelators. This means that they react with ferric iron in the labile pool using their phenolic hydroxyl groups that are attached to their aromatic rings, reducing into it into ferrous iron by forming bi- or di-dentate bonds. This means that the iron cannot participate in the Fenton reaction; production of hydroxyl reactive oxygen species via hydrogen peroxide. Essentially, they are sequestering the volatile iron.

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11
Q

How do you tradeoff phenols with iron?

A

Both are good! Return to oppocrop logic…

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12
Q

What is cubic spline analysis?

A

Restricted cubic splines can be used to assess non-linear relationships. It is natural to assume that total dietary antioxidant content might have a non-linear relationship with the odds ratio of developing type 2 diabetes mellitus, because there may be thresholds where certain extremely low antioxidant contents are not related to diabetes mellitus, because other health conditions are more prevalent first. From a statistical perspective, it is safer to assume a non-linear relationship, rather than a linear one. Restricted cubic splines are alsp constrained to avoid over-interpretation of a more rigid linear relationship.

Restricted cubic splines are also good at introducing confounding variables. For example, in this study confounding variables such as age, sex, smoking status, alcohol consumption, physical activity,BMI, hypertension and health supplement intake were controlled for in the model. I might also have controlled for socioeconomic status, for example.

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13
Q

What other ways could you have investigated this effect?

A

Piecewise model to elaborate on thresholds.

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14
Q

What is the significance of using an odds ratio?

A

Odds ratio are often used in case-control studies; individuals with the disease are compared to individuals without. Ideal for measuring risk vs odds. Since it isn’t a cohort study, you don’t have incidence of the disease; you can’t directly ascertain risk. Calculate the odds of exposure to the risk agent. Very practical in observational studies.

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15
Q

Are there other health conditions which also need to be tackled?

A

Yes! Lots. For example finger millet is famed for having high levels of calcium. Osteoporosis displays high rates in southeastern asia. 52% of women in India suffer with osteopenia, the precursor to osteoporosis.

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16
Q

What other symptoms of climate change could you have considered?

A

Drought stress, which finger millet also displays tolerance to through similar mechanisms in Nepalese landraces. These display qualities such as early maturity. For example, the Dibya Sinha variety takes just 80 days to mature (down from 180); a proxity trait for breeding drought escape. Completes life cycle before drought.

Also Striga parasitic weed tolerance is exhibited by some varieties of finger millet, which demonstrate an enhanced immune reaction to infection by the parasite (by preventing attachment, HR and cell death near haustoria).

Finally, resistance to Magnaporthe grisea is also selected for.

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17
Q

How does finger millet respond to low soil salinity? Is this even relevant?

A

No because the hotspots of decrease in salinity are in North America.

18
Q

How does proline osmoprotection work?

A

Proline is a highly soluble, hydrophilic amino acid that can accumulate in the cytoplasm of plant cells when they experience osmotic stress. This solubility enables it to be present in relatively high concentrations without disrupting the cell’s internal structure: it is a compatible solute. When proline accumulates, it increases the osmotic potential of the cell, which helps retain water and prevents the cell from losing too much water under stress conditions

19
Q

How was the proline extraction run?

A

Leaf tissue homogenisation: releases proline and stabilises it

Proline reacts with ninhydrin to form a hydrophobic chromophore, which can be extracted with toluene

Absorbance correlates with the amount of proline and compared to a standard.

20
Q

How does salinity result in scorching and necrosis?

A

High salinity can inhibit photosynthesis by affecting chloroplasts, stomatal conductance, and chlorophyll production. Leaf scorching is often seen in areas where photosynthesis is impaired, causing a decrease in the plant’s energy production.

In extreme cases, this water deficit can lead to necrosis, where cells in the leaf tissue die due to lack of hydration and proper nutrient flow (Munns, 2002; Ashraf & Harris, 2004).

21
Q

How does transcriptomic analysis work?

A

Sequencing a transcriptome allows for identification of DEGs, that are potentially implicated in a response under a certain stressor.

Transcriptome sequencing is completed by RNA-Seq:

Extract mRNA
Convert it to cDNA via reverse transcription; more suitable for amplifying and sequencing
Fragmented and adding adaptors
High throughput sequencing
Analysed bioinformatically; de novo synthesis of a transcriptome

22
Q

How is functional annotation completed?

A

Machine learning is often used when no reference genomes are available, and then functional validation is required through knockout/down or overexpression studies.

23
Q

Why does self-pollination require emasuculation and artificial hybridisation?

A

Self-pollinators require emasculation and artificial hybridisation in breeding programmes. If you think about it, if we are using a breeding programme to try and upregulate genes that result in high yield, we don’t want to keep this to just one plant; we want to spread the phenotype.

24
Q

What is the contact method?

A

Panicles are held together by intertwining the fingers of the male panicle inside the female panicle.
Covered with butter paper bags for protection and to exclude interaction with external pollen sources.
In the contact method for successful hybridization, genotypes with a dominant trait such as pigmentation on nodes are used as male parents (Gupta, 2006), and this helps in differentiating a crossed F1 from that of the selfed.
A handful of crossed seeds are obtained in this method, and all the seeds from female panicles are grown to identify true hybrids.
Growing all seeds to identify true hybrids requires more resources, time, space, and labor.

25
Q

What is genetic male sterility?

A

Application of gibberellic acid (GA3), a gametocide, at 1,600 parts per million (ppm) at the 5th leaf stage is effective in inducing male sterility.

However, this method is not utilized in hybridization programs due to maintenance problems; chemically induced male sterility needs to be induced for every season/generation, which is a resource- and time-consuming procedure and also hazardous to the people involved in it.

26
Q

How do virescence markers work?

A

Viresence markers are used in marker-assisted breeding, as they can be used to distinguish hybrids from parent plants. Cross-pollination is difficult to visually assess in naturally self-pollinating crops. However, is a virescence marker can be induced in a hybrid, then these can be tracked visually, and these hybrid individuals recovered. This is because virescence markers link to genetic changes that only occur during cross-pollination; self-pollinating crops usually do not have changes in their chlorophyll biosynthesis.

27
Q

What are the advantages of a reference genome?

A

A reference genome can be used for transcriptomics. Ultimately, the goal is to map each transcript to a gene, which is obviously facilitated by being aware of what the genome actually is.

Gene function can then be predicted with their ontology, by comparing to referecne genomes of other similar annotated crops; this is homology-based annotation (for example by InterPro).

Reference genome can therefore help us to understand genome architecture, in terms of genes and regulatory elements.

A reference genome can also speed up marker-assisted selection, as we know where certain genetic markers are that can be linked with desirable traits; and these markers can be screened for.

28
Q

What are the advantages (and disadvantages?) of CRISPR-Cas9

A

CRISPR-Cas9 is facilitated by having a fully sequenced genome because:

Functional annotation of specific genes and their regulators is possible
Guide RNA design for efficiency and precision, to prevent off-course cuts
Compare changes to make sure only the desired changes were made

CRISPR-Cas9 is superior to conventional breeding because it is:
Faster
Cheaper
Less resource intensive
More precise
More accurate

29
Q

Evaluate finger millet utility to both conventional breeding and transgenics

A

High genetic variation makes finger millet promising for conventional breeding programmes.

Transgenics less desirable due to regulatory strictness. However, trasngenic studies have been shownt o be successful. Take the case of Anjaneyulu et al. Who engineered a vacuolar H+-pyrophosphatase gene from Sorghum bicolor, another opportunity crop into finger millet. It displayed higher yields under greater salinity stress.

30
Q

VPPases

A

VPPases help maintain salt tolerance by pumping protons (H+) into vacuoles, creating a proton gradient across the vacuolar membrane. This gradient facilitates the sequestration of toxic sodium ions (Na+) into vacuoles, thus preventing their accumulation in the cytoplasm, which could disrupt cellular functions (Zhao et al., 2007; Zhang et al., 2014).

VPPases are involved in maintaining osmotic pressure by regulating vacuolar pH. This helps the plant retain water under saline conditions, thereby improving its overall water use efficiency (Li et al., 2017).

31
Q

How would you best utilise finger millet as an opportunity crop?

A

I would best use it as part of integrated system. Perhaps with intercropping. I would invest in research for the things its natural genetic diversity seem geared towards, to see whether this could be amplified. But I would not forgo other mega and opportunity crops to integrate within it in a local solution to a global problem.

32
Q

Why is finger millet grown where it is?

A

It evolved there.

Cultural preference.

Tradition.

Suitability to the environment.

33
Q

Why hasn’t finger millet already solvered these health issues?

A

In the same way that finger millet production does not fulfill its demand, finger millet health benefits do not satisfy all health concerns. There is no way of measuring how many people it does “help”. All I am outlining is the potential for finger millet to help as being worth exploring.

34
Q

What is the VACS?

A

A partnership between The US State Department, the African Union and The Food and Agriculture Organisation of the UN to build crop climate models.

35
Q

What is high performance liquid chromatography?

A

Products can be separated with regards to: Polarity, Size, Charge and Hydrophobicity. And are detected using UV-Vis, fluorescence, or mass spectrometer

36
Q

What is the “core collection”

A

Maximum germplasm potential; minimum redundancy; representative sample

37
Q

What makes protocatechurin a good iron chelator?

A

The hydroxyl group on its aromatic ring has a particularly high affinity for ferric iron; forming extremely stable complexes, reduces the likelihood of dissociation

38
Q

Why do you think the different genotypes had different salinity tolerances?

A

That’s literally the whole point bruh

39
Q

How to build core collection?

A
  1. assess for genetic, physiological, morphological and ecological traits
  2. group accessions based on similarities
  3. use PCA to generate the most representative pop
  4. test to validate
40
Q

How do the conditions for the Fenton reaction arise?

A
  • NADPH oxidase generates superoxide in immune cells
  • superoxide dismutase creates hydrogen peroxide