Week 2 Flashcards
How many people face problems with hunger?
Between 691 and 783 million people faced hunger in 2022 – around 9% of the world population
What drives food insecurity?
Major drivers of food insecurity: conflict, climate extremes and rising prices of food, agricultural inputs and energy
How will food insecurity increase?
Exposure to more complex, frequent and intense climate extremes is threatening to erode and reverse gains made in ending hunger and malnutrition
How has global hunger changed overtime as % population undernourished?
2005 to 2009 (12% decrease to 8.6%)
2009 to 2019 (8.6% to 7.9%)
2020 to 2022 (8.9% to 9.2%)
What is the distrubution of the prevalence of undernourishment in 2022?
Global - 9.2%
Africa - 19.7%
Asia - 8.5%
How much water does farming use?
Farming uses 70% of the world’s fresh water
What is the distrubution of the prevalence of undernourishment in 2015?
Global - 7.9%
Africa - 15.8%
Asia - 8%
What are the food challenges of the future?
An expanding population - 7 billion growing to 9 billion by 2050
Climate change/climate extremes/soil erosion/loss of biodiversity
Finite resources - Land availability/fertilisers /energy/water
Conflict
What are the predictions for how climate will change in two different scenarios?
RCP = Representative Concentration Pathway
RCP2.6: radiative forcing 2.6 W m-2 in 2100, CO2 ~400 ppm, 1.5 oC temperature rise
RCP8.5: radiative forcing 8.5 W m-2 in 2100, CO2 >900 ppm, 4.9 C temperature rise
What are the predictions for agricultural requirements?
100% increase in production required by 2050 (based on 2.4% yield increase per year based on data from 1989-2008
What was the past and future needs for cereal production for sustaining human population?
Global cereal production rose from 877 million metric tons in 1961 to 2351 million metric tons in 2007
To meet future demands this will need to rise to 4000 million+ metric tons p.a. by 2050 (70% increase compared to 2007).
What is the observed trend for global preciptation?
Areas like USA and North Europe will see an increase but areas with high farmland will see decrease so new crop varieties will need to be more efficient in their use of water
What is the breakdown of energy demand in agriculture?
29% - Fertilisers
Diesel - 24%
Electricity - 17%
Natural gas - 9%
Pesticide - 9%
Other - 12%
What are 2050 yield predictions based on currently used agricultural land?
Maize – 67%
Rice – 42%
Wheat – 38%
Soybean – 55%
What was the green revolution?
Research technology transfer initiatives in the 1950-1960s that increased agricultural production in parts of the world
What research was included in the green revolution?
High yielding crops, dwarf varieties
Use of fertilizers
Irrigation
mechanisation
What is an overview of wheat yields?
There are many areas with wheat yields as high as 10 metric tons/ha.
But the he majority of land cropped to wheat delivers yields below 3 metric tons/ha.
What areas have the lowest wheat yields?
These larger areas of low-yielding land/low-yielding environments (primarily in developing countries) offer the greatest opportunity for substantial increases in global food production
How will low income areas have substatial increase in food production?
The most gain will come from delivering these technologies in developing countries, but the new technologies will have to be economically accessible and readily disseminated.
What is the predicted wheat production in 2050?
Developing countries - 1750 millon tonnes
Industrial countries - 900 million tonnes
How will RCP 8.5 impact Maize yields?
2050 - global slight decrease averaging around 20%
2090 - Middle east + North Africa 30% increase but deacrease in europe ie France 30%
How will RCP 8.5 impact rice yields?
2050 - Global decrease by 20% eg Russia
2090 - Severe decrease 50% in Russia and europe but India decreasing by 20%
How will RCP 4.5 impact Maize yields?
Both 2050 and 2090 mostly unchanged though slight decrease in europe by 10% though Sahel africa increase by 10%
How will RCP 4.5 impact rice yields?
Both seeing a global decrease of approximately 20%
What is currently requried to maximise crop yields?
NPK fertilisers - require fossil fuels (c.1.5% of global fossil fuel consumption)
Pesticides - consequences for environment, biodiversity and human health
Irrigation (1/3 of crops are produced on irrigated land)
What are the challenged for future crop breeders/growers?
High yielding varieties
Lower fertiliser requirements
Adapted to climate change (abiotic stresses, including drought)
Resistance to pests and diseases
What is an overview of classical breeding?
Classical breeding relies largely on independent assortment and homologous recombination between chromosomes to generate genetic diversity
What techniques are used for classical breeding?
Classical plant breeding may also make use of a number of techniques such as protoplast fusion, embryo rescue or mutagenesis to generate diversity and produce hybrid plants that would not exist naturally.
What is independant assortment of alleles?
The alleles of two (or more) different genes get sorted into gametes independently of one another.
In other words, the allele a gamete receives for one gene does not influence the allele received for another gene
What are the combinations created from independant assortment of alleles?
For a plant with ‘n’ haploid chromosomes the number of possible combinations in gametes, produced by independent assortment alone is 2^n
What is incomplete linkage and crossing over?
Crossing Over is the process of separation of genes between homologous pairs into various gametes
Incomplete linkage occurs when two loci are located on the same chromosome but the loci are far enough apart so that crossovers occur between them during some, but not all, meioses
What is the aim of plant breeding?
Classical plant breeding uses deliberate interbreeding (crossing) of closely or distantly related individuals to produce new crop varieties or lines with desirable properties.
‘Cross the best with the best and hope for the best’
What happens after the breeding of two desired parents?
F2 progeny with desirable combinations of traits from both parents are then selected for further breeding to produce homozygous or pure breeding lines – genetic monoculture
What traditionally drives which crops are further selected for breeding?
Traditionally this would have been dependent upon phenotypic selection
What is the back crossing process?
Recombination occurs in F1
Need to select progeny containing the new gene at each generation. OR can use DNA marker technology to select appropriate progeny. Recombination can occur in each generation reducing the size of the introgressed DNA
At what backcross will the new line be 98% identical to P1?
At BC5-6 the new line should be greater than 98% identical to the original P1
What happens between F1 to F5 generations in the bulk method?
Hybridisation between chosen parents to create an F1
F1 to F5 generations are grown by selfing as bulk populations with no selection
Rationale - genotypes best suited to the environment will produce the most progeny
What happens between F6 to F10 generations in the bulk method?
Progeny showing desirable characters are selected at the F6 generation (nearly homozygous)
Select plants and a single head is sown as a row at F7
Initial yield trials (F8-9), then advanced (F9-10)
What happnes during the Pedigree method?
Selected F2 plants grown in plant/headrows at F3
‘Best’ plants are selected for F4 trials
Repeated until F6 when plants are near homozygous
Yield trials at F6 and beyond
What are the downsides to the Pedigree method?
Labour and resource intensive
Can discard valuable genotypes early in the programme
What is the history of plant breeding?
As a science, plant breeding originated with Sir Rowland Biffen in who identified a single recessive gene (Yr) for resistance to wheat yellow rust caused by Puccinia striiformis
Breeding linked to developments in Mendelian Genetics
What is a history of the green revolution?
The ‘Green Revolution’ in the first half of the 20th Century was initiated by breeders like Nobel Prize winner Norman Borlaug
Led to significant improvements in wheat, maize and rice
What traits where selected for in the green revolution?
Higher yield
Improved grain quality
Multiline varieties for resistance to diseases/pests
Tolerance of abiotic stresses
What is an example of a monogenetic trait found in wheat?
The introduction of ‘dwarf’ wheat varieties from Japanese varieties (e.g. Norin 10) increased grain yield. These wheat varieties are less responsive to natural plant growth regulators (Gibberellins).
What were the advantages of dwarf wheat like Norin 10 varients?
The semi-dwarf varieties he bred (half to two-thirds the height of standard varieties) produced more stalks and heads of grain per plant.
Also, larger amounts of assimilate were partitioned into grains, further increasing the yield.
What is an overview of Norin 10/ Brevor hybridisation?
Crossbred the semi-dwarf Norin 10/Brevor cultivar with disease-resistant cultivars to produce varieties that were adapted to tropical and sub-tropical climates.
What is an overview of the gene Rht?
Rht = Reduced height
Wheat dwarfing genes that led impressive yield increases in the Green Revolution. Rht genes encode mutant DELLA proteins that are more active in repressing GA-responsive growth
What is an overview of the yield increase of wheat from 1950 to 2000?
Mexico - 700 kg/Ha to 5000 kg/Ha
India - 600 kg/Ha to 2500 kg/Ha
Pakistan - 900 kg/Ha to 2200 kg/Ha
What is an overview of the major cereal crops?
Wheat, maize and rice - staple diet for much of the world’s population
Rich source of carbohydrate (starch), proteins, fats and nutrients
Grains used in baking, fermented for beverages or biofuel
Wheat and maize - subject to selective breeding for
c.10,000 years
Early domestication selected highly desirable characters
What is an overview of modern domesticated wheat?
Modern domesticated wheat Triticum aestivum is a hexaploid derived by the hybridization of three different diploid parents making its genetics quite complex
Commercial varieties are usually inbred lines
What is an overview of total wheat production?
Wheat is the third most-produced cereal (651 million tons) after maize (844 million tons) and rice (672 million tons)
Wheat is grown on more than 200,000,000 hectares - larger than for any other crop.
World trade in wheat is greater than for all other crops combined.
What are alternative uses of wheat?
Wheat grains are used to make flour for leavened, flat and steamed breads/biscuits etc. and for fermentation to make beer and other alcoholic beverages, or biofuel
Where does wheat originate?
Wheat originated in the Fertile Crescent in the near east
What was the first domestication event for agricultural wheat production?
A hybridization event between Aegilops speltoides (BB) and
Trictum urartu (AA) gave rise to the Emmer Wheat (AABB)
Triticum turgidum ~0.8 MYA
What was the second domestication event for agricultural wheat production?
Triticum aestivum arose from hybridisation event between Emmer Wheat (AABB) and Aegilops tauschii (DD) ~0.4 MYA
What traits where selected for in wheat?
Seed size
Growth habit (erect/prostrate; fewer tillers)
Reduced seed dormancy
Ease of threshing
What were the selection drivers for domestication?
Loss of spike shattering (Brittle rachis)
Free threshing (Tenacious glumes, Q)
What is brittle rachis?
Brittle rachis (Br) – grains remain attached to the spike in harvesting
What is free theshing?
Threshing separates the edible part of the grain from the chaff
Tenacious glumes 1 Tg1, Q –> free threshing
What are homologous chromosomes?
Homologous chromosomespair readily during meiosis
What are homoelogous?
Homoeologousdon’t pair or pair only occasionally during meiosis
What is an overview of wheats polyploid genome?
Genomes A B and D
Diploid at each point ie Chr 3A or Chr 7c these are homologous
Chromosomes from different genome but same number are homoeologous
What achieves genome stability in wheat?
Genome stability is achieved through the action of the Ph1 gene (Chr 5B)
What an overview of the production of maize?
The US produces in excess of 300 Million tonnes/pa (20% of cropland).
Used for a wide variety of purposes including starch, animal feeds and brewing.
Maize is a domesticated variant of teosinte, a wild grass.
What is an overview of the history of maize?
Maize was domesticated in Mexico and about 2500 BC the crop had spread throughout much of America.
Prior to domestication plants grew small, one-inch long corn cobs, and only one per plant
What is the overview of the domestication of maize?
Centuries of artificial selection resulted in the development of maize plants capable of growing several cobs per plant several inches long - a consequence of just 3 single gene mutations
What is an overview of the genetics of maize?
Maize is genetically diploid.
Male and female flowers are separated which makes F1 hybrid seed production much easier
What was farming of maize like in he early 1930s?
Prior to 1930 US farmers grew only open pollinated ‘varieties’ of maize.
The ‘Best ear’ was then selected by farmers for next year’s planting.
This resulted in little to no yield gain from year to year
Can maize self pollinate?
Maize is a natural out-crosser that can also self-pollinate. Self-pollination leads to reduced vigour, a phenomenon known as inbreeding depression.
Why was 90% of US maize a F1 hybrid by 1939?
This is due to a phenomenon known as heterosis or Hybrid Vigor - ‘An amazing phenomenon which two runty parents produce a giant offspring’.
It’s precise mechanistic basis is still disputed.
What are the different types of rice?
Oryza sativa = Asian rice. Oryza glaberrima= African rice
What is an overview of the domestication of rice?
Genetic evidence suggests that all forms of Asian rice (indica and japonica) arose from a single domestication event 8,200–13,500 years ago in China from the wild rice Oryza rufipogon
How important is rice?
Rice is the staple food for almost half of the world’s population (particularly in Asia). It provides more than 20% of the calories consumed worldwide by humans
What is an overview of the genetics of rice?
Rice exhibits simple diploid genetics. It is normally grown as an annual crop although perennial types are used
What is an overview of rice production?
It normally self-pollinates so most commercial varieties of rice are inbred lines
It’s production is highly labour-intensive
Rice is grown widely in Asia, Australasia, Africa and the Americas
What are the genetic limitations of conventional plant breeding?
Current high yielding genetically uniform crops are the result of thousands of years of domestication and selection
This has resulted in the creation of ‘bottlenecks’ in genetic diversity and a limited gene pool for further improvement
How can the reduced genetic variation in crops be improved?
Considerable genetic resources exist in the form of landraces of crop plants in addition to wild relatives, and closely related species
What can imporve the gene pools for in crops?
Technological advances mean that genes from the secondary and tertiary gene pools can now be incorporated into breeding programmes.
This is already impacting on disease resistance in wheat and rice, and tolerance to abiotic stresses.
What is an overview of PGR?
Therefore, the conservation of Plant Genetic Resources (PGR) has become increasingly important, as has the development of biotechnological approaches for its effective utilisation
What is an overview of genetic bottlenecks from domestication and breeding of crops?
allelic variations of genes originally found in the wild, but gradually lost through domestication and breeding.
Lost alleles can be recovered only by going back to the wild ancestors of crop species.
What are examples of genetic bottlenecks in domesticated varients?
Modern US soybean varieties can be traced back to a dozen strains from a small area in North-eastern China.
The majority of hard red winter wheat varieties in the US originated from 2 lines imported from Poland and Russia
What do pie diagrams depicting the proportion of genetic variation in crops show?
Oryza sativa indica and japonica have much small chunk compared to exotic species
Cultivated tomato very small slice compared to exotic species
What are exotic species?
Exotics include only those lines that cross readily with their domesticated counterparts.
What 3 main gene pools can increase genetic novelty?
Primary pool – Advanced cultivars and land races
Secondary pool - Closely related species
Tertiary pool – distantly related species
How can wild tomato species Solanum habrochaites improve domesticated tomato?
Introduce modern processing tomato cultivar E6203 with the near Isogenic line which genes for increased red pigment have been introgressed from S. habrochaites
How can wild tomato Solanum pimpinellifolium improve domesticated tomatoes?
From Peru produces small berries typical of most fruit-bearing wild species
An NIL into which genes for increased fruit size have been transferred from S. pimpinellifolium
Fruit of this NIL are significantly larger (10%) than the original E6203 variety
What is biotechnology?
Biotechnology is the use of living systems and organisms to develop or make useful products
What genetic approaches are used in biotechnology?
Mutagenesis
Marker–assisted selection
Genetic mapping
Genome sequencing
Transgenesis (GM)
Targeted genome modification
What is genetic mapping?
Genetic mapping establishes the order of elements on a chromosome and the genetic distance that separates them
What is the use of genetic mapping in plant breeders?
Plant breeders use modern genetic tools to ‘map’ genes to a specific chromosome and identify diagnostic DNA markers that are ‘linked’ to them.
‘Marker-assisted selection’ identifies progeny in a breeding experiment that contain desired gene combinations
What is an example of a molecular marker?
Cleaved Amplified Polymorphic Sequence (CAPS)
PCR section of DNA - parent 1 cleaved with EcoRI Parent 2 isnt cleaved
Parent 1 has 2 bands
Parent 2 has 1 band
F1 has both so 3 bands
What is chromosome mapping?
Chromosome mapping is a technique used in autosomal DNA testing which allows the testee to determine which segments of DNA came from which ancestor from genetic markers
What are the genotype outcomes of chromosome mapping?
Heterozygous
Parent 1
Parent 2
What is an example of using chromosome mapping?
Segregation patterns for 4 DNA markers in 24 F2 progeny (M1, M2 and M3 are linked).
Marker M20 is on a different chromosome and assorts independently
Progeny 2 - M1 P1, M2 P1 and M3 H shows recombination point inbetween
Progeny 22 - M1 H, M2 H and M3 P2 shows recombination point inbetween
What are the advantages of using DNA markers in plant breeding?
DNA sequence polymorphisms are a ubiquitous form of variation and arise naturally in isolated members of a species.
They are free from environmental effects and have no discernible effects on the phenotype being monitored.
Many can be scored and scored at the seedling stage
Most DNA markers can be detected using small amounts of tissue and exploit technologies that allow rapid and high throughput analysis.
How does DNA markers impact the breeding process?
The use of DNA markers can significantly expedite the breeding process.
What are QTLs?
Quantitative trait loci (QTL) genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment
What are examples of QTL mapping in papaya?
Plant height genes on chromosome 1 and 5
Stem diameter genes on chromosome 1, 3 and 5
Early flowering genes on chromosome 1 and 10
What is created on QTL mapping?
A segregating population is generated and the phenotypic trait scored in each plant
How do we get QTL maps?
Each plant is genotyped using molecular marker technologies
What is an overview of QTL mapping analysis?
Statistical analyses are used to identify QTLs that co-segregate with specific molecular markers.
The QTLs can now be followed in a breeding programme using molecular markers
TheLOD score =logarithm (base 10) of odds. A measure of the probability of loci being linked
What are the advantages of next generation sequencing?
Massively parallel (10’s of millions of reads are possible simultaneously).
No in vivo cloning is required.
Significant reduction in cost, and increase in throughput
What are the disadvantages of next generation sequencing?
Lack of contiguity information for many technologies (physical maps, BACs and paired-end reads etc.)
Short sequence reads initially (problems with G+C and repeat-rich genomes)
Requires considerable computing power and assembly algorithms
What is overcoming the problems with next generation sequencing?
Some problems are now being overcome with third generation sequencers such as the PACBIO and Nanopore sequence platforms, and new sequence assembly programmes: Single molecule real time sequencing (SMRTS
What are the advantages of PacBio single molecule sequencing?
No amplification of DNA required.
Rapid sequencing – up to 10 Mb in 45 mins but lower than most NGS platforms
Longer reads – started around 2-3 kb currently 10-100 kb!
Enables a single molecule of DNA to be sequenced multiple times
Potential for sequencing modified nucleotides (epigenetics)
What are the challenges of PacBio?
Relatively low accuracy – 85-87% but these are randomly distributed (re-sequencing of each template improves accuracy).
Sequencing sample preparation relatively costly – requires good quality high molecular weight DNA
What are the applications of PacBio?
Sequencing complex genomes and de novo assembly (sometimes in combination with higher throughput technology, e.g. Illumina) to improve assembly
What is the base of oxford nanopore technology?
Technology based on the concept that patterns in the flow of ions which occur when a single-stranded DNA molecule passes through a narrow channel can reveal the primary sequence of the strand
What is a major difference of oxford nanopore technology?
A major differentiator from other sequencing technologies is the extreme portability of nanopore devices, which can be as small as a memory (USB) stick, because they rely on the detection of electronic, rather than optical, signals
What is an overview of MinION?
MinION is a small (~3 cm × 10 cm for the MK1) USB-based device that runs off a personal computer, giving it smallest footprint of any current sequencing platform. This gives the MinION superior portability making it useful for rapid clinical applications and hard-to-reach field locations.
What are the uses of genome sequencing?
Protein coding and non-protein coding genes
Gene regulatory elements
Genome organisation and function
Mechanisms of genome evolution
How can genome resequencing be useful in plant breeding?
Helps to understand DNA variation between individuals (e.g. in wild germplasm stocks), and their phenotypic consequences.
Developing DNA markers for marker-assisted selection and genomic selection.
Characterise differences between strains / varieties / populations, or individuals in a breeding programme
What is an overview of whole genome resequencing for crop improvement?
Whole genome re-sequencing - short sequence reads are aligned to crop reference genome providing information on variants, mutations, and structural variations
What is an overview of genotyping by sequencing for crop improvement?
Genotyping-by-sequencing - sequencing a reduced representation library of the genome. Enables the detection of thousands of SNPs in large populations, or collections of lines, that can be used for mapping and genetic diversity analysis
What are the uses of genome-wide association studies for crop improvement?
Genome-wide association studies - utilizes collections of diverse, unrelated lines that are genotyped and phenotyped for traits of interest. DNA polymorphisms are then related to trait variation.
What creates crown galls?
Agrobacterium tumefaciens
What are the genes for Agrobacterium for transfering DNA into plant cells?
VirA and VirG detect and activate latter machinery
VirD1 istopoisomerase that unwinds the DNA strands on the pTi
VirD2 is an endonuclease that nicks one of DNA strands on the pTi
Creating a ss-T-DNA which transfers through pores created by VirB
What is the structure of the T-DNA of octopine-type Ti plasmid?
LB: left border repeat; RB right border repeat:
aux: auxin biosynthesis genes
cyt: isopentyl transferase (involved cytokinin biosynthesis)
tm1: tumour size regulation
ocs: octopine synthase
What can be done with the T-DNA?
Any DNA can be put in between the two border regions including selectable marker genes. E.g.: NPTII, confers resistance to neomycin-type antibiotics; ‘Bar’, confers resistance to phosphinothricin-based herbicides e.g. Basta
In addition to a gene of Interest (GoI)
What is an example of a selectable marker?
NPTII gene which confers resistance to neomycin antibiotics
What are the steps for generating a transgenic plant?
- Insert gene of interest into modified T-DNA:
- Transfer T-DNA-containing plasmid to Agrobacterium:
- Co-cultivate Agrobacterium with explant:
- Kill Agrobacterium with antibiotics and select for transformed plant cells
- Regenerate whole plants
What are the ratios to regenerate a whole plant?
Intermediate auxin to cytokinin ratio - promotes callus formation
Low auxin to cytokinin ratio - promotes shoot formation
High auxin to cytokinin ratio - promotes root formation
What is transcriptional fusion?
Transcriptional fusions are also known as promoter or operon fusions which attached is GUS, which produces blue coloration in plants upon integration into the genome
What is an example of transcriptional fusion?
When exposed to plant pathogen, lots of blue coloration produced showing gene expression
This is not produced when not exposed
How do you monitor proteins using translational fusion?
Gene X + GFP
Show where expressed and the movement throughout the plant/cell
How does the herbicide Glyphosate kill plants?
Inhibits EPSP synthase an important enzyme in the production of aromatic amino acids in the shikimate pathway
What are the 2 ways to resist glyphosate?
- Mutant EPSPS from Agrobacterium (resistant to glyphosate)
- Glyphosate oxidase from Orchrobactrum anthropi
How does glyphosate oxidase breakdown glyphosate?
Glyphosate –> Glyoxylate and aminomethyl phosphonate
What is an overview of the selling of glyphosate resistance?
Sold under Roundup
Roundup resistance oil seed rape contains both transgenes. Monsanto markets Roundup resistant soybean, maize, rape and tomato
What are Bt toxins?
Insecticidal crystal proteins (ICPs), products of cry genes of various subspecies and strains of Bacillus thuringiensis
How do Bt toxins work?
Binds to specific receptors in the insect midgut, creating pores that cause lysis of epithelial cells.
Different Cry proteins are active against different insects.
What are examples of transgenes of Bt toxins and the crop used on and insect specificity target?
cry3A Potato Colorado beetle
cry1Ab Maize European corn borer
cr3Bb Maize Corn rootworm larvae
What genes are involved in golden rice?
psy (phytoene synthase), daffodil
crt1 (carotene desaturase), Erwinia uredovora
lcy (lycopene cyclase), daffodil
What is the pathway to produce golden rice?
geranyl, geranyl diphosphate (psy) –> phytoene (crt1) –> lycopene (Icy) –> b-carotene (provitamin A)
Why is golden rice important?
~125 million children worldwide are Vitamin A deficient
~500 000 go blind each year as a consequence
Best strains: 37 mg g-1 b-carotene (sufficient for of daily requirement of vitamin A)
What are the advantages of genome editing over GM?
Can be used to ‘knockout’ or modify endogenous genes (as opposed to traditional mutagenesis approaches, which are time consuming and expensive).
Can facilitate targeted integration of foreign genes at defined locations in the genome (can then predict the consequences of integration).
Not limited by Agrobacterium tumefacien’s host range, so can be more broadly applied.
May prove to be more acceptable than conventional GM varieties.
