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Flashcards in AgriGenomics Deck (54)
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1
Q

what are the trends in crop production and yield?

A

both increase each year - due to better crop varieties through breeding and better crop management - fertiliser, pesticides, irrigation.
however, starting to plateau and unsure why, also, in the last 15 years or so, area used is increasing.
current gains in yield are insufficient to reach demands by 2050.

2
Q

is population growth the real problem?

A

yes, although technically we can manage it.

a greater problem is increasing affluence which means more people will want access to meat and more luxurious foods

3
Q

which countries are stressing their groundwater supplies?

A

Middle East, central/west US, Central Asia

not stressed: northern europe, Russia, Australia, much of Africa, South America

4
Q

basically- how are forward and reverse genetics used in agriculture

A

Reverse: Use genomic tools to understand how crops evolved after domestication.
Forward: Use genomics to actively assist breeding.

reverse will provide us with the basic knowledge needed to improve forward (eg neo-domestication).

5
Q

what causes the gap between actual yield and potential yield?

A

biotic stress: microbes, nematodes, insects, weeds, fungi

abiotic stress: nutrient availability
soil salinity
water availability
air pollution
temperature
6
Q

how can the yield be increased

A

1) increase yield potential. - remove limits of pests, nutrient limitation, effective control
2) decrease yield gap - increase disease resistance, abiotic stress tolerance etc

7
Q

what is the record and average wheat yield?

A

2017 - 16.8t/ha

average in 2017 - 3.5t/ha

8
Q

how long ago did the agricultural revolution start?

A

10000 ya people gave up hunter gatherer lifestyle and chose to settle.
domestication gradually occurred as farmers kept and replanted rare variants with useful traits.
when agri rev started, 5m people on earth. 5000 years later - Egyptian dynasty, approx 100m

9
Q

common features of domestication

A
Synchronisation of germination and ripening
apical dominance
loss of seed shattering
enlargements of fruit or seed
improved flavour/nutrition

these changes would be terrible for NS of the plant in the wild. Shows that engineered plants wouldn’t be able to survive in the wild anyway, we should not worry about this.

10
Q

what is the undomesticated ancestor of maize?

A

teosinte
has long tassels branches
few large kernels with rough exterior (modern corn grains would be digested by animals and not dispersed.)
maize is dependent on humans for sowing seed.

11
Q

how different are domestic plant genomes from wild progenitors?

A

little difference, because 10,000 years is a short time in evolutionary perspective.
dramatic changes in appearance are due to mutations in only a few domestication genes.
eg 50 genes contribute to domestication in maize
sites of selection show loss of genetic diversity, caused by selective sweep.

12
Q

what does tb1 gene do

A

teosinte branched 1

protein is a TF suppresses lateral shoot formation (apical dominance)

13
Q

how does tb1 diversity differ in maize and teosinte?

A

Dom maize has only 30% diversity in protein coding region of tb1 compared to teosinte - this reflects background diversity changes.
2% diversity in region 5’ to Tb1 gene.
selection has been applied to a regulatory region, not coding region.
maize tb1 carries retrotransposon in reg region and maize has higher mRNA levels of tb1 than teosinte.

14
Q

what types of genes are often targeted in domestication?

A

genes encoding TFs

15
Q

what does the hopscotch transposon do in teosinte?

A

hopscotch insertion into tb1 variant teosinte swept to high frequency yielding plants with few branches (gives apical dominance)

16
Q

example of orthologue of tb1

A

in wheat
regulates spike architecture
gives ‘hb’ - highly branched, phenotype.
extra pair of chr 4D = increased expression of tb1 gene.

17
Q

negative consequences of genetic sweep

A

loss of diversity - higher chance of getting wiped out in stressful conditions.

18
Q

what does a co-expression network show?

A

TF as ‘hubs’
many connections to other transcripts.
due to ability of TFs to bind to promoters of many genes and influence expression.
so a change in a TF can affect many genes = big phenotypic change, so often targeted.

19
Q

another gene which has been altered from teosinte to maize

A

tga1 - teosinte glume architecture 1. glume is surrounding seed, in teosinte it is a hard seed case. in maize, allele reduces to a soft membrane. tga1 similar expression levels in maize and teosinte, but SNP in one exon (lysine -> asparagine in maize)
this allele not found in teosinte, suggesting evolved after domestication.

20
Q

gene targeted for domestication of wheat.

A

Q gene - in domesticated wheat is responsible for cultivation of wheat, confers free thrashing trait (seeds separate easily from glumes).
also pleiotropically influences other domestication related traits.
encodes AP2 TF.

21
Q

what is de-domestication?

A

unique evolutionary process by which domesticated crops re-acquire wild-like traits to survive and persist in agricultural fields without the need for human cultivation.

22
Q

why is de-domestication a problem?

2 examples

A

species become noxious weeds
eg weedy rice - worldwide problem in rice fields.
tibetan semi wild wheat evolved from cultivated wheat. spontaneous transposon insertion in exon 5 of Q gene = non functional Q^t version with premature stop codon

23
Q

what is vavilovian mimicry?

why is it a problem?

A

adaptive evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans.
removal of weeds is difficult and requires the ability to discriminate between desirable crops and harmful weeds
eg Echinochoa weeds in paddy fields

24
Q

when was the green revolution?

A

1930-1960s

replacement of traditional, low-yielding landraces with new, high-yielding cultivars of rice and wheat.

25
Q

one breakthrough in green revolution?

A

dwarf cultivars that produced higher yields and were more tolerant to lodging.

26
Q

mechanism of dwarfing

A

Rht1 - reduced height 1
transferred from Japanese wheat cultivar Norin10 into others.
Rht1 encodes DELLA - transcriptional regulator, acts to repress signalling of gibberellic acid (GA).
GA promotes growth and stem elongation.
insensitivity of Rht1 containing plants to GA results in reduced stem elongation.

27
Q

what is Neo domestication?

A

contemporary domestication of plants that have not previously been used in agriculture, can be used to generate new crops for these systems.

28
Q

neo domestication of tomato

A

prior knowledge of domestication genes enables targeting of 6 genes in wild tomato with CRISPR cas9.
engineered lines have a threefold increase in fruit size and ten fold increase in fruit number
Fasciated (Fas) gene targeted - increase in fruit size

29
Q

what is the domestication bottleneck

A

domestication has reduced the number and genetic diversity of plants ready for food production.

30
Q

what is the domestication bottleneck

A

domestication has reduced the number and genetic diversity of plants ready for food production.
eg banana - all clones

31
Q

3 examples of domestic bottleneck causing crisis

A

banana - T4 banana disease in Colombia caused national emergency
Olive - italy, tree disease spreads
Wheat - cereal rust. threatens global food security.

32
Q

what is done to save genetic diversity?

A

huge germ plasm collections - seed banks - contain hundreds of thousands of different accessions of crops.
eg svalbard global seed vault.

33
Q

genebanks examples

A

store different accessions of crops
eg barley genebank in IPK Gatersleben, germanu
Tree gene bank in Zurich
Rice gene bank in international Rice research institute

34
Q

Challenges of using seed banks for breeding

A

which accessions should we choose for breeding program?
when crossing, how to make use of interesting traits without ‘polluting’ elite cultivars with inferior traits?
- genotype large germ plasm collections - PCA. shows genetic distance between accessions. instead of generating whole genome (100,000 USD) can instead probe with few thousand molecular markers.

35
Q

how can thousands of genomes be studies at once?

pros and cons of this method

A

use SNP array
Oligos made which are complementary to a known polymorphism, and hybridised to array. allelic sequences are hybridised onto the oligos (complementary to them) and then through single base extension, and differently labelled nucleotides the oligos are extended and can be distinguished. imaged, colours quantified.
cost per sample - $50
simple data analysis, but there is ascertainment bias, due to pre selection of SNPs. designing the array takes time.

36
Q

what makes genetic associations difficult?

A

continuous distribution of quantitative traits.

37
Q

2 approaches of mapping genotype to phenotype

A

GWAS and QTL analysis

38
Q

Basic outline of GWAS

A

analyses historic recombination events among different accessions of a species.
diversity panel genotyped with molecular markers and phenotype for the trait of interest.

39
Q

what is a diversity panel in GWAS?

A

population structure

40
Q

how to find the density of molecular markers

A

linkage disequilibrium* genome size

41
Q

what 4 things does success of GWAS experiment depend on?

A

size and composition of diversity panel
density of molecular markers
heritability of trait
quality of phenotypic observations (are replications similar)

42
Q

whats involved in a QTL analysis

A

performed on bi parental populations. 2 parental accessions differing for trait of interest are crossed.
progeny analysed phenotypically and genotypically
associations depicted as QTL peaks with log of odds score (LOD)

43
Q

differences between GWAS and QTL

A
  • GWAS can analyse geno-phenotype associations across hundreds of individuals whereas QTL is just 2
  • GWAS considers high number of historic recombinations occuring over a long period of time, QTL is for limited recombination events in well defines set of generations.
  • GWAS has more potential to find more associations for a given trait, but more demanding statistics needed.
  • QTL analyses better for detecting small effect loci - signal/noise ratio is lower.
44
Q

what is a drawback of both GWAS and QTL?

A

usually identifies molecular markers linked to trait of interest, but rarely finds casual genes.

45
Q
how many NT in each gneome?:
arabidopsis
rice
maize
human
barley
wheat
A
arabidopsis 125Mb
rice 430Mb
maize 2500 Mb
human 3000Mb
barley 5100 Mb
wheat 17000 Mb
46
Q

what is MutChromSeq?

A

sorting of individual chromosomes and comparison of chr seqs to parent and EMS induced loss of function mutants.
Involves mutagenesis of seeds and growing plants, chr flow sorting, DNA amplification, sequencing and then bioinformatic analysis.
compare homologous contigs in all samples with phenotype of interest and if mutation is at the same loci then you know this must be the resistance causing/gene of interest.
However, only works well with qualitative traits.

47
Q

4 shifts in plant breeding

A

1.0 - incidental breeding by farmers. majority of agri history
2.0 - plant breeding - deliberate crossing of cultivars, statistically analyse progeny. end of 19thC- 1920s.
PHENOTYPIC evaluation of plants.
3.0 molecular tools available from 1980s. large breeding programs apply thousands of molecular markers - shift to GENOTYPIC evaluation
4.0 shift from reliance on spontaneous natural variation to genome editing.

48
Q

during a typical plant breeding scheme, how does the number of genotypes change?

A

no. genotypes decreases but no. plants per genotype increases.
only a few genotypes make it to variety testing and only 1 or 2 are released as official cultivars.

49
Q

why is breeding for quantitative traits more difficult?

A

many loci with small effects contribute to the trait.

further challenged by environmental influences

50
Q

how to combine many beneficial alleles for a quantitative trait for breeding purposes?

A

molecular markers associated with the trait are identified through GWAS or QTL and are used to assist selection.
Marker-assisted selection.

51
Q

what determines the quality of a molecular marker?

distance

A

-distance from the casual gene
- because recombination can result in the non beneficial allele being wrongly selected if the between the marker and gene recombination has occurred.
likelihood of recombination is directly proportional to genetic distance in cM between marker and casual gene.
a perfect marker would be on the casual gene, but then the casual gene must be known.

52
Q

what is diagnostic value and how does it affect marker quality?

A

if there are a higher number of marker alleles it makes associations between marker alleles and phenotype more difficult
even if it is very close.

53
Q

how should marker assisted selection be used?

A

to assist but not replace phenotypic selection

54
Q

what will transform plant breeding?

A

genomic selection
very complex statistical models, tries to predict overall performance of a plant, including many traits. potential to select alleles with minor contributions to a phenotype which aren’t detectable by GWAS or QTL