Week 2 Flashcards

Question

What is currently requried to maximise crop yields?

Answer 1

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)

Answer 2

High yielding varieties Lower fertiliser requirements Adapted to climate change (abiotic stresses, including drought) Resistance to pests and diseases

Answer 3

Classical breeding relies largely on independent assortment and homologous recombination between chromosomes to generate genetic diversity

Answer 4

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.

Answer 5

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

Answer 6

For a plant with ‘n’ haploid chromosomes the number of possible combinations in gametes, produced by independent assortment alone is 2^n

Answer 7

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

Answer 8

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’

Answer 9

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

Answer 10

Traditionally this would have been dependent upon phenotypic selection

Answer 11

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

Answer 12

At BC5-6 the new line should be greater than 98% identical to the original P1

Answer 13

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

Answer 14

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)

Answer 15

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

Answer 16

Labour and resource intensive Can discard valuable genotypes early in the programme

Answer 17

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

Answer 18

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

Answer 19

Higher yield Improved grain quality Multiline varieties for resistance to diseases/pests Tolerance of abiotic stresses

Answer 20

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).

Answer 21

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.

Answer 22

Crossbred the semi-dwarf Norin 10/Brevor cultivar with disease-resistant cultivars to produce varieties that were adapted to tropical and sub-tropical climates.

Answer 23

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

Answer 24

Mexico - 700 kg/Ha to 5000 kg/Ha India - 600 kg/Ha to 2500 kg/Ha Pakistan - 900 kg/Ha to 2200 kg/Ha

Answer 25

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

Answer 26

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

Answer 27

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.

Answer 28

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

Answer 29

Wheat originated in the Fertile Crescent in the near east

Answer 30

A hybridization event between Aegilops speltoides (BB) and Trictum urartu (AA) gave rise to the Emmer Wheat (AABB) Triticum turgidum ~0.8 MYA

Answer 31

Triticum aestivum arose from hybridisation event between Emmer Wheat (AABB) and Aegilops tauschii (DD) ~0.4 MYA

Answer 32

Seed size Growth habit (erect/prostrate; fewer tillers) Reduced seed dormancy Ease of threshing

Answer 33

Loss of spike shattering (Brittle rachis) Free threshing (Tenacious glumes, Q)

Answer 34

Brittle rachis (Br) – grains remain attached to the spike in harvesting

Answer 35

Threshing separates the edible part of the grain from the chaff Tenacious glumes 1 Tg1, Q --> free threshing

Answer 36

Homologous chromosomes pair readily during meiosis

Answer 37

Homoeologous don’t pair or pair only occasionally during meiosis

Answer 38

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

Answer 39

Genome stability is achieved through the action of the Ph1 gene (Chr 5B)

Answer 40

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.

Answer 41

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

Answer 42

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

Answer 43

Maize is genetically diploid. Male and female flowers are separated which makes F1 hybrid seed production much easier

Answer 44

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

Answer 45

Maize is a natural out-crosser that can also self-pollinate. Self-pollination leads to reduced vigour, a phenomenon known as inbreeding depression.

Answer 46

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.

Answer 47

Oryza sativa = Asian rice. Oryza glaberrima = African rice

Answer 48

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

Answer 49

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

Answer 50

Rice exhibits simple diploid genetics. It is normally grown as an annual crop although perennial types are used

Answer 51

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

Answer 52

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

Answer 53

Considerable genetic resources exist in the form of landraces of crop plants in addition to wild relatives, and closely related species

Answer 54

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.

Answer 55

Therefore, the conservation of Plant Genetic Resources (PGR) has become increasingly important, as has the development of biotechnological approaches for its effective utilisation

Answer 56

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.

Answer 57

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

Answer 58

Oryza sativa indica and japonica have much small chunk compared to exotic species Cultivated tomato very small slice compared to exotic species

Answer 59

Exotics include only those lines that cross readily with their domesticated counterparts.

Answer 60

Primary pool – Advanced cultivars and land races Secondary pool - Closely related species Tertiary pool – distantly related species

Answer 61

Introduce modern processing tomato cultivar E6203 with the near Isogenic line which genes for increased red pigment have been introgressed from S. habrochaites

Answer 62

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

Answer 63

Biotechnology is the use of living systems and organisms to develop or make useful products

Answer 64

Mutagenesis Marker–assisted selection Genetic mapping Genome sequencing Transgenesis (GM) Targeted genome modification

Answer 65

Genetic mapping establishes the order of elements on a chromosome and the genetic distance that separates them

Answer 66

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

Answer 67

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

Answer 68

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

Answer 69

Heterozygous Parent 1 Parent 2

Answer 70

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

Answer 71

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.

Answer 72

The use of DNA markers can significantly expedite the breeding process.

Answer 73

Quantitative trait loci (QTL) genetic regions that influence phenotypic variation of a complex trait, often through genetic interactions with each other and the environment

Answer 74

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

Answer 75

A segregating population is generated and the phenotypic trait scored in each plant

Answer 76

Each plant is genotyped using molecular marker technologies

Answer 77

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 The LOD score = logarithm (base 10) of odds. A measure of the probability of loci being linked

Answer 78

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

Answer 79

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

Answer 80

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

Answer 81

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)

Answer 82

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

Answer 83

Sequencing complex genomes and de novo assembly (sometimes in combination with higher throughput technology, e.g. Illumina) to improve assembly

Answer 84

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

Answer 85

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

Answer 86

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.

Answer 87

Protein coding and non-protein coding genes Gene regulatory elements Genome organisation and function Mechanisms of genome evolution

Answer 88

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

Answer 89

Whole genome re-sequencing - short sequence reads are aligned to crop reference genome providing information on variants, mutations, and structural variations

Answer 90

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

Answer 91

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.

Answer 92

Agrobacterium tumefaciens

Answer 93

VirA and VirG detect and activate latter machinery VirD1 is topoisomerase 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

Answer 94

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

Answer 95

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)

Answer 96

NPTII gene which confers resistance to neomycin antibiotics

Answer 97

1. Insert gene of interest into modified T-DNA: 2. Transfer T-DNA-containing plasmid to Agrobacterium: 3. Co-cultivate Agrobacterium with explant: 4. Kill Agrobacterium with antibiotics and select for transformed plant cells 5. Regenerate whole plants

Answer 98

Intermediate auxin to cytokinin ratio - promotes callus formation Low auxin to cytokinin ratio - promotes shoot formation High auxin to cytokinin ratio - promotes root formation

Answer 99

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

Answer 100

When exposed to plant pathogen, lots of blue coloration produced showing gene expression This is not produced when not exposed

Answer 101

Gene X + GFP Show where expressed and the movement throughout the plant/cell

Answer 102

Inhibits EPSP synthase an important enzyme in the production of aromatic amino acids in the shikimate pathway

Answer 103

1. Mutant EPSPS from Agrobacterium (resistant to glyphosate) 2. Glyphosate oxidase from Orchrobactrum anthropi

Answer 104

Glyphosate --> Glyoxylate and aminomethyl phosphonate

Answer 105

Sold under Roundup Roundup resistance oil seed rape contains both transgenes. Monsanto markets Roundup resistant soybean, maize, rape and tomato

Answer 106

Insecticidal crystal proteins (ICPs), products of cry genes of various subspecies and strains of Bacillus thuringiensis

Answer 107

Binds to specific receptors in the insect midgut, creating pores that cause lysis of epithelial cells. Different Cry proteins are active against different insects.

Answer 108

cry3A Potato Colorado beetle cry1Ab Maize European corn borer cr3Bb Maize Corn rootworm larvae

Answer 109

psy (phytoene synthase), daffodil crt1 (carotene desaturase), Erwinia uredovora lcy (lycopene cyclase), daffodil

Answer 110

geranyl, geranyl diphosphate (psy) --> phytoene (crt1) --> lycopene (Icy) --> b-carotene (provitamin A)

Answer 111

~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)

Answer 112

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.