conservation of plant genetic resources.
shiva charan
1st_lecture.pdf
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Conservation of plant genetic resources (JAL402, 81041)
01.04.-06.05.2016
Helena Korpelainen 2016
Population ecology
Population genetics
Breeding
Scientific disciplines related to genetic resources
Population ecology recognizes variation in the environment; typical questions: density and distribution variation, interactions (competition, herbivory...)
Population genetics recognizes variation among individuals; typical questions: fitness, genetic variation, changes in gene and genotype frequencies
Plant breeding aims to change the genetic traits of plants to improve their utility to humans
Ecological genetics studies how populations adapt to their physical and biological environments, and the mechanisms that populations use when reacting to changes in the environment
Ecological genetics, when applied to questions in plant breeding, concentrates (instead of natural populations) on crop plants and forest trees (and their wild relatives)Genetic diversity/resources
necessary for both natural adaptation and for planned changes (breeding work)
Helena Korpelainen 2016
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Conservation of plant genetic resources
• The vision: the effective conservation and use of plant genetic resources and their increased availability for crop improvement, for the benefit of the environment and human society worldwide
• The mission: to help ensure plant genetic resources are adequately conserved and utilized, to enhance food security, aid poverty alleviation and improve the environment worldwide
Helena Korpelainen 2016
Conservation of plant genetic resources
• Convention on Biological Diversity
• International Treaty on Plant Genetic Resources for Food and Agriculture, etc…
…. all stress the need of conserving plant genetic resources for food and agriculture as a means of countering the current rate of biodiversity loss at the global and sub-global level
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Why does agricultural biodiversity matter?
Helena Korpelainen 2016
See the homepage of Bioversity International
See the introduction video: http://www.bioversityinternational. org/e-library/multimedia-library
Photo: Renzo Torricelli
Conservation threats and needs
• Natural plant populations:: Many threatened for a number of reasons, including habitat loss, increasing degradation of the environment, climate change and competition with introduced alien species
• Crop plants: Collections of genetic diversity of major crop species are generally sufficient, but further work is needed to increase holdings (and characterization) of landrace varieties, minor crops and crop wild relatives
• Crop plants contain only a small part of all plant genetic diversity
Helena Korpelainen 2016
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Are modern cultivars short-lived?
• While modern cultivars are more productive in most environments, growing a narrower range of cultivars with a narrow genetic basis over larger areas can increase the vulnerability of production systems to changes in climate, land use and disturbance regime, and exposure to biotic stresses, e.g., new races of pathogens
• Advanced cultivars may become less effective over time and are often of short duration, needing to be replaced at regular intervals
• For example, in Australia, cultivars of canola (Brassica napus var. napus) with resistance to the fungal disease blackleg (Leptosphaeria maculans) are continually being upgraded — few modern cultivars are used for longer than five years (Li et al. 2006).
Helena Korpelainen 2016
Analysis of genetic diversity • Morphological and agronomic traits for basic characterization
- information of high interest to the users of PGR - characterization can de done using simple techniques but it requires much human labour - allows the interpretation of relationships between the genotype and environmental conditions
• Molecular marker techniques and DNA sequencing - allow direct investigations of variation at the DNA level, thereby excluding all environmental influences - can be employed at very early growth stages - have marginalized other methods in diversity analyses
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DNA-markers in identification
- Accessions in collections and comparisons with potential new accessions
- Clonally propagated material: cultivars, sport mutations
- Seed propagated material (degree of homogeneity): self pollinating – crosspollinating, cultivars – landraces
- Suitable markers should be highly polymorphic and easily comparable between different laboratories: SNP (sequencing), microsatellites, AFLP etc.
Cinnamon apples, Hirvensalmi plant nursery
Helena Korpelainen 2016
Microsatellites Example: [gata]15 1 aatttttgta ttttttttag agacggggtt tcaccatgtt ggtcaggctg actatggagt
61 tattttaagg ttaatatata taaagggtat gatagaacac ttgtcatagt ttagaacgaa
121 ctaacgatag atagatagat agatagatag atagatagat agatagatag atagatagat 181 tgatagtttt tttttatctc actaaatagt ctatagtaaa catttaatta ccaatatttg 241 gtgcaattct gtcaatgagg ataaatgtgg aatcgttata attcttaaga atatatattc
Homozygote A1A1 (7 repeats) Heterozygote A1A2 (7 and 5 repeats) Heterozygote A3A4 (2 and 4 repeats)
Genotyping using capillary electrophoresis: heterozygote individual (two peaks, green) and ladder (red)
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Single nucleotide polymorphisms (SNPs)
• Single-base changes in DNA, discovered by sequencing
• Variation level varies, e.g. 1-2 bp per 1000 bp in humans, every 40 bp in maize
• For some applications (e.g. germplasm identification) SNPs are not as informative as microsatellites with multiple alleles
• Several detection methods; typical approach: design primers and conduct sequencing (also commercial kits available)
http://learn.genetics.utah.edu
Helena Korpelainen 2016
Limitations in practical applications of DNA techniques
•Need of comparison with different laboratories (repeatability and robustness)
•Bioinformatics: how to manage the marker data, availability of other data for comparison
•Which methods have previously been reported for the species under study? Need for development / optimization? •Available technical equipment and skills (both staff and the scientist!) •Costs: salaries, laboratory consumables, outsourcing services
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Preserving genetic diversity • The introduction of high-yielding varieties during the
1960s led to the concern that traditional varieties, local landraces, and wild relatives of crop species would be lost if they were not collected and preserved
• These resources are crucial for maintaining the genetic diversity that plant breeders need to continue to improve crop varieties
Helena Korpelainen 2016
Phaseolus vulgaris http://www.plantscienc es.ucdavis.edu/gepts/P B143/lec02
Background theory, the nature of taxonomic and genetic diversity
● Allele and genotype frequencies & Hardy-Weinberg law ● Genetic variation ● Fitness and adaptation
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Allele and genotype frequencies &
Hardy-Weinberg law
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Allele and genotype frequencies
Example: 1 locus, 2 alleles
Genotype Number of individuals Genotype frequencies
AA 30 AA=30/100=0.30 Aa 50 Aa=50/100=0.50 aa 20 aa=20/100=0.20 Total 100 1
Helena Korpelainen 2016
Allele (gene) frequencies (p is the frequency of A, q is the frequency of a)
p = (2 x 30 + 50)/(2 x 100) = 0.55 q = (2 x 20 + 50)/(2 x 100) = 0.45
p + q = 1
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Hardy-Weinberg law
• The basic theory of population genetics • It predicts how the allele frequencies are transmitted from
generation to generation if certain assumptions are valid • Assumptions:
- diploid organism - reproduction sexual - generations distinct - mating random - population size indefinite - no migration - no mutation - no selection at the locus in question
Helena Korpelainen 2016
Gene pool (www.brooklyn.cuny.edu)
Hardy-Weinberg law • If the H-W assumptions are valid, the allele frequencies
(p and q) do not change from generation to generation, and the genotype frequencies in the following generation are (independently from the genotype frequencies in the previous generation) the following:
• genotype AA: p2 • genotype Aa: 2pq • genotype aa: q2
• From the Hardy-Weinberg law and Mendelism it follows that if there are no affecting evolutionary factors, the pattern of genetic variation remains unchanged
Helena Korpelainen 2016
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Hardy-Weinberg law: AA: p2; Aa: 2pq; aa: q2
Female gamete p (A)
Female gamete q (a)
Male gamete p (A) p2 (AA) pq (Aa)
Male gamete q (a) pq (Aa) q2 (aa)
Helena Korpelainen 2016
Population achieves Hardy-Weinberg equilibrium after one generation
A1A1 A1A2 A2A2
Not in equilibrium A1A1 A1A2 A2A2 0.6 0 0.4
In equilibrium A1A1 A1A2 A2A2 0.36 0.48 0.16
Next generation
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allele frequency
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The relationship between the genotype and allele frequencies in a population with Hardy-Weinberg equilibrium
Helena Korpelainen 2016
Hardy-Weinberg law
• Relationship between allele and genotype frequencies:
• If 2 alleles: (p+q)2 = p2 + 2pq + q2 = 1
• If 3 alleles: (p+q+r)2 = p2 + q2 + r2 + 2pq + 2pr + 2qr = 1
• Even if the original genotype frequencies were not at the Hardy-Weinbergh equilibrium, the genotype frequencies of an autosomal locus will reach the equilibrium after one generation of random mating, if the population is large and there are no affecting evolutionary factors
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Deviations from the Hardy-Weinberg equilibrium (possible causes)
• Nonrandom mating
• Differences in viability (relatively easy to detect, frequency differences: zygote ... adult) or reproduction (more difficult to detect)
• The sample may actually represent several populations
• The influence of any evolutionary factor (selection, mutation, migration, genetic drift)
Helena Korpelainen 2016
Biodiversity
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Biodiversity: three levels
• ECOSYSTEM DIVERSITY
- The broadest level of biological diversity (e.g. deserts, rainforests, the deep sea, ponds and mountains)
- Diversity is determined by the types of plants, animals and microorganisms, as well as by the physical characteristics (e.g. substrate, light, nutrients, etc.) and interactions (e.g. predator-prey relationships)
• TAXONOMIC DIVERSITY
-Species, subspecies, cultivars,...
-Species diversity combines the number of different species (species richness) with the relative abundance of a species within a given area
• GENETIC DIVERSITY
-Genetic variation within and among populations of a species
Helena Korpelainen 2016
Taxonomy of a selected plant species. Note the increasing inclusivity of the "higher" taxonomic ranks. Kingdoms have a great deal more variety in them than do species. (Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates and WH Freeman)
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http://evolution.berkeley.edu/evolibrary/news/070201_corn
Crop plants tend to have less genetic variation than their counterparts in the wild population
Genetic diversity in crop plants
Wild and domesticated sunflowers
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Fitness and adaptation
Genetic variation is necessary for the adaptation of populations to changing
environmental conditions
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Fitness • Measures a genotype’s/individual’s adaptive value
• Absolute fitness: e.g., WAA = Σ lxbx in which lx= survival at age x and bx=reproduction at age x
• Relative fitness: e.g., WAA = WAA/Waa divided by the highest absolute fitness value; can be used if all fitness values known; sometimes divided by the mean fitness
• Malthusian parameter r: measures population growth, commonly used in ecology, calculated based on Lotka equation: Σ e-rxlxbx = 1
• r suitable expecially if generations overlapping; if used as a fitness measure then calculated separately for each genotype (not for the whole population)
Helena Korpelainen 2016
Difficulties in measuring fitness
• The biological complexity of fitness: which are the essential points of the life cycle for measuring fitness?
• The genetic complexity of fitness: in reality not just one but a great number of genes influence such features as viability or reproduction. How much does a single gene influence? In the case of lethal genes the influence is clear.
• Statistical problems: even apparently small differences (e.g. 1%) in viability or reproduction can have a considerable influence on the destiny of a gene. Hard to detect in experiments (sample size must be great enough).
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Fisher’s fundamental theorem
• The increase in fitness at any time is equal to the additive genetic variance of fitness at that time
• Any fitness predicted by the theorem will not necessarily lead to an increase in population size, because the size cannot exceed the carrying capacity of the habitat
• However, allele frequencies will change if there is additive variance of fitness, and the allele frequency changes may cause changes in characters correlated with fitness
Helena Korpelainen 2016
Fitness and artificial selection • Natural selection leads to an equilibrium population
(maximum average fitness) • If artificial selection is applied at some character,
fitness will possibly be reduced as a correlated response unless the character selected is entirely controlled by genes with no effects on fitness
• Typical: if artificial selection is carried out and then suspended before much of the variation has been lost by fixation, natural selection tends to bring the allele frequencies back toward their equilibrium values (and the mean of the character artificially selected is expected to revert towards its original value)
• This tendency for natural selection to resist allele frequency changes is known as genetic homeostasis
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Wild and domesticated forms of einkorn wheat
Wild forms need to disperse seeds effectively and have thus evolved easily shattered ears with brittle rachises and thin, arrow-shaped spikelets designed to penetrate surface litter and embed themselves in cracks in the ground. In domesticated forms, plumper spikelets have lost some of the key structures necessary for self- implantation, seed dispersal, and success in the soil.
(Smith 1995, p. 73)
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Gene pools and types of genetic resources
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Utility-based classification of germplasm resources (Harlan and de Wet 1971)
Primary gene pool (GP-1)
-Crossing among individuals possible with normal seed set, segregation and recombination
-Gene transfer possible through routine breeding
-Cultivated and wild races of a crop (example: raspberry, clover), usually the same species
Helena Korpelainen 2016
Secondary gene pool (GP-2)
• Some barriers of crossability, often sterile hybrids, chromosome pairing not normal
• Special efforts needed to overcome barriers of crossability and development of normal seed (pollen viability, greenhouse conditions, special genotypes)
• Usually different, closely related species, for instance wild relatives
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Tertiary gene pool (GP-3)
• Difficult to get hybrids, combinations often lethal or sterile due to abnormality in the development of embryo
• Special methods: embryo culture, induced polyploidy or use of bridging crosses (e.g. with members of GP-2)
• Examples: Trifolium, Solanum, Triticale
• Not as closely related species as in GP-2, for instance wild relatives
Helena Korpelainen 2016
Quaternary gene pool (GP-4)
• The extreme outer limit of genetic resources, requires radical methods to produce F1 hybrids
• Protoplast fusion, genetic transformation…
• Potentially all living organisms which contain DNA
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Types of genetic resources
• CULTIVARS: Varieties produced by plant breeders, usually uniform and adapted to high farm management standards
• LANDRACES: Varieties developed over time in traditional farming systems, usually variable and adapted to local conditions; therefore more or less dependent on continuous natural as well as human selection
• CROP WILD RELATIVES (CWR): All wild taxa within the same genus as a crop
Helena Korpelainen 2016
• ECOTYPES: Populations of wild forms of domesticated species or wild relatives of those, or other wild material; specific adaptations
• GENETIC STOCKS: Material undergone research or breeding programs resulting in specific information on gene or character or other data of value for breeding and research
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Definitions
• Landrace = Farmer-developed varieties of crops that are adapted to local environments and uses
• Old commercial cultivar = bred by professional plant breeders before the late 1960s
Landrace potato called ”Lemin punainen” (red from Lemi municipality). Photo: Hannu Ahokas
Helena Korpelainen 2016
Crop wild relatives (CWR) • CWR = all taxa within the same genus as a crop
[crop = any cultivated species including food, fodder, forage, medicinal plants, ornamental and forestry species, industrial crops…]
• CWR are taxa related to crops that can potentially donate genes or alleles of potential beneficial traits to them, such as pest or disease resistance, or yield improvement
• CWR also include the possible progenitors or direct ancestors of crops
• Natural crosses between crops and their wild relatives have occurred since the beginnings of agriculture
• See, www.cropwildrelatives.org, www.cwrsg.org
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Use of crop wild relatives (CWR)
• Farmers have used CWR in traditional breeding for millennia
• CWR genes have been used to improve crops, e.g. wheat, maize, rice, barley, potato, cassava, and legumes such as Phaseolus, Vicia, Vigna, Lens, Lathyrus and Cicer
• Improvements include resistance to pests and diseases, and abiotic stresses, such as drought and salinity
• Other uses include increased protein and vitamin content, and the improvement of medicinal plants/pharmaceuticals
• The global change will lead to an increased demand for the development of new cultivars adapted to changing conditions
Helena Korpelainen 2016
Examples of wild relatives of tomatoes (genera Lycopersicon and Solanum) used as a source of genetic material (from Rick and Chetelat 1995)
Taxa Characters L. esculentum var. cerasiformae Resistance to bacterial spot, wilt and broomrape
L. pimpinellifolium Increased fruit size
L. cheesmanii Resistance to TYLV, CMV and black mould
L. chmielewskii Increased fruit size, improved colour, increased soluble solids content
L. hirsutum Resistance to flea beetle, leaf miner and aphids
L. parviflorum Resistance to powdery mildew and Fusarium wilt
L. pennellii Resistance to whitefly, aphids and leaf miners, drought tolerance
L. chilense Resistance to gemini viruses, powdery mildew, bacterial spot and eel nematodes, drought and salinity tolerance
L. peruvianum Root knot nematode resistance
Solanum lycopersoides Resistance to cucumber mosaic virus
S. ochranthum Resistance to late blight
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Priority CWR
• CWR related to
- food crops (important for nutrition and food security)
- crops of economic value
- crops with multiple use values
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Prunus insititia. Photo: Emilio Laguna
Global priority genetic reserve locations for CWR of 12 food crops (Maxted and Kell 2009). The eight Vavilov Centres of origin/diversity, indicated by blue enclosed lines, are likely to contain further priority sites for crop gene pools
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Homework for the lecture (to be included in the study diary)
Helena Korpelainen 2016
Write comments (max. 1 page) of the topic ”FAO has estimated that ex situ plant germplasm collections comprise 7.4 million accessions” covered in the class. Specifically express your opinions of the questions:
1) Is this a lot or not?
2) Which aspects influence the quality of the collections?
3) Which aspects influence the usability of the collections?
