Zamir paper - Answers to the self study questions v4 PDF

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Questions to serve the discussion on Zamir – Exotic libraries.1. Consider a number of segregating populations and understand their differences, e. F2, BC1, RILs, NILs, BILs? All these populations are derived from a cross between two homozygous inbred parents. The F2 and BC1 do not represent immortal...

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Questions to serve the discussion on Zamir – Exotic libraries. 1. Consider a number of segregating populations and understand their differences, e.g. F2, BC1, RILs, NILs, BILs? All these populations are derived from a cross between two homozygous inbred parents. The F2 and BC1 do not represent immortalized material, because it is heterozygous. Infinite selfing results in recombinant inbred lines (RILs), recurrent backcrossing results in near isogenic lines (NILs) and BILs is more or less synonymous with exotic library. RILs are homozygous, but NILs and BILs require an additional round of selfing and selection to obtain homozygosity. 2. What is an “exotic library”. Describe the procedure to develop such a library. Answer this question IN YOUR OWN WORDS. It is a set of lines of an elite cultivar in which chromosome parts of an exotic donor have been introgressed. Together such homozygous introgression lines represent the entire exotic genome. Select an exotic accession and an elite line. Cross, and develop backcross lines. Also develop a molecular marker map to monitor the chromosome segments of the donor present in backcrossing progeny. in the end select descendants with only one (first heterozygous, since from BC) introgression, next self to select homozygous introgression line (by co-dominant markers!). 3. What is a “founder effect”? Do you know synonymous terms from literature? Fixation of alleles at many loci, or strongly biased by chance, when a population is based on only few original plants. More or less synonymous: Genetic bottleneck, selective sweep, random genetic drift. 4. How does it affect genetic variation? By chance many potentially useful alleles will not be present, which is an impoverishment of the genetic variation. 5. Would this effect be stronger or weaker in an autogamous compared to an allogamous plant species? In allogamous crops each plant is heterozygous at many loci. Therefore, a certain population of founding plants will contain more alleles than in the same limited number of plants of an autogamous species. So impoverishment is stronger in autogamous species. 6. What are domestication traits? Will domestication traits display a dominant or recessive inheritance (example bitterness)? Is the influence of recessive domestication traits on the strength of the founder effect stronger or weaker compared to a dominant domestication trait? Domestication traits are characters of the plant species that differ between the ancestral wild species and the derived cultivated species. In most cases domestication traits are recessively inherited mutations. In case of bitterness, the ancestral ‘wild’ trait is expected to be dominant. In this case only very few recessive homozygotes (= sweet) will be selected as basis of the domesticated population, leading to stronger impoverishment as compared to dominant traits.

7. Propose a number of possible reasons why tomato, soybean, flax contains much less variation than barley (all examples are autogamous crops). Spaniards took only few founder tomato plants from South America to Europe, so experienced a strong founder effect. Barley did not experience an extra bottleneck apart from its localized domestication process. It can be perceived that domestication took place only once or at more places, resulting in a wider genetic basis. Domestication could be based on immediate recognition of a qualitative favourable trait, or a gradual process of directional selection of quantitative traits. 8. Describe the genetics of crop domestication? Why this genetic improvement was a slow process? Do you expect this improvement to be slower in autogamous than in allogamous crops? Selection of improved plant types due to (1) recombination, (2) naturally occurring mutations, and (3) spontaneous outcrossing events with wild ancestors. Slow, because the farmers did not stimulate such outcrossing, and depended on rare events, and genetic principles were unknown. Slower in autogamous crops. Maize (allogamous) is an example of a crop where preMendelian breeding was relatively fast (see page 985). 9. Why breeders tend to hesitate crossing elite material with wild relatives. List several main reasons. Cross incompatibility, F1 sterility, infertility in segregating populations, reduced recombination between chromosomes, genes with negative effects on traits may be linked to useful genes (like resistance). Many breeders will have experienced the frustration to remove all undesirable traits and to regain an acceptable quality, while simultaneously trying not to loose the desirable traits. 10. Why is the Zamir approach solving this problem The removal of undesirable alleles is monitored with molecular markers without a priori assumptions on the desirable alleles. The effort mentioned in the previous question 10 is now only a matter of accurate phenotyping and identification of recombination events which remove undesirable linkage drag. 11. How many backcrosses are more or less required? What if you have not enough, what if you have too many backcrosses? About six according to Zamir (we think less). After only two backcrosses, almost all chromosomes of each BC2 plant still has some segment of the donor. In case of nine, too many plants will have no introgression at all, or only a very small one. Then we cannot compose a library that covers the whole exotic genome, or such a library should consist of too many lines (= inconvenient). 12. If an introgression line displays a useful trait (like higher sugar contents in fruits), how to proceed to develop a novel and successful cultivar?

Since the segment probably contains also some adverse effect genes, further backcrossing with that introgression line on the elite cultivar is required to keep the sugar content gene, but loose the adverse effect genes. 13. Explain what means that ‘the epistatic effects mediated by other regions of the exotic genome are removed’. Why is this advantageous? Two or more non-linked genes from the exotic donor may together bring about a particular phenotype, usually undesirable. Introgression of only one small segment, will reduce the chance for epistatic interactions. The BIL will display the effects of several genes of the wild donor (mostly for independent traits, that do not interact). A different answer in statistical terms can be given for quantitative traits. In elite material the genetic gain could be limited to a few percent. In a segregating population the trait values can show a very large variability. The aim is to identify a QTL allele with a positive contribution of 2 %. The statistical power to detect small QTL in a variable F2 or RIL offspring is reduced. The variability generates a large error term. In an exotic library the variability is highly reduced. All QTLs are tested in a near elite genetic background and the immortalised material may allow sufficient replications for accurate phenotyping. This results in a very small residual variance and a more statistical power for declaring QTL with small effects significant. The issue of epistatic interaction is also a disadvantage. If two interacting loci contribute to a desirable trait, the individual BILs will not display the phenotypic effect. On the other hand, breeders may not be interested in the transfer of such oligo/multi-genic traits into elite cultivars. 14. The exotic library principle is compared with the GM approach? What are advantages and advantages of the two approaches? GM is not faster (see page 986) but creates additional problems such as public concern, and requires expensive safety tests. Furthermore GM is focussing on a single trait only. Although exotic libraries may offer a wide range of novel/improved traits, the outcome of the effort is not predictable! 15. Is this method still advantageous in the era of next generation sequencing? The reason to use this method is not connected with the methods used (markers or sequencing). So this method remains uniquely suitable to find beneficial wild alleles and to measure their phenotypic effect in an elite genetic background. The current method requires many markers and accurate maps. Next generation sequencing can pinpoint the boundaries of the introgression segments with greater accuracy. But sequencing is the easy part. To map the reads to a reference genome to capture the information from NGS is not as easy as using markers. 16. The article is not clear about the disadvantages. Please summarise all important limitations of the exotic library approach advocated by Zamir. a) The concept is not feasible for outbreeders that cannot be selfed.

b) Accurate linkage maps should be available or developed (= laborious) to monitor the chromosome segments. c) Only few exotic accessions will be used to make a library. This cannot be done for 100-s of exotic germplasm accessions. So how to make your choice when thousands of accessions are stored in a Genebank? d) The phenotype of the exotic donor does not predict the presence of valuable alleles that may contribute to the elite recipient genotype. E.g. greater fruit size from donor with small fruits, darker red fruits from donor with green fruits. It is a “box with surprises” e) Tight genetic linkages (in cis / coupling phase) between useful alleles and undesirable alleles in the donor segment may require large efforts to remove ‘linkage drag’. f) It is not expected that epistatic effects can be observed. (Co-adapted gene complexes) g) Strong overestimation of the allele effects in individual BILs. Initially observed as additive effects, the law of diminishing returns may apply when additive effects are combined in one genetic background. Wageningen, January 2009 © Herman van Eck, Rients Niks and Jan-Kees Goud...