Qualitative and Quantitative traits Qualitative traits: Phenotypes with discrete and easy to measure values. Individuals can be correctly classified according

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Qualitative and Quantitative traits Qualitative traits: Phenotypes with discrete and easy to measure values. Individuals can be correctly classified according to phenotype. Show mendelian inheritance (monogene) Little environmental effect Molecular markers are qualitative traits Examples: Quantitative traits: Individuals cannot be classified by discrete values Quantitative trait distribution show a continuous range of variation and phenotypes can take any value Complex mode of inheritance (polygene) Moderate to great environmental effect) Examples: Plant height, yield, disease severity, grain weight, etc Plant Height (in) % of plants 2030 40 Slide 2 Inheritance of Quantitative traits The study of quantitative trait inheritance followed the same steps as for Mendelian traits. At the beginning they were thought to not follow Mendels laws. But it is not true PARENT 1: pure line, completely homozygote 40 inches PARENT 2: pure line, completely homozygote 20 inches F1: range of height distribution but no type of segregation F2: wider range of height distribution but no type of segregation F1 F2 Slide 3 Inheritance of Quantitative traits In 1903 the Danish botanist Wilhelm Johannsen measured the weight of seeds in the Princess variety of bean. This variety is a pure line since beans are self-fertilizing. From a seed lot he measured and classified the beans by weight and obtained the range of distribution for that variety. Then he selected 19 beans of different weights and self-pollinated them several generations Doing this he got 19 pure lines (completely homozygous) in case they were not at the beginning of the experiment He found that: The weight of the 5,494 beans he obtained followed a normal distribution All lines within each of the 19 groups were genetically identical but showed also a range of variation in weights. The average and distribution of weight in each pure line were similar to those of the original population Slide 4 Inheritance of Quantitative traits The Experiment of Johannsen Conclusions: There is a genetic control that keeps the same average weight and distribution However not all genetically identical seeds have the same weight. The phenotype of each individual must be determined by the genotype and the environmental conditions Without genetic variability, genetic improvement is not possible Slide 5 Inheritance of Quantitative traits Johannsen showed that quantitative traits are determined by genes. However he did not find any type of mendelian segregation. This was studied in 1909 by Swedish Herman Nilsson-Ehle who studied kernel color in wheat He had several pure lines of red and white colored kernels. When crossing red x white he got always red F1, but different proportions of red and white kernels depending on the cross: a)3 red : 1 white b)15 red : 1 White c)63 red : 1 white He deduced that the color was controlled by three loci. Only individuals with recessive homozygous alleles at the three loci showed the white phenotype. When a single dominant allele (A, B or C) is present at any of the three loci the red phenotype shows up. Slide 6 Inheritance of Quantitative traits a)3 red : 1 white b)15 red : 1 White c)63 red : 1 white AAbbcc X aabbcc P1 (red) P2 (white) AabbccF1(red) F2 (only one locus segregating) AAbbcc : Aabbcc : aabbcc (red) (red) (white) Segregation 3 red : 1 white For case a), allelic variation between the two parents was present only at one locus Slide 7 Inheritance of Quantitative traits a)3 red : 1 white b)15 red : 1 White c)63 red : 1 white AABBcc X aabbcc P1 (red) P2 (white) AaBbccF1(red) F2 (two loci segregating) 1/16 AABBcc (red) 2/16 AABbcc (red) 1/16 AAbbcc (red) 2/16 AaBBcc (red) 4/16 AaBbcc (red) 2/16 Aabbcc (red) 1/16 aaBBcc (red) 2/16 aaBbcc (red) 1/16 aabbcc (white) Segregation 15 red : 1 white Slide 8 Inheritance of Quantitative traits a)3 red : 1 white b)15 red : 1 White c)63 red : 1 white AABBCC X aabbcc P1 (red) P2 (white) AaBbCcF1(red) F2 (three loci segregating) 1/64 AABBCC (red) 2/64 AABbCC (red) 1/64 AabbCC (red) 2/64AaBBCC (red) 4/64 AaBbCC (red) 2/64 AabbCC (red) 1/64 aaBBCC (red) 2/64 aaBbCC (red) 1/64 aabbCC (red) Segregation 63 red : 1 white 2/64 AABBCc (red) 4/64 AABbCc (red) 2/64 AabbCc (red) 4/64 AaBBCc (red) 8/64 AaBbCc (red) 4/64 AabbCc (red) 2/64 aaBBCc (red) 4/64 aaBbCc (red) 2/64 aabbCc (red) 1/64 AABBcc (red) 2/64 AABbcc (red) 1/64 Aabbcc (red) 2/64 AaBBcc (red) 4/64 AaBbcc (red) 2/64 Aabbcc (red) 1/64 aaBBcc (red) 2/64 aaBbcc (red) 1/64 aabbcc (white) Slide 9 Inheritance of Quantitative traits However, Nilsson-Ehle not only classified the seeds by color. He also classified them by color intensity and saw that color intensity also had a defined segregation pattern AABB X aabb P1 (purple, very dark red) AaBb F1(red) 1/16 AABB (Purple) 2/16 AABb (dark-red) 1/16 AAbb (red) 2/16 AaBB (dark-red) 4/16 AaBb (red) 2/16 Aabb (light-red) 1/16 aaBB (red) 2/16 aaBb (light-red) 1/16 aabb (white) 1/16 : purple 4/16: dark-red 6/16: red 4/16: light-red 1/16: white P2 (white) P1 (purple, X very dark red) P2 (white) F1(red) He proposed that for this cross, color intensity was determined by two loci with two alleles each: one that produced red pigment (A and B) and other with no pigment (a and b). He determined that the effects of the alleles were additive and contributed equally to the phenotype, which depended on the number of alleles for pigment present Slide 10 Inheritance of Quantitative traits 1/16 : purple 4/16: dark-red 6/16: red 4/16: light-red 1/16: white P1 (purple, X very dark red) P2 (white) F1(red) Going one step further, He saw that within each of the groups there was also some variation Color intensity - white + purple Frequency Slide 11 Inheritance of Quantitative traits Color intensity - white+ purple Frequency He deduced that many loci were involved (not only two) in the trait and taking into account Johanssens findings: Phenotype=Genotype+Environment Then, the distribution of a quantitative trait would follow a normal distribution Analysis of quantitative traits is therefore complicated: Same genotype: 1 and 2 show different phenotype Same phenotype: 1, 3 and 4 is the result of three different genotypes 1 2 3 4 Slide 12 Inheritance of Quantitative traits The inheritance of quantitative traits also explains the phenomenon of transgressive segregation: In the progeny of a cross we can get phenotypes out of the range of the parents Frequency Cold tolerance P1 P2 0 10 Lets assume 5 loci with additive effects control the trait aabbccddEE X AABBCCDDee P1 AaBbCcDdEe F1 P2 All possible combinations of alleles at 5 loci. Between them: AABBCCDDEE (all favorable alleles) aabbccddee (all unfavorable alleles) F2 Slide 13 Inheritance of Quantitative traits Quantitative traits are usually controlled by several genes with small additive effects and influenced by the environment Heritability h 2 measures the proportion of phenotypic variation (variance) that is due to genetic causes P = G + E; V P = V G + V E A heritability of 40% for cold tolerance means that within that population, genetic differences among individuals are responsible of 40% of the variation. Therefore, 60% is due to environmental causes. However, that does not mean that the cold tolerance of a certain individual is due 40% to genetic causes and 60% to environmental causes. h 2 is a property of the population and not of individuals Slide 14 Inheritance of Quantitative traits Heritability h 2 measures the proportion of phenotypic variation (variance) that is due to genetic causes P = G + E; V P = V G + V E h 2 ranges between 0 and 1 If h 2 is 0 means : a)The trait is not genetically controlled. All the variation we see is due to environmental factors, or b)The trait is genetically controlled but all individuals have the same genotype h 2 is very useful because it allows us to predict the response to artificial selection Slide 15 Inheritance of Quantitative traits Heritability h 2 measures the proportion of phenotypic variation (variance) that is due to genetic causes P = G + E; V P = V G + V E h 2 is very useful because it allows us to predict the response to artificial selection 6000 In plant breeding, the starting point is a segregating population (with genetic variability). The best individuals are selected to be the progenitors of the next generation Frequency Grain yield (lb/A) 0 00 SS Selection differential (S) = S 0 Response to selection (R) = R 0 Realized heritability: Is the ratio of the single-generation progress of selection to the selection differential of the parents. The higher h 2, the higher the progress of selection in each generation Frequency Grain yield (lb/A) 0 00 RR 6000 Slide 16 Analysis of Quantitative traits The analysis of quantitative traits is based on the identification of the individual loci (QTL) controlling the trait, their location, effects and interactions A quantitative trait locus/loci (QTL) is the location of individual locus or multiple loci that affects a trait that is measured on a quantitative (linear) scale. These traits are typically affected by more than one gene, and also by the environment. Thus, mapping QTL is not as simple as mapping a single gene that affects a qualitative trait (such as flower color). Slide 17 Analysis of Quantitative traits There are two main approaches for QTL analysis: a) QTL analysis in mapping populations b) Association mapping Both approaches share a set of common elements: a) A population (array of individuals) that show variability for the trait of study b)Phenotypic information: We need to design an experiment to estimate the phenotypic value of each individual c) Genotypic information: A set of molecular markers that have been run in all the individuals of the population d)A statistical method to estimate QTL position, effects and interactions Slide 18 Analysis of Quantitative traits QTL analysis in mapping populations We need to develop a population from a