Genetic Factors and Interaction between genetics and environment.pdf

Colloquium CROP SCIENCE Genetic Factors and the Interaction between Genetics and Environment  INHERITANCE OF PLANT TRAITS Heritable variation fundamental principles of genetics analyze patterns of inheritance use phenotype to deduce genotype...

Colloquium CROP SCIENCE Genetic Factors and the Interaction between Genetics and Environment  INHERITANCE OF PLANT TRAITS Heritable variation fundamental principles of genetics analyze patterns of inheritance use phenotype to deduce genotypes carried out cross https://en.m.wikipedia.org/ pollination/ GREGOR JOHANN MENDEL fertilizations  INHERITANCE OF PLANT TRAITS Stages of Mendel’s experiment True breeding – self-fertilization of parent stocks to find out whether or not plant characters are passed on from parents to offspring Hybridization of pure plants – cross fertilization of purelines (true breeding parents) produced hybrids Self-pollination of hybrids – each F1 hybrid was self fertilized to produce segregating population (F2 generation)  INHERITANCE OF PLANT TRAITS Pattern of inheritance Mendel’s experiment (crosses) garden pea characteristics revealed the basics of heredity Law of inheritance law of dominance Dominant traits Recessive traits https://en.m.wikipedia.org/  INHERITANCE OF PLANT TRAITS Pattern of inheritance law of dominance ▪ In a cross of parents that are pure for contrasting traits, only one form of the trait will appear in the next generation. ▪ All the offspring will be heterozygous and express only the dominant trait. https://socratic.org/ alleles – alternative forms of genes that specify the variation Male Parent Female Parent in plant traits dominant or recessive  INHERITANCE OF PLANT TRAITS Pattern of inheritance Law of inheritance law of dominance law of segregation During the formation of gametes (eggs or sperm), the two alleles responsible https://courses.lumenlearning.com/ for a trait separate from each other. Alleles for a trait are then "recombined“ at fertilization, producing the https://courses.lumenlearning.com/ genotype for the traits of the offspring.  INHERITANCE OF PLANT TRAITS Pattern of inheritance Law of inheritance law of dominance law of segregation law of independent assortment Alleles for different traits are distributed to sex cells (& offspring) independently of one another https://courses.lumenlearning.com/  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance alternative to dominance and recessiveness incomplete dominance https://www.thoughtco.com/ ▪ Neither trait is completely Incomplete dominance in dominant over the other. https://socratic.org/ heterozygote snapdragon ▪ The hybrid (heterozygous) offspring displays a THIRD Phenotype. ▪ Offspring produced are a blending of both alleles  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance alternative to dominance and recessiveness incomplete dominance codominance Both traits are dominant, and show up in the offspring's phenotype together. https://biologywise.com/codominance-explained-with-examples  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance alternative to dominance and recessiveness multiple alleles When there are three or more types of alleles for a given trait, these are called multiple alleles. Multiple alleles exist in a population when there are many variations of a gene present. http://www.bio.miami.edu/  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance linked genes Linked genes are genes that are likely to be inherited together because they are physically close to one another on the same chromosome.  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance epistasis The interaction of different gene loci, so that one gene locus masks or suppresses the expression of another gene https://www.groupe-esa.com/ locus. Dominant epistasis Recessive epistasis The controlling allele is the epistatic allele The masked allele is the hypostatic allele  Dominant Epistasis Example: Fruit colour in summer squash (Cucurbita pepo) Genotypes and WWyy x wwYY Phenotypes: White Fruit Yellow Fruit W-/G = white AaBb W-/gg = white F1 White Fruit WY Wy wY wy ww/G- =yellow WY WWYY WWYy WwYY WwYy ww/gg = green Wy WWYy Wwyy WwYy Wwyy F2 wY WwYY WwYy wwYY wwYy Phenotypic ratio = wy WwYy Wwyy wwYy wwyy 12:3:1 If a dominant W allele is present, there will be no expression of any color regardless of whether there is a dominant Y allele present. Dominant allele at the W locus suppresses the expression of any allele at the Y locus W is epistatic to Y or y to give a 12:3:1 ratio  INHERITANCE OF PLANT TRAITS Extensions of the law of inheritance pleiotropy Pleiotropy is the expression of multiple traits by a single gene.  PHENOTYPE Phenotype - the physical manifestation of the genotype - physical appearance of an organism with respect to a particular character (macroscopic phenotype) -- wild-type phenotype – the phenotype of an organism common in the Source of article: Machine learning in plant science and plant breeding (Jan van Dijk et al., 2020) population - mutant phenotype – the alternative form of wild-type phenotype  PHENOTYPE Two types of phenotypic traits Classification of genes regulating yield-traits Qualitative traits Quantitative traits  QUALITATIVE AND QUANTITATIVE INHERITANCE Qualitative traits follows a Mendelian pattern of inheritance governed by “major” or “oligo” or few genes visually distinguishable color, shape, texture, presence or absence of certain characters segregation: discrete phenotypic variation and effect of a gene is large not easily influenced by the effects of environment the nature of inheritance is easy to analyze  QUALITATIVE AND QUANTITATIVE INHERITANCE Some important qualitative traits chlorophyll flower color seed color endosperm type morphological traits flowering habit and male sterility nodulation vertical resistance  QUALITATIVE AND QUANTITATIVE INHERITANCE Quantitative traits described in terms of the degree of expression controlled by “polygenes” or multiple genes the characters are metric (measurable) height, maturity period, seed size, vigor, tillering, yield, etc. segregation: classification forms a “continuous curve” individual effect of each gene is small easily influenced by the environment the nature of inheritance is difficult to analyze  QUALITATIVE AND QUANTITATIVE INHERITANCE Some important quantitative traits plant height plant size weight yield horizontal resistance protein content lipid content QUALITATIVE AND QUANTITATIVE INHERITANCE  NATURE VS NUTURE Phenotype the physical manifestation of the genotype physical appearance of an organism with respect to a particular character (macroscopic Source of article: Machine learning in plant science and plant breeding (Jan van Dijk et al., 2020) phenotype) wild-type phenotype – the P = G + E + (G x E) phenotype of an organism common in the population Where: mutant phenotype – the P = Phenotype alternative form of wild-type G = Genotype phenotype E = Environment G x E = Interaction of G and E  NATURE VS NUTURE Phenotype appearance Penetrance percent individuals with a genotype expressing the associated phenotype Expressivity variation in the degree of expression of the phenotype  NATURE VS NUTURE Phenotype appearance Penetrance percent individuals with a genotype expressing the associated phenotype Expressivity variation in the degree of expression of the phenotype http://www.cubocube.com/  NATURE VS NUTURE Phenotype appearance Modifier genes secondary genes effect which alters the phenotype produced by the primary gene for example: not all leaves are of the same length, another gene affects https://slideplayer.com/slide/13926358/ the actual length  NATURE VS NUTURE Phenotype appearance Modifier environment the environment may change or influence the effect of a genotype on the phenotype termed as Phenocopy for example: plant height may vary between regions, topography, or climate Source: Effects of size, competition and altitude on tree growth (Coomes and Allen, 2007)  NATURE VS NUTURE Types of phenotypic traits Qualitative Traits follows a Mendelian pattern of inheritance controlled by major genes discrete phenotypic variation less affected by the environment Quantitative Traits described in terms of the degree of expression controlled by polygenic genes continuous phenotypic variation highly affected by the environment  NATURE VS NUTURE P (Phenotype) = G (Genotype) + E (Environment) + G x E Source of article: Machine learning in plant science and plant breeding (Jan van Dijk et al., 2020) Qualitative traits: P=G interaction Quantitative traits: P=G+E+GxE  NATURE VS NUTURE P = G + E + (G x E) Genotype the genetic makeup of an organism the genetic design that gives rise to the phenotype complete set of genetic Source of article: Machine learning in plant science and plant breeding (Jan van Dijk et al., 2020) material the nature factor  NATURE VS NUTURE P = G + E + (G x E) Environment any external factors that could affect or influence the terminal phenotype (growth and development of plants) any phenotypic variation caused by non-genetic factors is Factors associated with the spatiotemporal variability of soil fertility attributes (adapted from Resende & Coelho, 2017). (A and B) Damage to growing crops by pests, diseases, or weather promotes heterogeneous nutrient export patterns in fields; (C) Exposure of the attributed to environmental subsoil in contour banks; (D) Non-uniform application of fertilizers and lime; (E) Limestone deposits; and (F) Abrupt natural changes in soil formation factors. factors the nurture factor  NATURE VS NUTURE P = G + E + (G x E) Environment a high-yielding variety grown under poor environment will have poor yield a low-yielding genotype will have low yield even if grown Factors associated with the spatiotemporal variability of soil fertility attributes (adapted from Resende & Coelho, 2017). (A and B) Damage to growing crops by pests, diseases, or in an optimum environment weather promotes heterogeneous nutrient export patterns in fields; (C) Exposure of the subsoil in contour banks; (D) Non-uniform application of fertilizers and lime; (E) Limestone deposits; and (F) Abrupt natural changes in soil formation factors.  NATURE VS NUTURE P = G + E + (G x E) Genotype x Environment Interaction when different genotypes respond to environmental variation in different ways some plants are exposed in a more favorable environment Overcoming the difficulty of breeding drought tolerant wheat (Koreis, 2019) genotype x location Year 1 Year 2 genotype x season genotype x year Is what you see, what you get? PBre 111: Principles and Methods of Plant Breeding  NATURE VS NUTURE P = G + E + (G x E) Genotype x Environment Interaction when different genotypes respond to environmental variation in different ways some plants are exposed in a more favorable environment genotype x location genotype x season genotype x year this observation relates to the concept of heritability Source of article: Genotype × Environment Interaction: A Prerequisite for Tomato Variety Development (Osie et al., 2018)  NATURE VS NUTURE Heritability the proportion of the phenotypic variance that is genetic in origin degree to which an offspring inherits the breeding value of its parent(s) the value of heritability ranges between 0 and 1 heritability values should be high (closer to 1) to improve the trait-of- https://www.integratedbreeding.net/ interest in the desired direction higher heritability values also indicates strong correspondence between parents and offspring  NATURE VS NUTURE Heritability if heritability is close to zero (0), the variation observed in the phenotype is due to environmental deviation if heritability is close to one (1), the variation observed in the phenotype is due to heritable genetic effects https://www.differencebetween.com/difference-between-genetic-variation-and-vs-environmental-variation/  NATURE VS NUTURE Estimates of heritability broad sense heritability and narrow sense heritability Additive-dominance model: VG = VA + VD Let us consider epistatic effect and G x E interaction effect to be not significant  NATURE VS NUTURE Estimates of heritability VG = VA + VD VP = VA + VD + VE 𝑽𝑮 𝑽𝑨 Broad sense heritability = 𝑯 = 𝟐 Narrow sense heritability = 𝒉 = 𝑽𝑷 𝑽𝑷  NATURE VS NUTURE Methods to estimate heritability Using variance component Through parent-offspring regression Broad sense heritability Narrow sense heritability https://www.chegg.com/ Narrow sense heritability  NATURE VS NUTURE Methods to estimate heritability Response to selection https://blog.uvm.edu/cgoodnig/page/10/ https://blog.uvm.edu/ Narrow sense heritability  NATURE VS NUTURE Response or genetic advance or genetic gain (𝑮𝑺 ) BREEDERS’ EQUATION genetic gain under selection Gs = kσPh2 = R improvement in the mean genotypic value of the selected families or superior individuals over that of the base population Narrow sense heritability Selection intensity (i) value based on the Phenotypic standard deviation Selection differential (k or S) – square root of the phenotypic variance (VP)  NATURE VS NUTURE Response or genetic advance or genetic gain (𝑮𝑺 ) genetic gain under selection improvement in the mean genotypic value of the selected families or superior individuals over that of the base population the equation has been suggested to be one of the fundamental equations of plant breeding the response equation is effective in predicting response to selection, provided that the heritability estimate (h2) is accurate but in terms of practical breeding, the parameters for the response equation are seldom available, hence, not widely used