class: center, middle, inverse, title-slide .title[ # Introduction ] .author[ ### Jinliang Yang ] .date[ ### Jan. 22, 2024 ] --- # About the course ### Course [website](https://jyanglab.com/agro931/) - Online HTML slides - Important dates ### Canvas - Announcements - Handouts - homework assignments (keys) ### Course format - In-person lecture session (with the Zoom option if needed) - In-class computational demo (Using [R software](https://www.r-project.org/) for statistical computing) --- # Scope of the Course ### Population genetics Study the genetic composition of natural populations and its evolutionary causes and consequences. - `Popgen` is the study of **evolution**. - The language of `popgen` is **Mathematics**. -- ### Quantitative genetics Study of the genetic basis of phenotypic variation. - `Quantgen` is the study of the **complex trait**, or **phenotype**. - The language of `Quantgen` is **Statistics**. -- - [AGRO-932](https://jyanglab.com/agro932/) (Biometrical genetics and plant breeding) - Spring of every odd-numbered year (next offfer: Spring 2025) --- # Population genetics .pull-left[ <div align="center"> <img src="Mendel.png" height=150> </div> - __Gregor Mendel__, the founder of modern genetics. ] .pull-right[ <div align="center"> <img src="Darwin.png" height=150> </div> - __Charles Darwin__, the founder of modern evolution. ] -- Population genetics emerged from early efforts to reconcile Mendelian genetics with Darwinian thought. - Many of the important ideas and mathematical models emerged before the 1940s - Before DNA was discovered and yet the usefulness of these models has not diminished --- # Quantitative genetics It almost synonymous with __statistics__! .pull-left[ <div align="center"> <img src="fisher.jpg" height=150> </div> - __R. A. Fisher__ is a founder of quantitative genetics but also of analysis of variance and randomization procedures in statistics. ] .pull-right[ <div align="center"> <img src="Karl_Pearson_1912.jpg" height=150> </div> - The early geneticist __Karl Pearson__ originated the concepts of regression and correlation. ] -- In the 2nd part of the course, we will be deeply involved with the statistical evaluation of the basic quantitative genetic models. --- # Texts and other readings Falconer & Mackay, 1996 Introduction to Quantitative Genetics. Fourth Edition. <div align="center"> <img src="qg_book.png" height=150> </div> ### __Study the material before class meets.__ - Pay attention to the problems in the textbook. - Note that problems and solutions are presented at the end of the text. --- # Definitions #### Locus (plural: loci) A __locus__ is a specific spot in the genome: maybe an entire gene, or a single base pair. - such as, chr1 from 1001-1005: A A __T__ C G. -- #### Alleles At each genetic locus, there may be multiple genetic variants segregating in the population --- these are known as __alleles__. - allele 1: A A __T__ C G. - allele 2: A A __C__ C G. Allele transfers from one generation to next -- #### Genotype - A __Genotype__ is a pair of alleles Genotype is not transferred from one generation to the next due to segregation of alleles. --- # Population A population is a group of interbreeding individuals - Same species - Close proximity - Share a gene pool -- .pull-left[ <div align="center"> <img src="dogs.jpg" height=150> </div> ] .pull-right[ - dog 1: AA AA __TT__ CC GG - dog 2: AA AA __CC__ CC GG - dog 3: AA AA __CT__ CC GG - dog 4: AA AA __CT__ CC GG - dog 5: AA AA __CC__ CC GG assuming 2 alleles per locus ] - Each offspring = random sample of one egg and one sperm from the gene pool - The probability of sampling a particular allele = the frequency of that allele in the gene pool, assuming equal fitness, random mating, ...