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The F2 progeny appeared in the phenotypic ratio of 9 round/yellow : 3 round/green : 3 wrinkled/yellow : 1 wrinkled/green.

How did Mendel go from this F2 phenotypic ratio to the second law? He ignored the wrinkled/smooth phenotype and just considered the yellow/green seed color phenotype in self-pollination crosses of F2 plants just like those for the first law. In the F2 progeny, 12/16 or three-quarters had a yellow seed coat and 4/16 or one-quarter had a green seed coat, or a 3 yellow : 1 green phenotypic ratio. Again using self-pollination of F2 plants like those in Fig. 2.3, he showed that the yellow phenotypes were one-quarter pure and one-half impure yellow. Thus, the segregation ratio for seed color was 1:2:1 and the wrinkled/smooth phenotype did not alter this result. Mendel obtained an identical result when focusing instead on the wrinkled/smooth phenotype and ignoring the seed color phenotype.

Mendel concluded that a phenotypic segregation ratio of 9:3:3:1 is the same as combining two independent 3 : 1 segregation ratios of two pheno-types since (3:1) x (3:1) = 9:3:3:1. Similarly, multiplication of two (1 : 2 : 1) phenotypic ratios will predict the two phenotype ratio (1 : 2 : 1) x (1:2:1) = 1:2:1:2:4:2:1:2:1. We now recognize that dominance in the first two phenotype ratios masks the ability to distinguish some of the homozygous and heterozygous genotypes, whereas the ratio in the second case would result if there was no dominance. You can confirm these conclusions by working out a Punnett square for the F2 progeny in the two-locus case.

Mendel performed similar breeding experiments with numerous other pea phenotypes and obtained similar results. Mendel described his work with peas and other plants in lectures and published it in 1866 in the Proceedings of the Natural Science Society of BrĂ¼nn in German. It went unnoticed for nearly 35 years. However, Mendel's results were eventually recognized and his paper was translated into several languages. Mendel's rediscovered hypothesis of particulate inheritance was also bolstered by evidence from microscopic observations of cell division that led Walter Sutton and Theodor Boveri to propose the chromosome theory of heredity in 1902.

Much of the currently used terminology was coined as the field of particulate genetics initially developed. Therefore, many of the critical terms in genetics have remained in use for long periods of time. However, the meanings and connotations of these terms have often changed as our understanding of genetics has also changed.

Unfortunately, this has lead to a situation where words can sometimes mislead. A common example is equating gene and allele. For example, it is commonplace for news media to report scientific breakthroughs where a "gene" has been identified as causing a particular phenotype, often a debilitating disease. Very often what is meant in these cases is that an allele with the phenotypic effect has been identified. Both unaffected and affected individuals all possess the gene, but they differ in their alleles and therefore in their genotype. If individuals of the same species really differed in their gene content (or loci they possessed), that would provide evidence of additions or deletions to genomes. For an interesting discussion of how terminology in genetics has changed - and some of the misunderstandings this can cause -see Judson (2001).

Gene Unit of particulate inheritance; in contemporary usage usually means an exon or series of exons, or a DNA sequence that codes for an RNA or protein. Locus (plural loci, pronounced "low-sigh") Literally "place" or location in the genome; in contemporary usage is the most general reference to any sequence or genomic region, including non-coding regions. Allele Variant or alternative form of the DNA sequence at a given locus. Genotype The set of alleles possessed by an individual at one locus; the genetic composition of an individual at one or many loci.

Mendel's second "law" Predicts independent assortment of multiple loci: during gamete formation, the segregation of alleles of one gene is independent of the segregation of alleles of another gene.

Phenotype The morphological, biochemical, physiological, and behavioral attributes of an individual; synonymous with character, trait.

Dominant Where the expressed phenotype of one allele takes precedence over the expressed phenotype of another allele. The allele associated with the expressed phenotype is said to be dominant. Dominance is seen on a continuous scale that ranges between "complete" dominance (one allele completely masks the phenotype of another allele so that the phenotype of a heterozygote is identical to a homozygote for the dominant allele), "partial," or "incomplete" dominance (masking effect is incomplete so that the phenotype of a heterozygote is intermediate to both homozygotes) and includes over- and under-dominance (phenotype is outside the range of phenotypes seen in the homozygous genotypes). The lack of dominance (heterozygote is exactly intermediate to phenotypes of both homozygotes) is sometimes termed "codominance" or "semi-dominance." Recessive The expressed phenotype of one allele is masked by the expressed phenotype of another allele. The allele associated with the concealed phenotype is said to be recessive.

(infrequent) alleles would disappear from populations over time. Godfrey H. Hardy (1908) and Wilhelm Weinberg (1908) worked independently to show that the laws of Mendelian heredity did not predict such a phenomenon (see Crow 1988). In 1908 they both formulated the relationship that can be used to predict allele frequencies given genotype frequencies or predict genotype frequencies given allele frequencies. This relationship is the well-known Hardy-Weinberg equation p2 + 2pq + q2 = 1 (2.1)

where p and q are allele frequencies for a genetic locus with two alleles.

Genotype frequencies predicted by the Hardy-Weinberg equation can be summarized graphically. Figure 2.5 shows Hardy-Weinberg expected genotype frequencies on the y axis for each genotype for any given value of the allele frequency on the x axis. Another graphical tool to depict genotype and allele frequencies simultaneously for a single locus with two alleles is the De Finetti diagram (Fig. 2.6). As we will see, De Finetti diagrams are helpful when examining how population genetic processes dictate allele and genotype frequencies. In both graphs it is apparent that heterozygotes are most frequent when the frequency of the two alleles is equal to 0.5. You can also see that when an allele is rare, the corresponding homozygote genotype is even rarer since the genotype frequency is the square of the allele frequency.

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