A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel’s second law

Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel’s second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter r¯ as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that r¯ is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of r¯ is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) r¯ in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.

Modeling Genetic Complexity in the Classroom

This classroom exercise aims to help students understand the three Ps of genetic complexity: polymorphic, polygenic, and pleiotropic. Using coin flips and dice rolls, students are able to generate the genotype and phenotype of a random individual. From there, students find a mate for this individual and determine the phenotype of their offspring. The randomness generated by the coin and dice mechanics illustrates the principles of independent assortment and segregation, variable gene expression, and environmental effects.

A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel’s second law

Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. However, such studies have been ham-pered by the fact that there has been no direct measure of this quantity. Existing measures consider crossing over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate because the positions of crossovers along a chromosome are also critical: a crossover towards the middle of a chromosome causes more shuffling than a crossover towards the tip. More-over, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel’s second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter r̅ as the probability that the alleles at two randomly chosen loci will be shuffled in the production of a gamete. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that r̅ is larger when crossovers are more evenly spaced, which suggests a novel selective advantage of crossover interference. Utilization of r̅ is enabled by powerful emergent methods for determining crossover positions, either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that: (i) r̅ in humans is close to its maximum possible value of 1/2, (ii) this high level of shuffling is due almost entirely to independent assortment, whose contribution is ~30 times greater than that of crossovers.

Target-Site Resistances to ALS and PPO Inhibitors Are Linked in Waterhemp (Amaranthus tuberculatus)

It is generally expected that, in the case of multiple herbicide resistance, different resistance mechanisms within a weed will follow Mendel’s law of independent assortment. Research was conducted to investigate anecdotal observations suggesting that target site–based resistances to inhibitors of acetolactate synthase (ALS) and protoporphyrinogen oxidase (PPO) did not follow independent assortment in common waterhemp. Cosegregation of the two resistances was observed in backcross lines (population sensitive to both herbicides as recurrent parent). Specifically, whereas 52% of backcross plants were resistant to a PPO inhibitor, this percentage increased to 92% when the backcross plants were preselected for resistance to an ALS inhibitor. Molecular marker analysis confirmed that the corresponding genes (ALSandPPX2) were genetically linked. When data from all plants analyzed were pooled, the genetic distance between the two genes was calculated to be 7.5 cM. The two genes were found to be about 195 kb apart in the recently published grain amaranth genome, explaining the observed genetic linkage. There is likely enough recombination that occurs between the linked genes to prevent the linkage from having significant implications in terms of resistance evolution. Nevertheless, documentation of the happenstance linkage between target-site genes for resistance to ALS and PPO inhibitors in waterhemp is a reminder that one should not assume distinct resistance mechanism will independently assort.

On the independent loci assumption in phylogenomic studies

Studies using multi-locus coalescent methods to infer species trees or historical demographic parameters usually require the assumption that the gene tree for each locus (or SNP) is genealogically independent from the gene trees of other sampled loci. In practice, however, researchers have used two different criteria to delimit independent loci in phylogenomic studies. The first criterion, which directly addresses the condition of genealogical independence of sampled loci, considers the long-term effects of homologous recombination and effective population size on linkage between two loci. In contrast, the second criterion, which only considers the single-generation effects of recombination in the meioses of individuals, identifies sampled loci as being independent of each other if they undergo Mendelian independent assortment. Methods that use these criteria to estimate the number of independent loci per genome as well as intra-chromosomal “distance thresholds” that can be used to delimit independent loci in phylogenomic datasets are reviewed. To compare the efficacy of each criterion, they are applied to two species (an invertebrate and vertebrate) for which relevant genetic and genomic data are available. Although the independent assortment criterion is relatively easy to apply, the results of this study show that it is overly conservative and therefore its use would unfairly restrict the sizes of phylogenomic datasets. It is therefore recommended that researchers only refer to genealogically independent loci when discussing the independent loci assumption in phylogenomics and avoid using terms that may conflate this assumption with independent assortment. Moreover, whenever feasible, researchers should use methods for delimiting putatively independent loci that take into account both homologous recombination and effective population size (i.e., long-term effective recombination).

Independent assortment of seed color and hairy leaf genes in Brassica rapa L.

Rahman, M. 2014. Independent assortment of seed color and hairy leaf genes in Brassica rapa L. Can. J. Plant Sci. 94: 615–620. A genetic study of seed color and hairy leaf in Brassica rapa was conducted in progeny originating from the brown-seeded, hairy leaf B. rapa subsp. chinensis line and the Bangladeshi B. rapa var. trilocularis line. A joint segregation of both traits was also examined in the F2 and backcross populations. Seed color segregated into brown, yellow–brown, and yellow, which suggests that digenic control of brown or yellow–brown color was dominant over yellow seed color. Hairy leaves were found to be under monogenic control, and hairy leaf was dominant over non-hairy leaf. The data show that genes controlling seed color and hairy leaf are inherited independently.

Cootie Genetics

“Cootie Genetics” is a hands-on, inquiry-based activity that enables students to learn the Mendelian laws of inheritance and gain an understanding of genetics principles and terminology. The activity begins with two true-breeding Cooties of the same species that exhibit five observable trait differences. Students observe the retention or loss of traits among first-generation heterozygotes, hypothesize what happened to these traits, and design an experiment to test their hypotheses by mating the first-generation Cooties. With the second generation, Mendel’s principles of segregation and independent assortment of alleles are observed; dominant and recessive traits and tools students need to construct Punnett squares are apparent.