Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.

The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

According to the invention, there is provided an inbred corn line, designated PHHB9. This invention thus relates to the plants and seeds of inbred corn line PHHB9 and to methods for producing a corn plant produced by crossing the inbred line PHHB9 with itself or with another corn plant. This invention further relates to hybrid corn seeds and plants produced by crossing the inbred line PHHB9 with another corn line or plant.

Inbred corn line PHHB9

An inbred maize line, designated PH0HC, the plants and seeds of inbred maize line PH0HC, methods for producing a maize plant produced by crossing the inbred line PH0HC with itself or with another maize plant, and hybrid maize seeds and plants produced by crossing the inbred line PH0HC with another maize line or plant.

Inbred maize line PH0HC

The utility of 131 simple sequence repeat (SSR) loci to characterize and identify maize inbred lines, validate pedigree, and show associations among inbred lines was evaluated using a set of 58 inbred lines and four hybrids. Thirteen sets of inbred parent-progeny triplet pedigrees together with four hybrids and their parental lines were used to quantify incidences of scoring that departed from expectations based upon simple Mendelian inheritance. Results were compared to those obtained using 80 restriction fragment length polymorphism (RFLP) probes. Over all inbred triplets, 2.2% of SSRs and 3.6% of RFLP loci resulted in profiles that were scored as having segregated in a non-Mendelian fashion. Polymorphic index content (PIC, a measure of discrimination ability) values ranged from 0.06 to 0.91 for SSRs and from 0.10 to 0.84 for RFLPs. Mean values for PIC for SSRs and RFLPs were similar, approximately 0.62. However, PIC values for nine SSRs exceeded the maximum PIC for RFLPs. Di-repeats gave the highest mean PIC scores for SSRs but this class of repeats can result in “stutter” bands that complicate accurate genotyping. Associations among inbreds were similar for SSR and RFLP data, closely approximating expectations from known pedigrees. SSR technology presents the potential advantages of reliability, reproducibility, discrimination, standardization and cost effectiveness over RFLPs. SSR profiles can be readily interpreted in terms of alleles at mapped loci across a broad range of maize germ plasm. Consequently, SSRs represent the optimum approach for the identification and pedigree validation of maize genotypes compared to other currently available methods.

An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree

Embryogenic callus consisting of both Type 1, firm, compact, translucent, relatively slow growing callus and Type 2, highly friable, rapidly growing callus with well-formed somatic embryos, were observed in elite maize germplasm, notably B73 and hybrids with B73. Parental genotype is very important in the ability to identify and isolate embryogenic callus after 14 and 28 days in culture. A partial diallel analysis revealed that a large proportion of the genotypic variation was of the additive type although heterosis did positively increase culture response in most cases. A significant negative maternal effect for culture response was noted for inbred B73 from Reid-type germplasm while four lines sampled from Lancaster germplasm showed similar response whether used as male or female. Although significant media differences were observed in some genotypes, culture media did not preclude observation of Type 1 or Type 2 embryogenic cultures in this study after 14 and 28 days. Plants could be regenerated from all genotypes in this study after 14-days of culture, but not all genotypes were capable of sustained subculture and plant regeneration. Plant regeneration from Type 2 cultures of B73 and B73 hybrids has been obtained up to a year after initiation.

The effect of parental genotype on initiation of embryogenic callus from elite maize (Zea mays L.) germplasm

Recent studies of ancestral maize populations indicate that linkage disequilibrium tends to dissipate rapidly, sometimes within 100 bp. We set out to examine the linkage disequilibrium and diversity in maize elite inbred lines, which have been subject to population bottlenecks and intense selection by breeders. Such population events are expected to increase the amount of linkage disequilibrium, but reduce diversity. The results of this study will inform the design of genetic association studies. We examined the frequency and distribution of DNA polymorphisms at 18 maize genes in 36 maize inbreds, chosen to represent most of the genetic diversity in U.S. elite maize breeding pool. The frequency of nucleotide changes is high, on average one polymorphism per 31 bp in non-coding regions and 1 polymorphism per 124 bp in coding regions. Insertions and deletions are frequent in non-coding regions (1 per 85 bp), but rare in coding regions. A small number (2–8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. No decline of linkage disequilibrium within a few hundred base pairs was found in the elite maize germplasm. This finding, as well as the small number of haplotypes, relative to neutral expectation, is consistent with the effects of breeding-induced bottlenecks and selection on the elite germplasm pool. The genetic distance between haplotypes is large, indicative of an ancient gene pool and of possible interspecific hybridization events in maize ancestry.

/pdf/snp-frequency-haplotype-structure-and-linkage-disequilibrium-1i2z4q5tv0.pdf

SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Genetic distances were calculated among 37 inbred lines representing a wide range of related and unrelated elite Corn Belt germ plasm of maize (Zea Mays L.), using 257 probe restriction enzyme combinations. Genetic distances based on RFLP data were highly correlated with coefficients of parentage among pairs of lines. The RFLP-based distance had a higher correlation with single-cross grain yield performance and grain yield heterosis than any of the other measures of similarity we calculated using these same lines. The coefficients of determination (r (2)) from regressing the coefficient of parentage, grain yield, and grain yield heterosis on Nei's measure of genetic similarity based on RFLP data were 0.81, 0.87 and 0.77, respectively. A cluster diagram based upon the RFLP data grouped the lines into families consistent with the breeding history and heterotic response of these lines. We believe that measures of similarity calculated from RFLP data, coupled with pedigree knowledge and using molecular markers to locate quantitative trait loci (QTL), could allow maize breeders to predict combinations of lines that result in high-yielding, single-cross hybrids.

Similarities among a group of elite maize inbreds as measured by pedigree, F1 grain yield, grain yield, heterosis, and RFLPs.

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.

/pdf/rate-and-pattern-of-mutation-at-microsatellite-loci-in-maize-1glipt5bg9.pdf

O. S. Smith

Papers

An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree

The effect of parental genotype on initiation of embryogenic callus from elite maize (Zea mays L.) germplasm

SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines

Similarities among a group of elite maize inbreds as measured by pedigree, F1 grain yield, grain yield, heterosis, and RFLPs.

Rate and Pattern of Mutation at Microsatellite Loci in Maize