History of plant population genetics.

This review of plant population genetics focuses on the genetic foundations of the processes that have led to documentable improvements in cultivated plants since the earliest domestications took place perhaps 13,000 years ago. Nearly all human civilizations have depended heavily on inbreeding plants (particularly wheat, barley, soybeans and other inbreeding legumes), as well as outbreeding vegetatively propagated species (white potatoes, yams) as their dietary standbys. The principal exception is maize (corn), an annual seed-produced outbreeder in nature. It is noteworthy that maize joined wheat, rice, and barley as a truly major crop worldwide only after its conversion to self-pollination combined with hybridization between favorably interacting inbred lines increased yield of maize several-fold in the twentieth century.

Evolution of ribosomal DNA (rDNA) genetic structure in colonial Californian populations of Avena barbata.

DNA samples from 980 plants of Avena barbata from 48 ecologically diverse sites in California and Oregon were assayed to determine their genotype for two duplicated loci governing rDNA variants. More than 40 different rDNA genotypes were observed among which 5 made up 96% of our sample in environmentally homogeneous sites; predominant genotypes were less frequent and recombinant genotypes were more frequent in environmentally heterogeneous sites. The spatial distribution of each predominant rDNA genotype was nearly an exact overlay on both macro- and microgeographical scales of a distinctive habitat and also of the distribution of an eight-locus morphological-allozyme variant genotype. In all, seven different habitat-genotype combinations (ecotypes) were distinguishable on the basis of their morphological-allozyme-rDNA genotypes. None of these seven genotypes has been found in ancestral Spanish populations; thus the above predominant multilocus genotypes (ecotypes) of the colonial populations evidently evolved subsequent to the recent introduction (within 150-200 generations) of A. barbata to California. The precise associations of specific alleles and genotypes of the morphological allozyme and rDNA loci with different specifiable habitats leads us to the conclusion that natural selection favoring particular multilocus combinations of alleles in different habitats was the main guiding force in shaping the internal genetic structure of local populations as well as the overall adaptive landscape of A. barbata over California and Oregon.

Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics.

This study was undertaken to assess the extent of genetic variation in barley simple sequence repeats (SSRs) and to study the evolutionary dynamics of SSR alleles. SSR polymorphisms were resolved by the polymerase chain reaction with four pairs of primers. In total, 71 variants were observed in a sample of 207 accessions of wild and cultivated barley. Analyses of wheat-barley addition lines and barley doubled haploids identified these variants (alleles) with four loci, each located on a different chromosome. The numbers of alleles detected at a locus corresponded to the number of nucleotide repeats in the microsatellite sequences. The numbers of alleles at two loci were 28 and 37; to our knowledge these are the largest numbers of alleles for single Mendelian loci reported in plants. Three alleles were resolved by each of the other two loci. Allelic diversity was greater in wild than in cultivated barley and surveys of two generations (F8 and F53) of Composite Cross II, an experimental population of cultivated barley, showed that few of the alleles present in the 28 parents survived into generation F53, whereas some infrequent alleles reached high frequencies. Such changes in frequency indicate that the chromosomal segments marked by the SSR alleles are under the influence of natural selection. The SSR variants allow specific DNA sequences to be followed through generations. Thus, the great resolving power of SSR assays may provide clues regarding the precise targets of natural and man-directed selection.

Ecogeographical distribution and differential adaptedness of multilocus allelic associations in Spanish Avena sativa L.

We determined the nine-locus isozyme genotype of 267 landrace accessions of Avena sativa from 31 provinces of Spain. Our results establish that level of genetic variability is usually high both within and among accessions of this heavily self-fertilizing hexaploid grass and that multilocus genetic structure differs in various ecogeographical regions of Spain. We concluded that selection favoring different multilocus genotypes in different environments was the main integrating force that shaped the internal genetic structure of local populations as well as the overall adaptive landscape of A. sativa in Spain. Implications in genetic resource conservation and utilization are discussed.

Evolution of multilocus genetic structure in Avena hirtula and Avena barbata.

Avena barbata, an autotetraploid grass, is much more widely adapted than Avena hirtula, its diploid ancestor. We have determined the 14-locus genotype of 754 diploid and 4751 tetraploid plants from 10 and 50 Spanish sites, respectively. Allelic diversity is much greater in the tetraploid (52 alleles) than in the diploid (38 alleles): the extra alleles of the tetraploid were present in nonsegregating heteroallelic quadriplexes. Seven loci were monomorphic for the same allele (genotypically 11) in all populations of the diploid: five of these loci were also monomorphic for the same allele (genotypically 1111) in all populations of the tetraploid whereas two loci each formed a heteroallelic quadriplex (1122) that was monomorphic or predominant in the tetraploid. Seven of the 14 loci formed one or more highly successful homoallelic and/or heteroallelic quadriplexes in the tetraploid. We attribute much of the greater heterosis and wider adaptedness of the tetraploid to favorable within-locus interactions and interlocus (epistatic) interactions among alleles of the loci that form heteroallelic quadriplexes. It is difficult to account for the observed patterns in which genotypes are distributed ecogeographically except in terms of natural selection favoring particular alleles and genotypes in specific habitats. We conclude that natural selection was the predominant integrating force in shaping the specific genetic structure of different local populations as well as the adaptive landscape of both the diploid and tetraploid.

Evolution of multilocus genetic structure in an experimental barley population.

Data from 311 selfed families isolated from four generations (F8, F13, F23, F45) of an experimental barley population were analyzed to determine patterns of change in character expression for seven quantitative traits, and in single-locus allelic frequencies, and multilocus genetic structure, for 16 Mendelian loci that code for discretely recognizable variants. The analyses showed that large changes in single-locus allelic frequencies and major reorganizations in multilocus genetic structure occurred in each of the generation-to-generation transitions examined. Although associations among a few traits persisted over generations, dynamic dissociations and reassociations occurred among several traits in each generation-transition period. Overall, the restructuring that occurred was characterized by gradual decreases in the number of clusters of associated traits and increases in the number of traits within each cluster. The observed changes in single-locus frequencies and in multilocus genetic structure were attributed to interplay among various evolutionary factors among which natural selection acting in a temporally heterogeneous environment was the guiding force.

Associations between nuclear loci and chloroplast DNA genotypes in wild barley.

Associations among alleles at nine nuclear loci and three chloroplast DNA (cpDNA) genotypes were assessed in a sample of 247 accessions of the wild barley, Hordeum vulgare ssp. spontaneum. Alleles at two of the nine nuclear loci are marked by length variations in the intergenic spacer region of ribosomal DNA (rDNA), and those of the other seven loci are well characterized allozymes. The three chloroplast DNA (cpDNA) genotypes are marked by restriction fragment length polymorphisms resulting from three polymorphic restriction sites detected by Southern blot hybridization. The analyses were performed by dividing the nine nuclear loci into a series of two-locus subsets and constructing log-linear models to characterize associations between the subsets of two nuclear loci and the cpDNA genotypes. Statistically significant associations were detected between six of the nine nuclear loci and the cpDNA genotypes, either individually as pairwise correlations, or through interaction with another nuclear locus to form three-variate complexes. Although the sample size of the present study was inadequate for statistical evaluation of higher order interactions, the results suggest the existence of interactions in which more than two nuclear loci are involved in associations with cpDNA genotypes. The observed cytonuclear associations appear to result from interplay among a number of evolutionary forces including a mating system of predominant selfing, differentiation among gene pools of local populations, and adaptation of barley genotypes to specific environmental conditions.

Pollen migration in predominantly self-fertilizing plants: barley.

In barley, a heavily self-fertilizing species (approximately 99%), most outcrosses occur between plants that grow closely adjacent to each other. Outcrosses have been detected only rarely between plants that are separated by a meter or more. In this article we present evidence that outcrosses can occur at distances up to 60 m and we discuss the implications of this longer-distance pollen migration on the maintenance of the genetic integrity of pedigreed stocks and experimental populations.

Multilocus genetic structure of ancestral Spanish and colonial Californian populations of Avena barbata.

We have applied a multivariate log-linear technique to the analysis of interlocus allelic associations among 14 allozyme loci in a sample of 4011 plants from 42 Spanish populations of Avena barbata. The loci fell into three natural groups of five, five, and four loci. The five loci of the first group are invariant, or nearly so, throughout the range of the species. The genetic organization of the loci of this set is defined by a single five-locus genotype; each allele of this predominant genotype is a "wild-type" allele that contributes favorably to adaptedness in all single-locus and multilocus configurations regardless of environment. Although allelic diversity is high in Spain for the nine loci of the second and third sets, log-linear analyses showed that these loci are tied together in Spanish populations through complex networks of overlapping lower-order interlocus interactions. The ancestral Spanish and colonial Californian gene pools are closely similar in allelic composition on a locus-by-locus basis; however, Spanish allelic configurations at two-locus and higher-order levels are usually different from and much less tightly organized than in Californian populations. We conclude that the major force involved in the evolution of the colonial populations was selection that led to reorganization, at the interlocus level, of the ancestral Spanish allelic ingredients into different multilocus genotypes adapted to Californian habitats.

Genetic diversity and adaptedness in tetraploid Avena barbata and its diploid ancestors Avena hirtula and Avena wiestii.

Avena barbata, a tetraploid grass, is much more widely adapted and successful in forming dense stands than its diploid ancestors. The success of such polyploids has often been attributed to heterosis associated with ability to breed true for a highly heterozygous state in which allelic differences between the parents are fixed in the polyploid by chromosome doubling. We have examined the relationship between genetic diversity and adaptedness for 14 allozyme loci in A. barbata and its diploid ancestors in samples collected from diverse habitats in Israel and Spain. The relationship varied from locus to locus: superior adaptedness was associated with genetic uniformity for five loci, in part with genetic uniformity and in part with genetic diversity (monomorphism for a single heteroallelic quadriplex) for one locus, and with allelic diversity in the form of heteroallelic quadriplexes combined with genotypic diversity in the form of complex polymorphisms among different homoallelic and/or heteroallelic quadriplexes for the eight remaining loci. These results indicate that allelic diversity fixed in nonsegregating form through chromosome doubling was an important factor in the evolution of adaptedness in A. barbata. However, it is unlikely that heterosis associated with heterozygosity contributed significantly to superior adaptedness in either the diploids or the tetraploid because virtually all loci (approximately 99%) were homozygous in the Avena diploids and tetraploid.

Genetic diversity and ecogeographical differentiation among ribosomal DNA alleles in wild and cultivated barley.

DNA from 267 accessions of wild barley from ecologically diverse habitats in Israel and Iran and from 92 accessions of cultivated barley from throughout the world were assayed for the 20 ribosomal DNA (rDNA) spacer-length variants that have been identified in the barley species. These 20 spacer-length variants, which are detectable by Southern blot hybridization, serve as markers of rDNA alleles of two Mendelian loci, Rrn1 and Rrn2. All of the populations of wild barley studied were polymorphic for both loci. In wild barley allele 112 (Rrn1) and allele 107 (Rrn2) behaved as widely adapted wild-type alleles; in our sample of cultivated barley allele 112 also behaved as a wild-type allele but allele 104 was somewhat more frequent than allele 107 in Rrn2. A few other alleles were locally frequent in wild barley. However, most of the 20 alleles were infrequent or rare and such alleles were often associated as "hitchhikers" with one of the wild-type alleles in compound two-component alleles. Allelic and genotypic frequencies differed widely in different habitats in correlation with eight of nine factors of the physical environment. Discrete log-linear multivariate analyses revealed statistically significant associations among alleles of Rrn1 and Rrn2. It was concluded that natural selection acting differentially on various rDNA alleles plays a major role in the development and maintenance of observed patterns of molecular and genetic organization of rDNA variability.

Genetic and molecular organization of ribosomal DNA (rDNA) variants in wild and cultivated barley.

Twenty rDNA spacer-length variants (slvs) have been identified in barley. These slvs form a ladder in which each variant (with one exception) differs from its immediate neighbors by a 115-bp subrepeat. The 20 slvs are organized in two families, one forming an eight-step ladder (slvs 100-107) in the nucleolus organizer region (NOR) of chromosome 7 and the other a 12-step ladder (slvs 108a-118) in the NOR of chromosome 6. The eight shorter slvs (100-107) segregate and serve as markers of eight alleles of Mendelian locus Rrn2 and the 12 longer slvs (108a-118) segregate and serve as markers of 12 alleles of Mendelian locus Rrn1. Most barley plants (90%) are homozygous for two alleles, including one from each the 100-107 and the 108a-118 series. Two types of departures from this typical pattern of molecular and genetic organization were identified, one featuring compound alleles marked by two slvs of Rrn1 or of Rrn2, and the other featuring presence in Rrn1 of alleles normally found in Rrn2, and vice versa. The individual and joint effects on adaptedness of the rDNA alleles are discussed. It was concluded that selection acting on specific genotypes plays a major role in molding the strikingly different allelic and genotypic frequency distributions seen in populations of wild and cultivated barley from different ecogeographical regions.

Effects on adaptedness of variations in ribosomal DNA copy number in populations of wild barley (Hordeum vulgare ssp. spontaneum).

Twenty alleles, 12 at Mendelian locus Rrn1 and 8 at locus Rrn2, control rRNA genes [ribosomal DNA (rDNA)] variability in barley. These alleles differ strikingly in their effects on adaptedness. In the present study, we determined variation in the copy number of 101 accessions of wild barley plants from 10 ecologically diverse sites in Israel and examined relationships between rDNA copy number and adaptedness. The average multiplicity of rDNA per haploid genome was 1881 copies and the average numbers of copies for Rrn1 and Rrn2 were 962 and 917, respectively. The total number of copies as well as the number of copies for Rrn1 and Rrn2 varied widely from plant to plant within sites and also from site to site. The predominant allele of Rrn2 had somewhat more copies on the average than the other alleles of this locus but differences between the predominant allele and other alleles of Rrn1 were not statistically significant. Overall, the results indicated that differing amounts of rDNA resulting from variations in copy number and/or number of subrepeats in the intergenic spacer region were not closely associated with adaptedness. This suggests that the high adaptedness of a few specific alleles results in large part from adaptatively favorable nucleotide sequences in the transcription units and/or the intergenic spacer regions of the favored alleles--i.e., that adaptedness in barley depends on the quality more than on the quantity of rDNA present.

Superstructure of the Drosophila ribosomal gene family.

Determining the spatial organization of middle repetitive DNA has proven difficult for several reasons. Repeated arrays are often so large that molecular methods alone cannot resolve their organization, and the lack of phenotypic markers within arrays limits the value of classical genetic analysis. We have characterized the superstructure of one repeated gene family, the ribosomal gene family of Drosophila melanogaster, by a combination of recombinational and molecular analyses of spacer-length variants. The resulting genetic maps demonstrate that some spacer variants are widely dispersed, while others are limited in their distribution. Moreover, exchange among ribosomal DNA (DNA encoding rRNA) arrays was often unequal, leading to a prediction of little or no relationship between physical location in an array and relatedness of gene family members. Extensions of our procedure may be generally useful for mapping the superstructure of repetitive DNA.

The genetics of host-pathogen coevolution: implications for genetic resource conservation.

The results of long-term studies of coevolution in the Hordeum vulgare-Rhynchosporium secalis pathosystem are summarized. The genetic systems of barley (host) and R. secalis (pathogen) are complementary: Gene-for-gene interactions among loci affect many traits, leading to self-regulating adjustments over generations between host and pathogen populations. Different pathotypes differ widely in their ability to damage the host, and different host-resistance alleles differ widely in their ability to protect the host from the pathogen. Among 29 resistance loci in the specific host population studied, several played major roles in providing stable resistance, but many had net detrimental effects on the yield and reproductive ability of the host. Resistance alleles that protected against the most damaging pathotypes increased sharply in frequency in the host populations. It is concluded that the evolutionary processes that take place in genetically variable populations propagated under conditions of cultivation can be highly effective in increasing the frequency of desirable alleles and useful multilocus genotypes. This enhances the value of the evolving populations as sources of genetic variability in breeding for disease resistance and other characters that affect adaptedness.

Worldwide pattern of multilocus structure in barley determined by discrete log-linear multivariate analyses.

Data from the electrophoretic assay for seven enzyme loci of 1,032 accessions of cultivated barley, Hordeum vulgare L., from the USDA world barley collection were analyzed for multilocus structure using discrete log-linear multivariate techniques. Three major steps were involved in the analysis: (i) identification and elimination of terms that have inconsequential effects in multilocus association; (ii) construction of a log-linear model that best describes the complete multilocus structure of the genetic system; and (iii) evaluation of each of the association terms included in the model. The results of analyses of two subsets of loci show that the multilocus genetic system of cultivated barley, including loci located on different chromosomes, is organized into hierarchically structured complexes of loci. Multilocus structure differs in various geographical regions of the world. The structure of barleys from Southwest Asia, the putative center of origin for cultivated barley, is intermediate for both subsets of loci. Differences increased progressively across the Eurasian-African landmasses in each direction with increasing distance from Southwest Asia, with the consequence that the barleys from West Europe, East Asia, and Ethiopia are maximally different from those of Southwest Asia and Middle South Asia.

Genetic variability for pathogenicity, isozyme, ribosomal DNA and colony color variants in populations of Rhynchosporium secalis.

Samples of Rhynchosporium secalis were collected from two experimental barley populations known to carry a diverse array of alleles for resistance to this fungal pathogen. Classification of 163 isolates for four putative isozyme systems, a colony color dimorphism and 20 ribosomal DNA restriction fragment length variants revealed 49 different multilocus phenotypes (haplotypes). The six most common haplotypes differed significantly in pathogenicity. Genetic analyses of the data indicated that effective population sizes of the fungus were very large, that the effects of genetic drift were small, and that negligible recombination occurred in the populations studied. Frequency dependent selection was suggested as an explanation for the maintenance of variation in pathogenicity in the fungus.

Allelic and genotypic composition of ancestral Spanish and colonial Californian gene pools of Avena barbata: evolutionary implications.

Spanish explorers and colonists inadvertently started a massive experiment in evolutionary genetics when they accidentally introduced Avena barbata to California from Spain during the seventeenth and eighteenth centuries. Assays of the Spanish and Californian gene pools of this species for 15 loci show that the present day Spanish gene pool, particularly that of Southwestern Spain, is identical or virtually identical to that of California for five loci and closely similar for nine loci. Despite their similar allelic and single-locus genotypic compositions, the present-day Spanish and Californian gene pools are differently structured on a multilocus genetic basis. Evolutionary implications of these results are discussed.

Coevolution of host and pathogen populations in the Hordeum vulgare-Rhynchosporium secalis pathosystem.

Isolates of Rhynchosporium secalis collected from two experimental barley populations were scored for putative isozyme, colony color, and virulence loci. Allelic frequencies, multilocus haplotype frequencies, and multilocus genetic structure differed in the two populations of R. secalis; haplotypes also differed widely from each other in virulence. The average virulence of isolates collected from the more resistant host population was greater than the average virulence of the isolates collected from the less resistant host population; also the least virulent haplotype, which made up 19% of the pathogen population collected from the less resistant host population, accounted for only 0.3% of the isolates collected from the more resistant host population. It was concluded that the genetic systems of the barley host and fungal pathogen interacted in a complementary fashion and that the genetic structures of both the host and pathogen populations were shaped by coevolutionary processes featuring interactions among loci affecting many different traits, including interactions among host resistance genes and pathogen virulence genes.