A. H. D. Brown

Plant population genetics, breeding, and genetic resources

A resource for students and research workers in population genetics, molecular evolution, evolutionary biology, ecological genetics, forestry and crop improvement.

Enzyme polymorphism in plant populations

Abstract This review encompasses a decade of studies of enzyme polymorphism in plant populations, in the light of both general theory and specific, simplified models. The patterns of the observed frequency of heterozygotes, compared with panmictic expectations adjusted only for inbreeding, are summarised for 23 outbreeding and 7 inbreeding plant species. There is a trend for outbreeders to show less heterozygosity than expected, and inbreeders to show more, despite the contrary evolutionary pressures on the mating system (the so-called heterozygosity paradox). An annual life cycle and pollination by animal vectors seem to increase the discrepancy in outbreeders. Of the several forces which might account for this paradox, the effects of intense microgeographic differentiation, of low gene flow, of self compatibility and of overdominance of linked segments are predominant. The evidence indicates that inbreeding plant species show more intense geographic and microgeographic differentiation, and more intense multilocus associations than outbreeders. Recent attempts to describe selection operating on variants by the analysis of life cycle components, of physiological processes, and of genetic demography are discussed. The fundamental importance of mating systems and their variation, as a distinctive feature of plant populations is already clear from the studies in hand. Therefore a closer integration of the joint microevolution of mating systems, and of genetic variation is required in both theoretical and experimental studies.

The conservation of plant biodiversity

Preface Part I. Introduction: 1. The biological system of conservation Part II. Diversity and Conservation of Plant Genes: 2. The genetic diversity of wild plants 3. The genetic diversity of cultivated plants 4. The conservation of cultivated plants Part III. Conservation of Plant Species: 5. Plant species conservation and population biology 6. The conservation in situ of useful or endangered wild species 7. Ex situ conservation of threatened and endangered plants Part IV. Conservation of Plant Communities: 8. Community structure and species interactions 9. Choosing plant community reserves 10. Managing plant community reserves 11. Conclusions References Index.

Isozymes, plant population genetic structure and genetic conservation.

SummaryThe exploration, conservation and use of the genetic resources of plants is a contemporary issue which requires a multidisciplinary approach. Here the role of population genetic data, particularly those derived from electrophoretic analysis of protein variation, is reviewed. Measures of the geographic structure of genetic variation are used to check on sampling theory. Current estimates justify the contention that alleles which have a highly localised distribution, yet are in high frequency in some neighbourhoods, represent a substantial fraction of the variation. This class, which is the most important class in the framing of sampling strategies, accounts for about 20–30% of variants found in 12 plant species. The importance of documenting possible coadapted complexes and gene-environment relationships is discussed. Furthermore, the genetic structure of natural populations of crop relatives might suggest the best structure to use in the breeding of crops for reduced vulnerability to pest and disease attack, or for adaptation to inferior environments. The studies reported to date show that whilst monomorphic natural populations do occur, particularly in inbreeding colonisers, or at the extreme margins of the distribution, polymorphism seems to be the more common mode. It is stressed here that the genetic resources of the wild relatives of crop plants should be systematically evaluated. These sources will supplement, and might even rival, the primitive land races in their effectiveness in breeding programmes. We may look forward to a wider application of gel electrophoresis in the evaluation of plant genetic resources because this technique is currently the best available for detecting genetic differences close to the DNA level on samples of reasonable size.

The use of plant genetic resources.

Preface Acknowledgements Part I. Role of Genetic Resource Collections in Research and Breeding: 1. Germplasm collections and the public plant breeder K. S. Gill 2. Germplasm collections and the private plant breeder J. S. C. Smith and D. N. Duvick 3. Germplasm collections and the experimental biologist R. G. Palmer Part II. Use of Collections: 4. International use of a sorghum germplasm collection K. E. Prasada Rao, M. H. Mengesha and V. G. Reddy 5. Current use of potato collections J. G. Th. Hermsen 6. Use of collections in cereal improvement in semi-arid areas J. P. Srivastava and A. B. Damania 7. Limitations to the use of germplasm collections D. R. Marshall Part III. Size and Structure of Collections: 8. The case for large collections T. T. Chang 9. The Case for core collections A. H. D. Brown 10. The role of networks of dispersed collections P. M. Perret Part IV. Evaluation: 11. Characterisation and evaluation of okra S. Hamon and D. H. van Sloten 12. Evaluation of cereals in Europe G. Fischbeck 13. Evaluatling the germplasm of groundnut (Arachis hypogaea) and wild Arachis species at ICRISAT J. P. Moss, V. Ramanatha Rao and R. W. Gibbons 14. Practical considerations relevant to effective evaluation J. T. Williams 15. Principles and strategies of evaluation O. H. Frankel Part V. Wild Relatives of Crops: 16. Collection strategies for the wild relatives of field crops C. G. D. Cahpman 17. Wild relatives as sources of disease resistance J. J. Burdon and A. M. Jarosz 18. Ecological and genetic considerations in collecting and using wild relatives G. Ladizinsky Part VI. Technological or Scientific Innovations that Affect the use of Genetic Resources: 19. In vitro conservation and germplasm utilisation L. A. Withers 20. Screening for resistance to diseases P. H. Williams 21. Restriction fragments as molecular markers for germplasm evaluation and utilisation R. Bernatsky and S. D. Tanksley 22. Molecular biology and genetic resources W. J. Peacock Index.

Outcrossing rates and heterozygosity in natural populations of Hordeum spontaneum Koch in Israel

SummaryThe extent of cross-pollination was estimated quantitatively in 26 populations of wild barley (H. spontaneum) in Israel, using allozyme variation at 22 polymorphic loci. Individual population estimates varied from 0 to 9·6 per cent outcrossing. The overall average was 1·6 per cent, with a 95 per cent confidence range of 0·8-2·7 per cent. The evidence indicated that outcrossing was significantly higher in populations growing in the more mesic (2·1 percent), than in the xeric regions (0·4 per cent). The average frequency of multilocus homozygosity for the 22 loci was 0·963 which was in agreement with the level expected under the observed high rate of self-fertilisation, indicating no heterozygous excess. However, the heterozygotes encountered, displayed a very high degree of multiple heterozygosity which arises from extensive gametic phase (or linkage) disequilibrium. In general, these results do not support the contention that the bulk of the genetic polymorphism found in H. spontaneum in Israel has arisen in recent times by periodic introgression from cultivated barley (H. vulgare L.). Rather they indicate that extensive genetic polymorphisms probably predates the domestication of the crop, and is maintained independently of introgression.

A global perspective of the richness and evenness of traditional crop-variety diversity maintained by farming communities

Varietal data from 27 crop species from five continents were drawn together to determine overall trends in crop varietal diversity on farm. Measurements of richness, evenness, and divergence showed that considerable crop genetic diversity continues to be maintained on farm, in the form of traditional crop varieties. Major staples had higher richness and evenness than nonstaples. Variety richness for clonal species was much higher than that of other breeding systems. A close linear relationship between traditional variety richness and evenness (both transformed), empirically derived from data spanning a wide range of crops and countries, was found both at household and community levels. Fitting a neutral “function” to traditional variety diversity relationships, comparable to a species abundance distribution of “neutral ecology,” provided a benchmark to assess the standing diversity on farm. In some cases, high dominance occurred, with much of the variety richness held at low frequencies. This suggested that diversity may be maintained as an insurance to meet future environmental changes or social and economic needs. In other cases, a more even frequency distribution of varieties was found, possibly implying that farmers are selecting varieties to service a diversity of current needs and purposes. Divergence estimates, measured as the proportion of community evenness displayed among farmers, underscore the importance of a large number of small farms adopting distinctly diverse varietal strategies as a major force that maintains crop genetic diversity on farm.

Genetic diversity and environmental associations of wild wheat, Triticum dicoccoides, in Israel

SummaryAllozyme variation in the tetraploid wild progenitor of wheat, Triticum dicoccoides, was studied for the proteins encoded by about 50 gene loci in 457 individuals representing 12 populations from Israel. Six spikelet morphological traits were measured in the same populations. The results indicate that: (a) 16 loci (= 32%) were monomorphic in all 12 populations, 15 loci (= 30%) were locally polymorphic, and 19 loci (= 38%) were regionally polymorphic. All polymorphic loci (but one) displayed high levels of polymorphism (≧ 10%). In Israel, the proportion of polymorphic loci per population, P, in wild wheat averaged 0.25 (range, 0.16–0.38), and the genetic diversity index, He averaged 0.07, (range, 0.03 – 0.12). (b) Altogether there were 110 alleles at the 50 putative loci tested (c) Genetic differentiation of populations included regional and local patterns: (i) The coefficients of genetic distance between populations were high (mean D = 0.10 range, 0.02 – 0.25), and indicated sharp genetic differentiation over short distances, (ii) Common (≧ 10%) but sporadic and localized alleles were frequent (76%), and (iii) Rare alleles were few (only 5 alleles). (d) The patterns of allozyme and spikelet variation in the wild gene pool were significantly correlated with, and partly predictable by, water factors, including those of precipitation, evaporation, and relative humidity as well as of soil type, (e) All six spikelet characters showed statistically significant variation among localities and (f) Allozymic variation was correlated with spikelet variation.These results suggest in T. dicoccoides: (i) the operation of natural selection in population genetic structure, (ii) local adaptive genetic differentiation caused by diversifying selection through climate and soil, and (iii) the guidelines for sampling these resources for use in wheat breeding programs.

Sample sizes required to detect linkage disequilibrium between two or three loci.

Abstract Estimates of the degree of nonrandom association among genes (linkage disequilibrium) can provide evidence of the role of natural selection in maintaining allozyme polymorphisms in natural populations. This paper outlines the maximum likelihood procedures for such estimates based on gametic or zygotic frequencies at the level of two loci. The analysis is extended to estimating disequilibrium between three loci. In particular, the question of the sampling requirements to detect different intensities of disequilibrium is considered. It is found that relatively large samples are required to detect nonrandom association, unless gene frequencies are intermediate and disequilibrium is relatively intense. This might be one reason why cases of linkage disequilibrium have so far proved to be the exception, rather than the rule, in population studies.

Internal transcribed spacer repeat‐specific primers and the analysis of hybridization in the Glycine tomentella (Leguminosae) polyploid complex

Polyploid and diploid hybridization is a ubiquitous and evolutionarily important phenomenon in the plant world. Determining the parental species of a hybrid, however, is difficult. Molecular markers such as the nuclear ribosomal DNA gene complex, particularly its internal transcribed spacer (ITS) region, have proved powerful in determining hybrid parentage. In some cases, population and genomic phenomena, such as genetic drift and concerted evolution, result in the loss of all or many of the tandemly repeated copies derived from one parental species, making the recovery of hybrid history difficult or impossible. Methods such as direct sequencing and cloning are typically used to find ITS sequences contributed from parental species, but are limited in their ability to detect rare repeat types. Here we report that repeat‐specific polymerase chain reaction primers can recover rare parental ITS sequences in the Glycine tomentella polyploid complex. In three allopolyploid lineages of this complex, repeat‐specific primers reliably detected rare repeats that both direct sequencing and the screening of many cloned sequences failed to detect. Other strategies, such as the use of exclusion primers, may detect rare parental repeat types in hybrids when previous hypotheses regarding the second parental species are lacking.