Plant molecular diversity and applications to genomics

doi:10.1016/S1369-5266(02)00238-8

Current Opinion in Plant Biology

Volume 5, Issue 2, 1 April 2002, Pages 107-111

https://doi.org/10.1016/S1369-5266(02)00238-8 Get rights and content

Abstract

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.

Introduction

Surveys of nucleotide diversity provide a snap shot of evolution at its most basic level. This nucleotide diversity reflects a rich history of selection, migration, recombination, and mating systems. Additionally, the nucleotide diversity across a genome is the source of most of the phenotypic variation.

In the past few years, there has been tremendous progress in studying diversity within plant genomes, particularly those of maize and Arabidopsis. In this review, we describe some of the processes that are shaping diversity within species and across their genomes, and how some of this nucleotide variation can be related to phenotypic variation.

Section snippets

Plant diversity

Molecular diversity has been studied in plants for about three decades. The most comprehensive early studies were done using isozymes [1], which provided many insights into population structure and breeding systems. Although these markers allowed large numbers of samples to be analyzed, comparisons of samples from different species, loci, and laboratories were problematic. More importantly, only a limited number of loci could be scored easily. In the past decade, the focus has shifted to

Dissecting diversity

Across a large genome, such as that of maize, diversity can accumulate so that 150 million sites are commonly polymorphic. A small but important proportion of these polymorphisms is responsible for the complex variation in phenotypic traits. This naturally occurring nucleotide diversity is a treasure trove for investigating and harnessing quantitative variation. To improve crops, it is essential that we sort through this diversity to find the alleles and polymorphisms that are beneficial.

The

Conclusions

High-throughput DNA sequencing allows surveys of nucleotide diversity to be conducted for a wide range of species and loci, and evolutionary questions are starting to be addressed using this wealth of data. Until carefully designed studies of multiple orthologous loci across several species are conducted, our understanding of the processes underlying nucleotide diversity will be limited. Association tests in natural populations are providing an exciting opportunity to simultaneously use

Acknowledgements

We thank Brad Rauh for his help in researching this topic, and Sandra Andaluz, Carlyn Buckler, and Sherry Whitt for commenting on the manuscript. JMT was supported by National Science Foundation grant DBI-9872631.

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

• of special interest
•• of outstanding interest

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View full text

ReviewPlant molecular diversity and applications to genomics

Abstract

Introduction

Section snippets

Plant diversity

Dissecting diversity

Conclusions

Acknowledgements

References and recommended reading

Curr Opin Plant Biol

Am J Hum Genet

Am J Hum Genet

Am J Hum Genet

Allozyme diversity in plant species

Properties of statistical tests of neutrality for DNA polymorphism data

Genetics

Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.)

Mol Biol Evol

DNA polymorphism, haplotype structure and balancing selection in the Leavenworthia PgiC locus

Genetics

High rates of polymorphism and recombination at the Opaque-2 locus in cultivated maize

Mol Gen Genet

Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.)

Proc Natl Acad Sci USA

Molecular diversity, structure and domestication of grasses

Genet Res

The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations

Genetics

Comparing patterns of nucleotide substitution rates among chloroplast loci using the relative ratio test

Genetics

Examining rates and patterns of nucleotide substitution in plants

Plant Mol Biol

Molecular population genetics of floral homeotic loci: departures from the equilibrium-neutral model at the APETALA3 and PISTILLATA genes of Arabidopsis thaliana

Genetics

Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana

Genetics

DNA polymorphism at the cytosolic phosphoglucose isomerase (PgiC) locus of the wild plant Arabidopsis thaliana

Genetics

The effect of deleterious mutations on neutral molecular variation

Genetics

Levels of naturally occurring DNA polymorphism correlate with recombination rate in D. melanogaster

Nature

Species and recombination effects on DNA variability in the tomato genus

Genetics

DNA polymorphism in Lycopersicon and crossing-over per physical length

Genetics

Positive correlation between recombination rates and levels of genetic variation in natural populations of sea beet (Beta vulgaris subsp. maritima)

Genetics

The highly recombinogenic bz locus lies in an unusually gene-rich region of the maize genome

Proc Natl Acad Sci USA

Molecular evolution of the Adh1 locus in the genus Zea

Proc Natl Acad Sci USA

Nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae)

Genetics

Intragenic recombination in the Adh locus of the wild plant Arabidopsis thaliana

Genetics

Intra- and interspecific variation of the alcohol dehydrogenase locus region in wild plants Arabis gemmifera and Arabidopsis thaliana

Mol Biol Evol

Nucleotide sequence diversity at the alcohol dehydrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): an evaluation of the background selection hypothesis

Proc Natl Acad Sci USA

DNA variation in the 5′ upstream region of the Adh locus of the wild plants Arabidopsis thaliana and Arabis gemmifera

Mol Biol Evol

The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia

Genetics

Genetic diversity in Leavenworthia populations with different inbreeding levels

Proc R Soc London B Biol Sci

Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana

Mol Biol Evol

Review
Plant molecular diversity and applications to genomics