ReviewApplications of single nucleotide polymorphisms in crop genetics
Introduction
As more genomes, including those of humans, Arabidopsis and soon rice, are completely sequenced, interest is re-focusing on the discovery and analysis of intraspecific sequence differences. This is particularly evident in research into the human genome, in which over one million single nucleotide polymorphisms (SNPs) (the most common type of sequence differences between alleles) have been catalogued recently. These polymorphisms could be used as simple genetic markers, which may be identified in the vicinity of virtually every gene. There is also great potential for the use of SNPs in the detection of associations between allelic forms of a gene and phenotypes, especially for common diseases that have multifactorial genetics 1., 2.. Very recently, studies of the level of linkage disequilibrium (LD) in human populations revealed that large islands of high LD extend over much larger distances than predicted previously [3••]. This finding suggests that the analysis of SNP haplotypes, rather than of individual SNPs, provides a more effective way of associating alleles with traits.
When working with SNPs, plant scientists could take advantage of the investment in technology development that has already been made by the broader community, especially by the Human Genome Project. Considerable progress has been made in the areas of SNP discovery and SNP assay development, and in the use of haplotype diversity for association mapping. At the same time, plant genomes offer some unique advantages for researchers using SNP-based technologies. The high level of polymorphism of many plant species, such as maize, facilitates SNP identification. Inbred lines, when available, enable direct read-off of haplotypes. Populations that are suitable for high-resolution genetic mapping make the detailed analysis of the relationship between genetic and physical distance relatively straightforward.
In an accompanying review, Buckler and Thornsberry (this issue) discuss recent advances in understanding sequence diversity in higher plants and the factors that influence diversity distribution. Here, we focus on the methodology of SNP discovery, the applications of SNPs in plant genetics and breeding, and some of the implications of recent advances in human association studies for work on higher plants.
Section snippets
SNP discovery
Several different routes to the discovery of SNPs may be taken. These include the re-sequencing of PCR amplicons with or without pre-screening; electronic SNP (eSNP) discovery in shotgun genomic libraries; and eSNP discovery in expressed sequence tag (EST) libraries.
Direct sequencing of DNA segments (amplified by PCR) from several individuals is the most direct way to identify SNP polymorphisms 4., 5.. PCR primers are designed to amplify 400–700 bp segments of DNA, which are frequently derived
SNP assays
Several methods are available for SNP genotyping, which have already been discussed in several reviews 23•., 24•., 25., 26., 27.. The choice of a method for a particular assay depends on many factors, including cost, throughput, equipment needed, difficulty of assay development, and potential for multiplexing. There is intense commercial activity in this area and no dominant assay has emerged yet. Marker-assisted breeding of soybean in a commercial setting has been facilitated by the use of a
SNPs and indels as genetic markers
Numerous types of DNA markers that are based on the indirect detection of sequence-level polymorphism have been developed 28., 29.. Frequently, highly informative simple sequence repeat (SSR) markers are preferred [30]. SSRs are less suitable for association studies, however, because of the occurrence of homoplasy; that is, the occurrence of SSR alleles of identical size but different evolutionary origin 31., 32.. Conversely, it is also likely that SSRs of different size are embedded in
Conclusions
Single nucleotide polymorphisms and indels are an essentially inexhaustible source of polymorphic markers for use in the high-resolution genetic mapping of traits, and for association studies that are based on candidate genes or possibly whole genomes. A better understanding of the distribution of LD and of recombination frequencies along plant chromosomes is needed, especially in crop plants. Much may be learned from the recent progress in this area in human and animal genomics. The rapid
Acknowledgements
I would like to thank Michele Morgante and Ed Buckler for helpful suggestions. Ada Ching and Kelly Palaisa supplied some unpublished data.
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
References (59)
- et al.
Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection
Genomics
(1998) - et al.
Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction
Genomics
(1989) Current methods of mutation detection
Mutat Res
(1993)- et al.
Detection of 81 of 81 known mouse beta-globin promoter mutations with T4 endonuclease VII — the EMC method
Genomics
(1996) - et al.
Single-nucleotide polymorphism analysis by pyrosequencing
Anal Biochem
(2000) Linkage disequilibrium as a gene-mapping tool
Am J Hum Genet
(1995)Linkage disequilibrium and the search for complex disease genes
Genome Res
(2000)Islands of linkage disequilibrium
Nat Genet
(2001)- et al.
Nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae)
Genetics
(1993) - et al.
DNA sequence variation within maize and melon: observations from polymerase chain reaction amplification and direct sequencing
Genetics
(1990)
PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
Nucleic Acids Res
Inference of haplotypes from PCR-amplified samples of diploid populations
Mol Biol Evol
Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize
Proc Natl Acad Sci USA
Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography
Genome Res
Detection of single-nucleotide polymorphisms with the WAVE(tm) DNA fragment analysis system
Genetic Testing
Detection of polymorphisms of human DNA by gel electrophoresis as single-strand conformation polymorphisms
Proc Natl Acad Sci USA
Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases
Nat Genet
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
Nature
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Nature
Mining single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) databases
Genome Res
Identification of candidate coding region single nucleotide polymorphisms (cSNPs) using assembled expressed sequence tags (ESTs)
Genome Res
Reliable identification of large numbers of candidate SNPs from public EST data
Nat Genet
Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies
Clin Chem
Automation in genotyping single nucleotide polymorphisms
Hum Mutat
High-throughput genotyping assay approaches
Pharmacogenomics
Discovery and application of single nucleotide polymorphism markers in plants
Plant genotyping based on analysis of single nucleotide polymorphisms using microarrays
Cited by (843)
Development of polymorphic simple sequence repeat markers in Agastache rugosa and their application in genetic evaluation and cross-taxon transferability of Agastache species
2024, Journal of Applied Research on Medicinal and Aromatic PlantsAssessment of the genetic diversity in plants using molecular markers: a review and perspective
2024, Tropical AgricultureGenomic Selection in Animal Breeding
2024, BIO Web of ConferencesKappa-Casein Gene (CSN3) Polymorphisms Detection in Three Indigenous Iraqi Goat Breeds, Using PCR-RFLP and SNP Markers
2024, Egyptian Journal of Veterinary Science(Egypt)