New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology

Abstract

Welcome to this, the first special issue of the Plant Biotechnology Journal devoted to one specific area of plant biotechnology. In this issue, we have responded to you, our readers, and devoted an entire issue to the subject of single nucleotide polymorphism (SNP) discovery and high-throughput genotyping in crops. This area is sufficiently important for its own special issue for two reasons: first, SNPs define the individual or variety; and second, SNPs, when present in genes (as alleles), determine how the individual interacts with the environment. It is, of course, this interaction, in the form of yield, disease resistance and product quality, which is important to the plant breeder and farmer. Although molecular markers were first discovered in the 1920s with the use of isoenzymes, they were employed only infrequently until the late 1980s, when the use of restriction fragment length polymorphisms (RFLPs) became widespread within plant breeding companies, such as Pioneer and Garst Seeds. With the advent of commercial molecular breeding, molecular geneticists endeavoured to develop cheaper and more efficient tools to tag those regions of the genome associated with agronomic traits. Hence, since their discovery, RFLPs, randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLPs) and microsatellites have, at one time or another, all been the focus of much attention (and expense). Many of these marker systems are still in active use for those species which, unlike humans, are limited by a lack of funds and/or resources. Each of these marker types, including isoenzymes, has one thing in common: they are all underpinned by differences in the DNA sequence of the individuals being screened. It is this obvious fact that was bound to lead, eventually, to the use of SNPs as the marker system of choice. The use of SNPs as the marker of choice is obvious when one considers their high frequency and ability to be automatically processed. However, although in humans and other well-resourced species, SNPs are the marker of choice, their use in most plants has been limited. Why is this the case? First, there are the cost implications of developing and using SNPs; and second, the development of SNPs in plants is complicated by the presence (in polyploid crops) of homoeologues, i.e. non-allelic versions of genes residing on homoeologous chromosomes. The cost implications of the development of SNPs have been directly related to the requirement for high-quality sequence data from several varieties, and hence are directly related to the costs of sequencing and data analysis. The issue relating to homoeologues has, until recently, appeared to be insurmountable. The impact of this ‘polyploidy problem’ on SNP discovery and utilization is clear to see when one remembers that, in diploid barley, there are several thousand SNPs, which are now being used to great effect and are, as a consequence, revolutionizing barley genetics and breeding, whereas, in allohexaploid wheat, the routine use of SNPs (in wheat breeding) has been limited to a handful of genes important to the breeder, such as the high-molecular-weight glutenins. In this issue, we have gathered together eight articles which, between them, address the issues surrounding the discovery, development and use of SNPs in rice, barley, oilseed rape, sugarcane and wheat. It is interesting to note that all of the articles that describe the discovery and development of SNPs utilize either bioinformatics or next-generation sequencing platforms to improve the speed and efficiency of SNP discovery. We, at the Plant Biotechnology Journal, see these technical advances as the first step towards complete SNP maps of all the important crop plants, including those with complex genomes, such as wheat. In the remaining papers of this special issue, the authors present possible methodologies for the use of SNPs via cost-effective, high-throughput genotyping. Of significant interest is the fact that two of these articles demonstrate the use of SNPs to genotype hexaploid wheat and one the even more highly polyploid sugarcane. The Plant Biotechnology Journal hopes to publish more articles on the subject of SNPs and high-throughput genotyping in the coming months and years.