Marker‐Assisted Crop Breeding

Abstract

Molecular genetic markers are tools that provide an opportunity to assist crop breeders in the development of new cultivars. They can be used as a proxy for costly or difficult‐to‐phenotype traits, enabling the screening of germplasm in a more efficient and robust way. The approach of using molecular markers in breeding programs is not new, and the key aim when developing such markers is to identify loci that are in linkage disequilibrium with the trait of interest. However, interesting developments in the technology underpinning contemporary crop genetics, such as next‐generation sequencing and high‐density genotyping platforms, can be translated and applied to crop breeding, potentially improving this process.

Key Concepts

  • Genetic loci in linkage disequilibrium with a trait of interest can be used to design molecular markers for breeding.
  • Large numbers of single‐nucleotide polymorphisms (SNPs) enable marker discovery when mapping the trait, with coverage of around one marker per 2 cM to map a trait for marker‐assisted selection (MAS) in crops. A much smaller number can be used for tracking preferred alleles during the breeding process. A denser set of markers than those used in MAS would be needed for genomic selection.

Keywords: linkage disequilibrium; allele; genotyping; introgression; crop breeding

Figure 1. Overview of use of genetic markers for plant breeding.
Figure 2. Genetic marker overview. An alignment of two homologous DNA sequences, for example, gene sequence from two different varieties of a crop, a single base pair change in one sequence relative to the other is described as an SNP (single nucleotide polymorphism). In the example shown, variety 1 has the G allele of the SNP and variety 2 the C allele. Their bi‐allelic nature makes SNP genotype calling relatively easy compared to other marker systems and also amenable to multiplexing, so that a single DNA source can be genotyped for multiple SNPs in a single reaction. For these reasons, SNPs are the predominant marker system of choice in current crop‐breeding programmes. A number of different techniques are available for the identification of SNPs, but they vary widely with respect to the cost, bioinformatic processing and the generic/targeted nature of the SNP identified.
Figure 3. Linkage disequilibrium. (a) Linkage equilibrium and disequilibrium of five loci (1–5) in six accessions, represented by horizontal black lines. At each locus, two alternative alleles are present, illustrated by the same shape highlighted in different colours. (b) Extent of pairwise linkage disequilibrium (LD) along barley chromosome 2H between loci in an elite barley cultivar. The white horizontal bar at the top represents genetic map of chromosome 2H, with the genetic marker location indicated by vertical lines. In the genetic centromere, these markers are closer together due to lower rates/lack of recombination, and this translates into higher rates of LD. A colour scale of blue (no LD), yellow (moderate levels of LD) through to red (complete LD) is used. (c) Matrix of pair‐wise LD for several genes between elite barley cultivars and barley landraces. Above the diagonal line are the R2 values; P values are below the diagonal line. A key to the colour scale used is provided, but it is clear that levels of LD are much lower in the barley landraces than the elite cultivars. Adapted from Caldwell et al. (2006) © Genetics Society of America.
Figure 4. Using molecular markers to assist in the introgression of a section of donor accession (in blue, B) genome into a recipient accession (in white, A) using repeated backcrosses (BC) to the recipient accession. The first four BC generations are illustrated; however, in practice more are often used. The percentage contribution of each accessions genome to each generation is provided in black boxes, and the phenotypic state for the trait of interest is represented as white for recipient phenotype, and blue for individuals with the donor phenotype. At each generation, the accession that is homozygous for the trait of interest, circled in red, is crossed back to the recipient accession A. The amount of the donor accession genome introgressed decreases by 50% in every generation (backcross). After each BC, markers (1 and 2) that have been designed to flank the required introgression can be used to screen the progeny to identify which contain the donor introgression.
Figure 5. Schematic of the use of bulked segregant analysis to identify loci that could be used to develop genetic markers for marker assisted breeding. This figure illustrates a low‐throughput scenario using a SNP‐based genotyping platform and NGS data, in this case RNA‐seq, to identify regions of the genome suitable for marker development for the trait of interest. The example included here for RNA‐seq is oversimplified; this approach would identify multiple putative candidates that would need to be validated.
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Further reading

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Houston, Kelly, Russell, Joanne, Ramsey, Luke, Bull, Hazel, Thomas, Bill, and Waugh, Robbie(May 2016) Marker‐Assisted Crop Breeding. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023711]