Molecular Markers


Our lab started to develop molecular markers linked to economic traits in beans in 1990 when Dr. Phillip Miklas joined the lab as a post doctoral scientist. The marker of choice at that time was RAPD marker(s) and we were able to ‘tag’ the first gene for rust resistance in common bean with a RAPD marker. That work expanded to tagging other genes conditioning resistance to rust, anthracnose, and bean common mosaic virus. All these pathogens are controlled by major genes and finding linked markers became routine. The approach taken differed from that used in other crop species where the goal was to develop genetic linkage maps. Genetic populations such as NILs were developed to allow us to specifically tag a gene in the absence of a saturated genetic map. Other approaches such as segregant bulk analysis improved that effort. Both coupling and repulsion phase markers were identified and differences in efficiency between these types in marker-assisted selection (MAS) was documented. As the technology was refined, the RAPD markers were converted to SCAR markers and many of these SCAR markers have been widely used in other labs for MAS. The availability and easy-use of molecular markers encouraged bean breeders to use this technology and allowed for the selection of resistance traits in the absence of the pathogen. The molecular markers were also used to expand the bean genetic linkage map and permitted the mapping of many of the resistance genes and the discovery of resistance gene clusters controlling major pathogens. This work has been published and summarized in a series of review articles by the same authors in 1995, 1998, 2003, 2004 and 2006 and the SCAR markers  linked to wide range of resistance genes.

As the science advanced to a genotypic analysis of quantitative traits (QTL analysis), new marker systems that provided broader genomic coverage were deployed in common bean. These included AFLP, TRAP, SRAP and microsatellite or SSR markers. Many QTL associated with disease resistance, yield and quality were detected using these marker systems. However many QTL were minor in effect and their utilization was suspect in different genetic backgrounds and/or environments. In addition, the lack of adequate level of polymorphic markers between highly related bean breeding materials greatly limited the use of MAS in bean breeding except for major gene traits. Most mapping studies involved inter gene pool crosses that were too diverse for use in bean breeding. Overall QTL analysis of quantitative traits has not been widely deployed in bean breeding and is reflected bysimilar experiences in other crops.

Current advances in bean genomics and the availability of bean sequence information from the sequencing of the bean genotype G19833 are providing exciting new marker systems for bean breeding. The BeanCAP project is developing SNP markers and a 6K SNP chip is expected to be available in 2011. In addition, colleagues at NDSU are developing Indel markers with good genomic coverage. They are selecting markers with a minimum fragment length difference of 10bp that are polymorphic within different bean market classes. Since bean breeders are used to working with SCAR markers these Indel markers are ‘breeder-friendly’ since they can be run in small labs on agarose gels and are easily scored without the need for chemical staining. These new marker systems under development for common bean are more abundant in the genome and will be more polymorphic than the markers previously used a decade ago. In addition, these markers are more robust since they are likely to be more close to or within the gene rather than linked at some distance from the gene of interest. Having polymorphic markers available within commercial bean market classes where most breeding and selection work is conducted will enhance the use of MAS to speed up the selection process and provide opportunities for gene pyramiding. The close synteny with soybean will continue to provide new opportunities to locate genes of interest that are not easily detected in common bean.


Select References:

Kelly, J.D. 1995. Use of Random Amplified Polymorphic DNA markers in breeding for major gene resistance to plant pathogens. HortScience 30:461-465.
Kelly, J.D., and P.N. Miklas. 1998. The role of RAPD markers in breeding for disease resistance in common bean. Molecular Breeding 4:1-11.
Kelly, J.D., P. Gepts, P.N. Miklas, and D.P. Coyne. 2003. Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crops Research 82:135-154.
Kelly, J.D. and V. A. Vallejo. 2004. A comprehensive review of the major genes conditioning resistance to anthracnose in common bean. HortScience 39:1196-1207.
Miklas, P.N., J.D. Kelly, S.E. Beebe, and M. W. Blair. 2006. Common bean breeding for resistance against biotic and abiotic stresses: From classical to MAS breeding. Euphytica 147:105-131.


Table 1. Markers Types & Abbreviations

RAPD -           Randomly Amplified PolymorphicDNA
SCAR -     Sequence Characterized Amplified Regions
AFLP -        Amplified Fragment Length Polymorphism
TRAP -   Target Region Amplification Polymorphism
SRAP -            Sequence-Related Amplification Polymorphism
SSR -       Simple Sequence Repeats, aka Microsatellites
SNP - Single Nucleotide Polymorphism
InDel -             Insertion-Deletion
QTL -              Quantitative Trait Loci
NIL -               Near-Isogenic Line
MAS -             Marker-Assisted Selection