A Genome Wide Association Study Biology Essay


Common bean (Phaseolus vulgaris) belongs to the family Fabacaea and is related to such legume species as Glycine max (soybean) and Vigna unguiculata (Cowpea) from which it diverted 18 and 4.9 MYA respectively. The diploid number for Phaseolus is 22. (Stefanovic et al, 2009)

The genus Phaseolus originated from Central America in Ecuador and P. vulgaris is the most important cultivated species. The other related species are P. coccineus (scarlet runner), P. acutifolius (tepary bean) P. polyanthus and P. lunatus. The species P. vulgaris is divided into two gene pools; Andean and Middle American depending on the growth habit, seed type and reproductive isolation. (Gepts et al, 1986). The Andean gene pool has large seeded market classes which are further subdivided into three races containing kidney and cranberry beans while the Middle American gene pool is composed of medium and small seeded beans. (Papa and Gepts, 2003).

Common bean is a very important legume food crop. It is an important source of dietary protein in most developing countries and its consumption is promoted in developing countries to combat chronic illness like diabetes, heart disease and obesity (Broughton et al, 2003). Current production is estimated at 6 MT in the Americas and is much lower (2.1 MT) in other parts of the world like Africa. (Miklas and Singh, 2007). Production is hindered by many factors which include both biotic and abiotic stresses. The most important diseases in dry bean are common bacterial blight, anthracnose, bean common mosaic virus, fusarium wilts, angular leaf spot, rusts and white mold. White mold has been ranked as most limiting factor to bean production in the Midwest.


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White mold is caused by the fungus Sclerotinia sclerotiorum which is a soil born pathogen. It is an ascomycete that persists in the soil for up to 5 years through its resting structures called sclerotia. (Bolton et al, 2006). The disease causes yield losses ranging from 20-80% in particularly bad years such that disease management requires an intergrated approach. Agronomic practices that help control white mold in the field involve reducing the efficiency of sclerotia and ascospore germination by controlling humidity. High moisture within the plant canopy creates a favorable microclimate for ascospore germination such that increasing plant and row spacing helps in managing the disease. This however may not always economically feasible. Timing irrigations to allow drying of plant canopy and avoiding excessive irrigation during flowering and after petal drop also reduces disease severity (Schwartz, 1987).

The use of resistant varieties of beans is the most economical and effective way of controlling the disease. Resistance to white mold is known to be complexly inherited (Fuller et al., 1984). When crosses are made between resistant and susceptible cultivars the progeny exhibit continuous variation indicating that trait is controlled by many genes and is affected by environmental conditions. There are no common bean lines with complete resistance but moderate levels of resistance to white mold have been identified in common bean (Kolkman and Kelly, 2002; Miklas and Grafton, 1992). The moderate levels of resistance are usually affected by plant morphological avoidance mechanisms (Kolkman and Kelly, 2002; Miklas et al., 2001).

Mapping for Resistance

To expedite germplasm enhancement and cultivar development marker assisted selection (MAS) has been incorporated in efforts to breed for white mold resistance. MAS involves scoring indirectly for the presence or absence of a desired phenotype or phenotypic component based on the sequences or banding patterns of molecular markers located in or near the genes controlling the phenotype. Since phenotypic disease scoring for white mold is confounded by plant architecture and environment in the field, MAS offers an efficient and reliable way to separate avoidance from genetic resistance through tagging genes or genomic regions that are associated with physiological resistance.

Quantitative trait loci (QTL) analysis relies on the differences among the trait means of genotypes at a marker locus, based on the principle of association between the phenotype and genotype of markers. Several QTL studies have been conducted on different genetic backgrounds; using different marker systems to identify white mold resistance in beans. The RIL populations developed for QTL identification in dry beans have used several sources of white mold resistance PC-50 (pompadour bean), NY6020-4 (snap bean), Bunsi (navy bean) and G122 (cranberry bean) and some wild and landrace lines. Mutiple QTL have been identified in different pedigree populations explaining variation ranging from 5 to 38% of observed phenotypes. Soule et al, 2011 summarized the QTL on an integrated linkage map consisting mostly of SSR AFLP and RAPD markers. Some of the markers associated with the QTL have been validated in an independent study in snap beans (Chung et al., 2008). However QTL mapping is coarse and results in low resolution maps that do not result in efficient selection when associated markers are used for MAS. It is also difficult to identify underlying candidate genes from QTL linkage maps due to long cM distances between adjacent markers.

Genome wide association mapping

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Association mapping (AM) is a relatively new and promising approach for the dissection of complex traits in plants. It offers higher resolution mapping through the exploitation of historical recombination events at the population level and can enable gene level mapping.The concept of linkage disequilibrium is the basis of this mapping and it can be defined as the non-random co-segregation of alleles at two loci. Genome wide association studies can be used to localise causative genes with minor effects within populations of unrelated individuals. This is due to the concept that chromosomes from unrelated individuals in a population are likely to be more distantly related than those sampled from members of traditional pedigrees in mapping populations. In other words, the time to most recent common ancestor of any given two individuals from a population of unrelated individuals would be greater than that of a pedigree population. Association mapping is well suited for fine-scale mapping because there are more opportunities for recombination to take place over several generations, between many alleles, in a species, while there can be only a few generations of recombination present in pedigree populations. When recombination occurs it leads to rearrangement of the chromosomal segments into smaller pieces. This will lead to reduction of the LD in short distances around loci, and lead to significant co-occurrence (i.e. LD) between only loci physically close, allowing high resolution. Whereas pedigree studies work with recombination events in few generations that enable exchange between chromosomes at the order of megabases, association studies deal with segmental exchanges measured in kilobases.

Bolton, M. D., Thomma, B. P. H. J. and Nelson, B. D. (2006), Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen. Molecular Plant Pathology, 7: 1-16. doi: 10.1111/j.1364-3703.2005.00316.x

Miklas, P.N., and Singh S.P (2007). Common bean. p. 1-31. In C. Kole (ed.) Genome mapping and molecular breeding in plants. Vol. 3. Pulses, sugar and tuber crops. Springer, Berlin.

Stefanović S, Pfeil BE, Palmer JD, Doyle JJ. (2009) Relationships among phaseoloid legumes based on sequences from eight chloroplast regions. Systematic Botany, 34:115-128.

Gepts P, Osborn TC, Rashka K, Bliss FA (1986) Phaseolin-protein variability in wild forms and landraces of common bean (Phaseolus vulgaris): Evidence of multiple centres of domestication. Econ Bot 40:451-458

Papa R, Gepts P (2003) Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica. Theor. Appl. Genet. 106:239250

Broughton WJ, Hernández G, Blair M, Beebe S, Gepts P, Vanderleyden J. (2003). Beans (Phaseolus spp.) - Model food legumes. Plant Soil 252: 55-128

Schwartz, H.F., Casciano D.H., JAsenga J.A, and Wood D.R, 1987: Field Measurement of White Mold Effects upon Dry Beans with Genetic Resistance or Upright Plant Architecture. Crop Sci 27, 699-702.