Project Number: 5348-21000-020-05
Project Type: Specific C/A

Start Date: Sep 30, 2002
End Date: Aug 01, 2006

Objective:
The development of microsatellite markers distinguishing closely related genotypes in bean germplasm.

Approach:
The research proposed will consist of three steps: 1) assembling a panel of microsatellite markers; 2) testing the degree of polymorphism among both a) a wide representation of the domesticated common bean germplasm; and b) a group of closely related lines; and 3) calculate frequency data of microsatellite alleles and genotypes and make inferences on the probability of occurrence of two identical genotypes just by chance. For Step 1, three sources of microsatellite markers will be examined. These include 1) existing microsatellite markers. Yue et al. (2000) identified 37 microsatellite arrays were identified, of which 16 were polymorphic between the two parents (BAT93, Jalo EEP558) of the core mapping population of beans and 15 could be mapped; 2) RFLP sequence probes: We propose to sequence the inserts of these clones in the PstI library (several hundreds of clones) and identify those clones that contain microsatellite arrays. In the next step, PCR primers will be designed using online software Primer3 (http://www.genome.wi.mit.edu/cgi-bin/primer/ primer3_www. cgi). Following the design, these primers will be assayed as to their suitability for amplification in common bean; and 3) Develop a small insert genomic library and a cDNA library for microsatellite isolation if insufficient microsatellites can be developed using the two previous approaches. For Step 2, we will screen both a broadly-based array of domesticated common bean germplasm. We have established a small (n = 37) collection of landrace genotypes from the Andean and Mesoamerican gene pools, representing the six domesticated races (Singh et al. 1991) (see Appendix A). Seeds of these accessions have already been provided by CIAT. Plants of these accessions will be grown in the greenhouse and DNA will be extracted according to established procedures. Depending on the amount of funding, one or more groups of closely related genotypes will be analyzed with the microsatellite markers for their ability to distinguish these genotypes. We propose here to focus on the yellow-seeded beans, but obviously results could be extended to major commercial bean classes if funds were available. For step 3, we propose to calculate the probability of matching two genotypes. This probability can be calculated as the product of the frequencies of the individual alleles at the different loci based on Bayesian statistics as is done in forensic testing (Weir 1996, pp. 215-221). This assumes independence of the individual loci, which will have to be tested by the appropriate test of independence. Alternatively, a likelihood ratio can be calculated as the ratio of the probability that observing a match given that the lines are the same over the probability that the lines are not related. Weir (1996) also discuss cases when individual lines are related (e.g., here, members of the yellow-seeded group, potentially). Formerly 5348-21000-017-02S (6/04).

Project Team

Welsh, Molly Paul Gepts - Research Scientist 509-335-3692

Project Annual Reports

FY 2003

Related National Programs

Plant, Microbial & Insect Genetic Res., Genomics, & Genetic Improv. I (301)