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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Publications at this Location » Publication #304927
Title: Molecular genetic analysis of the Phaseolus vulgaris P locus

Author
item MOGHADDAM, MAFI - North Dakota State University
item STONEHOUSE, R - University Of Saskatchewan
item LEE, R - North Dakota State University
item MAMIDI, S - University Of North Dakota
item BELLO, MARCO - Former ARS Employee
item Miklas, Phillip - Phil
item MCLEAN, P.E. - University Of North Dakota
item BETT, K.E - University Of Saskatchewan

Submitted to: Bean Improvement Cooperative Annual Report
Publication Type: Proceedings
Publication Acceptance Date: 2/11/2014
Publication Date: 3/1/2014
Citation: Moghaddam, M.S., Stonehouse, R., Lee, R., Mamidi, S., Bello, M., Miklas, P.N., Mclean, P., Bett, K. 2014. Molecular genetic analysis of the Phaseolus vulgaris P locus. Bean Improvement Cooperative Annual Report. 57: 15-16.

Interpretive Summary: Common bean market classes are distinguished by their many seed colors, patterns, and size. At least 23 genes, acting independently or in an epistatic manner, affect the seed coat color and pattern. The P locus which is described as the “ground factor” by Emerson, has multiple alleles and controls all color expression. The presence of its recessive allele p results in white seeds and flowers due to its epistatic effect on the expression of the other color/pattern genes. Different molecular markers mapped the P locus on Pv07. The availability of a reference genome (Schmutz, McClean et al. submitted) facilitates the Identification of a candidate gene based on comparative genomics approach. Previous studies in Arabidopsis indicates that multiple mechanisms are involved in seed coat color expression. One possibility is that the P locus encodes a transcription factor that regulates the flavonoid biosynthesis pathway in a manner similar to the Arabidopsis TT89 or pea A6 genes. Our objectives were to 1) physically fine-map the P locus using known linked markers, 2) use a comparative genomics approach to find a candidate bean ortholog to AtTT8 and A, and 3) characterize different alleles of the P gene candidate. We also performed an independent genome wide association study (GWAS) to find the genomic regions associated with the seed coat color.

Technical Abstract: Common bean market classes are distinguished by their many seed colors, patterns, and size. At least 23 genes, acting independently or in an epistatic manner, affect the seed coat color and pattern. The P locus which is described as the “ground factor” by Emerson, has multiple alleles and controls all color expression. The presence of its recessive allele p results in white seeds and flowers due to its epistatic effect on the expression of the other color/pattern genes. Different molecular markers mapped the P locus on Pv07. The availability of a reference genome (Schmutz, McClean et al. submitted) facilitates the Identification of a candidate gene based on comparative genomics approach. Previous studies in Arabidopsis indicates that multiple mechanisms are involved in seed coat color expression. One possibility is that the P locus encodes a transcription factor that regulates the flavonoid biosynthesis pathway in a manner similar to the Arabidopsis TT89 or pea A6 genes. Our objectives were to 1) physically fine-map the P locus using known linked markers, 2) use a comparative genomics approach to find a candidate bean ortholog to AtTT8 and A, and 3) characterize different alleles of the P gene candidate. We also performed an independent genome wide association study (GWAS) to find the genomic regions associated with the seed coat color.