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ARS Home » Southeast Area » Mayaguez, Puerto Rico » Tropical Crops and Germplasm Research » Research » Publications at this Location » Publication #205744
Title: Genetics and mapping of the C1 gene for circumlineated pattern in common bean using AFLP and SNP-based bulk segregated analysis

Author
item Porch, Timothy - Tim
item ARANDA, LUWBIA - GRADUATE STUDENT
item BASSETT, M.J. - UF, GAINESVILLE
item LARA, L - University Of Puerto Rico
item Cregan, Perry

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/16/2013
Publication Date: 3/14/2014
Citation: Porch Clay, T.G., Aranda, L., Bassett, M., Lara, L., Cregan, P.B. 2014. Genetics and mapping of the C1 gene for circumlineated pattern in common bean using AFLP and SNP-based bulk segregated analysis. Journal of the American Society for Horticultural Science. 139(2):213-218.

Interpretive Summary: Circumlineatus in common bean is a seed trait identified by a precipitation line in the seed coat at the boundary of the white and colored zones. It is recessive and is expressed in partly colored seed coats. In this study, molecular markers (AFLP and SNP) and the common bean genome sequence were used to identify the genetic location of circumlineated. SNP markers with known genetic lociation were identified that were associated with the trait. The genetic sequence from two AFLP markers, also associated with the trait, was determined. The two sequences were used to interrogate the common bean whole genome sequence, identifying a region also found through genetic mapping with the molecular markers. Thus, the circumlineated gene was localized on Pv9.

Technical Abstract: Circumlineatus (cl) in common bean (Phaseolus vulgaris L.) is identified by a precipitation line in the seed coat at the boundary of the white and colored zones. Circumlineatus is recessive and is expressed in partly colored seed coats (t) with restricted patterns, such as virgarcus. In this study, AFLP (amplified fragment length polymorphism) and SNP (single nucleotide polymorphism) markers, and the common bean genome sequence were used in combination with BSA (bulk segregant analysis) to identify the genetic location of Cl. Markers were identified that co-segregated with Cl using Cl/Cl and cl/cl F3 and F5 progeny bulks from the cross t z cl G b v virgarcus BC3 5-593 ' t zsel Cl G b v sellatus BC3 5-593. Two bands associated with an AFLP primer combination, which yielded unambiguous polymorphisms between the bulks, were cloned and sequenced. The two sequences were used to interrogate the common bean whole genome sequence, identifying a region also found using bulk segregant analysis. Thus, the cl gene was localized on Pv9, using AFLP and SNP markers that co-segregated with Cl, and the physical location was confirmed with the whole genome sequence.