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Title: Simple sequence repeats linked with Slow Darkening Trait in Pinto bean discovered by SNP assay and whole genome sequencing

Author
item Felicetti, Erin
item Song, Qijian
item JIA, GAOFENG - Nanjing Agricultural University
item Cregan, Perry
item BETT, KIRSTEN - University Of Saskatchewan
item Miklas, Phillip - Phil

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2012
Publication Date: 7/1/2012
Citation: Felicetti, E.E., Song, Q., Jia, G., Cregan, P.B., Bett, K., Miklas, P.N. 2012. Simple sequence repeats linked with Slow Darkening Trait in Pinto bean discovered by SNP assay and whole genome sequencing. Crop Science. 52:1600-1608.

Interpretive Summary: Slow darkening trait in pinto bean is conditioned by a single gene which helps to perserve seed coat color in storage as well as reducing weathering of the seed coat due to delayed harvests. Breeders are working to transfer this gene into commercial pintos which darken in storage and succomb to darkening under adverse weather contions at harvest. The gene can be difficult to transfer because it has recessive inheritance and is expressed in maternal tissue which delays detection of the trait by one full generation. We developed genetic markers which can be used to rapidly detect the gene. These markers will facilitate development of slow darkening pinto bean cultivars which will save growers and dealers millions of dollars each year by preserving seed quality appearance from the field to the table.

Technical Abstract: Seed coat darkening in pinto bean (Phaseolus vulgaris L.) primarily occurs during prolonged storage and can result in significant loss in value based on it being a consumer perceived product flaw. Several slow darkening (SD) pintos, conditioned by the presence of the recessive sd gene, exist but are poorly adapted. Breeding for improved SD pintos is complicated by the recessive inheritance and expression of the trait in maternal tissue. We sought to develop capacity for marker-assisted selection (MAS) for the SD trait. Three F2 populations (159 individuals) derived from crosses between SD parents, representing two different sources (1533-15 and SDIP-1) for the trait, and commercial regular dark (RD) pintos, were used to screen for single nucleotide polymorphisms (SNPs) linked with the sd locus. Separate DNA pools from SD and from RD F2 individuals genotyped for the sd locus were used to detect putative sd-linked SNPs using the bulked-segregant analysis strategy. Two of 1536 SNPs differentiated between the SD and RD DNA bulks for all three populations. The whole genome sequence scaffold possessing the two SNPs was canvassed for simple sequence repeats (SSRs). Three of 12 SSRs from the SNP region distinguished between the SD and RD lines. The three SSRs, Pvsd-1157, Pvsd-1158, and Pvsd-0028 were observed to be tightly linked with the sd locus at 0.9, 0.4, and 3.1 cM, respectively across the F2 populations. The SSRs assayed across a recombinant inbred line mapping population (CDC Pintium x 1533-15) placed the sd gene on bean linkage group 7, between framework SSR markers BM210 and PvBR35. A survey of SD and RD advanced lines and cultivars revealed the SSRs will have utility for marker-assisted selection (MAS) of the SD trait in pinto bean and perhaps in other dry bean market classes as well.