Characterization of AT-rich microsatellites in common bean (Phaseolus vulgaris L.)

Abstract

Polymorphism of microsatellite markers is often associated with the simple sequence repeat motif targeted. AT-rich microsatellites tend to be highly variable and this appears to be notable, especially in legume genomes. To analyze the value of AT-rich microsatellites for common bean (Phaseolus vulgaris L.), we developed a total of 85 new microsatellite markers, 74 of which targeted ATA or other AT-rich motif loci and 11 of which were made for GA, CA or CAC motif loci. We evaluated the loci for the level of allelic diversity in comparison to previously characterized microsatellites using a panel of 18 standard genotypes and genetically mapped any loci polymorphic in the DOR364 x G19833 population. The majority of the microsatellites produced single bands and detected single loci, however, 15 of the AT-rich microsatellites produced multiple or double banding patterns; while only one of the GA or CA-rich microsatellites did. The polymorphism information content (PIC) values averaged 0.892 and 0.600 for the AT and ATA motif microsatellites, respectively, but only 0.140 for the CA-rich microsatellites. GA microsatellites, which had a large average number of repeats, had high to intermediate PIC, averaging 0.706. A total of 45 loci could be genetically mapped and distribution of the loci across the genome was skewed towards non-distal locations with a greater prevalence of loci on linkage groups b02, b09 and b11. AT-rich microsatellites were found to be a useful source of polymorphic markers for mapping and diversity assessment in common bean that appears to uncover higher diversity than other types of simple sequence repeat markers.

Identification of QTLs of resistance to white mold in common bean from multiple markers by using Bayesian analysis

“…The ME1 marker was initially marked in LG 1 by Blair et al (2008) and then reported in LG 9, and is present in the linkage map published by Galeano et al (2009) and Blair et al (2010). In this study, ME1 was found near a QTL (2.29 cM) and showed an effect of increasing resistance to white mold, but with low heritability (0.55%).…”

“…The BM184 marker was initially mapped in LG 11 (Blair et al, 2003(Blair et al, , 2008. However, Maxwell et al (2007) identified this marker in LG 9, evaluating the RIL G122/CO72548 population.…”

“…This marker was initially mapped by Yu et al (2000) in 2 RIL populations, DOR364/G19833 and BAT93/JaloEEP558, in LG 4, and has frequently been reported in the literature (Blair et al, 2003(Blair et al, , 2008Mkwaila et al, 2011;Soule et al, 2011;Miklas et al, 2013). In its linkage group, there are 2 QTLs-WM4.1 PX and WM4.2 R31 , identified by Park et al (2001) and Soule et al (2011), respectively.…”

Microsatellite markers in common bean (Phaseolus vulgaris L.)

“…The most frequent were AG, GAA, CAT, TGG motifs. Blair et al (2008) developed 85 new SSRs, 71 were developed from an ATA-enriched library, 3 AT-rich SSRs from gene-based sequences and 11 were based on non-AT-rich sequences and were made for GA, CA or CAC motif loci. A total of 45 new loci could be mapped on the DG integrated map and this brings to over 160 mapped loci for common bean with the previous genetic mapping of SSRs conducted by Yu et al (2000), Blair et al (2003) and Grisi et al (2007).…”

“…They integrated 99 new BMb markers into the genetic map with a high LOD score with the most common motifs AT/TA and ATA/TAT. The new genetic map had a total of 215 SSRs and included 116 previously mapped SSR loci from Blair et al (2003Blair et al ( , 2008. Hanai et al (2010) developed a set of new 282 markers (50 EST-SSR, 32 RGA (resistance gene analogs), and 200 AFLP) and a new, expanded version of the core linkage map, using the BJ population.…”