Characterization of wheat DArT markers: genetic and functional features

Mol. Genet. Genomics

Marone D, Panio G, Ficco DBM, Russo MA, De Vita P, Rubiales D, Papa R, Cattivelli L, Mastrangelo AM

Corresponding author: Anna Maria Mastrangelo, CRA-Cereal Research Centre SS 16 - km 675 71122 Foggia, Italy. E-mail:

EMS_5

Map comparisons

The order of the DArT and PCR-based markers was compared across the three durum wheat genetic maps presented in this study. The common markers generally showed good correspondence across the maps, in terms of the orders and the relative genetic distances. Only a few markers showed ambiguous orders across two or more maps. Two inversions were observed on chromosome 2A between CP and OC (the Xwmc170 and tPt-3136 markers) and on chromosome 4A between CP and CN (the Xgwm834 and Xwmc718 markers). Three cases of different genetic distances were observed across the segregating populations analyzed in this study. A distance of about 20 cM was found between the Xbarc308 and Xwm235 markers on chromosome 5B for OC, while the two markers were separated by 9 cMfor CN. The distance between rPt-3887 and the group comprising the wPt-4743, wPt-5585 and wPt-4038 markers on chromosome 7B was about 62 cMfor CP, and 28 cMfor OC. On the same chromosome, the wPt-3730 and Xgwm302 markers were at distances of 4 cMfor OC and 26 cMfor CN.

Furthermore, the positions of DArT and PCR-based markers mapped in this study were compared with recently published maps of bread and durum wheat. The ITMI map (Song et al. 2005) and the consensus map developed by Somers et al. (2004), which represent two well-saturated bread wheat maps, were considered for the PCR-based markers, while the durum wheat map described by Trebbi et al. (2011) wasusedfor comparisons of both the DArT and PCR-basedmarker positions.The genetic positions of most DArT and PCR-basedloci in the three genetic maps showed general good consistency with respect to the reference maps. In some cases, differences in the relative distances between two markers were found, although these could be explained by duplication of small chromosomal regions indicated by the presence of paralogous loci mapped on the same chromosomes.An example is seenby the rPt-1040 DArT marker, positioned on chromosome 7A at a distance of 10 cM from a group of markers comprising wPt-7489, wPt-8721 and Xwmc265for CN, while a distance of 34 cM was found in the durum wheat map published by Trebbi et al. (2011). Nevertheless, two different loci were amplified for the Xwmc265marker for CNand mapped in paralogous positions on chromosome 7A. This suggests that duplication might have occurred in this region, which would account for the discrepancy described above.

Other discrepancies were observed for distances between pairs of markers on different chromosomes. The mapping data from the genetic maps presented in this study disagreed with some of the published maps, but were consistent with others. Some cases were represented by pairs of markers that were shown as co-segregating by Somers et al. (2004) and were separated by distancesgreater than 15 cM in our maps. For example, thedistance of about 15 cM reported between the Xbarc181 and Xbarc240markers on chromosome 1B forCN is supported bysimilar distances between these two markers also forCP and OC. A distance of 25 cM was found for the markers Xwmc257 and Xgwm429 on chromosome 2B, and the Xbarc70 and Xbarc78 markers were positioned in two different linkage groups on chromosome 4A forOC. Both marker pairsshared the same map position in the study by Somers et al. (2004); however, the positions identified forOC in both cases agreed with the map data presented by Song et al. (2005). Finally, the Xgwm495 and Xwmc48 markers that co-mappedin the map by Somers et al. (2004) are positioned at a distance of 24 cM on chromosome 4B for OC, according to the P92201D5-2 × P91190D1-10 segregating populationdata reported by Francki et al. (2009).A few more discrepancies were identified by comparing the three maps presented in this study with those available in the literature, as seen forthe Xbarc69 and wPt-5133 markers, which were located at a distance of 40 cM by Trebbi et al. (2011) and about 5 cMfor CP, on chromosome 3A.

Two inconsistencies were found in terms of marker orders. The Xgwm334 marker was mapped on the short arm of chromosome 6Ain a distal position with respect to the wPt-3468 DArT marker for CP, and in the inverted order in the consensus map by Somers et al. (2004). However, the data reported by Tsilo et al. (2010) and Wang et al. (2011) support the order found forCP in the present study.Similarly, the Xgwm471 marker was positioned on the short arm of chromosome 7A in a distal position with respect to Xbarc70; this is consistent with data reported by Xue et al. (2008), while the inverted order is seen in the map by Somers et al. (2004).

References

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