SSR and e-PCR Provide a Bridge Between Genetic Map and Genome Sequence of Potato for Marker Development in Target QTL Region

Abstract

The aim of this study was to increase marker density in a previously identified late blight resistance QTL in a diploid potato population. SSR markers from the reference potato genome sequence were located by e-PCR in the QTL region in the chromosome 9 genetic map of the diploid potato population B3C1HP, and utilized to identify more candidate genes locating between the SSR markers. After verified by PCR and genetic mapping, two SSR markers and two DM candidate genes were mapped in the QTL peak in the maternal genetic map of B3C1HP. The new markers narrowed down the average 2-LOD support interval from 2.6 to 1.4 cM. The new markers on the LOD peak are valuable for fine mapping and positional cloning of the alleles in late blight resistance QTL. This study proves that combination of SSR and e-PCR is an effective way to develop markers in target QTL region.Resumen El objetivo de este estudio era aumentar la densidad de marcadores en un QTL de resistencia a tizón tardío previamente identificado en una población diploide de papa cultivada. Marcadores de SSR de la secuencia del genoma de la papa fueron localizados por e-PCR en la región QTL en el mapa genético del cromosoma 9 del diploide población B3C1HP, y utilizadas para identificar más genes candidatos con la localización entre los marcadores de SSR. Después de verificación por PCR y mapeo genético dos marcadores de SSR y dos genes candidatos DM fueron asignadas en el pico de QTL en el mapa genético de B3C1HP. Los nuevos marcadores redujeron el intervalo medio de soporte 2-LOD de 2.6 a 1.4 cM. Los nuevos marcadores en el pico LOD son valiosos para el mapeo fino y la clonación posicional de los alelos de QTL de resistencia al tizón tardío. Este estudio demuestra que la combinación de SSR y e-PCR es una manera eficaz para desarrollar marcadores en la región QTL.

Potato late blight field resistance from QTL dPI09c is conferred by the NB-LRR gene R8

“…Initial mapping carried out in the population B3C1HP 100 placed the QTL dPI09c within the proximity of the marker DMG400031529 ( Li et al , 2015 ), which resides near R gene clusters with homology to Tm-2 2 and Sw-5 on potato linkage group 9 ( Jo et al , 2011 , 2015 ; Jupe et al , 2012 ; Li et al , 2012 ). To fine map the resistance, a larger population comprising 4000 additional clones (B3C1HP 4000 ) was assessed with initially identified markers Rpi-svnt1_367, DMC42152bf, DMC42144af, and At3g24160f2, which resulted in 106 recombinants ( Fig.…”

“…Marker names and chromosomal positions are presented above and below the physical map, respectively. Marker names in red represent the markers developed in our previous study ( Li et al , 2012 , 2015 ); markers in black were developed in this study. The transition between black and white rectangles indicates that the cross-over happened in the progenies.…”