Comparative mapping and marker-assisted selection in Rosaceae fruit crops

Abstract

The development of saturated linkage maps using transferable markers, restriction fragment length polymorphisms, and micro-satellites has provided a foundation for fruit tree genetics and breeding. A Prunus reference map with 562 such markers is available, and a further set of 13 maps constructed with a subset of these markers has allowed genome comparison among seven Prunus diploid (x = 8) species (almond, peach, apricot, cherry, Prunus ferganensis, Prunus davidiana, and Prunus cerasifera); marker colinearity was the rule with all of them. Preliminary results of the comparison between apple and Prunus maps suggest a high level of synteny between these two genera. Conserved genomic regions have also been detected between Prunus and Arabidopsis. By using the data from different linkage maps anchored with the reference Prunus map, it has been possible to establish, in a general map, the position of 28 major genes affecting agronomic characters found in different species. Markers tightly linked to the major genes responsible for the expression of important traits (disease/pest resistances, fruit/nut quality, self-incompatibility, etc.) have been developed in apple and Prunus and are currently in use for marker-assisted selection in breeding programs. Quantitative character dissection using linkage maps and candidate gene approaches has already started. Genomic tools such as the Prunus physical map, large EST collections in both Prunus and Malus, and the establishment of the map position of high numbers of ESTs are required for a better understanding of the Rosaceae genome and to foster additional research and applications on fruit tree genetics.

Fig. 1.

Comparison among the SSR maps of linkage group 1 in the almond × peach Prunus reference map (TxE), peach (cv. Ferjalou Jalusia × cv. Fantasia = FxJ), almond × peach (cv. Felinem), P. cerasifera (P.2175), and cherry (cv. Lapins and cv. Regina). Positions of anchor loci between maps are indicated by connecting lines. Only marker positions as in ref. are indicated for the TxE map.

Fig. 2.

Comparison between Prunus (5) and apple (21) linkage maps. Only the position of anchor loci is shown. Linkage groups in Prunus are noted as G and apple groups are noted as L followed by a number. The positions of markers in parenthesis in Prunus were inferred from other maps. Marker positions in apple were obtained by using the maps of both parents of the F₁ cross cv. Prima × cv. Fiesta. Two parallel oblique lines indicate that only a fragment of the linkage group is included. Arrows pointing to the left in the Prunus map are anchors to markers located in the indicated linkage groups of the apple map.

Fig. 3.

Approximate position of 28 major genes mapped in different populations of apricot (blue background), peach (orange background), almond or almond × peach (yellow background), and Myrobalan plum (green background) on the framework of the Prunus reference map (5). Gene abbreviations correspond to: Y, peach flesh color; B, almond/peach petal color; sharka, plum pox virus resistance; B, flower color in almond x peach; Mi, nematode resistance from peach; D, almond shell hardness; Br, broomy plant habit; Dl, double flower; Cs, flesh color around the stone; Ag, anther color; Pcp, polycarpel; Fc, flower color; Lb, blooming date; F, flesh adherence to stone; D, non-acid fruit in peach, Sk, bitter kernel; G, fruit skin pubescence; Nl, leaf shape; Dw, dwarf plant; Ps, male sterility; Sc, fruit skin color; Gr, leaf color; S^*, fruit shape; S, self-incompatibility (almond and apricot); Ma, nematode resistance from Myrobalan plum; E, leaf gland shape; Sf, resistance to powdey mildew. Genes Dl and Br are located on an unknown position of G2.