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 microsatellites 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 (disease͞ pest resistances, fruit͞nut 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. T he major temperate fruit tree crops, apple (Malus ϫ domestica), peach (Prunus persica), cherry (Prunus avium and Prunus cerasus), plum (Prunus domestica and Prunus salicina), apricot (Prunus armeniaca), almond (Prunus dulcis), pear (Pyrus communis), quince (Cydonia oblonga), and loquat (Eriobotrya japonica), belong to the Rosaceae family. This also includes some other important crops such as strawberry (Fragaria ϫ ananassa) and rose (Rosa spp.). Most of these species are woody perennials with a long intergeneration period due to their juvenile phase and large plant sizes, which make them poorly suited organisms for classical genetic analysis. On the other hand, fruit trees have some advantageous features such as a long life, the existence of efficient methods of vegetative reproduction, the possibility of making interspecific crosses (frequent at the congeneric level), and a small basic genome; e.g., wild strawberry (Fragaria vesca) has a haploid genome size of 164 Mbp (1), and peach has a haploid genome size of 290 Mbp (2). Until recently, only very limited information existed on the genetics of phenotypic characters of simple inheritance; only 31 major genes had been described in peach (3), the best characterized of the Prunus species, or three genes in almond (4).The breeding methods used in these species have undergone very few changes over the last 50 years, and th...

Towards a unified genetic map for diploid roses

“…Some additional genes were added from the MASAKO gene family (Kitahara and Matsumoto 2000;Remay et al 2009). Also, three markers were developed for sequences of EST BAC contigs of the Prunus T £ E reference map (Dirlewanger et al 2004). In these map, these BACs Xank the S-locus.…”

“…1). Additional molecular markers, TE3-SSCP and TE22_2, derived from the TEXAS £ EARLYGOLD Prunus reference map (Dirlewanger et al 2004) could be mapped on this LG. The EST sequences that were used to design these primer pairs are linked to the S-locus in Prunus without any recombination.…”

“…Interestingly these loci map in-between two loci involved in self-incompatibility (S, TE3-SSCP) and within 20 cM distance of the Blfo locus, which controls the switch from single to double Xowers. A locus controlling the presence of double Xowers in Prunus is mapped on an unknown position on LG G2 on the T £ E reference map separated from the S-locus from almond and apricot on the lower end of group G6 on the same comparative map (Dirlewanger et al 2004). In addition to the molecular bridge markers, the homologous LGs could also be veriWed by the co-localization of phenotypic traits, either QTL or single gene markers, also in cases where the original LG numbering had not revealed this.…”

“…But the beneWts from the linkage map information remain limited by the genetic background of the population that was mapped. To overcome this restriction consensus or integrated linkage maps have been constructed for many cultivated plant species including peach (Dirlewanger et al 2004), apple (N'Diaye et al 2008, grapevine (Doligez et al 2006;Vezzulli et al 2008), soybean (Cregan et al 1999), rapeseed (Lombard and Delourme 2001), barley (Wenzl et al 2006), red clover (Isobe et al 2009), eucalyptus (Brondani et al 2006), and loblolly pine (Sewell et al 1999). Integrated maps not only increase the genome coverage but also make it possible to compare locations of major genes controlling important phenotypic traits or QTL positions between populations from multiple crosses.…”

“…Integrated maps not only increase the genome coverage but also make it possible to compare locations of major genes controlling important phenotypic traits or QTL positions between populations from multiple crosses. Although small chromosome rearrangements have been detected in some closely related species of the Pinaceae (Pelgas et al 2006) comparative mapping in the Rosaceae genus Prunus showed a very high degree of colinearity between the genomes of the diploid species peach, almond, apricot, and cherry (Dirlewanger et al 2004). Furthermore consensus maps of various genera of the Rosaceae have been linked with a conserved orthologue set of sequence-based markers (Sargent et al 2009).…”