Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species

Abstract

We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with the addition of some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F 2 and F 3) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F 2. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: selfcompatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F 2 seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F 1 hybrids, is discussed.

Inheritance of Fruit Red-Flesh Patterns in Peach

“…The first segregating population used was an F 1 segregating population called Bb × Nl, comprising 98 individuals from the cross between Belbinette and Nectalady [ 31 , 32 ]. The second population was an F 2 segregating population of 431 individuals, called SDF2, that was derived from the selfing of Sweet Dream [ 33 ]. The third one was an interspecific BC 1 segregating population of 190 individuals called T1E that was generated by backcrossing the F 1 hybrid between the Texas almond cultivar and the Earlygold peach cultivar, and backcrossed to Earlygold (Donoso et al 2016).…”

“…Linkage group terminology was according to the Prunus reference genome v2.0 [ 19 ]. The second map used was for the SDF2 population already described by Eduardo et al [ 33 ]. We added three new SSRs in the regions not covered with an initial set of 64 SNPs.…”

Breeding New Premium Quality Cultivars by Citrus Breeding 2.0 in Japan: An Integrative Approach Suggested by Genealogy

“…The rebreeding approach intends to provide a new strategy for mutation breeding by selecting new hybrids with traits that are equal or superior to those of the original cultivar. Eduardo et al proposed a similar approach, called resynthesis, to select elite genotypes using marker-based partial reconstruction [48]. They demonstrated the potential of this approach in peach by selecting seven individuals 76-94% identical to the reference from the 416 F2 population.…”