Progress in molecular markers and localization of functional genes of main traits in peach

Abstract: Peach is considered as a model plant for genetic studies of perennial fruit trees due to its small genome and abundant genetic resources. The study of the characteristics of peach mainly focuses on fruit, flower, tree and the resistance to diseases and insect pests. A large number of studies have been carried out on the heredity of peach characteristics. So far, some functional genes have been obtained and corresponding molecular markers have also been developed. Marker assisted selection has greatly improved the efficiency of peach breeding as the development of molecular markers and the localization of functional genes related to important agronomic traits. The characteristic of peach/nectarine was regulated by a MYB transcription factor gene Ppe MYB25 with the insertion of a LTR retro element in exon 3 in the cause of the nectarine phenotype. The functional marker (Indel G) was also developed for the LTR insertion to efficiently discriminate peach and nectarine seedlings. Fresh color (white or yellow) was controlled by the carotenoid cleavage dioxygenase 4 gene (CCD4) . The yellow peach alleles have evolved from various ancestral haplotypes by at least three independent mutational events involved nucleotide substitutions, small insertions and transposable element insertions. The functional markers (SNP, SSR and RE) were developed for these mutations. Melting flesh and flesh adhesion to the stone was controlled by the F-M locus which has three allelic copy number variants of the twogenes encoding endopolygalacturonase (endo PG) designated as Ppendo PGF and Ppendo PGM. The functional markers (P13, P29, P38, P39) were developed for discriminating the genotype of F-M locus. The Stony hard trait was controlled by a single recessive gene (Pp YUC11) and was inherited independently of the F-M locus. The SSR marker developed on the intron TC microsatellite genotypes of Pp YUC11 was used to identify the stony hard genotype. The non-acid and acid fruit were divided by their pH value (above 4.0 and below 3.9) . The locus was mapped in the linkage group 5 and co-segregated with SCAR marker D-Scar0. The locus controlling round and flat fruit was mapped in the linkage group 6 and co-segregated with SSR marker MA040 a and MA014 a. The genome-wide association study of round and flat fruit trait showed that the variation was highly associated with an A/T polymorphism detected in the fifth intron of the CAD1 gene (ppa003772 m) . A large number of QTLs for sugar and acid content were mapped and genes coding the enzymes of sugar and acid metabolism were predicted as the candidate genes. The study of dynamic QTLs for sugar and acid content could provide reference for identifying the underlying genes and establishing the model of metabolism in sugar and acid. Meanwhile, a candidate gene (ppa008301 m) for a major locus controlling maturity date had been identified.Showy flower and non-showy flower, pollen fertility and pollen sterility were qualitative traits. Showy flower and pollen fertility were dominant characters. The locus of flower shape was mapped in the linkage group 8, the nearest marker (CPPCT006) being located at 1.4 cM. The genome-wide association study of flower shape showed that a clear association signal was located on the scaffold 8, while the gene (ppa016980 m) was a predicted protein. The locus of pollen fertility and pollen sterility was located on the linkage group 6, the nearest marker (SSR: CPPCT004) being located at 9.7 cM. The characters of tree growing habit including normal and brachytic dwarf, standard and pillar, standard and temperature sensitive semi-dwarf, normal and evergrowing were correspondingly controlled by one pair of alleles.Brachytic dwarfism was a recessive trait and was caused by a nonsense mutation within the Pp GID1 c gene (gibberllic acid receptor) . The peach individuals could be genotyped using the HRM marker (gid1 c) based on the nonsense allele. The locus of temperature sensitive semi-dwarf was located in a region spanning 500 kb in the scaffold 3 containing 69 predicted protein-coding gene models. The pillar trait (originally called“broomy”, br) was shown to be incompletely dominant, as heterozygous individuals had intermediate branch angles, referred to as“upright”. The Ppe TAC1 in which insertion happened in‘Italian pillar'and SNP happened in‘New Jersey pillar'had proven to be a candidate gene for the br mutation. All or part of four of six genes cluster of MIKC-type MADS-box transcription factors were lost and did not expressed in the evergrowing (evg) mutant. These genes as the candidate genes for regulation of terminal bud formation had been named as dormancy-associated MADS-box (DAM) genes. The study of peach resistance to diseases and insect pests mainly focused on resistance to root-knot nematode and the green peach aphid. A resistance gene belonging to the NBS-LRR resistance gene family was identified and co-segregated with the major locus of resistance to M. incoginta, Pk Mi. There were many non-synonymous SNPs distributed in the TIR and NBS motifs in the genic region among different levels of resistance to M. incoginta genotype. The green peach aphid resistance was controlled by a single dominant gene. The Rm2 gene from‘Rubira'conferring resistance to the green peach aphid (Myzus persicae Sulzer) was mapped on the linkage group 1, the markers tightly linked with Rm2 could be used to increase the efficiency of selection for resistant plants. Moreover, the applications of molecular marker in MAS and identification of germplasm resource were prospected.