Genetic Linkage Map Construction And QTLs Analyses For Phenotypic Traits Of Mei

Belonging to the Rosaceae, sub-family Prunoideae, mei(Prunus mume Sieb. et Zucc.,2n=2x=16) possesses early blossom, varying types of flowers, colorful corollas, and pleasant fragrance and is extensively grown as a garden ornamental plant. Up to now, new cultivars of mei are always bred using traditional hybridizations which spend a lot of time. Meanwhile, the origin of mei isn’t still revealed as a result of the lack of the comparative genomic analyses between mei and related species. Here, a high density genetic linkage map using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers based on190F1segregating progeny generated from a cross between female P. mume ’Fenban’ and male P. mume ’Kouzi Yudie’ was constructed and was anchored genomic assembly sequences of mei, depanding on which not only the macro-colinearity between mei genome and Prunus T×E reference map [an interspecific almond ’Texas’×peach ’Earlygold’(T×E) F2mapping population] was identified, but also the quantitative trait loci (QTLs) for main phenotypic traits were detected in this study. The main results and conclusions are indicated as follows:1. We performed the genome-wide characterization of SSRs ranging in length from1to8bp in the mei genome and the results were shown as follows:A total of188,149SSRs were identified at a frequency of793.9SSR/Mb using MIcroSAtellites identification tool (MISA) and mononucleotide repeats (67,183) were the most common type of SSRs.2. We analysed the distribution of the repeat motifs of SSRs in the genomic and different genomic regions of mei, apple, and strawberry. The results were indicated as follows:The frequency of SSRs decreased with the increasing the repeat motif length, AT-rich repeat motifs were more common than GC-rich repeat motifs, and the frequency of SSRs was more common in intergenic regions than CDS regions in three genomes of Rosaceae.3.670SSRs were chosen from the total SSRs identified in mei genome and were detected among parental lines and190Fi segregating progeny generated from a cross between P. mutne ’Fenban’ and P. mume ’Kouzi Yudie’. The results were indicated as follows:A framework genetic linkage map of mei was constructed based on144polymorphic SSRs according to pseudo-test-cross strategy, containing eight linkage groups (LGs). The total genetic distance was668.7cM. Seventy one scaffolds covering about28.1%of mei assembled sequences were anchored to this genetic map, totaling to66.5Mb.4. According to the restriction-site associated with DNA-tag (RAD-tag) strategy, about2,166polymorphic SNPs were detected among the parental lines and190F1segregating progeny using bioinformatics analysis. The polymorphic1,484SNPs exhibited standard Mendelian segregation (1:1or1:2:1) by χ2test at cutoff of P<0.05. About3,229SNPs polymorphic loci were found in this mapping population, occurring at an average two polymorphic loci of each SNPs.5. We constructed a high density genetic linkage map including1,613markers based on the framework genetic linkage map added density using1,484polymorphic SNPs. This genetic map contained eight LGs, totaling to780.9cM. The average marker interval is0.5cM.513scaffolds covering about84.0%of mei assembled sequences were anchored to this high density genetic map, totaling to199.0Mb.6. A high level of macro-collinearity was revealed by aligning the199.0Mb assembled sequences anchored to the mei genetic map and613sequences of Rosaceae Conserved Ortholog Set (RosCOS) anchored to the Prunus T×E reference map. The results were indicated as follows:Among the process of mei evolution, PM3and PM4underwent chromosome rearrangement and PM3was originated from PG1, PG6and PG7of Prunus, and PM4was originated from PG2and PG5of Prunus.7. Hereditary variations of plant height, ground diameter, leafblade length, leafblade width, leafblade area and leafblade vein number were measured and analyzed based on F1mapping population of mei. These QTLs for these phenotypic traits using composit interval mapping. The results were shown as follows:There were84QTLs for these six phenotypic traits using composit interval mapping. Of these QTLs,35QTLs for leafblade area and for leafblade vein number were the most common, while only one QTL for ground diameter was the least.In summary, this study may facilitate genomic structure and function, maker-assisted selection breeding, and comparative genomic analyses between mei and relative species, may further provide an important reference for molecular marker polymerization breeding of mei, and pave the way for the study of genetic mechanism of important ornamental traits and the origin of mei.