Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

Ha, Young‐Ho; Gil, Hee-Young; Kim, Sang‐Chul; Choi, Kyung; Kim, Joohwan

doi:10.1038/s41598-022-20513-z

Cited by 2 publications

(2 citation statements)

References 78 publications

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“…As a very important genus in the Rosaceae family, Malus includes apple, rootstock and a large number of ornamental crabapple species that have rich germplasm resources and biological value [ 5 ]. However, due to extensive hybridization and complex morphology, species classification and germplasm identification of Malus are extremely difficult [ 11 ].…”

Section: Discussionmentioning

confidence: 99%

“…It is native to China and has a wide range of natural distributions, including Northeast China, North China and Southwest China [ 3 , 4 ]. M. baccata has good fertility and a certain degree of resistance, so it is used in the production of grafting seedling rootstock and apple breeding parents [ 5 ]. Due to the differences in ecological environment and the influence of species adaptability, M. baccata has accumulated abundant variation types, such as broad leaves, hanging branches, early flowering, large fruit and so on [ 6 , 7 ].…”

Section: Introductionmentioning

confidence: 99%

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Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species

Wang,

Zhang,

Wang

et al. 2023

Biomolecules

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Malus baccata (L.) Borkh. is an important wild species of Malus. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly and annotation, six complete cp genome sequences, ranging in size from 160,083 to 160,295 bp, were obtained. The GC content of stable IR regions (42.7%) was significantly higher than that of full length (36.5%) and SC regions (LSC-34.2%, SSC-30.4%). Compared with other Malus species, it was found that there were more sites of polymorphisms and hotspots of variation in LSC and SSC regions, with high variation sites including trnR/UCU-atpA, trnT/UGU-trnL/UAA, ndhF-rpl32 and ccsA-ndhD. The intraspecific and interspecific collinearity was good, and no structural rearrangement was observed. A large number of repeating elements and different boundary expansions may be involved in shaping the cp genome size. Up to 77 or 78 coding genes were annotated in the cp genomes of M. baccata, and high frequency codons such as UUA (Leu), GCU (Ala) and AGA (Arg) were identified by relative synonymous codon usage analysis. Phylogeographic analysis showed that 12 individuals of M. baccata clustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related to M. baccata evolutionarily. The phylogenetic analysis suggested that two main clades of different M. baccata in the genus Malus were formed and that I and II diverged about 9.7 MYA. In conclusion, through cp genome assembly and comparison, the interspecific relationships and molecular variations of M. baccata were further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation of M. baccata and Malus.

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Section: Discussionmentioning

confidence: 99%