Identification, genealogical structure and population genetics of S-alleles in Malus sieversii, the wild ancestor of domesticated apple

Genetic Admixture in the Population of Wild Apple (Malus Sieversii) from the Tien Shan Mountains, Kazakhstan

There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.

Full-length transcriptome and targeted metabolome analyses provide insights into defense mechanisms of Malus sieversii against Agrilus mali

Malus sieversii is the wild progenitor for many cultivars of domesticated apple and an important germplasm resource for breeding. However, this valuable species faces a significant threat in the areas north of the Tianshan Mountains in China, by the invasion of Agrilus mali, a destructive pest of apple trees belonging to the family Buprestidae. Our preliminary study has has shown that there may be resistance to this insect in M. sieversii plants in the field, but the corresponding molecular mechanisms remain unclear. In this study, we compared the response of insect-resistant and insect-susceptible plants of M. sieversii to insect feeding using full-length transcriptome and targeted metabolome. 112,103 non-chimeric full-length reads (FLNC) totaling 10.52 Gb of data were generating with Pacific Biosciences SingleMolecule, Real-Time (PacBio SMRT) sequencing. A total of 130.06 Gb data of long reads were acquired with an Illumina HiSeq. Function annotation indicated that the different expressed genes (DEGs) were mainly involved in signal transduction pathway of plant hormones and in the synthesis of compounds such as terpenes, quinones, flavonoids, and jasmonic acid. Through targeted metabolome analysis resistant strains showed higher levels of trans-cinnamic acid, caffeine and ferulic acid after pest infestation. This study helps to decipher the transcriptional changes and related signaling paths in M. sieversii after an insect feeding, which lays a foundation for further research on molecular mechanisms of insect resistance in apples.

Differential Allelic Richness between Malus sylvestris L. and Malus × domestica Borkh. from Finland as a Measure of Genetic Loss

European wild apple (Malus sylvestris L.) is the only Malus wild species native to Europe which is a relative of cultivated apples (Malus × domestica Borkh.). It grows on forests’ edges, farmland hedges, and marginal sites; by living in those scattered meta-populations, it is exposed to genetic erosion in relation to hybridization and habitat degradation. In Finland, it grows at the northern edge of its distribution in Europe and is considered as a near-threatened taxon requiring urgent conservation. In order to evaluate the molecular genetic diversity of M. sylvestris, five populations including 43 trees were analyzed using 15 microsatellite markers. Additionally, a similar number of samples from cultivated apples, which are common to the same region, was included in order to estimate gene diversity gaps and give an insight into putative hybridization. European wild apple in Finland proved to be populationally structured, and seems not to be threatened by introgression events from its cultivated relative. They were all separated into different clusters, except for one individual. However, urgent conservation is indeed needed, especially due to the very low total number of trees (four) in some of the analyzed populations. These populations should be restored in order to enable permanent access to the wild relatives’ diversity, as they might be a critical source of gene variants for future needs.

A Multifaceted Overview of Apple Tree Domestication

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.