Genetic structure analysis of cultivated and wild chestnut populations reveals gene flow from cultivars to natural stands

Abstract

Japanese chestnut (Castanea crenata Sieb. et Zucc.), the only fruit tree species domesticated in Japan, has been cultivated alongside natural stands since prehistorical times. Understanding the genetic diversity of this species and the relationships between cultivated and wild chestnut is important for clarifying its breeding history and determining conservation strategies. We assessed 3 chestnut cultivar populations and 29 wild chestnut populations (618 accessions). Genetic distance analysis revealed that wild populations in the Kyushu region are genetically distant from other populations, whereas other wild and cultivar populations are comparatively similar. Assignment tests suggested that cultivars were relatively similar to populations from central to western Honshu. Bayesian structure analyses showed that wild individuals were roughly classified according to geographical distribution along the Japanese archipelago, except that some wild individuals carried the genetic cluster prevalent in cultivars. Parentage analyses between cultivars and wild individuals identified 26 wild individuals presumed to have a parent–offspring relationship with a cultivar. These results suggested that the genetic structure of some wild individuals in natural stands was influenced by gene flow from cultivars. To conserve wild individuals carrying true “wild” genetic clusters, these individuals should be collected and preserved by ex situ conservation programs.

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

“…The genome sequence data generated in this study would enhance the genetics and genomics of Japanese chestnut, in which classical molecular markers, such as simple sequence repeats, previously played a key role in (i) the identification of genetic loci affecting agronomically important traits 3 , 4 , 18 ; (ii) chestnut breeding programs with marker-assisted selection 19 ; and (iii) the assessment of the genetic structure of cultivated and wild chestnut populations. 20 Furthermore, the highly conserved genome sequence and structure of woody members of rosids might help us better understand their evolutionary history and facilitate the identification of common genetic mechanisms affecting agronomic traits across various orders, families, species, and genera.…”

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

“…The genome sequence data generated in this study would enhance the genetics and genomics of Japanese chestnut, in which classical molecular markers, such as simple sequence repeats, previously played a key role in 1) the identification of genetic loci affecting agronomically important traits 4,15,17 ; 2) chestnut breeding programs with marker-assisted selection 18 ; and 3) the assessment of the genetic structure of cultivated and wild chestnut populations 19 . Furthermore, the highly conserved genome sequence and structure of woody members of rosids might help us better understand their evolutionary history and facilitate the identification of common genetic mechanisms affecting agronomic traits across various orders, families, species, and genera.…”

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

“…While the cultivated plants are characterized by limited genetic diversity, resulting from the process of domestication 1 , their wild relatives display greater genetic variability, which can be utilized as a source of genes lost during this process 2 . On the other hand, genes originating from cultivated populations have been shown to influence the genetic structure of wild populations in numerous species 3 . This gene flow between wild populations and cultivated varieties of the same or closely related species is well-known 4 and has been observed when cultivated varieties are planted within the natural range of their wild relatives 5 – 7 , with spontaneous hybrids known to form their own distinct populations and persist in the wild 8 , 9 .…”

“…The diversity of European marron varieties has been analyzed using gSSRs in Switzerland 32 , Italy 12 , 33 – 35 and the Iberian Peninsula 36 – 41 , as well as using the EST-SSRs markers in Italy and Spain 42 . In addition, researchers looked into introgression and hybridization between cultivated and wild populations 3 , 22 , 35 , 43 – 45 .…”