Abstract
Chestnuts (Castanea) are major nut crops in East Asia and southern Europe, and are unique among temperate nut crops in that the harvested seeds are starchy rather than oily. Chestnut species have been cultivated for three millennia or more in China, so it is likely that artificial selection has affected the genome of orchard-grown chestnuts. The genetics of Chinese chestnut (Castanea mollissima Blume) domestication are also of interest to breeders of hybrid American chestnut, especially if the low-growing, branching habit of Chinese chestnut, an impediment to American chestnut restoration, is partly the result of artificial selection. We resequenced genomes of wild and orchard-derived Chinese chestnuts and identified selective sweeps based on pooled whole-genome SNP datasets. We present candidate gene loci for chestnut domestication and discuss the potential phenotypic effects of candidate loci, some of which may be useful genes for chestnut improvement in Asia and North America. Selective sweeps included predicted genes potentially related to flower phenology and development, fruit maturation, and secondary metabolism, and included some genes homologous to domestication candidates in other woody plants.
Highlights
We investigated the following questions: 1) Is genetic diversity on the genomic scale lower in orchardderived Chinese chestnut than it is in wild Chinese chestnut?
Our study provides a first glimpse into the complex pathways of selection by which humans transformed a forest tree into a reliable food crop, and has practical importance for chestnut improvement
For breeders who are interested in improving Chinese chestnut for increased nut production or nut size, genes that were selected during domestication to promote heavier fruiting, such as the male-sterility genes identified here, could be a pathway to trees with shorter catkins and more female flowers
Summary
Traits relevant to plant domestication show genomic evidence of selection in diverse crop species, including grains (Cockram et al, 2007), legumes (Kaga et al, 2008; Lam et al, 2010; Li et al, 2013; Schmutz et al, 2014), annual fruit-bearing crops such as tomato and squash (Lefebvre et al, 1998; Frary et al, 2000; Ronen et al, 2000; Vrebalov et al, 2002; Rao and Paran, 2003; Guo et al, 2013), and woody perennial fruit crops (Cao et al, 2014; Khan et al, 2014) Some traits, such as flowering time and plant architecture, show genomic evidence of selection in many crops (Mao et al, 2000; Clark et al, 2006; Paran and van der Knaap, 2007; Tan et al, 2008; Zhou et al, 2009; Li et al, 2013). Broad-sense heritability estimates for these traits ranged from 0.40 (nut weight) to 0.91 (harvest date) (Nishio et al, 2014)
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