The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication

Ping Lin,Kailiang Wang,Jiyuan Li,Wei Long,Zhengqi Fan,Xianjin Ma,Weixin Liu,Yupeng Wang,Huadong Ren,Zhikang Hu,Chao Yan,Hu Huang,Ning Ye,Xinlei Li,Yongqing Cao,Hengfu Yin,Xiaohua Yao

doi:10.1186/s13059-021-02599-2

Abstract

BackgroundAs a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. Camellia oleifera Abel. is a sister species to the tea plant, which is extensively cultivated for edible oil production. However, the molecular mechanism of the domestication of oil-Camellia is still limited due to the lack of sufficient genomic information.ResultsTo elucidate the genetic and genomic basis of evolution and domestication, here we report a chromosome-scale reference genome of wild oil-Camellia (2.95 Gb), together with transcriptome sequencing data of 221 cultivars. The oil-Camellia genome, assembled by an integrative approach of multiple sequencing technologies, consists of a large proportion of repetitive elements (76.1%) and high heterozygosity (2.52%). We construct a genetic map of high-density corrected markers by sequencing the controlled-pollination hybrids. Genome-wide association studies reveal a subset of artificially selected genes that are involved in the oil biosynthesis and phytohormone pathways. Particularly, we identify the elite alleles of genes encoding sugar-dependent triacylglycerol lipase 1, β-ketoacyl-acyl carrier protein synthase III, and stearoyl-acyl carrier protein desaturases; these alleles play important roles in enhancing the yield and quality of seed oil during oil-Camellia domestication.ConclusionsWe generate a chromosome-scale reference genome for oil-Camellia plants and demonstrate that the artificial selection of elite alleles of genes involved in oil biosynthesis contributes to oil-Camellia domestication.

Highlights

As a perennial crop, oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health
To further evaluate the genome complexity, we examined the genome based on short sequencing reads
We identified 1,849,953 single nucleotide polymorphism (SNPs) (Additional File 1: Table S14) and 85,440 short genomic insertions and deletions (InDels; Additional File 1: Table S15), 59.80% of SNPs located in intergenic regions and 19.64% were in the exon regions

Summary

Introduction

Oil-Camellia possesses a long domestication history and produces high-quality seed oil that is beneficial to human health. The usage of oil-Camellia for edible oil has a long history (over 2300 years) in China [7], and the content and quality of seed oil have been continuously selected as the primary targets of breeding programs [7]. Compared to their wild progenitors, cultivated oilCamellia plants often have larger fruit and thinner pericarp, allowing for a boost of seed oil yield. Oil-Camellia is cultivated extensively as an oil crop in many countries, including China, The Philippines, India, Japan, Brazil, Thailand, and South Korea [8, 9]

Methods

Results

Discussion

Conclusion