RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

Lei Zhang,Wenqing Su,Hanhui Kuang,Rong Tao,Peiyao Wu,Richard W Michelmore,Robert M Larkin,Sebastian Reyes Chin-Wo,Weiyi Zhang,Chenghuan Yan,Dean Lavelle,Yue Jia,Jiongjiong Chen,Maria-Jose Truco

doi:10.1038/s41467-017-02445-9

Abstract

Different horticultural types of lettuce exhibit tremendous morphological variation. However, the molecular basis for domestication and divergence among the different horticultural types of lettuce remains unknown. Here, we report the RNA sequencing of 240 lettuce accessions sampled from the major horticultural types and wild relatives, generating 1.1 million single-nucleotide polymorphisms (SNPs). Demographic modeling indicates that there was a single domestication event for lettuce. We identify a list of regions as putative selective sweeps that occurred during domestication and divergence, respectively. Genome-wide association studies (GWAS) identify 5311 expression quantitative trait loci (eQTL) regulating the expression of 4105 genes, including nine eQTLs regulating genes associated with flavonoid biosynthesis. GWAS for leaf color detects six candidate loci responsible for the variation of anthocyanins in lettuce leaves. Our study provides a comprehensive understanding of the domestication and the accumulation of anthocyanins in lettuce, and will facilitate the breeding of cultivars with improved nutritional value.

Highlights

Different horticultural types of lettuce exhibit tremendous morphological variation
In addition to these 200 accessions, we included 40 inbred lines derived from a cross between a looseleaf cultivar (S1) and a stem lettuce cultivar (Y37), which were only used for expression quantitative trait loci (eQTL) and Genome-wide association studies (GWAS) analysis in this study
Our results suggested that lettuce undergo a single domestication from L. serriola, and it was estimated to be domesticated 10,829 y B.P. in the Middle East and the Fertile Crescent

Summary

Introduction

Different horticultural types of lettuce exhibit tremendous morphological variation. the molecular basis for domestication and divergence among the different horticultural types of lettuce remains unknown. Our study provides a comprehensive understanding of the domestication and the accumulation of anthocyanins in lettuce, and will facilitate the breeding of cultivars with improved nutritional value. 2500 BCE, indicating that lettuce has been cultivated for at least 4500 years[3,4] Based on their morphological characteristics, cultivars of lettuce are classified into six horticultural types: butterhead, crisphead, looseleaf, romaine, stem, and oilseed. The former four types are harvested and consumed for their leaves and they are collectively referred to as “leafy” types. The domestication of lettuce, its population structure, and the genetic and molecular mechanisms underlying the variations among different horticultural types remain to be investigated[16]. The results in this study shed light on lettuce evolution and provide useful information for future lettuce breeding programs

Methods

Results

Conclusion