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

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

Research output: Contribution to journalArticle

21 Citations (Scopus)

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.

Original languageEnglish (US)
Article number2264
JournalNature Communications
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2017

Fingerprint

RNA Sequence Analysis
Lettuce
biosynthesis
sequencing
genome
Biosynthesis
loci
Flavonoids
genes
leaves
divergence
Genes
RNA
Anthocyanins
polymorphism
nucleotides
lists
Genome-Wide Association Study
Association reactions
color

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. / Zhang, Lei; Su, Wenqing; Tao, Rong; Zhang, Weiyi; Chen, Jiongjiong; Wu, Peiyao; Yan, Chenghuan; Jia, Yue; Larkin, Robert M.; Lavelle, Dean; Truco, Maria Jose; Chin-Wo, Sebastian Reyes; Michelmore, Richard W; Kuang, Hanhui.

In: Nature Communications, Vol. 8, No. 1, 2264, 01.12.2017.

Research output: Contribution to journalArticle

Zhang, L, Su, W, Tao, R, Zhang, W, Chen, J, Wu, P, Yan, C, Jia, Y, Larkin, RM, Lavelle, D, Truco, MJ, Chin-Wo, SR, Michelmore, RW & Kuang, H 2017, 'RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis', Nature Communications, vol. 8, no. 1, 2264. https://doi.org/10.1038/s41467-017-02445-9
Zhang, Lei ; Su, Wenqing ; Tao, Rong ; Zhang, Weiyi ; Chen, Jiongjiong ; Wu, Peiyao ; Yan, Chenghuan ; Jia, Yue ; Larkin, Robert M. ; Lavelle, Dean ; Truco, Maria Jose ; Chin-Wo, Sebastian Reyes ; Michelmore, Richard W ; Kuang, Hanhui. / RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis. In: Nature Communications. 2017 ; Vol. 8, No. 1.
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