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 and Hanhui Kuang ()
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Lei Zhang: Huazhong Agricultural University
Wenqing Su: Huazhong Agricultural University
Rong Tao: Huazhong Agricultural University
Weiyi Zhang: Huazhong Agricultural University
Jiongjiong Chen: Huazhong Agricultural University
Peiyao Wu: Huazhong Agricultural University
Chenghuan Yan: Huazhong Agricultural University
Yue Jia: Huazhong Agricultural University
Robert M. Larkin: Huazhong Agricultural University
Dean Lavelle: University of California
Maria-Jose Truco: University of California
Sebastian Reyes Chin-Wo: University of California
Richard W. Michelmore: University of California
Hanhui Kuang: Huazhong Agricultural University

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: 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.

Date: 2017
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DOI: 10.1038/s41467-017-02445-9

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