A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.)

Abstract

To improve several agronomic traits in crisphead lettuce (Lactuca sativa L.) under high-temperature growth conditions, we investigated the correlation among those traits in multiple cultivars and performed genetic mapping of their causal genes. In a field cultivation test of Empire type (serrated leaf) and Salinas type (wavy leaf) cultivars, Empire type cultivars showed increased tipburn susceptibility and late bolting compared with Salinas type cultivars. We attempted genetic mapping of leaf shape and bolting time by ddRAD-seq using the F 2 population derived from a cross between 'VI185' (Empire type) and 'ShinanoGreen' (Salinas type). These analyses suggested that both traits are controlled by a single locus in LG5. Genotyping of 51 commercial lettuce cultivars with a tightly linked marker (LG5_v8_252.743Mbp) at this locus showed an association between its genotype and the serrated leaf phenotype. By further fine mapping and transcriptome analysis, a gene encoding putative CIN-like TCP transcription factor was determined to be a candidate gene at this locus and was designated as LsTCP4. An insertion of retrotransposable element was found in the allele of 'VI185', and its transcript level in the leaves was lower than that in 'ShinanoGreen'. Because shapes of leaf epidermal cells in 'VI185' were similar to those in the TCP family mutant of Arabidopsis thaliana, the leaf shape phenotype was likely caused by reduced expression of LsTCP4. Furthermore, because it is known that the TCP family protein also controls flowering time via interaction with FT in A. thaliana, it was highly possible that LsTCP4 gave pleiotropic effects on both leaf shape and bolting time in lettuce.

Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

“…In petunia, seven closest homologs of the CIN -like genes ( PaTCP3a , 3b , 4a , 4b , 10 , 24a and 24b ) have the putative binding sites for PamiR319 ( Figure 2 c). High expression levels of PaTCP3a , PaTCP4a/PaTCP4b , PaTCP10 and PaTCP24a/PaTCP24b in leaves suggest their potential roles in leaf development, which may be conserved for the TCP genes targeted by miR319 [ 8 , 55 , 57 , 58 , 59 ]. Moreover, the transcripts of most putative miR319-regulated PaTCP genes are detected in most tested tissues, including seedlings, cotyledons, leaves, axillary buds, inflorescences and flower buds, suggesting that these PaTCPs may play diverse regulatory roles at multiple developmental processes in petunia.…”

The Regulation of CIN-like TCP Transcription Factors

“…The molecular base is that Empire type cultivars carry a retrotransposable element inserted in the upstream of LsTCP4 gene, causing lower expression level of LsTCP4 than that in the Salina type cultivars. The downregulation of LsTCP4 by the insertion led to the severer leaf serration in Empire type cultivars [ 61 ]. However, differential expression analysis between broad- and curly-leaved plants of Cichorium endivia , a close relative of L. sativa that also displayed wavy or serrated leaves, did not identify TCP4-like homologous genes as differentially expressed in leaves with different morphologies, and the two transcripts were abundant in both leaf types [ 62 ].…”

A Composite Analysis of Flowering Time Regulation in Lettuce

“…Physical coordinates of the markers flanking significant QTLs were reported in seven studies ( Niroula, 2017 ; Mamo et al, 2019 ; Sandoya et al, 2020 ; Seki et al, 2020 ; Sthapit Kandel et al, 2020 ; Niroula et al, unpublished; You et al, unpublished). DNA variant detector array probe sequences of the lettuce expression sequence tag (EST)-based single nucleotide polymorphism (SNP) markers used in four studies ( Hartman et al, 2013b ; Jenni et al, 2013 ; Kwon et al, 2013 ; Niroula, 2017 ) were blasted against version 8 of the reference genome ( Reyes-Chin-Wo et al, 2017 ; NCBI: GCA_002870075.2) to determine their physical locations.…”

“…Two of these genes, Lsat_1_v5_gn_2_86121 and Lsat_1_v5_gn_5_122401, show oscillating expression in 24-hour periods. Lsat_1_v5_gn_5_122401 is within qFLT5.3 (Seki et al, 2020). No CO-like gene has been analyzed functionally in lettuce.…”