Characterization of four polymorphic genes controlling red leaf colour in lettuce that have undergone disruptive selection since domestication.

Anthocyanins protect plants from biotic and abiotic stressors and provide great health benefits to consumers. In this study, we cloned four genes (Red Lettuce Leaves 1 to 4: RLL1 to RLL4) that contribute to colour variations in lettuce. The RLL1 gene encodes a bHLH transcription factor, and a 5-bp deletion in some cultivars abolishes its function to activate the anthocyanin biosynthesis pathway. The RLL2 gene encodes an R2R3-MYB transcription factor, which was derived from a duplication followed by mutations in its promoter region. The RLL3 gene encodes an R2-MYB transcription factor, which down-regulates anthocyanin biosynthesis through competing with RLL2 for interaction with RLL1; a mis-sense mutation compromises the capacity of RLL3 to bind RLL1. The RLL4 gene encodes a WD-40 transcription factor, homologous to the RUP genes suppressing the UV-B signal transduction pathway in Arabidopsis; a mis-sense mutation in rll4 attenuates its suppressing function, leading to a high concentration of anthocyanins. Sequence analysis of the RLL1-RLL4 genes from wild and cultivated lettuce showed that their function-changing mutations occurred after domestication. The mutations in rll1 disrupt anthocyanin biosynthesis, while the mutations in RLL2, rll3 and rll4 activate anthocyanin biosynthesis, showing disruptive selection for leaf colour during domestication of lettuce. The characterization of multiple polymorphic genes in this study provides the necessary molecular resources for the rational breeding of lettuce cultivars with distinct levels of red pigments and green cultivars with high levels of health-promoting flavonoids.

Introduction

Anthocyanins are naturally occurring flavonoid chromophores that are largely responsible for the variation in colour among flowers and fruits, an important adaptive trait in plants. Anthocyanins may also accumulate in leaves to protect the photosynthetic apparatus and photolabile compounds from ultraviolet radiation (Gould, 2004). The accumulation of anthocyanins may be induced by environmental stressors such as UV damage, extreme temperatures and drought (Winkel‐Shirley, 2002). Elevated levels of anthocyanins participate in abiotic or biotic stress tolerance in plants by scavenging reactive oxygen species (Winkel‐Shirley, 2002). The antioxidant activity of anthocyanins also provides great health benefits to consumers (Liobikas et al., 2016; Morais et al., 2016; Qin et al., 2018).

The flavonoid biosynthetic pathway in plants has been well studied. Flavonoid biosynthetic genes can be divided into early biosynthetic genes (EBGs), which catalyse the production of dihydroflavonols and late biosynthetic genes (LBGs), which lead to the biosynthesis of proanthocyanidins and anthocyanins (Ferreyra et al., 2012; Xu et al., 2015). The flavonoid biosynthetic pathway is mainly regulated by a complex of three transcription factors: MYB, bHLH and WD40 (MBW) (Hichri et al., 2011). The MBW complex is regulated by several factors (Li, 2014). In Arabidopsis, MYBL2 negatively regulates the MBW complex by competing with R2R3‐MYBs for interactions with the bHLH component of the MBW complex (Dubos et al., 2008; Matsui et al., 2008). SPL9, a target of miR156/157, disrupts the MBW complex by competitively binding to the R2R3‐MYB subunit of the MBW complex (Gou et al., 2011). TCP3 interacts with R2R3‐MYB proteins and promotes flavonoid biosynthesis (Li and Zachgo, 2013). The RUP1 and RUP2 proteins are two WD40‐repeat proteins that serve as negative regulators of UV‐B signalling and anthocyanin biosynthesis by down‐regulating the expression of HY5, which regulates the expression of genes in the anthocyanin biosynthesis pathway (Gruber et al., 2010). The R2R3‐MYB subunit of the MBW complex may also be regulated by other proteins such as nitrate‐responsive proteins and RING E3 ligase (An et al., 2017; Gruber et al., 2010; Wang et al., 2018b). The expression of genes associated with anthocyanin biosynthesis is often regulated by biotic and abiotic stress and by environmental factors, such as light and temperature.

Genetic cloning of genes responsible for the natural variation in anthocyanin levels in crops may provide novel insights into the regulation of anthocyanin biosynthesis in diverse plants and will provide tools that are directly applicable to breeding programs. High‐throughput sequencing technology has revolutionized the genetic analysis of important traits in crops. The combination of bulked segregant analysis (BSA) and high‐throughput sequencing has been proven to be an efficient and cost‐effective method for the genetic analysis of important traits in crops (Dou et al., 2018; Huo et al., 2016; Michelmore et al., 1991). It can be also used for genetic analysis of QTLs, which was termed QTL‐seq (Illa‐Berenguer et al., 2015; Lu et al., 2014; Singh et al., 2016). Another powerful genetic approach is the genome‐wide association study (GWAS), which has been used to study QTLs controlling important traits in many crops (Bazakos et al., 2017).

Lettuce (Lactuca sativa) is one of the most important vegetable crops worldwide. Lettuce genomics has advanced rapidly in recent years (Reyes‐Chin‐Wo et al., 2017; Zhang et al., 2017). Cultivated lettuce shows dramatic variations in morphology and leaf colour. Previous studies on the inheritance of anthocyanin in lettuce suggested several loci controlling anthocyanin accumulation (Robinson et al., 1983). In our previous GWAS, we identified 12 expression quantitative trait loci (eQTL) that regulate the expression of 24 genes associated with flavonoid biosynthesis (Zhang et al., 2017) and several candidate loci controlling the accumulation of anthocyanins in lettuce leaves (Zhang et al., 2017). However, functional analysis of these candidate genes on the accumulation of anthocyanins was beyond the scope of our initial study. In addition, their evolution and their impact on the regulatory mechanisms that drive the accumulation of anthocyanins remained to be studied.

In this report, we used BSA + RNA‐seq to determine the genetics underlying the red colour of lettuce leaves. Four genes controlling leaf colour in lettuce were genetically mapped, cloned and characterized. We studied the impact of these genes on the mechanisms that regulate the accumulation of anthocyanins in lettuce. The evolution and applied significance of these genes controlling leaf colour of lettuce are discussed.

Results

Colour variation in wild and domesticated lettuce

The leaf colours of 240 lettuce genotypes used previously for GWAS in Zhang et al. (2017) were investigated (Zhang et al., 2017). We also expanded the sampling to include 123 additional wild lettuce genotypes, which typically have green leaves, from different parts of the world (Table S1). In total, 145 genotypes were investigated in this study, including the 22 genotypes from the GWAS population. After treatment with cold or drought, the leaves of wild lettuce may, to some extent, appear red. Unlike wild lettuce, some cultivars do not accumulate red pigments in response to stress. However, other cultivars of lettuce may develop light to dark red leaves when grown under non‐stress conditions. A red cultivar, a green cultivar and a wild progenitor of lettuce were randomly chosen to investigate the types and relative concentrations of anthocyanins (Figure 1a). Using HPLC‐tandem mass spectrometry (MS/MS), three peaks were identified in red cultivars (Figure 1c). Peaks 1, 2 and 3 correspond to three cyanidin derivatives: cyanidin‐3‐O‐(6″‐malonyl‐β‐glucopyranoside), cyanidin‐3‐O‐(6″‐malonyl‐β‐glucopyranoside methyl ester) and cyanidin‐3‐O‐β‐glucopyranoside, respectively (Mulabagal et al., 2010). We quantified the relative levels of anthocyanins in the different genotypes using HPLC (Figure 1b). The green cultivar has no detectable anthocyanin, the red cultivar has abundant anthocyanin, while the wild progenitor accumulated intermediate levels of anthocyanins.

Figure 1

Disruptive selection of anthocyanin accumulation in lettuce. (a) Leaf colour of a red cultivar (left), a wild lettuce (middle) and a green cultivar (right). (b) HPLC analysis of methanolic extracts from the red cultivar (top), the wild genotype (middle) and the green cultivar (bottom). HPLC chromatograms were recorded at 525 nm. Each chromatogram was generated using identical quantities of injected samples. (c) LC‐MS profile of anthocyanins extracted from the red cultivar. Peak 1: cyanidin‐3‐O‐(6″‐malonyl‐β‐glucopyranoside); Peak 2: cyanidin‐3‐O‐β‐glucopyranoside; and Peak 3: cyanidin‐3‐O‐(6″‐malonyl‐β‐glucopyranoside methyl ester).

QTL‐seq evidence for multiple loci controlling the accumulation of anthocyanins in lettuce

To identify loci that affect the accumulation of anthocyanins in lettuce, a lettuce cultivar (S1, with dark red leaves) was crossed with a cultivar of stem lettuce (Y37, with green leaves). The F1 population was selfed to generate a segregating F2 population. Among 218 F2 individuals, 113 plants had green leaves and the other 105 developed pigmentation phenotypes that ranged from light red to dark red. This pattern of phenotypic segregation suggests that the accumulation of anthocyanins in leaves is controlled by both qualitative and quantitative polymorphic loci in this population.

From this F2 population, 50 plants with the most intense red colour were chosen for a ‘red pool’ and 50 plants with green leaves were randomly chosen for a ‘green pool’. Equal amounts of leaf tissue were collected from each individual and pooled. RNA was extracted from each contrasting pool of leaves. The RNA‐seq libraries were sequenced, and reads were mapped to the lettuce genome sequence v8 (Reyes‐Chin‐Wo et al., 2017). Single nucleotide polymorphisms (SNPs) were detected, and allele frequencies for these SNPs were calculated for each pool. The difference in the allele frequency (index) between the two pools was calculated for each SNP and was plotted along the nine chromosomes (Figure 2). The plot figure exhibited multiple peaks of SNP values. These data provide evidence that several loci contributed to the variation in leaf colour in this F2 population. To verify these loci, markers were designed at four loci and were used to screen the F2 population (Table S2). Two loci, Red Lettuce Leaf 1 (RLL1) and Red Lettuce Leaf 2 (RLL2), were shown to be statistically associated with variations in leaf colour (i.e. green or red leaves) in this population. F2 individuals that are homozygous for the Y37 allele at the RLL1 locus (i.e. rll1/rll1) always have green leaves. Similarly, most F2 individuals that are homozygous for the Y37 allele at the RLL2 locus (i.e. rll2/rll2) have green leaves. The combination of the RLL1 and RLL2 loci explained the colour variation (i.e. green or red leaves) for the majority of individuals in the F population. Based on these data, we concluded that RLL1 and RLL2 are two qualitative loci.

Figure 2

Differences in allele frequencies between the red and green pools from the F2 population. The x‐axis represents the nine chromosomes of lettuce. The y‐axis indicates the difference in allele frequencies (SNP values) between the red pool and the green pool. Multiple peaks of SNP values are shown along the nine chromosomes, suggesting several loci contributing to the variation in leaf colour variation in the segregating population. The positions of the four genes that we cloned from this population are marked with arrows. 84 × 24 mm.

The RLL1 gene encodes a bHLH transcription factor

To fine map and clone the RLL1 gene, F individuals with RLL1/rll1 and RLL2/RLL2 genotypes were selfed to generate F2:3 families. One F2:3 family (S9) with red to green phenotypes segregating in an approximately 3:1 ratio was chosen for fine mapping of the RLL1 gene (Figure 3a). RNA‐seq analysis of a red pool and a green pool from the S9 F2:3 family confirmed that the leaf colour was controlled by a single locus on chromosome 5. We named this locus Red Lettuce Leaves 1 (RLL1) (Figure 3b). Using 1751 green individuals (chosen from an F2:3 family of 5100 individuals), the RLL1 gene was mapped between 335.69 and 337.92 Mb on chromosome 5 (Table S2). This interval contains a gene that encodes a putative bHLH transcription factor. Based on a GWAS and a gene expression network analysis, this gene had been predicted to be associated with the accumulation of anthocyanins (Zhang et al., 2017). Comparison of gene sequences of the bHLH gene from the two parents revealed a 5‐bp deletion at the beginning of exon 7 in the green parent that is not present in the red parent (Figure 3c). This 5‐bp deletion in the green parent causes a frameshift and consequently a null allele (rll1). Transformation of a green individual from the segregating population with the wild‐type RLL1 gene from the red parent (S1) yielded transgenic progeny with red leaves. These data indicate that this bHLH‐encoding gene is RLL1 and that RLL1 promotes the accumulation of anthocyanins in lettuce (Figure 3a).

Figure 3

Cloning of the RLL1 gene. (a) The leaf colour of RLL1 and rll1 in the segregating population (left panel), and a green individual (rll1 genotype) from the segregating population and its transgenic rll1 + 35S::RLL1 (right panel). (b) Mapping of the RLL1 gene using BSA. The red and blue curves represent confidence probability of P = 0.01 and P = 0.05, respectively. (c) Structure of the RLL1 gene. The black boxes represent exons, and the lines between the boxes represent introns. The 5‐bp deletion in rll1 is indicated below the relevant exon.

The RLL1 gene up‐regulates the expression of anthocyanin biosynthetic pathway genes

The RNA‐seq data from the red and green pools that were prepared from the S9 F2:3 family indicated that four differentially expressed genes (DEGs) are associated with anthocyanin biosynthesis (CHS, DFR, ANS and GST) in this subpopulation. The differences in their expression were confirmed with a qRT‐PCR analysis that utilized near‐isogenic lines (NILs) that differed in the genomic region containing the RLL1 and rll1 alleles (Figure S1A). Y1H assays demonstrated that the RLL1 transcription factor binds the promoters of the DFR and ANS genes (Figure S1B). Therefore, the loss‐of‐function mutation in the bHLH‐encoding gene (i.e. rll1) down‐regulates the expression of multiple genes in the biosynthetic pathway of anthocyanin and leads to constitutively green leaves.

RLL2 encodes a MYB transcription factor

A F2:3 family (Q16) that was homozygous for RLL1 (from the red parent) and that was segregating the RLL2 locus was used to clone the RLL2 gene. The Q16 F2:3 family had 4058 red and 1372 green individuals (Figure 4a), with a phenotypic ratio of approximately 3:1 (P > 0.5). A BSA + RNA‐seq experiment confirmed that a single locus on chromosome 5 was responsible for the segregating leaf colour in this family (Figure 4b). By genotyping the green individuals (recessive homozygotes), the RLL2 gene was mapped to a 2.6‐Mb region on chromosome 5 (Figure S2A and Table S2). Based on a GWAS and a gene expression network analysis, a gene encoding a MYB transcription factor from this locus was predicted to be associated with the accumulation of anthocyanins (Zhang et al., 2017). To test this hypothesis, we PCR amplified the homologs of this MYB‐encoding gene from the red (S1) and the green parents (Y37). Three homologs (RLL2A, RLL2B and RLL2C) were amplified from the genome of the red parent, which were all mapped to the same locus using gene‐specific markers (Figure 4c). In contrast, one homolog (RLL2B‐Y37) was found in the genome of the green parent, which is identical to the gene in the reference genome. Only the RLL2A gene from the red parent is highly expressed (Figure S2B). Transformation of the green genotype with the RLL2A gene from the red parent yielded transgenic lines with red leaves (Figure 4a). These data demonstrate that the RLL2A copy is the RLL2 gene, which promotes the accumulation of anthocyanins in lettuce.

Figure 4

Cloning of the RLL2 gene. (a) Leaf colour of RLL2 and rll2 in the segregating population (left panel), rll2 and rll2 + 35S::RLL2A (middle panel) and rll2 and rll2 + 35S::RLL2B (right panel). Note that the three rll2 genotypes in the three panels have different genetic backgrounds. (b) Mapping of the RLL2 gene using BSA. The red and blue curves represent confidence probability of P = 0.01 and P = 0.05, respectively. (c) Haplotypes of the RLL2 locus in the green and red parents. The relative positions of the three copies in the red parent are undetermined.

Members of the RLL2 gene family regulate anthocyanin biosynthesis

Both the RLL2B and RLL2B‐Y37 alleles were expressed at low levels and therefore probably do not contribute to the observed colour variation in the Q16 family. To test whether the RLL2B gene can regulate anthocyanin biosynthesis when expressed, the coding sequences of RLL2B driven by the 35S promoter were transformed into a green genotype from the segregating population, and the green phenotype successfully changed to red phenotype. Therefore, when expressed at elevated levels, RLL2B can promote the accumulation of anthocyanins.

From an RNA‐seq analysis of the red and green pools from the Q16 family, we identified 93 DEGs, including four from the anthocyanin biosynthesis pathway (F3H, DFR, ANS and AAC). The differential expression of these four genes was confirmed using qRT‐PCR (Figure S2B). Y1H assays indicated that the RLL2 protein binds the promoters of the DFR and ANS genes (Figure S2C). Therefore, the RLL2 protein appears to promote the accumulation of anthocyanins by directly binding the promoters of genes that encode anthocyanin biosynthetic enzymes. Y1H assays demonstrated that the RLL2B proteins could also bind to the promoter of the ANS and DFR genes, which is consistent with the overexpression of RLL2B promoting the accumulation of anthocyanin (Figure S2C).

RLL3 encodes a MYB transcription factor and repressor of anthocyanin biosynthesis

Although most individuals with RLL1/RLL1_rll2/rll2 (null allele) genotypes have green leaves, some individuals became light red when the seedlings were approximately 1 month old (Figure 5a). Thus, we hypothesized that there is an additional locus that promotes the accumulation of anthocyanins that partially rescues the rll2 green phenotype. We chose an F2:3 family with a RLL1/RLL1_rll2/rll2 genetic background that segregated green to light red phenotypes in a 3:1 ratio to study this locus controlling leaf colour. A BSA + RNA‐seq analysis demonstrated that the colour variation in this subpopulation was controlled by a single locus on chromosome 4 that we named RLL3 (Figure 5b). However, we originally failed to independently confirm this result with the F2 population due to interference from RLL1 and RLL2. Our previous GWAS also identified a significant locus in this region and gene expression network analysis suggested CAD as a candidate gene (Zhang et al., 2017). This locus contributed a moderate peak of SNP values to our earlier BSA + RNA‐seq experiment (Figure 2). However, using a large segregating population (864 recessive homozygotes with red leaves), the CAD gene was excluded as the candidate gene. Instead, the 500‐kb candidate region contains a gene encoding a R3‐MYB transcription factor. Two SNPs (G/A and G/C) in the CDS of this MYB gene cause amino acid substitutions (C42Y and W52S) (Figure 5c).

Figure 5

Cloning of the RLL3 gene. (a) Leaf colour of RLL3 and rll3 in the segregating population. (b) Mapping of the RLL3 gene using BSA. The red and blue curves represent confidence probability of P = 0.01 and P = 0.05, respectively. (c) Gene structure of the RLL3 gene. The black boxes represent exons. The lines between the boxes represent introns. The two SNPs are shown. (d) Yeast two‐hybrid assays. These data indicate that RLL1 and RLL3 can interact and that the W52S substitution in RLL3 but not the C42Y substitution in RLL3 compromised these interactions.

RLL3 negatively regulates anthocyanin biosynthesis by competing with RLL2 for a binding site on RLL1

The predicted RLL3 protein has the conserved [D/E]Lx2[R/K]x3Lx6Lx3R motif in the R3 domain and belongs to the R3‐MYB group of MYB transcription factors. The results from our Y1H experiments indicate that RLL3 does not bind the promoters of the genes that contribute to anthocyanin biosynthesis, probably due to the lack of a DNA‐binding domain in the C‐terminus. We hypothesized that the R3‐MYB RLL3 protein negatively regulates anthocyanin biosynthesis by competing with the RLL2 protein for a binding site on the bHLH subunit of the MBW complex (Baudry et al., 2004).

Y2H assays were used to test the above hypothesis. Y2H showed that RLL1 (bHLH) interacted with RLL2 (R2R3‐MYB) and LsTTG1, the WD40 component in the MBW complex (Walker et al., 1999) (Figure 5d). Interestingly, RLL1 also interacted with the negative regulator RLL3 (R3‐MYB). This interaction was abolished by the W52S substitution present in the rll3 protein (Figure 5d). These results are consistent with our hypothesis that RLL3 suppresses anthocyanin biosynthesis by competing with RLL2 for a binding site on RLL1. Additionally, these data are in accordance with the amino acid substitution in rll3 abolishing this suppression and consequently promoting the accumulation of anthocyanins in the leaves of rll3.

RLL4 is homologous to the RUP genes in Arabidopsis

Mutations in RLL1, RLL2 and RLL3 did not explain all of the colour variation in the F2 population, indicating the presence of an additional locus/loci contributing to the colour variation in lettuce. To test this idea, we planted 114 F4 families and found that leaf colour segregated in 32 of these families. The colour variation in the 32 F4 families was screened using markers derived from RLL1, RLL2 and RLL3 (Table S2). One F4 family, Q54, was homozygous at all three loci but still segregated light red and dark red leaves at a ratio of 195:75 (light red leaves to dark red leaves), which provided evidence for an additional locus (RLL4) controlling leaf colour (Figure 6a). We mapped this gene to chromosome 9 using BSA + RNA‐seq (Figure 6b) and used 3100 individuals to fine map this gene to a 358‐kb region containing five candidate genes (Table S2). One of these genes encodes a WD40 transcription factor. Bi‐direction BLAST and phylogenetic analyses indicated that this WD40‐encoding gene is an ortholog of the RUP1 and RUP2 genes in Arabidopsis, which are negative regulators of UV‐B signalling and anthocyanin biosynthesis (Gruber et al., 2010) (Figure S3). Transgenics with the 35S promoter driving the expression of this RLL4 candidate gene had considerably attenuated the red colour in leaves, which confirmed that the RLL4 gene suppresses the accumulation of anthocyanins (Figure 6a).

Figure 6

Cloning of the RLL4 gene. (a) Leaf colour of plants in the segregating population (left panel), red cultivar THZ (rll4) and transgenic plants with 35S::RLL4 and 35S::rll4 (right panel). (b) Mapping of the RLL4 gene using BSA. A NIL was used as the mapping population. The red and blue curves represent confidence probability of P = 0.01 and P = 0.05, respectively. (c) Structure of the RLL4 gene. The black boxes represent exons, and the lines between the boxes represent introns. The two SNPs are shown. (d) Expression of anthocyanin‐associated genes in the RLL4 and rll4 genotypes of NIL. Gene expression was quantified using qRT‐PCR. The expression of RLL2 and several genes required for anthocyanin biosynthesis was down‐regulated in RLL4 relative to rll4. RLL4 did not affect the expression of HY5a or HY5b. Data are means ± SEM (n = 3 biological replicates).

Point mutation at the conserved WD40 domain‐encoding region abolishes the function of RLL4, leading to up‐regulation of flavonoid biosynthesis genes

Unexpectedly, the RLL4 gene was expressed at slightly higher levels in the dark red individuals than in the light red individuals, which appears to conflict with its function as a suppressor of anthocyanin accumulation. We speculated that its sequence rather than its expression level was responsible for the variation in leaf colour in the segregating population. Sequence comparisons showed two SNPs between RLL4 and rll4. One of them results in an amino acid change (V134D) in the conserved WD40 domain (Figure 6c). Overexpression of the mutated rll4 had no obvious phenotypic change, which is consistent with the above hypothesis that the point mutation in the WD40 domain‐encoding region rather than its expression level determines the functional variations of the RLL4 alleles (Figure 6a).

A qRT‐PCR analysis demonstrated that RLL4 significantly down‐regulated the expression of anthocyanin biosynthesis genes such as RLL2, CHS, F3H, DFR, ANS and AAC in the NILs (Figure 6d). The down‐regulation of anthocyanin biosynthesis genes by RLL4 orthologs (RUP1 and RUP2) was also found in Arabidopsis (Gruber et al., 2010). This down‐regulation functions through the HY5 gene, which connects the UV‐B pathway and the anthocyanin pathway (Brown et al., 2005; Gruber et al., 2010). Unlike in Arabidopsis, the expression of the two HY5 genes in lettuce (HY5a and HY5b) was not affected by the RLL4 gene (Figure 6d), suggesting an alternative regulatory mechanism of RLL4 on anthocyanin biosynthesis in lettuce.

Genetic deficiencies that prevent the accumulation of anthocyanins were selected at an early stage of domestication

To understand the evolution of the four genes cloned in this study, their sequences were obtained from a panel of Lactuca genotypes that includes 124 cultivars from all horticultural types and 145 wild genotypes. The 5‐bp deletion in the RLL1 gene, which abolished its function, was found in 32 cultivars including both leafy and stem lettuce. All cultivars with this rll1 allele have green leaves. On the other hand, all of the 145 wild genotypes collected from all over the world have the wild‐type RLL1 allele. Based on these data, we conclude that the loss‐of‐function mutation in the RLL1 gene occurred in an ancient cultivated population of lettuce.

The red colour of lettuce leaves was selected after domestication

We also investigated the evolution of the three genes that promote the accumulation of anthocyanins in lettuce (RLL2, RLL3 and RLL4). The RLL3 gene is a negative regulator of anthocyanin biosynthesis. The mis‐sense mutation in RLL3 that is responsible for the pigmentation phenotype was not found in the wild genotypes, but was found in three cultivars of loose leaf, eight romaine, three butterhead and four crisphead. Similarly, the causal mis‐sense mutation responsible for the V134A substitution in RLL4 was found only in five cultivated genotypes. Therefore, the loss‐of‐function mutations in the RLL3 and RLL4 genes that promote the accumulation of anthocyanins in lettuce leaves were selected after domestication.

To investigate the evolution of the RLL2 gene family in Lactuca, PCR primers were designed at conserved regions and used to amplify ~700‐bp PCR products from 124 cultivars and 145 wild genotypes of lettuce (Table S2). The PCR products were sequenced directly; 228 of the 269 genotypes have a single homolog of RLL2 that could be classified into 21 distinct groups (with at least one SNP between two groups). The other 41 genotypes have two or more homologs of RLL2 that could be grouped into three distinct RLL2 haplotypes. Genotypes CGN05092, CGN09365 and CGN13325 representing the three haplotypes were chosen to characterize their RLL2 homologs. TA cloning and subsequent sequencing discovered three RLL2 homologs from CGN05092, CGN09365 and CGN13325, respectively. Consequently, a total of 34 distinct RLL2 genes were obtained from the 269 genotypes and a phylogenetic tree was constructed (Figure 7a).

Figure 7

Evolution of the RLL2 gene. (a) Distance tree of the RLL2 homologs from different Lactuca species. A neighbour‐joining (NJ) tree was constructed for RLL2 using DNA sequences containing part of exon II, part of exon III and all of intron II. The three genes from S1 are marked by red triangles, and RLL2B_Y37 is indicated by a circle. Bootstrap values are percentages from 1000 replicates. Values lower than 65 are not shown. The RLL2 homologs amplified from an accession are named with the accession number followed by the species name. (b) The evolution of the RLL2 locus in Lactuca. I, II and III refer to the three clades in (a). The mutation at the promoter of the gene (in red) in clade II in some cultivars led to its accelerated expression. Represented genotypes are listed on the left.

The sequences of the approximately 700‐bp fragments from 39 of the 269 genotypes are identical to the RLL2 sequences, including two genotypes of L. serriola (CGN05092 and CGN11333). Further analysis showed that these two wild genotypes have the RLL2 haplotype similar to that of the S1 parent, that is with three copies of RLL2 homologs (RLL2_CGN05092 and RLL2_CGN11333). However, the expression of the RLL2_CGN05092 gene was significantly lower than that of the RLL2 gene in S1. We obtained the genomic sequences of RLL2_CGN05092, including 1.43 kb of sequences in the promoter region. The difference between RLL2 and RLL2_CGN05092 is a 2‐bp (TA) insertion in RLL2 at −411 bp and three SNPs in the coding region. It is most likely that the 2‐bp insertion in the promoter of the RLL2 gene from S1 activates the gene, resulting in red leaves. Therefore, spontaneous mutations in the RLL2 gene might have been selected after domestication (Figure 7b).

Discussion

Anthocyanin in lettuce is one of the earliest Mendelian traits studied in plants (Dahlgren, 1918; Durst, 1915). In this study, we identified five polymorphic genes controlling anthocyanin accumulation in lettuce. Based on the description of the inheritance and phenotypes, the C and T genes investigated by Thompson 80 years ago are likely the RLL1 genes characterized in this study, because (i) RLL1 is complementary to each other and (ii) homozygotes of loss‐of‐function mutation for either of them completely block anthocyanin biosynthesis in lettuce, which were also the characteristics of the C and T genes (Thompson, 1938). The i gene reported by Lindqvist (1960) resembles the RLL3 or RLL4 gene in this study, since they are recessive intensifiers (Lindqvist, 1960). The R locus studied by Thompson (1938) is very likely to be the RLL2 locus, which controls the intensity of the pigment and spots on lettuce leaves (Thompson, 1938).

Application of BSA + high‐throughput sequencing to study complex genetic traits

Bulked segregant analysis is a fast, economical and efficient method for genetic analysis (Michelmore et al., 1991). High‐throughput sequencing technology is now frequently used with BSA to provide large numbers of informative markers (Ding et al., 2017; Dou et al., 2018; Wang et al., 2018a). In this study, we used BSA + RNA‐seq to efficiently analyse the genetics of red leaf colour in lettuce. Two qualitative loci (RLL1 and RLL2) were easily identified through an analysis of allele frequencies in two contrasting pools. Due to several factors, the other two loci (RLL3 and RLL4), which are QTLs, were not detected in our initial analysis. First, the two qualitative loci are epistatic to the two quantitative loci, and consequently, the differences in the allele frequencies of the two quantitative loci were below detection limits. Second, although a large number of individuals (50) in the green pool may reduce sampling error, a large number of individuals in the red pool may decrease the frequencies of the two colour‐promoting quantitative loci. Furthermore, if the original F2 population had been larger, we would have identified the two quantitative loci using only the dark red individuals for the red pool. Furthermore, due to the epistatic effects of RLL1 and RLL2, we needed to use only red individuals rather than the entire F2 population to identify RLL3 and RLL4. Since the biosynthetic pathway and the regulatory network that drives the accumulation of anthocyanins are highly conserved in plants, homology searches in combination with expression profiling analysis are commonly used to identify genes that are associated with the accumulation of flavonoids in non‐model species, such as lettuce (Zhang et al., 2016). On the other hand, the genetic dissection of the natural variation of anthocyanin levels in crops will show its underlying genetic events, which may provide novel insight into anthocyanin biosynthesis and the regulatory factors that drive the accumulation of anthocyanins, such as the case for the RLL4 gene in this study. This information may be valuable to future breeding programs.

Negative regulators of anthocyanin biosynthesis

Loss‐of‐function mutations in any gene that contributes to anthocyanin biosynthesis may attenuate the accumulation of anthocyanins. For example, a mutation in the ANS gene characterized in this study blocks the conversion of leucoanthocyanidin, a colourless flavonoid, to downstream coloured products. Furthermore, loss‐of‐function alleles can arise from different types of mutations, such as indels that cause frameshifts (Quattrocchio et al., 1999; Tang et al., 2017). Therefore, mutations that attenuate the accumulation of anthocyanins may occur frequently in nature. In contrast, gain‐of‐function mutations are relatively rare. Moreover, a gain‐of‐function mutation in a single gene will only affect the accumulation of the final products of a particular biosynthetic pathway (e.g. the anthocyanin biosynthetic pathway) if the gain‐of‐function mutation affects a rate‐limiting step in the pathway. Transcription factors, such as R2R3‐MYB transcription factors, regulate entire pathways. Thus, we expect that gain‐of‐function mutations in genes encoding transcription factors more commonly promote high‐level accumulation of final products than genes encoding biosynthetic enzymes. In this study, we discovered that high‐level expression of a MYB transcription factor leads to the high‐level accumulation of anthocyanins in lettuce leaves. Similar results were reported in cauliflower, orange and rice (Butelli et al., 2012; Chiu et al., 2010; Oikawa et al., 2015).

Negative regulators of anthocyanin biosynthesis have been reported in plants, such as the RUP1 and RUP2 genes and the R3‐MYB genes (Dubos et al., 2008; Gruber et al., 2010; Matsui et al., 2008) (Aharoni et al., 2001; Cao et al., 2017). As mentioned above, spontaneous loss‐of‐function mutations should occur at a much higher rate than spontaneous gain‐of‐function mutations. Interestingly, we discovered loss‐of‐function mutations in the orthologs of a R3‐MYB gene and the RUP1 and RUP2 genes in lettuce (i.e. RLL3 and RLL4). These mutations considerably increased the abundance of anthocyanins in several cultivars.

The role of RLL4 in anthocyanin biosynthesis in lettuce is highly similar to that of RUP1 and RUP2 in Arabidopsis, since their loss‐of‐function mutations up‐regulate the expression of anthocyanin‐associated genes. However, in contrast to Arabidopsis, RLL4 in lettuce does not regulate anthocyanin biosynthesis through HY5. Our Y2H experiments suggested no interactions between RLL4 and RLL2, therefore ruling out RLL4 as a competitor of TTG1 (the WD40 component of the MBW complex). Nevertheless, anthocyanin biosynthesis in lettuce is UV‐B dependent, and UV‐B treatment induces the expression of HY5. Therefore, it is most likely that HY5 also bridges the UV‐B pathway and anthocyanin biosynthesis pathway in lettuce. Knockout of genes in the UV‐B pathway, such as HY5 and UVR8, in future studies, may shed light on the regulatory mechanism of RLL4 on anthocyanin biosynthesis.

Disruptive selection for leaf colour in lettuce

When grown in optimal conditions, wild lettuce usually develops green leaves with occasional accumulation of anthocyanins near the edge of the leaf lamina. Stress, such as drought, promotes the accumulation of anthocyanins leading to visibly red colour of wild lettuce leaves. However, some lettuce cultivars lost this stress response because of loss‐of‐function mutations in a bHLH‐encoding gene. On the other hand, some lettuce cultivars develop red leaves when they are grown in optimal conditions. The constitutive up‐regulation of anthocyanin biosynthesis is due to a gain‐of‐function mutation in a gene encoding a MYB transcription factor and loss‐of‐function mutations in two negative regulators. Therefore, lettuce cultivars that develop green leaves and cultivars that develop red leaves were both selected during domestication and in modern breeding programmes, showing typical artificial disruptive selection, that is selection favouring extreme values over intermediate values (Krakauer, 2018). Cultivars lacking anthocyanins may decrease their ability against biotic and abiotic stresses. On the other hand, cultivars with high concentration of anthocyanins in their epidermal cells will block the penetration of lights and consequently reduce photosynthesis and plant growth. The selection on green and/or red leaves of a vegetable has been carried out by human being, that is artificial selection. Selection on leaf colour may also exist in nature. For example, trees with bright colour of leaves may reduce their parasite load since insects tend to avoid laying their eggs on bright trees (Archetti and Brown, 2004).

As a salad vegetable, it is important for lettuce to develop diverse colours. Although anthocyanins are appreciated for their health‐promoting benefits, green lettuce is still the main type of lettuce sold on the market. The combination of the anthocyanin‐promoting alleles of four genes (RLL1, RLL2, rll3 and rll4) with the mutated ans gene is predicted to generate a green lettuce cultivar, which accumulates abundant colourless flavonoids, providing health benefits to consumers.

Materials and methods

Mapping population

To study the genetics underlying leaf colour in lettuce, a loose‐leaf cultivar with red leaves (Figure 1) was crossed with a green stem cultivar (Y37). The F1 hybrid was selfed to generate a segregating F2 population of 218 plants. The association of a marker with leaf colour was tested using a chi‐square test. Each F2 individual was selfed for three generations. A large number of seeds were obtained for each line in each generation. These lines were screened to choose informative families for genetic mapping. The lettuce plants were grown in the National Center for Vegetable Improvement (Central China) on the campus of Huazhong Agricultural University in Wuhan, China.

BSA RNA‐seq

For each segregating population, two pools each containing 50 individuals with contrasting phenotypes were constructed. Tissue from the young leaves of 1‐month‐old plants was pooled, and total RNA was extracted using the TRIzol reagent (Invitrogen, Paisley, UK). RNA was quantified and assessed using a Qubit Fluorometer and a Nanodrop spectrophotometer (Novogene, Beijing, China). Paired‐end sequencing was carried out on an Illumina HiSeq 2500 instrument. Raw RNA‐seq data were mapped to the lettuce genome assembly v8 (Reyes‐Chin‐Wo et al., 2017), and SNPs were called. The frequency of each SNP was calculated for both pools. The frequency difference (∆Index) between the two pools was calculated, and their positions on the nine lettuce chromosomes were plotted. A region with a high ∆Index potentially harboured a gene controlling the trait that was used to construct the contrasting pools. RNA‐seq data were available at GenBank under the following accession number PRJNA512330.

Yeast one‐hybrid (Y1H)

To perform Y1H assays, the oligonucleotide sequences containing the core elements of the bHLH binding region (G‐box and E‐box) and MYB binding site (MBS) were arrayed in tandem and cloned into pHIS2, respectively. The coding region of the transcription factors was cloned into pGADT7. The yeast strain AH109 was transformed with each construct using the LiAc‐PEG method as described in the manual from the manufacturer (Clontech, Mountain view, CA, http://www.clontech.com/). The transformed yeast strains were grown on SD/‐Trp/‐Leu medium, and then, different dilutions were spotted on SD/‐Trp/‐Leu/‐His medium in the presence or absence of 45 mm 3‐aminotriazole (Sigma‐Aldrich, http://www.sigmaaldrich.com). The plates were incubated for 3 days at 28 °C. Cell growth was used to assay the activity of the reporter gene.

To test whether the RLL1 transcription factor binds the promoters of the genes encoding anthocyanin biosynthetic enzymes, the oligonucleotide sequences containing the core elements of the bHLH binding regions, the E‐box (CANNTG) and the G‐box (CACGTG) in the promoters of the anthocyanin structural genes were identified at PlantCARE (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/), arrayed in tandem and cloned into pHIS2 vectors. Three truncated fragments of the RLL1 coding sequence were fused to the AD domain coding sequence to test whether RLL1 can interact with the promoter sequences of CHS, CHI, DFR, F3H and ANS because the RLL1 protein had a strong autoactivation activity when fused to the GAL4 activation domain.

Yeast two‐hybrid (Y2H)

Y2H analysis was performed using the Matchmaker Gold Yeast Two‐Hybrid Library Screening System (Clontech). The ORF of bHLH genes were amplified by PCR and inserted into pGBKT7. MYB genes were cloned into pGADT7 vector. All fusion constructs were introduced into yeast strain AH109 using the LiAc‐PEG method as described in the manual from the manufacturer (Clontech). The transformants were selected on SD/‐Leu/‐Trp medium. The positive colonies were transferred to SD/‐Leu/‐Trp/‐His/‐Ade medium containing X‐α‐Gal (5‐bromo‐4‐chloro‐3‐indolyl‐α‐d‐galactopyranoside) to test for interactions between pairs of proteins. Photographs were taken after 3–5 days of growth on the medium at 28 °C.

Transformation and complementation tests

To transform lettuce, the full‐length cDNAs from genes of interest were amplified and cloned into pHellsgate8 (Invitrogen), pRI101 and p06 vectors driven by CaMV 35S promoter. Agrobacterium tumefaciens strain GV3101 was transformed with the constructs that were used for plant transformation using the freeze–thaw method. Transgenic plants were generated using cotyledon explants (Michelmore et al., 1987) and were selected on MS medium supplemented with 40 mg/L kanamycin or 30 mg/L hygromycin by the UC Davis Parsons Plant Transformation Facility (http://ucdptf.ucdavis.edu).

Extraction of anthocyanins and LC‐MS analyses

Lettuce leaves were lyophilized and ground into a fine powder. A total of 0.2 g of this fine powder was extracted with 3 mL of extraction solution (CH3OH containing 1% HCl) at 4 °C for 16 h. The extracts were centrifuged at 1878 at 4 °C for 10 min. The supernatants were transferred to new 2‐mL centrifuge tubes. The extracts were filtered using 0.22‐μm nylon syringe filters before being analysed by LC‐MS. Gradient elution was performed at a flow rate of 0.3 mL/min with solvent A (1% aqueous acetic acid) and solvent B (1% acetic acid and 95% acetonitrile) as follows: 0–20 min, 5%–95% B; 20–24 min, 95% B; 24–26 min, 95%–5% B; and 26–30 min, 5% B. The positive ion mode (m/z M+H+) was used to detect the anthocyanins.

Sequence analysis

RLL2 homologs were amplified using primers that annealed to conserved sequences. The PCR products were cloned into pEASY‐T5 Zero vector (TransGen Biotech, Beijing, China). For the last five clones that were sequenced, individual clones were sequenced until no new sequence data were obtained. Sequences were aligned using Geneious (Drummond, 2010), and phylogenetic trees were constructed using MEGA7.0 (Kumar et al., 2016).

Quantitative RT‐PCR analysis

RNA was extracted using TRIzol reagent (Invitrogen). Approximately 2 μg of total RNA per sample was used to synthesize first‐strand cDNA using TransScript One‐Step gDNA Removal and cDNA Synthesis SuperMix (TransGen Biotech). Quantitative RT‐PCR was performed using SYBR premix Ex Taq (ABMgood, Vancouver, Canada) and the CFX96 Touch System (Bio‐Rad, Hercules, CA). The amplification programme was performed at 95 °C for 30 s, followed by 95 °C for 1 s and 60 °C for 10 s (40 cycles). Ubiquitin was used to normalize the qPCR data.

Accession numbers

RNA‐seq data are available at GenBank under the following accession number PRJNA512330, and gene sequences have accession numbers of MK522155–MK522161.

Author contributions

J.C. and H.K. designed the project. W.S., R.T., W.L., C.Y., Z.Y., S.H., D. L. and G.A. performed the experiments. W.Z., L.Z., Y.Z., Q.H. and D. L. analysed the experimental data. J.C., W.S and R.T. wrote the manuscript with the help of H.K., R.M.L. and R.W.M.

Conflict of interest

The authors declare no conflict of interests.

Figure S1 Characterization of RLL1.

Figure S2 Mapping and functional analysis of the RLL2 gene.

Figure S3 Phylogenetic analysis of RLL4 and its homologs.

Table S1 Summary of the 145 wild lettuce accessions.

Table S2 Primers used in this study.

Click here for additional data file.