Phylogenetic relationships among Lactuca (Asteraceae) species and related genera based on ITS-1 DNA sequences

Genetic Diversity and Evaluation of Agro-Morphological Traits in Lettuce Core Collection

Lettuce (Lactuca sativa) is a globally significant leafy vegetable, valued for both its economic and nutritional contributions. The efficient conservation and use of the lettuce germplasm are crucial for breeding and genetic improvement. This study examined the genetic diversity and population structure of a core collection of the lettuce germplasm using genotyping by sequencing (GBS). A total of 7136 high-quality single-nucleotide polymorphisms (SNPs) were identified across nine chromosomes. Population analysis through Bayesian clustering and discriminant analysis of principal components (DAPC) revealed three distinct genetic clusters. Cluster 2 exhibited the greatest genetic diversity (He = 0.29, I = 0.44), while Cluster 3 had high levels of inbreeding (F = 0.79). Agro-morphological trait evaluation further identified significant differences in leaf length, plant weight, and head height across clusters. These findings provide valuable insights into the genetic and phenotypic diversity of lettuce, facilitating the development of more robust breeding programs. Additionally, the core collection established in this study offers a representative subset of the lettuce germplasm for future genomic research and conservation efforts.

Plastome-based phylogeny and biogeography of Lactuca L. (Asteraceae) support revised lettuce gene pool categories

This study generated and analyzed complete plastome and internal transcribed spacer (ITS) data of 46 Lactuca species, 13 African endemic (AE) Lactuca species, and 15 species from eight related genera in Lactucinae. The new plastome and nuclear ITS sequences were then used to reconstruct the phylogenetic relationships of Lactuca species. The whole-plastome data were used to estimate divergence time and ancestral area reconstruction of the identified major Lactuca lineages. The results showed that Lactuca species are generally similar in plastome size, Guanine and Cytosine (GC) content, gene structure, and categories, although crop lettuce (Lactuca sativa L.) and its gene pool relatives were found to have one unique pseudogene (ψ ndhF), and accD, atpF, cemA, clpP, and rpl22 showed signs of positive selection. Our phylogenomic analysis demonstrated that Lactuca is monophyletic after excluding Lactuca alatipes Collett and Hemsl and AE Lactuca species. AE Lactuca species are morphologically distinct from core Lactuca lineage and need to be excluded from Lactua. The core Lactuca species most likely originated from Asia-Temperate W ~6.82 Mya and then dispersed globally and formed nine clades. Finally, the lettuce gene pool concept was amended according to the phylogenetic and historical biogeographic analyses. This study revised the circumscription of Lactuca, revealed robust phylogenetic relationships within the genus, and provided insights into Lactucinae phylogeny. The lettuce gene pool species could be used as potential genetic resources for lettuce breeding.

Nutritional value of commercial and traditional lettuce (Lactuca sativa L.) and wild relatives: Vitamin C and anthocyanin content

Lettuce is the most consumed leafy vegetable though the most popular varieties have a low nutritional value. Our objective was to accurately quantify vitamin C and anthocyanins in wild relatives, and commercial and traditional varieties. Wild species and traditional varieties contained more total ascorbic acid (TAA) than commercial varieties (21% and 8%, respectively). In contrast, commercial varieties had significantly higher content of anthocyanins than traditional varieties and wild species (6 and 8 times more, respectively). TAA was significantly higher in green than in red lettuces (18%). TAA was also significantly higher in the leaves of two wild species than in stems. Cyanidin 3-O-(6'-O-malonylglucoside) was the most abundant anthocyanin (97%), present in most samples. The rankings of accessions by vitamin C and anthocyanin contents can be useful for consumers worried about the impacts of food on their wellbeing and for breeders aiming to improve lettuce by biofortification with health-promoting compounds.

Sequence of the Mitochondrial Genome of Lactuca virosa Suggests an Unexpected Role in Lactuca sativa's Evolution

The involvement of the different Lactuca species in the domestication and diversification of cultivated lettuce is not totally understood. Lactuca serriola is considered as the direct ancestor and the closest relative to Lactuca sativa, while the other wild species that can be crossed with L. sativa, Lactuca virosa, and Lactuca saligna, would have just contributed to the latter diversification of cultivated typologies. To contribute to the study of Lactuca evolution, we assembled the mtDNA genomes of nine Lactuca spp. accessions, among them three from L. virosa, whose mtDNA had not been studied so far. Our results unveiled little to no intraspecies variation among Lactuca species, with the exception of L. serriola where the accessions we sequenced diverge significantly from the mtDNA of a L. serriola accession already reported. Furthermore, we found a remarkable phylogenetic closeness between the mtDNA of L. sativa and the mtDNA of L. virosa, contrasting to the L. serriola origin of the nuclear and plastidial genomes. These results suggest that a cross between L. virosa and the ancestor of cultivated lettuce is at the origin of the actual mitochondrial genome of L. sativa.

Population genetics and genome-wide association studies provide insights into the influence of selective breeding on genetic variation in lettuce

Genetic diversity is an important resource in crop breeding to improve cultivars with desirable traits. Selective breeding can lead to a reduction of genetic diversity. However, our understanding on this subject remains limited in lettuce (Lactuca sativa L.). Genotyping-by-sequencing (GBS) can provide a reduced version of the genome as a cost-effective method to identify genetic variants across the genome. We genotyped a diverse set of 441 lettuce accessions using the GBS method. Phylogenetic and population genetic analyses indicated substantial genetic divergence among four horticultural types of lettuce: butterhead, crisphead, leaf, and romaine. Genetic-diversity estimates between and within the four types indicated that the crisphead type was the most differentiated from other types, whereas its population was the most homogenous with the slowest linkage disequilibrium (LD) decay among the four types. These results suggested that crisphead lettuces had relatively less genetic variation across the genome as well as low gene flow from other types. We identified putative selective sweep regions that showed low genetic variation in the crisphead type. Genome-wide association study (GWAS) and quantitative trait loci (QTL) analyses provided evidence that these genomic regions were, in part, associated with delayed bolting, implicating the positive selection of delayed bolting in reducing variation. Our findings enhance the current understanding of genetic diversity and the impacts of selective breeding on patterning genetic variation in lettuce.

Chemical constituents from Lactuca plumieri (L.) Gren. & Godr. (Asteraceae)

This is the first report concerning the natural products of the hitherto unstudied Lactuca plumieri (L.) Gren. & Godr., a member of the tribe Cichorieae (Asteraceae). From aerial parts and roots of this plant, five sesquiterpene lactones and one coumarin were isolated. The compounds were identified as sonchuside A, 11β,13-dihydrolactucin-8-O-acetate, 11β,13-dihydrolactucin, cichorioside B, 11β,13-dihydrolactucin-8-O-acetate-15-O-β-glucopyranoside and coumarin - cichoriin. Their structures were established by ¹H NMR. Moreover, HPLC/PAD analysis of a hydroalcoholic extract from the aerial parts of the plant revealed the presence of caffeic acid derivatives, coumarins and flavonoids commonly found in lettuces.

Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce

Lettuce (Lactuca sativa) is an important vegetable crop worldwide. Cultivated lettuce is believed to be domesticated from L. serriola; however, its origins and domestication history remain to be elucidated. Here, we sequenced a total of 445 Lactuca accessions, including major lettuce crop types and wild relative species, and generated a comprehensive map of lettuce genome variations. In-depth analyses of population structure and demography revealed that lettuce was first domesticated near the Caucasus, which was marked by loss of seed shattering. We also identified the genetic architecture of other domestication traits and wild introgressions in major resistance clusters in the lettuce genome. This study provides valuable genomic resources for crop breeding and sheds light on the domestication history of cultivated lettuce.

Metabolite variation in the lettuce gene pool: towards healthier crop varieties and food

INTRODUCTION

Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals.

OBJECTIVES

We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties.

METHODS

Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information.

RESULTS

A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types.

CONCLUSION

Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

Phylogeography of the Macaronesian Lettuce Species Lactuca watsoniana and L. palmensis (Asteraceae)

The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae. Maximum parsimony, Maximum likelihood and Bayesian analysis of a combined molecular dataset (ITS and four chloroplast DNA regions) and molecular clock analyses were performed with the Macaronesian Lactuca species, as well as a TCS haplotype network. The analyses revealed that L. watsoniana and L. palmensis belong to different subclades of the Lactuca clade. Lactuca watsoniana showed a strongly supported phylogenetic relationship with North American species, while L. palmensis was closely related to L. tenerrima and L. inermis, from Europe and Africa. Lactuca watsoniana showed four single-island haplotypes. A divergence time estimation of the Macaronesian lineages was used to examine island colonization pathways. Results obtained with BEAST suggest a divergence of L. palmensis and L. watsoniana clades c. 11 million years ago, L. watsoniana diverged from its North American sister species c. 3.8 million years ago and L. palmensis diverged from its sister L. tenerrima, c. 1.3 million years ago, probably originating from an African ancestral lineage which colonized the Canary Islands. Divergence analyses with *BEAST indicate a more recent divergence of the L. watsoniana crown, c. 0.9 million years ago. In the Azores colonization, in a stepping stone, east-to-west dispersal pattern, associated with geological events might explain the current distribution range of L. watsoniana.

Development of genic-SSR markers and genetic diversity of Indian lettuce (Lactuca indica L.) in South Korea

Indian lettuce (Lactuca indica L.) is an undomesticated wild plant with high economic potential. We know little about the plant's genome, such as its DNA markers, making genetic research using this plant difficult. In this study, 100 genic simple sequence repeat (SSR) primers with a 99-250 bp target amplicon were synthesized from L. indica transcriptomic sequences. These primers were examined in 8 diverse L. indica accessions, and 90 polymorphic SSRs were obtained. Twenty-three of the 90 polymorphic SSRs were used to investigate transferability to another two Lactuca species, Lactuca serriola and Lactuca sativa. Genetic diversity was investigated in 77 Lactuca accessions, including 73 L. indica collected from across South Korea, 2 L. serriola, and 2 L. sativa. Our genic-SSR markers were highly polymorphic with a mean polymorphic information content of 0.61 and, on average, 10.83 alleles per locus. The average expected heterozygosity (0.76) was higher than the observed heterozygosity. An analysis of molecular variance revealed that most of the total variance in our population is attributable to genetic variation among accessions, rather than among provinces. STRUCTURE, unweighted neighbor-joining phylogenetic trees, and principal coordinate analyses resulted in three clusters, where northern and central-southern L. indica accessions were grouped into two clusters with some admixture. The L. serriola and L. sativa accessions did not produce a separate cluster due to a small sample size. These results show our SSR markers will be useful in germplasm assessment and genetic studies of L. indica and other Lactuca species.

Pattern of callose deposition during the course of meiotic diplospory in Chondrilla juncea (Asteraceae, Cichorioideae)

Total absence of callose in the ovules of diplosporous species has been previously suggested. This paper is the first description of callose events in the ovules of Chondrilla juncea, which exhibits meiotic diplospory of the Taraxacum type. We found the presence of callose in the megasporocyte wall and stated that the pattern of callose deposition is dynamically changing during megasporogenesis. At the premeiotic stage, no callose was observed in the ovules. Callose appeared at the micropylar pole of the cell entering prophase of the first meioticdivision restitution but did not surround the megasporocyte. After the formation of a restitution nucleus, a conspicuous callose micropylar cap and dispersed deposits of callose were detected in the megasporocyte wall. During the formation of a diplodyad, the micropylar callose cap decreased and the walls of a newly formed megaspores showed scattered distribution of callose. Within the older diplodyad, callose was mainly accumulated in the wall between megaspores, as well as in the wall of the micropylar cell; however, a dotted fluorescence of callose was also visible in the wall of the chalazal megaspore. Gradual degradation of callose in the wall of the chalazal cell and intense callose accumulation in the wall of the micropylar cell were related to the selection of the functional megaspore. Thus, our findings may suggest that callose fulfills a similar role both during megasporogenesis in sexual angiosperms and in the course of meiotic diplospory in apomicts and seems to form a regulatory interface between reproductive and somatic cells.

Towards new sources of resistance to the currant-lettuce aphid (Nasonovia ribisnigri)

Domesticated lettuce varieties encompass much morphological variation across a range of crop type groups, with large collections of cultivars and landrace accessions maintained in genebanks. Additional variation not captured during domestication, present in ancestral wild relatives, represents a potentially rich source of alleles that can deliver to sustainable crop production. However, these large collections are difficult and costly to screen for many agronomically important traits. In this paper, we describe the generation of a diversity collection of 96 lettuce and wild species accessions that are amenable to routine phenotypic analysis and their genotypic characterization with a panel of 682 newly developed expressed sequence tag (EST)-linked KASP™ single nucleotide polymorphism (SNP) markers that are anchored to the draft Lactuca sativa genome assembly. To exemplify the utility of these resources, we screened the collection for putative sources of resistance to currant-lettuce aphid (Nasonovia ribisnigri) and carried out association analyses to look for potential SNPs linked to resistance.

Molecular phylogeny of the Lactuca alliance (Cichorieae subtribe Lactucinae, Asteraceae) with focus on their Chinese centre of diversity detects potential events of reticulation and chloroplast capture

The first comprehensive molecular phylogenetic reconstruction of the Cichorieae subtribe Lactucinae is provided. Sequences for two datasets, one of the nuclear rDNA ITS region, the other of five concatenated non-coding chloroplast DNA markers including the petD region and the psbA-trnH, 5'trnL((UAA))-trnF, rpl32-trnL((UAG)) and trnQ((UUG))-5'rps16 spacers, were, with few exceptions, newly generated for 130 samples of 78 species. The sampling spans the entire subtribe Lactucinae while focusing on its Chinese centre of diversity; more than 3/4 of the Chinese Lactucinae species are represented. The nuclear and plastid phylogenies inferred from the two independent datasets show various hard topological incongruences. They concern the internal topology of major lineages, in one case the placement of taxa in major lineages, the relationships between major lineages and even the circumscription of the subtribe, indicating potential events of ancient as well as of more recent reticulation and chloroplast capture in the evolution of the subtribe. The core of the subtribe is clearly monophyletic, consisting of the six lineages, Cicerbita, Cicerbita II, Lactuca, Melanoseris, Notoseris and Paraprenanthes. The Faberia lineage and the monospecific Prenanthes purpurea lineage are part of a monophyletic subtribe Lactucinae only in the nuclear or plastid phylogeny, respectively. Morphological and karyological support for their placement is considered. In the light of the molecular phylogenetic reconstruction and of additional morphological data, the conflicting taxonomies of the Chinese Lactuca alliance are discussed and it is concluded that the major lineages revealed are best treated at generic rank. An improved species level taxonomy of the Chinese Lactucinae is outlined; new synonymies and some new combinations are provided.

Hybridization between crops and wild relatives: the contribution of cultivated lettuce to the vigour of crop-wild hybrids under drought, salinity and nutrient deficiency conditions

With the development of transgenic crop varieties, crop-wild hybridization has received considerable consideration with regard to the potential of transgenes to be transferred to wild species. Although many studies have shown that crops can hybridize with their wild relatives and that the resulting hybrids may show improved fitness over the wild parents, little is still known on the genetic contribution of the crop parent to the performance of the hybrids. In this study, we investigated the vigour of lettuce hybrids using 98 F(2:3) families from a cross between cultivated lettuce and its wild relative Lactuca serriola under non-stress conditions and under drought, salinity and nutrient deficiency. Using single nucleotide polymorphism markers, we mapped quantitative trait loci associated with plant vigour in the F(2:3) families and determined the allelic contribution of the two parents. Seventeen QTLs (quantitative trait loci) associated with vigour and six QTLs associated with the accumulation of ions (Na(+), Cl(-) and K(+)) were mapped on the nine linkage groups of lettuce. Seven of the vigour QTLs had a positive effect from the crop allele and six had a positive effect from the wild allele across treatments, and four QTLs had a positive effect from the crop allele in one treatment and from the wild allele in another treatment. Based on the allelic effect of the QTLs and their location on the genetic map, we could suggest genomic locations where transgene integration should be avoided when aiming at the mitigation of its persistence once crop-wild hybridization takes place.

Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers

The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.

A high-density, integrated genetic linkage map of lettuce (Lactuca spp.)

An integrated map for lettuce comprising of 2,744 markers was developed from seven intra- and inter-specific mapping populations. A total of 560 markers that segregated in two or more populations were used to align the individual maps. 2,073 AFLP, 152 RFLP, 130 SSR, and 360 RAPD as well as 29 other markers were assigned to nine chromosomal linkage groups that spanned a total of 1,505 cM and ranged from 136 to 238 cM. The maximum interval between markers in the integrated map is 43 cM and the mean interval is 0.7 cM. The majority of markers segregated close to Mendelian expectations in the intra-specific crosses. In the two L. saligna x L. sativa inter-specific crosses, a total of 155 and 116 markers in 13 regions exhibited significant segregation distortion. Data visualization tools were developed to curate, display and query the data. The integrated map provides a framework for mapping ESTs in one core mapping population relative to phenotypes that segregate in other populations. It also provides large numbers of markers for marker assisted selection, candidate gene identification, and studies of genome evolution in the Compositae.

Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for EST sequences

Using likelihood-based variable selection models, we determined if positive selection was acting on 523 EST sequence pairs from two lineages of sunflower and lettuce. Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates. However, previous studies have shown that the likelihood ratio test (LRT) is reliable for detecting positive selection, even with low numbers of sequences. These analyses identified 56 genes that show a signature of selection, of which 75% were not identified by simpler models that average selection across codons. Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs. We discuss the validity and limitations of using variable rate models for comparisons of sequence pairs, as well as the limitations of using ESTs for identification of positively selected genes.

Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South American Hypochaeris (Asteraceae, Cichorieae)

Hypochaeris has a disjunct distribution, with more than 15 species in the Mediterranean region, the Canary Islands, Europe, and Asia, and more than 40 species in South America. Previous studies have suggested that the New World taxa have evolved from ancestors similar to the central European H. maculata. Based on internal transcribed spacer (ITS) sequences and fluorescence in situ hybridization (FISH) with 5S and 18S-25S rDNA of the previously overlooked Hypochaeris angustifolia from Moyen Atlas, Morocco, we show that it is sister to the entire South American group. A biogeographic analysis supports the hypothesis of long-distance dispersal from NW Africa across the Atlantic Ocean for the origin of the South American taxa rather than migration from North America, through the Panamian land bridge, followed by subsequent extinction in North America. With the assumption of a molecular clock, the trans-Atlantic dispersal from NW Africa to South America is roughly estimated to have taken place during Pliocene or Pleistocene.

Phylogenetic signal in AFLP data sets

AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative.

Species relationships in Lactuca s.l. (Lactuceae, Asteraceae) inferred from AFLP fingerprints

An AFLP data set comprising 95 accessions from 20 species of Lactuca s.l. (sensu lato) and related genera was generated using the primer combinations E35/M48 and E35/M49. In phenetic analyses of a data subset, clustering with UPGMA based on Jaccard's similarity coefficient resulted in the highest cophenetic correlation, and the results were comparable to those of a principal coordinates analysis. In analyses of the total data set, phenetic and cladistic analyses showed similar tree topologies for the well-supported parts of the trees. The validity of cladistic analysis of AFLP data is discussed. The results do not support a distinction among the serriola-like species L. sativa, L. serriola, L. dregeana, and L. altaica, which is in line with previous results. Therefore, we postulate that these species are conspecific. The serriola-like species L. aculeata occupies a clearly separate position, making it an ideal outgroup for studies of the closest relatives of L. sativa. The subsect. Lactuca as a group is well supported by our data, but the positions of L. saligna and L. virosa relative to the serriola-like species remain unclear. The close relationship between the sect. Mulgedium species L. tatarica and L. sibirica is corroborated by the present AFLP results and by additional crossability data.