9 research outputs found
Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1
Background: Lettuce (Lactuca saliva L.) is susceptible to dieback, a soilborne disease caused by two
viruses from the family Tombusviridae. Susceptibility to dieback is widespread in romaine and leaf-type
lettuce, while modern iceberg cultivars are resistant to this disease. Resistance in iceberg cultivars is
conferred by Tvr1 - a single, dominant gene that provides durable resistance. This study describes fine
mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the Tvr1
region, and development of molecular markers for marker-assisted selection.
Results: A combination of classical linkage mapping and association mapping allowed us to pinpoint the
location of the Tvr1 resistance gene on chromosomal linkage group 2. Nine molecular markers, based on
expressed sequence tags (EST), were closely linked to Tvr1 in the mapping population, developed from
crosses between resistant (Salinas and Salinas 88) and susceptible (Valmaine) cultivars. Sequencing of these
markers from a set of 68 cultivars revealed a relatively high level of nucleotide polymorphism (θ = 6.7 ×
10-3) and extensive linkage disequilibrium (r2 = 0.124 at 8 cM) in this region. However, the extent of linkage
disequilibrium was affected by population structure and the values were substantially larger when the
analysis was performed only for romaine (r2 = 0.247) and crisphead (r2 = 0.345) accessions. The association
mapping approach revealed that one of the nine markers (Cntg10192) in the Tvr1 region matched exactly
with resistant and susceptible phenotypes when tested on a set of 200 L. sativa accessions from all
horticultural types of lettuce. The marker-trait association was also confirmed on two accessions of
Lactuca serriola - a wild relative of cultivated lettuce. The combination of three single-nucleotide
polymorphisms (SNPs) at the Cntg10192 marker identified four haplotypes. Three of the haplotypes were
associated with resistance and one of them was always associated with susceptibility to the disease.
Conclusion: We have successfully applied high-resolution DNA melting (HRM) analysis to distinguish all
four haplotypes of the Cntg10192 marker in a single analysis. Marker-assisted selection for dieback
resistance with HRM is now an integral part of our breeding program that is focused on the development
of improved lettuce cultivars
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A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.).
Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC(3)S(2) near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2-3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds
Associating Phenotype to Genotype in Lettuce Using NGS, in silico Analyses, High Resolution Genetic Maps and Targeted Fine Mapping: abstract
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Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.
Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence