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Heatmap of estimated recombination fractions (upper-left triangle) and logarithm of the odds (LOD) scores (lower-right triangle) for all pairs of markers in the F 2 population (n = 181) of Solanum lycopersicum RvT1 · S. cheesmaniae Lche4. Red indicates markers are linked (large LOD score or small recombination fraction), and blue indicates markers are not linked (small LOD score or large recombination fraction).
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Roots impact plants’ capacity to absorb water and nutrients and thus play a vital role in tolerance to drought, salinity, and nutrient stress. In tomato ( Solanum lycopersicum ) breeding programs, wild tomato species have been commonly used to increase disease resistance and fruit quality and yield. However, tomato has seldom been bred for water/nu...
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... gap between markers was 19.68 cM on chromosome 5 (Table 3, Supplemental Fig. 2). Given the tomato genome size of %950 Mb, the current genetic map is %0.72 Mb/cM. The heatmap of estimated recombination and LOD scores of mapped markers showed consistent heat across the diagonal line within chromosomes, suggesting this is a good-quality linkage map (Fig. 5). QTL ANALYSIS. The QTL analysis included 181 F 2 seedlings. When two or more QTLs overlapped within the same confidence interval, they were identified as the same QTL. The threshold LOD score declaring a significant QTL was calculated as 3.7 to 4.0 for all traits. A total of 29 putative QTLs for root and shoot traits were detected on ...
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... Bacteral canker resistance F2 mapping population Abebe et al. (2022) pest resistance, abiotic stress etc (Celik et al., 2017, Xie et al., 2019100 Tomato Genome Sequencing Consortium, 2014). A combination of RNA-seq and QTL mapping approaches has been applied to map QTLs to identify candidate genes. ...
Tomato is an important vegetable of the human diet. In tomatoes, through conventional breeding methods, many cultivars with desirable traits have been developed. With the advancement in sequencing technologies combined with reducing cost per sample, high-throughput genotyping platforms and bioinformatics pipelines have revolutionized tomato improvement. After the tomato genome sequencing in 2012, thousands of cultivated and wild species have been sequenced with respect to studies on population structure, genetic diversity, high-density maps and structural variants analysis so on. Now, genomics-assisted research would aim to discover of QTLs/genes and associated single nucleotide polymorphisms (SNP) markers by genome-wide association studies (GWAS) using high-throughput genotyping (SNP array or genotyping-by-sequencing) for rapid breeding. Moreover, genome editing and genomics selection tools would increase breeding efficiency and higher genetic gain in tomatoes.
... Identified haplotypes associated with quality traits, and candidate genes for fruit weight and metabolites. of these QTLs in the domestication of tomatoes (Ye et al., 2017;Zhang et al., 2018a). Moreover, the availability of the reference tomato genome (Tomato Genome Consortium, 2012) has advanced the genetic mapping in tomatoes for various traits, such as plant phenotype, root, leaf, fruit, disease-pest resistance, and abiotic stress tolerance (Celik et al., 2017;Xie et al., 2019). Recent genomics approaches have greatly increased fine mapping to discover new genes in tomatoes for breeding purposes. ...
Tomato is an important vegetable crop for fresh and processed products. In the past decades, conventional breeding cum marker-assisted selection (MAS) has been deployed widely to develop modern tomato cultivars with desirable agronomic traits, market classes, and consumer preferences. The rapid developments in sequencing technologies with the reduced costs per sample, high-throughput single nucleotide polymorphism (SNP) genotyping platforms, and bioinformatics tools have revolutionized crop improvement programs, and deciphered the tomato genome sequence in 2012. Since then thousands of cultivated, its close relatives, and wild species have been genome resequenced to analyze structural variants population structure, genetic diversity, high-density map construction so on. Further, tomato pan-genomes have been constructed to search genomics regions associated with agronomic traits to expedite the breeding process. Importantly, genomics-assisted research has begun in tomatoes with the identification of genes, and SNP markers associated with phenotypic variation by applying genome resequencing, genome-wide association studies (GWAS) using SNP array, and genotyping-by-sequencing techniques. Further, the genomic selection (GS) method is expected to increase breeding efficiency and genetic gain rapidly. This review provides the latest information on progress in MAS to genome resequencing, pan-genomes, SNP genotyping, GWAS, and GS for genomics-assisted breeding in tomatoes.
... In the pairwise recombination fraction plot, some markers had high recombination frequencies (>0.5), but low LOD scores ( Supplementary Fig. 5a). The heatmap of estimated recombination and LOD scores of mapped markers showed a low level of off-diagonal association between marker pairs and consistency of square-like heat blocks across the diagonal line within chromosomes, suggesting this is a good-quality linkage map ( Supplementary Fig. 5b) 35 . Of the 996 mapped SNP markers, 121 (12.1%) showed significant (P < 0.01) distortion from the 1:2:1 segregation ratio in the F2 population, with heterozygote deficiency (LG11 and LG13) or heterozygote excess (LG1 and LG8) (Fig. 5). ...
The freshwater snail Biomphalaria glabrata is an important intermediate host of the parasite Schistosoma mansoni that causes human intestinal schistosomiasis. To better understand vector snail biology and help advance innovative snail control strategies, we have developed a new snail model consisting of two homozygous B. glabrata lines (iM line and iBS90) with sharply contrasting schistosome-resistance phenotypes. We produced and compared high-quality genome sequences for iM line and iBS90 which were assembled from 255 (N50 = 22.7 Mb) and 346 (N50 = 19.4 Mb) scaffolds, respectively. Using F2 offspring bred from the two lines and the newly generated iM line genome, we constructed 18 linkage groups (representing the 18 haploid chromosomes) covering 96% of the genome and identified three new QTLs (quantitative trait loci), two involved in snail resistance/susceptibility and one relating to body pigmentation. This study provides excellent genomic resources for unveiling complex vector snail biology, reveals genomic difference between resistant and susceptible lines, and offers novel insights into genetic mechanism of the compatibility between snail and schistosome. Using newly developed genetic resources, comparative genomics, and genetic mapping, this study provides novel insights into schistosome resistance in the snail Biomphalaria glabrata, an important intermediate host of Schistosoma mansoni, a causative agent of human schistosomiasis.
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Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on the status of genomics and marker-assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop, we present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies.
