Backcross Inbred Lines Research Articles

Solanum pimpinellifolium exhibits complex genetic resistance to Pseudomonas syringae pv. tomato

Pseudomonas syringae pv. tomato (Pst) is the causal agent of bacterial speck disease in tomatoes. The Pto/Prf gene cluster from Solanum pimpinellifolium was introgressed into several modern tomato cultivars and provided protection against Pst race 0 strains for many decades. However, virulent Pst race 1 strains that evade Pto-mediated immunity now predominate in tomato-growing regions worldwide. Here we report the identification of resistance to a Pst race 1 strain (Pst19) in the wild tomato accession S. pimpinellifolium LA1589 (hereafter LA1589), using our rapid high-throughput seedling screen. LA1589 supports less bacterial growth than cultivars, and does not exhibit a hypersensitive response to Pst19. We tested an existing set of 87 Inbred Backcross Lines (IBLs) derived from a cross between susceptible Solanum lycopersicum E-6203 and Solanum pimpinellifolium LA1589 for resistance to Pst19. Using single-marker analysis, we identified three genomic regions associated with resistance. Bacterial growth assays on IBLs confirmed that these regions contribute to resistance in planta. We also mapped candidate genes associated with resistance in a cross between the Solanum lycopersicum var. lycopersicum cultivar Heinz BG-1706 and S. pimpinellifolium LA1589. By comparing candidates from the two mapping approaches, we were able to identify 3 QTL and 5 candidate genes in LA1589 for a role in resistance to Pst19. This work will assist in molecular marker-assisted breeding to protect tomato from bacterial speck disease.

The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites

Capsicum (pepper) is among the most economically important species worldwide, and its fruits accumulate specialized metabolites with essential roles in plant environmental interaction and human health benefits as well as in conferring their unique taste. However, the genetics underlying differences in metabolite presence/absence and/or accumulation remain largely unknown. In this study, we carried out a genome-wide association study as well as generating and characterizing a novel backcross inbred line mapping population to determine the genetic architecture of the pepper metabolome. This genetic analysis provided over 1,000 metabolic quantitative trait loci (mQTL) for over 250 annotated metabolites. We identified 92 candidate genes involved in various mQTLs. Among the identified loci, we described and validated a gene cluster of eleven UDP-glycosyltransferases (UGTs) involved in monomeric capsianoside biosynthesis. We additionally constructed the gene-by-gene-based biosynthetic pathway of pepper capsianoside biosynthesis, including both core and decorative reactions. Given that one of these decorative pathways, namely the glycosylation of acyclic diterpenoid glycosides, contributes to plant resistance, these data provide new insights and breeding resources for pepper. They additionally provide a blueprint for the better understanding of the biosynthesis of species-specific natural compounds in general.

Comparative transcriptome profiling to untie the drought tolerance molecular mechanism of backcross rice (Oryza sativa L.) inbred

AbstractRice production is severely hampered by drought stress, which causes enormous economic losses. The issue of global climate change is gaining importance, and hence development of rice genotypes tolerant to drought stress is becoming more critical. To address this issue, backcross inbred lines (BILs) developed were subjected to drought stress, and their molecular mechanism was studied. The drought‐tolerant parent Apo and drought‐susceptible, high‐yielding IR64 along with two BILs, namely, CB 229 (qDTY2.2 + qDTY3.1 + qDTY8.1) and CB 193‐3 (qDTY3.1 + qDTY8.1) were tested in a greenhouse for their response to drought. In this study, CB 229 showed better performance under water stress irrigated conditions; it was on par with IR64. Drought‐responsive transcriptome profiling was carried out in both the parents and the superior BIL CB 229 through the RNA‐Seq approach. About 3050 differentially expressed genes (DEGs) (2021 upregulated and 1029 downregulated) were detected in tolerant BIL CB 229 in drought stress. Most of the DEGs were involved in carbohydrate metabolism and the formation of cell walls, as well as genes associated with metabolite adaptability, ROS homeostasis and post‐transcriptional regulation. Genes such as chaperone protein, senescence‐induced receptor‐like serine, mannose‐6‐phosphate isomerase, aquaporin and heat shock proteins (LOC_Os02g26840, LOC_Os02g25720, LOC_Os07g35570, LOC_Os01g64970, etc.) were upregulated in the tolerant Apo and CB 229. It was observed that the BIL CB 229 yielded higher grains than both parents under moisture stress. Ninety‐four genes in the quantitative trait loci (QTLs) region were found to be differentially regulated in CB 229, Apo and IR64. Out of 94, nine genes co‐localized within the QTL qDTY2.2, 12 genes within qDTY3.1 and four genes within qDTY8.1 were differentially upregulated in CB 229 and downregulated in the susceptible genotype. The study revealed that the QTLs qDTY2.2, qDTY3.1 and qDTY8.1 are found to have complementary effects and offer enhanced levels of tolerance against drought due to complementation. Additionally, this analysis discovered new DEGs that may be involved in functions related to drought tolerance but lack function annotations. Future research can focus on a few of the significant DEGs found in this study. Taken together, our findings provide insight into drought tolerance mechanisms and could assist the development of novel strategies for improving drought tolerance in rice.

New population of Solanum pimpinellifolium backcross inbred lines as a resource for heat stress tolerance in tomato.

The occurring temperature increase in crop production areas worldwide is generating conditions of heat stress that negatively affect crop productivity. Tomato (Solanum lycopersicum), a major vegetable crop, is highly susceptible to elevated temperatures. Under such conditions, fruit set is dramatically reduced, leading to significant yield losses. Solanum pimpinellifolium, a wild species closely related to the cultivated tomato, was shown to have beneficial attributes under various abiotic stress growth conditions. We have utilized a new population of backcross inbred lines originated from a cross between S. pimpinellifolium and S. lycopersicum, in order to evaluate its potential as a new genetic resource for improvement of reproductive performance of cultivated tomato under heat stress conditions. This population was screened for various heat stress-related traits, under controlled heat stress and non-stress conditions. Our results show that significant variation exists for all the heat stress related traits that were examined and point at individual lines with better reproductive performance under heat stress conditions that share a common introgression from the wild S. pimpinellifolium parent, suggesting several candidate genes as potential drivers of thermotolerance. Thus, our results place this population as a valuable new resource for the discovery of heat stress related genetic loci for the future development of heat stress tolerant tomato cultivars.

Identification of genomic regions controlling spikelet degeneration under FRIZZLE PANICLE (FZP) defect genetic background in rice

The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts.

Co-localization and analysis of miR477b with fiber length quantitative trait loci in cotton.

Cotton is an important cash crop for the textile industry. However, the understanding of natural genetic variation of fiber elongation in relation to miRNA is lacking. A miRNA gene (miR477b) was found to co-localize with a previously mapped fiber length (FL) quantitative trait locus (QTL). The miR477b was differentially expressed during fiber elongation between two backcross inbred lines (BILs) differing in FL and its precursor sequences. Bioinformatics and qRT-PCR analysis were further used to analyse the miRNA genes, which could produce mature miR477b. Cotton plants with virus-induced gene silencing (VIGS) constructs to over-express the allele of miR477b from the BIL with longer fibers had significantly longer fibers as compared with negative control plants, while the VIGS plants with suppressed miRNA expression had significantly shorter fibers. The expression level of the target gene (DELLA) and related genes (RDL1 and EXPA1 for DELLA through HOX3 protein) in the two BILs and/or the VIGS plants were generally congruent, as expected. This report represents one of the first comprehensive studies to integrate QTL linkage mapping and physical mapping of small RNAs with both small and mRNA transcriptome analysis, followed by VIGS, to identify candidate small RNA genes affecting the natural variation of fiber elongation in cotton.

Fine Mapping of qAL5.2 Controlling Anther Length in Oryza sativa.

Anther length is the critical floral trait determining hybrid rice seed production and is controlled by many quantitative trait loci (QTL). However, the cloning of genes specifically controlling anther size has yet to be reported. Here, we report the fine mapping of qAL5.2 for anther size using backcross inbred lines (BILs) in the genetic background of Oryza sativa indica Huazhan (HZ). Gene chip analysis on the BC4F2 and BC5F1 population identified effective loci on Chr1, Chr5, and Chr8 and two genomic regions on Chr5, named qAL5.1 and qAL5.2. qAL5.2 was identified in both populations with LOD values of 17.54 and 10.19, which explained 35.73% and 25.1% of the phenotypic variances, respectively. Ultimately qAL5.2 was localized to a 73 kb region between HK139 and HK140 on chromosome 5. And we constructed two near-isogenic lines (NILs) for RNA-seq analysis, named NIL-qAL5.2HZ and NIL-qAL5.2KLY, respectively. The result of the GO enrichment analysis revealed that differential genes were significantly enriched in the carbohydrate metabolic process, extracellular region, and nucleic acid binding transcription, and KEGG enrichment analysis revealed that alpha-linolenic acid metabolism was significantly enriched. Meanwhile, candidate genes of qAL5.2 were analyzed in RNA-seq, and it was found that ORF8 is differentially expressed between NIL-qAL5.2HZ and NIL-qAL5.2KLY. The fine mapping of qAL5.2 conferring anther length will promote the breed improvement of the restorer line and understanding of the mechanisms driving crop mating patterns.

Solanum pennellii (LA5240) backcross inbred lines (BILs) for high resolution mapping in tomato.

Wild species are an invaluable source of new traits for crop improvement. Over the years, the tomato community bred cultivated lines that carry introgressions from different species of the tomato tribe to facilitate trait discovery and mapping. The next phase in such projects is to find the genes that drive the identified phenotypes. This can be achieved by genotyping a few thousand individuals resulting in fine mapping that can potentially identify the causative gene. To couple trait discovery and fine mapping, we are presenting large, recombination-rich, Backcross Inbred Line (BIL) populations involving an unexplored accession of the wild, green-fruited species Solanum pennellii (LA5240; the 'Lost' Accession) with two modern tomato inbreds: LEA, determinate, and TOP, indeterminate. The LEA and TOP BILs are in BC2F6-8 generation and include 1400 and 500 lines, respectively. The BILs were genotyped with 5000 SPET markers, showing that in the euchromatic regions there was one recombinant every 17-18 Kb while in the heterochromatin a recombinant every 600-700 Kb (TOP and LEA respectively). To gain perspective on the topography of recombination we compared five independent members of the Self-pruning gene family with their respective neighboring genes; based on PCR markers, in all cases we found recombinants. Further mapping analysis of two known morphological mutations that segregated in the BILs (self-pruning and hairless) showed that the maximal delimited intervals were 73 Kb and 210 Kb, respectively, and included the known causative genes. The 'Lost'_BILs provide a solid framework to study traits derived from a drought-tolerant wild tomato.

Genetic Improvement of Drought Tolerance in a Mega-Rice Variety Improved White Ponni through Marker-Assisted Backcross Breeding

In the ever-changing climatic conditions, it has become important to enhance rice productivity to ensure global food security. Drought is one of the major limiting factors in rice pro- duction. Drought during the reproductive stage results in maximum or complete yield loss. Efforts have been taken to develop drought-tolerant rice lines by introgressing three major drought-effect QTLs, viz. qDTY1.1, qDTY2.1, and qDTY3.1, from Apo into a susceptible popular rice variety, Improved White Ponni (IWP). Backcross inbred lines of IWP × Apo were developed through the marker-assisted backcross breeding approach. Foreground analysis using linked markers resulted in the identification of 17 progenies carrying two or more QTLs, and the recurrent parent genome recoveries of these lines were >95.6% using 72 genome-wide SSR markers distributed throughout all chromosomes. Upon phenotypic evaluation of 17 IWP BILs, the water limited condition resulted in the identification of improved lines by recording the yield and the yield-related parameters. The promising performance of IWP BILs in terms of spikelet fertility (63.3%) and grain yield per plant (>10 g) under drought stress indicated the positive effects of introgressed qDTYs, while IWP recorded complete yield loss (94.2%). Out of the cultivars considered, the best-performing lines which truly exhibited drought tolerance, with more increased yield than the recurrent parent under water-limited conditions, and the effects of these QTLs and their interactions were examined in this research work.

The QTL and Candidate Genes Regulating the Early Tillering Vigor Traits of Late-Season Rice in Double-Cropping Systems.

Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes and the molecular mechanism underlying rice-regulating ETV traits are unclear. In this study, the candidate genes in regulating ETV traits have been sought by quantitative trait locus (QTL) mapping and bulk-segregation analysis by resequencing method (BSA-seq) conjoint analysis using rice backcross inbred line (BIL) populations, which were cultivated as late-season rice of double-cropping rice systems. By QTL mapping, seven QTLs were detected on chromosomes 1, 3, 4, and 9, with the logarithm of the odds (LOD) values ranging from 3.52 to 7.57 and explained 3.23% to 12.98% of the observed phenotypic variance. By BSA-seq analysis, seven QTLs on chromosomes 1, 2, 4, 5, 7, and 9 were identified using single-nucleotide polymorphism (SNP) and insertions/deletions (InDel) index algorithm and Euclidean distance (ED) algorithm. The overlapping QTL resulting from QTL mapping and BSA-seq analysis was shown in a 1.39 Mb interval on chromosome 4. In the overlap interval, six genes, including the functional unknown genes Os04g0455650, Os04g0470901, Os04g0500600, and ethylene-insensitive 3 (Os04g0456900), sialyltransferase family domain containing protein (Os04g0506800), and ATOZI1 (Os04g0497300), showed the differential expression between ETV rice lines and late tillering vigor (LTV) rice lines and have a missense base mutation in the genomic DNA sequences of the parents. We speculate that the six genes are the candidate genes regulating the ETV trait in rice, which provides a research basis for revealing the molecular mechanism behind the ETV traits in rice.

Mapping QTLs for grain iron, zinc, and yield traits in advanced backcross inbred lines of Samba mahsuri (BPT5204)/Oryza rufipogon

Mapping QTLs for grain iron, zinc, and yield traits in advanced backcross inbred lines of Samba mahsuri (BPT5204)/Oryza rufipogon

Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum).

Integrated QTL mapping and WGCNA condense the potential gene regulatory network involved in oil accumulation. A glycosyl hydrolases gene (GhHSD1) for oil biosynthesis was confirmed in Arabidopsis, which will provide useful knowledge to understand the functional mechanism of oil biosynthesis in cotton. Cotton is an economical source of edible oil for the food industry. The genetic mechanism that regulates oil biosynthesis in cottonseeds is essential for the genetic enhancement of oil content (OC). To explore the functional genomics of OC, this study utilized an interspecific backcross inbred line population to dissect the quantitative trait locus (QTL) interlinked with OC. In total, nine OC QTLs were identified, four of which were novel, and each QTL explained 3.62-34.73% of the phenotypic variation of OC. The comprehensive transcript profiling of developing cottonseeds revealed 3,646 core genes differentially expressed in both inbred parents. Functional enrichment analysis determined 43 genes were annotated with oil biosynthesis processes. Implementation of weighted gene co-expression network analysis showed that 803 differential genes had a significant correlation with the OC phenotype. Further integrated analysis identified seven important genes located in OC QTLs. Of which, the GhHSD1 gene located in stable QTL qOC-Dt3-1 exhibited the highest functional linkages with the other network genes. Phylogenetic analysis showed significant evolutionary differences in the HSD1 sequences between oilseed- and starch- crops. Furthermore, the overexpression of GhHSD1 in Arabidopsis yielded almost 6.78% higher seed oil. This study not only uncovers important genetic loci for oil accumulation in cottonseed, but also provides a set of new candidate genes that potentially influence the oil biosynthesis pathway in cottonseed.

Study on Genetic Variability and Correlation of Yield Traits in the F3 Population Derived from Wild Introgression Lines of Swarna/Oryza nivara

Wild and related species are a source of wide genetic diversity. Back cross inbred line 166-2S derived from Swarna/Oryza nivara was crossed with Swarna to generate F3 population. This F3 population was raised in wet season of 2018 and data was collected for ten yield traits. Among all ten yield traits, single plant yield was highly associated with PH, TN, PTN, BM, TDM, HI, PL, PW and GW. HI was observed with a highly significant negative association with PH and BM. Positive skewness was observed for TN, PTN, SPY, BM, TDM and GW with platykurtic distribution and complementary gene action, suggesting an intense selection for better genetic gain. The panicle weight showed positive skewness with leptokurtic distribution, indicating the genetic regulation by only a few segregating genes. The negatively skewed and platykurtic distribution of PH, PL and HI indicated the governance of large number of dominant genes with duplicate interaction in the inheritance of these traits.

Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy.

Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.

Identification and Functional Characterization of Two Major Loci Associated with Resistance against Brown Planthoppers (Nilaparvata lugens (Stål)) Derived from Oryza nivara.

The brown planthopper (BPH) is a highly destructive pest of rice, causing significant economic losses in various regions of South and Southeast Asia. Researchers have made promising strides in developing resistance against BPH in rice. Introgression line RPBio4918-230S, derived from Oryza nivara, has shown consistent resistance to BPH at both the seedling and adult stages of rice plants. Segregation analysis has revealed that this resistance is governed by two recessive loci, known as bph39(t) and bph40(t), contributing to 21% and 22% of the phenotypic variance, respectively. We later mapped the genes using a backcross population derived from a cross between Swarna and RPBio4918-230S. We identified specific marker loci, namely RM8213, RM5953, and R4M17, on chromosome 4, flanking the bph39(t) and bph40(t) loci. Furthermore, quantitative expression analysis of candidate genes situated between the RM8213 and R4M17 markers was conducted. It was observed that eight genes exhibited up-regulation in RPBio4918-230S and down-regulation in Swarna after BPH infestation. One gene of particular interest, a serine/threonine-protein kinase receptor (STPKR), showed significant up-regulation in RPBio4918-230S. In-depth sequencing of the susceptible and resistant alleles of STPKR from Swarna and RPBio4918-230S, respectively, revealed numerous single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) mutations, both in the coding and regulatory regions of the gene. Notably, six of these mutations resulted in amino acid substitutions in the coding region of STPKR (R5K, I38L, S120N, T319A, T320S, and F348S) when compared to Swarna and the reference sequence of Nipponbare. Further validation of these mutations in a set of highly resistant and susceptible backcross inbred lines confirmed the candidacy of the STPKR gene with respect to BPH resistance controlled by bph39(t) and bph40(t). Functional markers specific for STPKR have been developed and validated and can be used for accelerated transfer of the resistant locus to elite rice cultivars.

Genotypic and phenotypic analysis of backcross inbred lines for brown plant hopper resistance in rice

Genotypic and phenotypic analysis of backcross inbred lines for brown plant hopper resistance in rice

Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat (Triticum aestivum L.) line Chuanyu12D7.

Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.

Resequencing-based QTL mapping for yield and resistance traits reveals great potential of Oryza longistaminata in rice breeding

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC2F20 backcross inbred line (BIL) population of 152 lines from the cross of 9311 × O. longistaminat. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13 QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species. A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and 27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement.

Mapping of quantitative trait loci for the nutritional value of fresh market tomato.

The incidence of many diseases, such as cancer, cardiovascular diseases, and diabetes, is associated with malnutrition and an unbalanced daily diet. Vegetables are an important source of vitamins and essential compounds for human health. As a result, such metabolites have increasingly become the focus of breeding programs. Tomato is one of the most popular components of our daily diet. Therefore, the improvement of tomato's nutritional quality is an important goal. In the present study, we performed targeted metabolic profiling of an interspecific Solanum pimpinellifolium × S. lycopersicum inbred backcross line (IBL) population and identified quantitative trait loci responsible for the nutritional value of tomato. Transgressive segregation was apparent for many of the nutritional compounds such that some IBLs had extremely high levels of various amino acids and vitamins compared to their parents. A total of 117 QTLs for nutritional traits including 62 QTLs for amino acids, 18 QTLs for fatty acids, 12 QTLs for water-soluble vitamins, and 25 QTLs for fat-soluble vitamins were identified. Moreover, almost 24% of identified QTLs were confirmed in previous studies, and 40 possible gene candidates were found for 18 identified QTLs. These findings can help breeders to improve the nutritional value of tomato.

Epistatic QTLs for yield heterosis in tomato

Controlled population development and genome-wide association studies have proven powerful in uncovering genes and alleles underlying complex traits. An underexplored dimension of such studies is the phenotypic contribution of nonadditive interactions between quantitative trait loci (QTLs). Capturing of such epistasis in a genome-wide manner requires very large populations to represent replicated combinations of loci whose interactions determine phenotypic outcomes. Here, we dissect epistasis using a densely genotyped population of 1,400 backcross inbred lines (BILs) between a modern processing tomato inbred (Solanum lycopersicum) and the Lost Accession (LA5240) of a distant, green-fruited, drought-tolerant wild species, Solanum pennellii. The homozygous BILs, each harboring an average of 11 introgressions and their hybrids with the recurrent parents, were phenotyped for tomato yield components. Population-wide mean yield of the BILs was less than 50% of that of their hybrids (BILHs). All the homozygous introgressions across the genome reduced yield relative to recurrent parent, while several QTLs of the BILHs independently improved productivity. Analysis of two QTL scans showed 61 cases of less-than-additive interactions and 19 cases of more-than-additive interactions. Strikingly, a single epistatic interaction involving S. pennellii QTLs on chromosomes 1 and 7, that independently did not affect yield, increased fruit yield by 20 to 50% in the double introgression hybrid grown in irrigated and dry fields over a period of 4 y. Our work demonstrates the power of large, interspecific controlled population development to uncover hidden QTL phenotypes and how rare epistatic interactions can improve crop productivity via heterosis.