A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum)

Precise colocalization of sorghum's major chilling tolerance locus with Tannin1 due to tight linkage drag rather than antagonistic pleiotropy

Chilling tolerance in crops can increase resilience through longer growing seasons, drought escape, and nitrogen use efficiency. In sorghum (Sorghum bicolor [L.] Moench), breeding for chilling tolerance has been stymied by coinheritance of the largest-effect chilling tolerance locus, qSbCT04.62, with the major gene underlying undesirable grain proanthocyanidins, WD40 transcriptional regulator Tannin1. To test if this coinheritance is due to antagonistic pleiotropy of Tannin1, we developed and studied near-isogenic lines (NILs) carrying chilling tolerant haplotypes at qCT04.62. Whole-genome sequencing of the NILs revealed introgressions spanning part of the qCT04.62 confidence interval, including the Tannin1 gene and an ortholog of Arabidopsis cold regulator CBF/DREB1G. Segregation pattern of grain tannin in NILs confirmed the presence of wildtype Tannin1 and the reconstitution of a functional MYB-bHLH-WD40 regulatory complex. Low-temperature germination did not differ between NILs, suggesting that Tannin1 does not modulate this component of chilling tolerance. Similarly, NILs did not differ in seedling growth rate under either of two contrasting controlled environment chilling scenarios. Finally, while the chilling tolerant parent line had notably different photosynthetic responses from the susceptible parent line - including greater non-photochemical quenching before, during, and after chilling - the NIL responses match the susceptible parent. Thus, our findings suggest that tight linkage drag, not pleiotropy, underlies the precise colocalization of Tan1 with qCT04.62 and the qCT04.62 quantitative trait nucleotide lies outside the NIL introgressions. Breaking linkage at this locus should advance chilling tolerance breeding in sorghum and the identification of a novel chilling tolerance regulator.

Identification and assessment of alleles in the promoter of the Cyc-B gene that modulate levels of β-carotene in ripe tomato fruit

Novel diversity may be mined from databases and de novo sequencing, but functional characterization remains a limiting step to identifying new alleles. Classical breeding approaches augmented by marker-assisted selection offer a means to rapidly assess the function of new variation in coding or regulatory regions to modulate traits. We used the Cyc-B gene (B) of tomato (Solanum lycopersicum L.) for a proof of concept because of its role in the production of β-carotene, a provitamin A carotenoid with importance to human nutrition. We measured carotenoid content in vintage and contemporary varieties and the profiles had a range of β-carotene from 0.2 to 4.06 mg 100 g^-1 fresh weight. We characterized variation in B from 84 sequences recovered from public databases and from an additional 29 high β-carotene tomato, S. galapagense S. C. Darwin & Peralta, and S. cheesmaniae (L. Riley) Fosberg accessions. Thirteen unique haplotypes across 1600 bp of sequence 5' to the first ATG were identified with 11 occurring in high β-carotene accessions we sequenced, and additional haplotypes were identified in public data. Phylogenetic analysis suggested that the alleles in high β-carotene varieties were derived from wild species. Association analysis suggested two single nucleotide polymorphisms (SNPs) as the most likely causes of high β-carotene, presumably through their influence on transcription of B that is elevated in ripening fruit. A marker-assisted backcross breeding scheme leveraging SNPs for background genome selection was used to rapidly develop germplasm resources containing different alleles of B in a uniform genetic background. Evaluation demonstrated that distinct promoter haplotypes function as different alleles that can be used to modulate the levels of β-carotene in tomato.

Bactericera cockerelli resistance in the wild tomato Solanum habrochaites is polygenic and influenced by the presence of Candidatus Liberibacter solanacearum

The tomato-potato psyllid (TPP), Bactericera cockerelli, is a vector for the phloem-limited bacterium Candidatus Liberibacter solanacearum (Lso), the causative agent of economically important diseases including tomato vein-greening and potato zebra chip. Here, we screened 11 wild tomato relatives for TPP resistance as potential resources for tomato (Solanum lycopersicum) cultivar development. Six accessions with strong TPP resistance (survival <10%) were identified within S. habrochaites, S. pennelli, S. huaylasense, S. chmielewskii, S. corneliomulleri, and S. galapagense. Two S. pennelli and S. corneliomulleri accessions also showed resistance to Lso. We evaluated recombinant inbred lines (RILs) carrying resistance from S. habrochaites accession LA1777 in the S. lycopersicum background and identified major quantitative trait loci (QTLs) responsible for adult TPP mortality and fecundity in several RILs carrying insertions in different chromosomes, indicating the polygenic nature of these traits. Analysis of a major resistance QTL in RIL LA3952 on chromosome 8 revealed that the presence of Lso is required to increase adult TPP mortality. By contrast, the reduced TPP oviposition trait in LA3952 is independent of Lso. Therefore, resistance traits are available in wild-tomato species, although their complex inheritance and modes of action require further characterisation to optimise their utilisation for tomato improvement.

Dissecting the Genetic Architecture of Melon Chilling Tolerance at the Seedling Stage by Association Mapping and Identification of the Elite Alleles

Low temperature is an important abiotic stress that negatively affects morphological growth and fruit development in melon (Cucumis melo L.). Chilling stress at the seedling stage causes seedling injury and poor stand establishment, prolonging vegetative growth and delaying fruit harvest. In this study, association mapping was performed for chilling tolerance at the seedling stage on an expanded melon core collection containing 212 diverse accessions by 272 SSRs and 27 CAPSs. Chilling tolerance of the melon seedlings was evaluated by calculating the chilling injury index (CII) in 2016 and 2017. Genetic diversity analysis of the whole accession panel presented two main groups, which corresponded to the two subspecies of C. melo, melo, and agrestis. Both the subspecies were sensitive to chilling but with agrestis being more tolerant. Genome-wide association study (GWAS) was conducted, respectively, on the whole panel and the two subspecies, totally detecting 51 loci that contributed to 74 marker-trait associations. Of these associations, 35 were detected in the whole panel, 21 in melo, and 18 in agrestis. About half of the associations identified in the two subspecies were also observed in the whole panel, and seven associations were shared by both the subspecies. CMCT505_Chr.1 was repeatedly detected in different populations with high phenotypic contribution and could be a key locus controlling chilling tolerance in C. melo. Nine loci were selected for evaluation of the phenotypic effects related to their alleles, which identified 11 elite alleles contributing to seedling chilling tolerance. Four such alleles existed in both the subspecies and six in either of the two subspecies. Analysis of 20 parental combinations for their allelic status and phenotypic values showed that the elite alleles collectively contributed to enhancement of the chilling tolerance. Tagging the loci responsible for chilling tolerance may simultaneously favor dissecting the complex adaptability traits and elevate the efficiency to improve chilling tolerance using marker-assisted selection in melon.

Rootstock Sub-Optimal Temperature Tolerance Determines Transcriptomic Responses after Long-Term Root Cooling in Rootstocks and Scions of Grafted Tomato Plants

Grafting of elite cultivars onto tolerant rootstocks is an advanced strategy to increase tomato tolerance to sub-optimal temperature. However, a detailed understanding of adaptive mechanisms to sub-optimal temperature in rootstocks and scions of grafting combinations on a physiological and molecular level is lacking. Here, the commercial cultivar Kommeet was grafted either onto 'Moneymaker' (sensitive) or onto the line accession LA 1777 of Solanum habrochaites (tolerant). Grafted plants were grown in NFT-system at either optimal (25°C) or sub-optimal (15°C) temperatures in the root environment with optimal air temperature (25°C) for 22 days. Grafting onto the differently tolerant rootstocks caused differences in shoot fresh and dry weight, total leaf area and dry matter content of roots, in stomatal conductance and intercellular CO2 and guaiacol peroxidase activity but not in net photosynthesis, sugar, starch and amino acid content, lipid peroxidation and antioxidant enzyme activity. In leaves, comparative transcriptome analysis identified 361 differentially expressed genes (DEG) responding to sub-optimal root temperature when 'Kommeet' was grafted onto the sensitive but no when grafted onto the tolerant rootstock. 1509 and 2036 DEG responding to sub-optimal temperature were identified in LA 1777 and 'Moneymaker' rootstocks, respectively. In tolerant rootstocks down-regulated genes were enriched in main stress-responsive functional categories and up-regulated genes in cellulose synthesis suggesting that cellulose synthesis may be one of the main adaptation mechanisms to long-term sub-optimal temperature. Down-regulated genes of the sensitive rootstock showed a similar response, but functional categories of up-regulated genes pointed to induced stress responses. Rootstocks of the sensitive cultivar Moneymaker showed in addition an enrichment of up-regulated genes in the functional categories fatty acid desaturation, phenylpropanoids, biotic stress, cytochrome P450 and protein degradation, indicating that the sensitive cultivar showed more transcriptional adaptation to low temperature than the tolerant cultivar that did not show these changes. Mainly defense-related genes were highly differentially expressed between the tolerant and sensitive rootstock genotypes under sub-optimal temperature in the root environment. These results provide new insights into the molecular mechanisms of long-term sub-optimal temperature tolerance of tomato.

Differential Transcriptional Regulation in Roots of Tomato Near-Isogenic Lines in Response to Rapid-Onset Water Stress

Cultivated tomato (Solanum lycopersicum L.) is susceptible to abiotic stresses, including drought and chilling stress, while its wild relative (Solanum habrochaites) exhibits tolerance to many abiotic stresses. Chilling roots to 6°C induces rapid-onset water stress by impeding water movement from roots to shoots. Wild S. habrochaites responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato fails to close stomata and wilts. This phenotypic response (shoot turgor maintenance under root chilling) is controlled by a major QTL stm9 on chromosome 9 from S. habrochaites that was previously high-resolution mapped to a 0.32 cM region, but its effects on transcriptional regulation were unknown. Here we used paired near isogenic lines (NILs) differing only for the presence or absence of the S. habrochaites introgression containing stm9 in an otherwise S. lycopersicum background to investigate global transcriptional regulation in response to rapid-onset water stress induced by root chilling. NIL175 contains the S. habrochaites introgression and exhibits tolerance to root chilling stress, while NIL163 does not contain the introgression and is susceptible. RNA from roots of the two NILs was obtained at five time points during exposure to root chilling and mRNA-Seq performed. Differential expression analysis and hierarchical clustering of transcript levels were used to determine patterns of and changes in mRNA levels. Our results show that the transcriptional response of roots exposed to chilling stress is complex, with both overlapping and unique responses in tolerant and susceptible lines. In general, susceptible NIL 163 had a more complex transcriptional response to root chilling, while NIL175 exhibited a more targeted response to the imposed stress. Our evidence suggests that both the tolerant and susceptible NILs may be primed for response to root-chilling, with many of these response genes located on chromosome 9. Furthermore, serine/threonine kinase activity likely has an important role in the root chilling response of tolerant NIL175.

Breeding approaches and genomics technologies to increase crop yield under low-temperature stress

Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions. Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders' toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.

SSR Mapping of QTLs Conferring Cold Tolerance in an Interspecific Cross of Tomato

A population of 146 RILs (Recombinant Inbred Line) was derived from the cross between a cold-sensitive cultivated Solanum lycopersicum L. XF98-7 and a cold-tolerant wild Solanum pimpinellifolium LA2184. Relative germination ratio (RGR) and chilling index (CI) were used to evaluate the cold tolerance of the parental lines and RILs. It was found that the RGR and CI were significantly different between S. lycopersicum XF98-7 and S. pimpinellifolium LA2184 under cold treatment, indicating that wild species was more adapted to chilling temperature. The continuous and normal distribution of RGR and CI in RIL population suggested that the trait of cold tolerance was a typically quantitative trait controlled by multigenes. The molecular linkage map was constructed by using 120 simple-sequence repeat (SSR) markers, resulting in 15 linkage groups, with a total distance of 256.8 cM and average interval of 2.14 cM. Five QTLs controlling RGR and four QTLs for CI were detected with genetic contribution ranging from 0.95% to 19.55%. Thus, the nine QTLs will provide references for further fine position mapping for cold tolerance. The polymorphic markers could be used as a way of indirectly selecting the plant trait of interest and would promote developing new tomato variety by marker-assisted selection.

Clair DA. High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling

QTL stm9 controlling rapid-onset water stress tolerance in S. habrochaites was high-resolution mapped to a chromosome 9 region that contains genes associated with abiotic stress tolerances. Wild tomato (Solanum habrochaites) exhibits tolerance to abiotic stresses, including drought and chilling. Root chilling (6 °C) induces rapid-onset water stress by impeding water movement from roots to shoots. S. habrochaites responds to such changes by closing stomata and maintaining shoot turgor, while cultivated tomato (S. lycopersicum) fails to close stomata and wilts. This response (shoot turgor maintenance under root chilling) is controlled by a major QTL (designated stm9) on chromosome 9, which was previously fine-mapped to a 2.7-cM region. Recombinant sub-near-isogenic lines for chromosome 9 were marker-selected, phenotyped for shoot turgor maintenance under root chilling in two sets of replicated experiments (Fall and Spring), and the data were used to high-resolution map QTL stm9 to a 0.32-cM region. QTL mapping revealed a single QTL that was coincident for both the Spring and Fall datasets, suggesting that the gene or genes contributing to shoot turgor maintenance under root chilling reside within the marker interval H9-T1673. In the S. lycopersicum reference genome sequence, this chromosome 9 region is gene-rich and contains representatives of gene families that have been associated with abiotic stress tolerance.

Chilling-induced water stress: variation in shoot turgor maintenance among wild tomato species from diverse habitats

PREMISE OF THE STUDY

Cultivated tomato, Solanum lycopersicum, suffers chilling induced wilting because water movement through its roots decreases with declining soil temperatures. Certain wild tomato species exhibit resistance to chilling-induced wilting, but the extent of this chilling tolerance in wild tomatoes is not known. •

METHODS

We measured shoot wilting during root chilling in wild Solanum accessions from habitats differing in elevation, temperature, and precipitation. We also measured shoot wilting during root chilling in introgression lines (ILs) with chromosome 9 segments collinear to the shoot turgor maintenance QTL stm9 region from chilling-tolerant S. habrochaites, chilling and drought-tolerant S. lycopersicoides, or drought-tolerant S. pennellii. •

KEY RESULTS

Wild tomato species, which experience chilling temperatures (<10°C) in their native habitat, maintain shoot turgor under root chilling. Among accessions of S. lycopersicum var. cerasiforme, a typically chilling sensitive species, shoot turgor maintenance during root chilling was correlated with the precipitation of the native habitat. By contrast, S. pennellii, a species that is typically drought adapted, did not maintain turgor under root chilling. Grafted plants with roots containing S. habrochaites and S. lycopersicoides introgressions improved shoot turgor maintenance under root chilling. •

CONCLUSIONS

Resistance to chilling-induced water stress is an important adaptation to chilling temperatures in wild tomatoes. There is some overlap in adaptation to drought and chilling stress in some tomato species. Root-based resistance to chilling-induced water stress in wild tomatoes may involve orthologous gene(s).

Differential modulation of photosynthesis, signaling, and transcriptional regulation between tolerant and sensitive tomato genotypes under cold stress

The wild species Solanum habrochaites is more cold tolerant than the cultivated tomato (S. lycopersicum). To explore the mechanisms underlying cold tolerance of S. habrochaites, seedlings of S. habrochaites LA1777 introgression lines (ILs), as well as the two parents, were evaluated under low temperature (4°C). The IL LA3969 and its donor parent LA1777 were found to be more cold tolerant than the recurrent parent S. lycopersicum LA4024. The differences in physiology and global gene expression between cold-tolerant (LA1777 and LA3969) and -sensitive (LA4024) genotypes under cold stress were further investigated. Comparative transcriptome analysis identified 1613, 1456, and 1523 cold-responsive genes in LA1777, LA3969, and LA4024, respectively. Gene ontology (GO) term enrichment analysis revealed that more GO biological process terms were significantly enriched among the up-regulated genes in the two tolerant genotypes, whereas more biological processes were significantly repressed by cold stress in the sensitive one. A total of 92 genes with significant differential expression between tolerant and sensitive genotypes under cold stress were identified. Among these, many stress-related GO terms were significantly enriched, such as 'response to stimulus' and 'response to stress'. Moreover, GO terms 'response to hormone stimulus', 'response to reactive oxygen species (ROS)', and 'calcium-mediated signaling' were also overrepresented. Several transcripts involved in hormone or ROS homeostasis were also differentially expressed. ROS, hormones, and calcium as signaling molecules may play important roles in regulating gene expression in response to cold stress. Moreover, the expression of various transcription factors, post-translational proteins, metabolic enzymes, and photosynthesis-related genes was also specifically modulated. These specific modifications may play pivotal roles in conferring cold tolerance in tomato. These results not only provide new insights into the molecular mechanisms of cold tolerance in tomato, but also provide potential candidate genes for genetic improvement.

Dissection and fine mapping of a major QTL for preharvest sprouting resistance in white wheat Rio Blanco

Preharvest sprouting (PHS) is a major constraint to white wheat production. Previously, we mapped quantitative trait loci (QTL) for PHS resistance in white wheat by using a recombinant inbred line (RIL) population derived from the cross Rio Blanco/NW97S186. One QTL, QPhs.pseru-3A, showed a major effect on PHS resistance, and three simple sequence repeat (SSR) markers were mapped in the QTL region. To determine the flanking markers for the QTL and narrow down the QTL to a smaller chromosome region, we developed a new fine mapping population of 1,874 secondary segregating F(2) plants by selfing an F6 RIL (RIL25) that was heterozygous in the three SSR marker loci. Segregation of PHS resistance in the population fitted monogenic inheritance. An additive effect of the QTL played a major role on PHS resistance, but a dominant effect was also observed. Fifty-six recombinants among the three SSR markers were identified in the population and selfed to produce homozygous recombinants or QTL near-isogenic lines (NIL). PHS evaluation of the recombinants delineated the QTL in the region close to Xbarc57 flanked by Xbarc321 and Xbarc12. To saturate the QTL region, 11 amplified fragment length polymorphism (AFLP) markers were mapped in the QTL region with 7 AFLP co-segregated with Xbarc57 by using the NIL population. Dissection of the QTL as a Mendelian factor and saturation of the QTL region with additional markers created a solid foundation for positional cloning of the major QTL.

Enzyme activity profiles during fruit development in tomato cultivars and Solanum pennellii

Enzymes interact to generate metabolic networks. The activities of more than 22 enzymes from central metabolism were profiled during the development of fruit of the modern tomato cultivar Solanum lycopersicum 'M82' and its wild relative Solanum pennellii (LA0716). In S. pennellii, the mature fruit remains green and contains lower sugar and higher organic acid levels. These genotypes are the parents of a widely used near introgression line population. Enzymes were also profiled in a second cultivar, S. lycopersicum 'Moneymaker', for which data sets for the developmental changes of metabolites and transcripts are available. Whereas most enzyme activities declined during fruit development in the modern S. lycopersicum cultivars, they remained high or even increased in S. pennellii, especially enzymes required for organic acid synthesis. The enzyme profiles were sufficiently characteristic to allow stages of development and cultivars and the wild species to be distinguished by principal component analysis and clustering. Many enzymes showed coordinated changes during fruit development of a given genotype. Comparison of the correlation matrices revealed a large overlap between the two modern cultivars and considerable overlap with S. pennellii, indicating that despite the very different development responses, some basic modules are retained. Comparison of enzyme activity, metabolite profiles, and transcript profiles in S. lycopersicum 'Moneymaker' revealed remarkably little connectivity between the developmental changes of transcripts and enzymes and even less between enzymes and metabolites. We discuss the concept that the metabolite profile is an emergent property that is generated by complex network interactions.

Antagonistic epistasis for ecophysiological trait differences between Solanum species

Epistasis, the nonadditive interaction between loci, is thought to play a role in many fundamental evolutionary processes, including adaptive differentiation and speciation. Focusing on species differences in ecophysiological traits, we examined the strength and direction of pairwise epistatic interactions between target chromosomal regions from one species, when co-introgressed into the genetic background of a foreign species. A full diallel cross was performed using 15 near-isogenic lines (NILs) constructed between two tomato species (Solanum habrochaites and Solanum lycopersicum) to compare the phenotypic effects of each chromosomal region singly and in combination with each other region. We detected main effect quantitative trait loci (QTLs) for two of our three focal traits. Epistatic effects accounted for c. 25% of detected effects on trait means, depending on the trait. Strikingly, all but two interactions were antagonistic, with the combined effect of chromosomal regions acting in the opposite direction from that of one or both individual chromosomal regions. Our study is one of the few to systematically examine pairwise epistatic effects in a nonmicrobial system. Our results suggest that epistatic interactions can contribute substantially to the genetic basis of traits involved in adaptive species differentiation, especially highly complex, multivariate traits.

Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range

This paper characterizes the transcriptional and metabolic response of a chilling-tolerant species to an increasingly large decrease of the temperature. Arabidopsis Col-0 was grown at 20 degrees C and transferred to 17, 14, 12, 10 or 8 degrees C for 6 and 78 h, before harvesting the rosette and profiling >22 000 transcripts, >20 enzyme activities and >80 metabolites. Most parameters showed a qualitatively similar response across the entire temperature range, with the amplitude increasing as the temperature decreased. Transcripts typically showed large changes after 6 h, which were often damped by 78 h. Genes were induced for sucrose, proline, raffinose, tocopherol and polyamine synthesis, phenylpropanoid and flavonoid metabolism, fermentation, non-phosphorylating mitochondrial electron transport, RNA processing, and protein synthesis, targeting and folding. Genes were repressed for carbonic anhydrases, vacuolar invertase, and ethylene and jasmonic acid signalling. While some enzyme activities and metabolites changed rapidly, most changed slowly. After 6 h, there was an accumulation of phosphorylated intermediates, a shift of partitioning towards sucrose, and a perturbation of glycine decarboxylation and nitrogen metabolism. By 78 h, there was an increase of the overall protein content and many enzyme activities, a general increase of carbohydrates, organic and amino acids, and an increase of many stress-responsive metabolites including raffinose, proline, tocopherol and polyamines. When the responses of transcripts and metabolism were compared, there was little agreement after 6 h, but considerable agreement after 78 h. Comparison with the published studies indicated that much, but not all, of the response was orchestrated by the CBF programme. Overall, our results showed that transcription and metabolism responded in a continuous manner across a wide range of temperatures. The general increase of enzyme activities and metabolites emphasized the positive and compensatory nature of this response.