Co-selection of low cadmium accumulation and high yield during tomato breeding

doi:10.21203/rs.3.rs-4819784/v1

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Co-selection of low cadmium accumulation and high yield during tomato breeding

https://doi.org/10.21203/rs.3.rs-4819784/v1

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Enhancing crop production and yield is necessary to feed an increasing population but cadmium (Cd) accumulation in crops poses a serious threat to human health. We found that there has been a trend during domestication for co-selection of improved tomato yield and reduced Cd accumulation. A genome-wide association study (GWAS) of 506 tomato accessions identified a natural allele, SlF3’H^AA, which confers low Cd accumulation in the shoots of tomato. The linkage disequilibrium (LD) analysis revealed a tight linkage between

SlF3’H^AA and a fruit weight gene fw3.2. Evolution analysis showed that fw3.2 and SlF3’H experienced similar selection pressure. These findings indicate that the widespread presence of low Cd accumulating types in cultivated tomato is due to genetic hitchhiking and co-selection of SlF3’H with fw3.2 during yield breeding.

Biological sciences/Plant sciences/Plant genetics

Biological sciences/Plant sciences/Plant breeding

Biological sciences/Genetics/Agricultural genetics

Since the onset of global industrialization in the modern era, human activities such as mining, metal smelting, industrial wastewater discharge and nuclear pollution have led to a gradual deterioration of the global environment (1-4). Heavy metal pollution, typified by Cd, is silently threatening human health. Cd has a fast migration rate and a long half-life, typically accumulating in the human body through the food chain (5). Prolonged accumulation of Cd can easily lead to diseases such as lung cancer, kidney cancer, and “itai-itai disease”(6, 7). Tomato is one of the most widely consumed plant species globally. It is consumed not only in its raw or cooked form, but also predominantly as processed products such as juice, soup, and ketchup (8, 9). The safety of tomato and its by-products for consumption is closely tied to human health. Thus, breeding “low Cd” crops such as tomato is of high importance to address ongoing severe heavy metal pollution.

Cultivated tomato varieties accumulate less Cd in shoot than wild ancestors

Here, we investigated the differences in Cd accumulation capacity among 506 tomato accessions. These 506 accessions represent various geographical origins and improvement status, consisting of 53 wild accessions of Solanum pimpinellifolium (PIM), 179 domesticated accessions of Solanum lycopersicum var. cerasiforme (CER), and 274 improved accessions of Solanum lycopersicum (BIG) (Fig. 1A, fig. S1, and table S1). We found that the Cd content in the roots of the BIG group was significantly higher than that of the PIM and CER groups, while the Cd content in the shoots of the BIG group was significantly lower than that of the PIM and CER groups. Additionally, the Cd translocation factor of the BIG group was significantly lower than that of the PIM and CER groups. There were no significant differences observed in the Cd contents in the roots and shoots, as well as the translocation factor between the PIM and CER groups (Fig. 1, B to D, and table S2).

Taking the median value (3.0463 mg/kg) of Cd content in the shoots of 506 tomato accessions as the threshold, we found that the proportion of “low Cd” tomato (Cd content < 3.0463 mg/kg) increased gradually from the PIM group to the CER group and then to the BIG group, especially during the transition from CER to BIG, where it increased from 32.40–64.96% (Fig. 1E). This discovery suggests that unintentionally, as humans have domesticated and improved tomato yields, they have preserved the excellent trait of “low Cd” during the process. This is promising as it indicates that we can use existing cultivars for breeding to rapidly develop low Cd accumulating cultivars. Thus, the domestication and improvement of species for higher yields has not always resulted in the loss of desirable but invisible traits such as flavor(10) or stress resistance(11, 12), and may fortunately have led to the preservation of outstanding traits like “low Cd”.

Identification of a major locus for low Cd accumulation in tomato

The “Cd accumulation” trait has received relatively little attention during the process of tomato domestication and breeding. To understand why this trait underwent directional selection, we investigated the genetic mechanisms behind low Cd accumulation in tomato. Genome-wide association study (GWAS) is an effective strategy for uncovering the genetic basis of ion accumulation in plants(11, 13, 14). Here, 5,096,140 common SNPs with a minor allele frequency (MAF) > 0.05 and missing ratio < 10% were used to perform a GWAS. The P-values of 1.0 × 10^− 7 were set as the significance threshold after Bonferroni-adjusted correction (Fig. 2A and fig. S2). One strong association signal (named LCT1 (Low Cadmium in Tomato 1)) on chromosome 3 was observed in the GWAS of Cd content in shoots, which includes 27 significant SNPs (Fig. 2A). We then analyzed the physical positions, genomic elements, and functional annotations surrounding the significant SNPs to select candidate genes underlying Cd content in shoots. Notably, three significant SNPs were found within the promoter region (SNP15-T), exon 2 (SNP16-T), and 3’UTR (SNP3-A) of the gene Solyc03g115220 (fig. S3 and table S3). The SNP15-T, located within the promoter region, is predicted not to reside within any known cis-regulatory elements. SNP16-T is a synonymous mutation. SNP3-A is predicted to be a binding site for miR8762, which is supposed to disrupt the miR8762 binding (fig. S4 and table S3). Haplotype analysis reveals that accessions with the 3’UTR^AA genotype had lower Cd content compared to those with the 3’UTR^TT genotype (Fig. 2B). The Solyc03g115220 encodes a flavonoid 3’-hydroxylase (SlF3’H), which belongs to the CYP450 family. Previous studies have reported that CYP450 is involved in regulating ion transport processes (15, 16). Hence, we focused on SlF3’H to understand its potential genetic mechanism underlying low Cd accumulation in tomato.

We generated two tomato SlF3’H overexpression (SlF3’H-OE) lines in background of “high Cd” accession TS-222 and confirmed their elevated SlF3'H RNA levels (fig. S5A). We measured the Cd accumulation abilities of SlF3’H-OE#1 and #2 lines together with TS-222 and found that overexpressing SlF3’H in tomato reduced the Cd content in the shoots while it had no significant effect on the Cd content in the roots (Fig. 2, C to F). Additionally, a functional experiment was performed by using CRISPR/Cas9 to knock out SlF3’H in TS-222 (fig. S5B). Interestingly, the successful knockout of SlF3’H also reduced the Cd content in the shoots (fig. S5, C to J). We speculate that this is due to the SlF3’H-OE and SlF3’H-CR lines affecting different pathways of Cd accumulation. The SlF3’H-OE lines likely function primarily through the cell wall and chelation pathways, whereas the SlF3’H-CR lines likely function mainly through the transporter pathway (fig. S6). Therefore, we proposed that SlF3’H was the causal gene for SlLCT1.

To validate the function of the flavonoid hydroxylase F3’H in other species, the rice orthologs, OsCYP75B2 and OsCYP75B4, were overexpressed in rice ZH11 (Oryza sativa L. ssp. japonica), and AtCYP75B1 was overexpressed in Arabidopsis, respectively (fig. S7). The results demonstrated that overexpressing OsCYP75B2 and OsCYP75B4 both reduced the Cd content in the leaves, stems, and grains of rice, while overexpressing AtCYP75B1 decreased the Cd content in the shoots of Arabidopsis (Fig. 2, G to L). Thus, these results suggested that the function of F3’H in reducing plant Cd accumulation is relatively conserved across different species. This could potentially provide a solution to the current issue of excessive Cd in rice production (17).

SlF3’H expression variance: a key to low Cd in cultivated tomato

In our analysis of SlF3’H expression levels in tomato, we observed that “low Cd” accessions exhibited higher expression levels relative to “high Cd” accessions, and that Cd treatment induced the expression of SlF3’H (Fig. 3, A and B). The 3’UTR of transcripts typically functions as a binding site for miRNA, negatively regulating gene expression (18, 19). Hence, employing the dual-luciferase reporter assay system, we fused the two 3’UTR sequences (3’UTR^TT and 3’UTR^AA) of SlF3’H with the luciferase gene sequence and co-expressed them separately with miR8762 in tobacco (Nicotiana tabacum) leaves (fig. S8). The results indicated that miR8762 exerted inhibitory effects on the luciferase fused with both types of 3’UTRs, but the luciferase construct fused with the 3’UTR^AA showed a weaker inhibition (Fig. 3, C and D). Therefore, we speculate that the 3’UTR variation (SNP3-A) of SlF3’H buffered the inhibitory effect of miR8762 on SlF3’H expression, resulting in a reduced accumulation of Cd in tomato.

Promoter-GUS analysis revealed that SlF3’H is primarily expressed in the tomato hypocotyl (Fig. 3F) and subcellular localization indicated that SlF3’H is mainly located on the endoplasmic reticulum membrane (Fig. 3E). In hypocotyl cross sections, GUS activity was primarily detected in the vascular bundle sheath (Fig. 3, G and H). This implied that SlF3’H might be involved in the transport of Cd from the tomato root to the shoot.

Co-selection of LCT1 and fruit weight locus fw3.2

The findings above indicated that SlF3’H is the major gene controlling low Cd accumulation in tomato and plays a significant role in the low Cd accumulation in important crops like tomato and rice. Accordingly, we carried out an investigation to evaluate whether the trait of “Cd accumulation” in tomato, which has received little attention from breeders, has undergone directional selection. Since SNP3-A is supposed to be the casual variation underling the Cd content, the evolution and selection of 3'UTR of SlLCT1 was investigated.

We found that the majority of accessions in the PIM group belong to the SlLCT1^TT genotype, while most of the accessions in the BIG group had the SlLCT1^AA genotype (Fig. 4A). Throughout the domestication and improvement of tomato, there has been a gradual increase in the prevalence of the SlLCT1^AA genotype, particularly during the transition from CER to BIG, where it rose from 20.67–85.77% (Fig. 4A). This is consistent with the trend for the change in proportion of tomato with “low Cd” phenotype in the three groups (Fig. 1E). We hypothesized that this phenomenon may be attributed to genetic hitchhiking, since there is no record of targeted selection for Cd accumulation traits during the tomato domestication and improvement process. Thus, our focus turned to fruit weight, a trait closely linked to yield, which is a major target for breeders. A significant negative correlation between fruit weight and Cd content in shoots was found among the 164 tomato accessions (Fig. 4B), providing preliminary validation for our hypothesis.

For genetic hitchhiking to occur, it is essential that two loci are located on the same chromosome and separated by a relatively short genetic distance (20, 21). In our study, we investigated QTLs associated with yield and identified a QTL, fw3.2, on chromosome 3 that controls fruit size, with a highly correlated SNP (ch03_64799226) in its promoter region (22, 23) (table S4). The linkage disequilibrium (LD) analysis revealed a tight linkage between the SNP (ch03_64799226) in the promoter of fw3.2 and the SNP (ch03_65001793) in the 3’UTR of SlF3’H (Fig. 4C). We examined the distribution of fw3.2^CC and fw3.2^TT alleles in the PIM, CER, and BIG accessions. The prevalence of the fw3.2^TT allele, representing large fruit, gradually increased within the population, notably rising from 24.02–92.34% during the transition from CER to BIG (Fig. 4D). This trend closely paralleled changes in the prevalence of the LCT1 within the population (Fig. 4A). Accessions carrying the fw3.2^CC allele mostly co-carried the LCT1^TT allele, associated with “high Cd”, whereas accessions carrying the fw3.2^TT allele predominantly co-carried the LCT1^AA allele, linked to “low Cd” (Fig. 4E). Furthermore, analysis of near-isogenic lines (NILs) of LCT1 indicated that all accessions of the NIL (TT) genotype contain the fw3.2^CC allele, while all accessions of the NIL (AA) genotype contain the fw3.2^TT allele (Fig. 4F and fig. S9). We scanned the regions surrounding the LCT1 and fw3.2 genes on chromosome 3 and compared the ratios of nucleotide diversity between PIM and CER accessions, as well as between CER and BIG accessions. The results showed that both fw3.2 and LCT1 were found to be in the region associated with improvement sweep (Fig. 4, G and H). This suggests that fw3.2 and LCT1 experienced similar selection pressures during the improvement process from CER to BIG in tomato. Furthermore, the geographical distribution indicates that LCT1^TT is mainly distributed in regions where tomato originate, such as Peru and Ecuador, whereas LCT1^AA is mainly found in the United States, Russia, and along the Mediterranean coast (e.g., in Italy) (Fig. 5A). Thus, we proposed that the “low Cd” genotype LCT1^AA has been retained in tomato during long-term domestication, and underwent strong selective pressure by genetic hitchhiking with fw3.2^TT during the breeding process from CER to BIG. These events have led to the dominance of the “low Cd” genotype SlF3’H^AA in cultivated tomato today (Fig. 5, A and B).

In the process of targeted selection for crop yield, it is often regrettable that numerous genes are lost, leading to a series of threats faced by global food production such as salt, cold, and drought stress (11, 24, 25). Researchers had proposed strategies such as distant hybridization, induced mutation, and de novo domestication to address these challenges (26–28). It is noteworthy that retention of “invisible traits” during plant domestication is not always unfortunate outcome; the “low Cd” trait highlighted in this study serves as a fortunate example. Another, from previous research, is the significant increases in nicotinic acid and succinyladenosine during tomato domestication and improvement processes, metabolites with benefits to both human health and plant growth (29) (fig. S10, A and B). Evolutionary analysis indicated that the leading SNPs regulating these metabolites were found to be in the region associated containing the fruit weight gene fw11.3 and associated with improvement sweep (29) (fig. S10, C and D). These findings suggest that there are still many fortunate “invisible traits” and identification of their major QTLs await further exploration. Here, we refer to this phenomenon as “Cryptic Selection”, which involves selecting advantageous variations for an invisible trait in concert with a visible trait during yield domestication and improvement.

In summary, we have identified a quantitative trait locus for “low Cd” in tomato, named LCT1, and its causal gene, SlF3’H. Furthermore, we provided an explanation for why cultivated tomato today mainly exhibit “low Cd” traits, which is attributed to the genetic hitchhiking and cryptic selection between SlF3’H and the fruit weight gene fw3.2. Currently, we can utilize existing varieties with “low Cd” genotypes (SlF3’H^AA) to improve some major cultivars with “high Cd” genotypes (SlF3’H^TT) to produce healthier and safer tomato. The converged function of SlF3’H and its orthologues in Arabidopsis and rice make brighter prospect in crop improvement.

Plant material and growth conditions

A tomato collection, consisting of 506 tomato accessions from around the world, was used for the genome-wide association analysis (29, 30). The accessions comprised 53 Solanum pimpinellifolium (PIM), 179 Solanum lycopersicum var. cerasiforme (CER), and 274 Solanum lycopersicum (BIG) (Fig. 1A and table S1). Regarding the risk control standard for soil contamination of agricultural land (China) (GB 15618 − 2018) and the standard level of pollution of soils in China, the concentration of Cd in the substrate was set to a light pollution level, 1 mg/kg. Cd was added as CdCl₂·2.5H₂O, mixed well with the cultivation substrate, and then loaded into the planting groove. The 506 tomato accessions were sown in greenhouse conditions in Cd-treated substrates. After germination, each accession was maintained with five individual plants and allowed to grow for an additional 30 days. For Arabidopsis thaliana growth, both transgenic and wild-type seeds were sown on 1/2 MS media with or without 100 mg/L kanamycin to select positive seedlings. Selected seedlings were transplanted into substrates containing 1.5 mg/kg Cd and grown under controlled conditions (25°C, 12-hour light/12-hour dark cycle) for 30 days. For rice growth, approximately 3-week-old seedlings were transplanted into paddy soil containing 0.5 mg/kg Cd and cultivated in a greenhouse with temperatures ranging from 26–32°C and a photoperiod of 10-h light/14-h dark until harvest. Cd-contaminated substrates and paddy soil were professionally processed by the Department of Hazardous Waste Recovery at Huazhong Agricultural University.

Measurement of Cd²⁺ contents

Tomato seedlings were exposed to 1 mg/kg Cd for 30 d, after which their roots and shoots were harvested separately. Arabidopsis shoots, including rosette leaves and inflorescence stems, were harvested. For rice, once the grains ripened, the stems, leaves, and grains were harvested individually. After harvesting, the samples were initially dried at 110°C for 15 min and then dried to a constant weight at 75°C. The dried samples were ground and sieved through a 0.149 mm nylon mesh for chemical analysis. Samples of 0.2 g were digested with 10 mL of nitric acid using a MARS6 microwave at a temperature gradient of 120–180°C for 1 h. After digestion, the samples were diluted with deionized water and analyzed for Cd content using Agilent graphite furnace (Agilent AA 240Z), with a detection limit of 0.019 µg/L. The translocation factor (TF) is defined as the ratio of Cd content in shoots to that in roots (31).

Genome-wide association study

We used a linear mixed model (LMM) within the Tassel software suite, with 5,096,140 SNPs (MAFs > 0.05, missing ratio < 10%) to perform GWAS for Cd content and TF in 506 accessions. The SNPs were acquired from previous studies (22, 29, 30). The genome-wide significance thresholds of all the three traits were set at a uniform threshold (1.0 × 10^− 7). The physical positions of the SNPs were identified using the tomato genome sequence, version SL2.50 (http://solgenomics.net).

Generation of transgenic tomato

The full-length coding sequence of SlF3’H was amplified from TS-222 cDNA and then cloned into pHELLSGATE8 downstream of the CaMV35S promoter to yield the overexpression construct 35Spro:F3’H. TS-222 was transformed with the 35Spro:F3’H transgene using Agrobacterium (strain GV3101)-mediated transformation (32). The CRISPR-Cas9 vector pTX was used to generate SlF3’H mutants in the TS-222 backgrounds by targeting two sites in the second exon of SlF3’H using the single guide RNAs (sgRNA) sgRNA1 and sgRNA2 (fig S5). The sgRNAs were designed using CRISPR-GE (http://skl.scau.edu.cn/targetdesign/). All primers and sgRNA sequences are listed in table S5.

Gene expression analysis

After a month of Cd exposure, the primary leaves were collected from the tomato seedlings' tips and immediately frozen in liquid nitrogen. Total RNA was extracted using TRIzol reagent (RN0102, Aidlab, China). First-strand cDNA was synthesized using HiScript II 1st Strand cDNA Synthesis Kit (+ gDNA wiper) (R212-01, Vazyme, China), following the manufacturer’s instructions. Gene expression levels were quantified using quantitative real-time PCR (qRT-PCR) conducted on a QuantStudioTM 6 Flex System (ABI, USA). The tomato actin gene (Solyc11g005330.1) was used as an internal control. Primer sequences (designed with Primer Premier 5) are listed in table S5.

Dual luciferase reporter assay

Based on the method described by Zhang (33), we constructed a plasmid for the functional analysis of the 3’UTR. The 3’UTRs of both genotypes, along with their corresponding 3-kb promoters, were amplified using the genomic DNA of TS-9 and TS-222 as templates. Subsequently, the sequences of the 3’UTRs were integrated downstream of the luc sequence, while the 3-kb promoters were integrated upstream to generate the reporter vector. The full-length pre-miRNA for miR8762 was amplified from TS-9 genomic DNA and then cloned into pHELLSGATE8 downstream of the CaMV35S promoter to generate the overexpression construct 35Spro: miR8762. Agrobacterium strains containing a reporter construct and an effector construct were infiltrated into tobacco leaves. After 3 days of incubation, firefly luciferase (LUC) and Renilla luciferase (REN) activities were determined and the ratios of LUC to REN were calculated to indicate transactivation activity. The primers used for the constructs are listed in table S5.

Subcellular localization

The full-length coding sequence of SlF3’H without the stop codon was amplified from cDNA prepared from TS-9, and then cloned into 101LYFP (34). The CaMV35S: SlF3’H-YFP construct was generated using homologous recombination. The fusion proteins of CaMV35S: SlF3’H-YFP and the endoplasmic reticulum marker RFP-HDEL (35) were co-injected and transiently expressed in the leaves of Nicotiana benthamiana. Fluorescence of the N. benthamiana leaf cells was examined and imaged using a confocal laser scanning microscope (SP8, LEICA) two days after infiltration.

GUS staining

To construct a SlF3’H^TS−9pro: GUS transgene, the promoter of SlF3’H was amplified and cloned into an expression vector (pHELLSGATE8-GUS) derived from pHELLSGATE8 that lacked the CaMV35S promoter. Histochemical staining was performed using at least three independent SlF3’H^TS−9pro: GUS transgenic T₁ lines as described previously (36).

Detection of domestication and improvement sweeps

To identify the selection region around SlF3’H, the SNPs near the SlF3’H locus in the tomato genome were obtained (corresponding to ch03: 64.0–67.0 Mb, SL2.50). We measured the level of nucleotide diversity (π) using a 100-kb window with a step size of 10 kb in PIM, CER, and BIG accessions. The ratios of nucleotide diversity between PIM and CER (π_PIM/π_CER) and CER and BIG (π_CER/π_BIG) also were calculated as described in a previous study (22).

Acknowledgments

We thank B. Ouyang, C.X. Li and C. M. Shi (Huazhong Agricultural University) for providing technical support in bioinformatics; C. Zhang (Huazhong Agricultural University) for his contribution to the development of the near-isogenic lines; and J.W. Song (Huazhong Agricultural University) for valuable discussions.

Funding

National Key Research & Development Plan 2022YFD1200502, 2021YFD1200201 (YZ)

National Natural Science Foundation of China 32372696, 31991182 (YZ, ZY)

Wuhan Biological Breeding Major Project 2022021302024852 (YZ)

Hubei Agriculture Research System 2023HBSTX4-06 (YZ)

HZAU-AGIS Cooperation Fund SZYJY2023022 (YZ)

Funds for High Quality Development of Hubei Seed Industry HBZY2023B004 (YZ)

Author contributions

Conceptualization: X.Z., M.Q., W.W., Z.Y., and Y.Z.

Methodology: X.Z., M.Q., J.T., F.L., P.G., and Y.Y.

Investigation: X.Z. and M.Q.

Visualization: X.Z., H.B.X.

Funding acquisition: Y.Z.

Project administration: Z.Y. and Y.Z.

Supervision: Y.Z.

Writing – original draft: X.Z.

Writing – review & editing: X.Z., D.G., Z.Y., and Y.Z.

Competing interests

The authors declare no competing interests.

X. Liang, S. L. Yang, Z. C. Lou, A. Ali, The impact of Japan's discharge of nuclear-contaminated water on aquaculture production, trade, and food security in China and Japan. Sustainability 16, 1285 (2024). doi: 10.3390/su16031285.
I. Thornton, Impacts of mining on the environment; Some local, regional and global issues. Appl. Geochem. 11, 355–361 (1996). doi: 10.1016/0883-2927(95)00064-x.
H. Gui, Q. C. Yang, X. Y. Lu, H. L. Wang, Q. B. Gu, J. D. Martín, Spatial distribution, contamination characteristics and ecological-health risk assessment of toxic heavy metals in soils near a smelting area. Environ. Res. 222, 115328 (2023). doi: 10.1016/j.envres.2023.115328.
Y. S. Xu, S. H. Xiang, X. Y. Zhang, H. J. Zhou, H. M. Zhang, High-performance pseudocapacitive removal of cadmium via synergistic valence conversion in perovskite-type FeMnO₃. J. Hazard. Mater. 439, 129575 (2022). doi: 10.1016/j.jhazmat.2022.129575.
S. Soni, A. B. Jha, R. S. Dubey, P. Sharma, Mitigating cadmium accumulation and toxicity in plants: The promising role of nanoparticles. Sci. Total Environ. 912, 168826 (2024). doi: 10.1016/j.scitotenv.2023.168826.
T. Inaba, E. Kobayashi, Y. Suwazono, M. Uetani, M. Oishi, H. Nakagawa, K. Nogawa, Estimation of cumulative cadmium intake causing Itai-itai disease. Toxicol. Lett. 159, 192–201 (2005). doi: 10.1016/j.toxlet.2005.05.011.
M. Peana, A. Pelucelli, C. T. Chasapis, S. P. Perlepes, V. Bekiari, S. Medici, M. A. Zoroddu, Biological effects of human exposure to environmental cadmium. Biomolecules 13, 36 (2023). doi: 10.3390/biom13010036.
M. Viuda-Martos, E. Sanchez-Zapata, E. Sayas-Barberá, E. Sendra, J. A. Pérez-Alvarez, J. Fernández-López, Tomato and tomato byproducts. Human health benefits of lycopene and its application to meat products: A review. Crit. Rev. Food Sci. Nutr. 54, 1032–1049 (2014). doi: 10.1080/10408398.2011.623799.
C. M. Bai, C. E. Wu, L. L. Ma, A. Z. Fu, Y. Y. Zheng, J. W. Han, C. B. Li, S. Z. Yuan, S. F. Zheng, L. P. Gao, X. H. Zhang, Q. Wang, D. M. Meng, J. H. Zuo, Transcriptomics and metabolomics analyses provide insights into postharvest ripening and senescence of tomato fruit under low temperature. Hortic. Plant J. 9, 109–121 (2023). doi: 10.1016/j.hpj.2021.09.001.
D. Tieman, G. T. Zhu, M. F. R. Resende, T. Lin, M. Taylor, B. Zhang, H. Ikeda, Z. Y. Liu, J. Fisher, I. Zemach, A. J. Monforte, D. Zamir, A. Granell, M. Kirst, S. Huang, H. Klee, C. Nguyen, D. Bies, J. L. Rambla, K. S. O. Beltran, A chemical genetic roadmap to improved tomato flavor. Science 355, 391–394 (2017). doi: 10.1126/science.aal1556.
Z. Wang, Y. C. Hong, G. T. Zhu, Y. M. Li, Q. F. Niu, J. J. Yao, K. Hua, J. J. Bai, Y. F. Zhu, H. Z. Shi, S. W. Huang, J. K. Zhu, Loss of salt tolerance during tomato domestication conferred by variation in a Na⁺/K⁺ transporter. Embo J. 39, e103256 (2020). doi: 10.15252/embj.2019103256.
M. J. L. Morton, M. Awlia, N. Al-Tamimi, S. Saade, Y. Pailles, S. Negrao, M. Tester, Salt stress under the scalpel - dissecting the genetics of salt tolerance. Plant J. 97, 148–163 (2019). doi: 10.1111/tpj.14189.
Z. L. Guo, H. R. Cao, J. Zhao, S. Bai, W. T. Peng, J. Li, L. L. Sun, L. Y. Chen, Z. H. Lin, C. Shi, Q. Yang, Y. Q. Yang, X. R. Wang, J. Tian, Z. C. Chen, H. Liao, A natural uORF variant confers phosphorus acquisition diversity in soybean. Nat. Commun. 13, 3796 (2022). doi: 10.1038/s41467-022-31555-2.
M. Yang, K. Lu, F. J. Zhao, W. B. Xie, P. Ramakrishna, G. Y. Wang, Q. Q. Du, L. M. Liang, C. J. Sun, H. Zhao, Z. Y. Zhang, Z. H. Liu, J. J. Tian, X. Y. Huang, W. S. Wang, H. X. Dong, J. T. Hu, L. C. Ming, Y. Z. Xing, G. W. Wang, J. H. Xiao, D. E. Salt, X. M. Lian, Genome-wide association studies reveal the genetic basis of ionomic variation in rice. Plant Cell 30, 2720–2740 (2018). doi: 10.1105/tpc.18.00375.
B. Escalante, D. Erlij, J. R. Falck, J. C. McGiff, Effect of cytochrome-P450 arachidonate metabolites on ion-transport in rabbit kidney loop of henle. Science 251, 799–802 (1991). doi: 10.1126/science.1846705.
J. Vriens, H. Watanabe, A. Janssens, G. Droogmans, T. Voets, B. Nilius, Cell swelling, heat, and chemical agonists use distinct pathways for the activation of the cation channel TRPV4. Proc. Natl. Acad. Sci. U. S. A. 101, 396–401 (2004). doi: 10.1073/pnas.0303329101.
H. L. Yan, W. X. Xu, J. Y. Xie, Y. W. Gao, L. L. Wu, L. Sun, L. Feng, X. Chen, T. Zhang, C. H. Dai, T. Li, X. N. Lin, Z. Y. Zhang, X. Q. Wang, F. M. Li, X. Y. Zhu, J. J. Li, Z. C. Li, C. Y. Chen, M. Ma, H. L. Zhang, Z. Y. He, Variation of a major facilitator superfamily gene contributes to differential cadmium accumulation between rice subspecies. Nat. Commun. 10, 2562 (2019). doi: 10.1038/s41467-019-10544-y.
S. Bagga, J. Bracht, S. Hunter, K. Massirer, J. Holtz, R. Eachus, A. E. Pasquinelli, Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122, 553–563 (2005). doi: 10.1016/j.cell.2005.07.031.
L. Fattore, R. Mancini, M. Acunzo, G. Romano, A. Laganà, M. E. Pisanu, D. Malpicci, G. Madonna, D. Mallardo, M. Capone, F. Fulciniti, L. Mazzucchelli, G. Botti, C. M. Croce, P. A. Ascierto, G. Ciliberto, miR-579-3p controls melanoma progression and resistance to target therapy. Proc. Natl. Acad. Sci. U. S. A. 113, E5005-E5013 (2016). doi: 10.1073/pnas.1607753113.
B. Harr, M. Kauer, C. Schlötterer, Hitchhiking mapping: A population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proc. Natl. Acad. Sci. U. S. A. 99, 12949–12954 (2002). doi: 10.1073/pnas.202336899.
J. Maynard-Smith, J. Haigh, Hitch-hiking effect of a favorable gene. Genet. Res. 23, 23–35 (1974). doi: 10.1017/s0016672300014634.
T. Lin, G. T. Zhu, J. H. Zhang, X. Y. Xu, Q. H. Yu, Z. Zheng, Z. H. Zhang, Y. Y. Lun, S. Li, X. X. Wang, Z. J. Huang, J. M. Li, C. Z. Zhang, T. T. Wang, Y. Y. Zhang, A. X. Wang, Y. C. Zhang, K. Lin, C. Y. Li, G. S. Xiong, Y. B. Xue, A. Mazzucato, M. Causse, Z. J. Fei, J. J. Giovannoni, R. T. Chetelat, D. Zamir, T. Städler, J. F. Li, Z. B. Ye, Y. C. Du, S. W. Huang, Genomic analyses provide insights into the history of tomato breeding. Nature Genet. 46, 1220–1226 (2014). doi: 10.1038/ng.3117.
M. Chakrabarti, N. Zhang, C. Sauvage, S. Muños, J. Blanca, J. Cañizares, M. J. Diez, R. Schneider, M. Mazourek, J. McClead, M. Causse, E. van der Knaap, A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc. Natl. Acad. Sci. U. S. A. 110, 17125–17130 (2013). doi: 10.1073/pnas.1307313110.
X. M. Ji, B. D. Dong, B. Shiran, M. J. Talbot, J. E. Edlington, T. Hughes, R. G. White, F. Gubler, R. Dolferus, Control of abscisic acid catabolism and abscisic acid homeostasis is important for reproductive stage stress tolerance in cereals. Plant Physiol. 156, 647–662 (2011). doi: 10.1104/pp.111.176164.
C. F. Su, Y. C. Wang, T. H. Hsieh, C. A. Lu, T. H. Tseng, S. M. Yu, A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol. 153, 145–158 (2010). doi: 10.1104/pp.110.153015.
H. Yu, T. Lin, X. B. Meng, H. L. Du, J. K. Zhang, G. F. Liu, M. J. Chen, Y. H. Jing, L. Q. Kou, X. X. Li, Q. Gao, Y. Liang, X. D. Liu, Z. L. Fan, Y. T. Liang, Z. K. Cheng, M. S. Chen, Z. X. Tian, Y. H. Wang, C. C. Chu, J. R. Zuo, J. M. Wan, Q. Qian, B. Han, A. Zuccolo, R. Wing, C. X. Gao, C. Z. Liang, J. Y. Li, A route to de novo domestication of wild allotetraploid rice. Cell 184, 1156–1170 (2021). doi: 10.1016/j.cell.2021.01.013.
J. Zeng, C. L. Zhou, Z. M. He, Y. Wang, L. L. Xu, G. D. Chen, W. Zhu, Y. H. Zhou, H. Y. Kang, Disomic substitution of 3D chromosome with its homoeologue 3E in tetraploid Thinopyrum Elongatum enhances wheat seedlings tolerance to salt stress. Int. J. Mol. Sci. 24, 1609 (2023). doi: 10.3390/ijms24021609.
L. Z. Chen, L. Duan, M. H. Sun, Z. Yang, H. Y. Li, K. M. Hu, H. Yang, L. Liu, Current trends and insights on EMS mutagenesis application to studies on plant abiotic stress tolerance and development. Front. Plant Sci. 13, 1052569 (2023). doi: 10.3389/fpls.2022.1052569.
G. T. Zhu, S. C. Wang, Z. J. Huang, S. B. Zhang, Q. G. Liao, C. Z. Zhang, T. Lin, M. Qin, M. Peng, C. K. Yang, X. Cao, X. Han, X. X. Wang, E. van der Knaap, Z. H. Zhang, X. Cui, H. Klee, A. R. Fernie, J. Luo, S. W. Huang, Rewiring of the fruit metabolome in tomato breeding. Cell 172, 249–261 (2018). doi: 10.1016/j.cell.2017.12.019.
J. Ye, X. Wang, W. Q. Wang, H. Y. Yu, G. Ai, C. X. Li, P. Y. Sun, X. Y. Wang, H. X. Li, B. Ouyang, J. H. Zhang, Y. Y. Zhang, H. Y. Han, J. J. Giovannoni, Z. J. Fei, Z. B. Ye, Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. Plant Physiol. 186, 2078–2092 (2021). doi: 10.1093/plphys/kiab230.
F. Rastmanesh, F. Moore, B. Keshavarzi, Speciation and phytoavailability of heavy metals in contaminated soils in sarcheshmeh area, Kerman Province, Iran. Bull. Environ. Contam. Toxicol. 85, 515–519 (2010). doi: 10.1007/s00128-010-0149-z.
B. Ouyang, Y. H. Chen, H. X. Li, C. J. Qian, S. L. Huang, Z. B. Ye, Transformation of tomatoes with osmotin and chitinase genes and their resistance to Fusarium wilt. J. Horticult. Sci. Biotechnol. 80, 517–522 (2005). doi: 10.1080/14620316.2005.11511971.
S. B. Zhang, Z. C. Jiao, L. Liu, K. T. Wang, D. Y. Zhong, S. B. Li, T. T. Zhao, X. Y. Xu, X. Cui, Enhancer-promoter interaction of SELF PRUNING 5G shapes photoperiod adaptation. Plant Physiol. 178, 1631–1642 (2018). doi: 10.1104/pp.18.01137.
Y. Zhang, R. H. Ming, M. Khan, Y. Wang, B. Dahro, W. Xiao, C. L. Li, J. H. Liu, ERF9 of Poncirus trifoliata (L.) Raf. undergoes feedback regulation by ethylene and modulates cold tolerance via regulating a glutathione S-transferase U17 gene. Plant Biotechnol. J. 20, 183–200 (2022). doi: 10.1111/pbi.13705.
J. Z. Zang, V. Kriechbaumer, P. W. Wang, Plant cytoskeletons and the endoplasmic reticulum network organization. J. Plant Physiol. 264, 7 (2021). doi: 10.1016/j.jplph.2021.153473.
L. L. Shang, J. W. Song, H. Y. Yu, X. Wang, C. Y. Yu, Y. Wang, F. M. Li, Y. G. Lu, T. T. Wang, B. Ouyang, J. H. Zhang, R. M. Larkin, Z. B. Ye, Y. Y. Zhang, A mutation in a C₂H₂-type zinc finger transcription factor contributed to the transition toward self-pollination in cultivated tomato. Plant Cell 33, 3293–3308 (2021). doi: 10.1093/plcell/koab201.

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Co-selection of low cadmium accumulation and high yield during tomato breeding

Status:

Version 1

Abstract

Introduction

Results

Cultivated tomato varieties accumulate less Cd in shoot than wild ancestors

Identification of a major locus for low Cd accumulation in tomato

Discussion

Methods

Plant material and growth conditions

Measurement of Cd²⁺ contents

Genome-wide association study

Generation of transgenic tomato

Gene expression analysis

Dual luciferase reporter assay

Subcellular localization

GUS staining

Detection of domestication and improvement sweeps

Declarations

Acknowledgments

Funding

Author contributions

Competing interests

References

Additional Declarations

Supplementary Files

Status:

Version 1

Co-selection of low cadmium accumulation and high yield during tomato breeding

Status:

Version 1

Abstract

Introduction

Results

Cultivated tomato varieties accumulate less Cd in shoot than wild ancestors

Identification of a major locus for low Cd accumulation in tomato

Discussion

Methods

Plant material and growth conditions

Measurement of Cd2+ contents

Genome-wide association study

Generation of transgenic tomato

Gene expression analysis

Dual luciferase reporter assay

Subcellular localization

GUS staining

Detection of domestication and improvement sweeps

Declarations

Acknowledgments

Funding

Author contributions

Competing interests

References

Additional Declarations

Supplementary Files

Status:

Version 1

Measurement of Cd²⁺ contents