Candidate Gene Identification and Transcriptome Analysis of Tomato male sterile-30 and Functional Marker Development for ms-30 and Its Alleles, ms-33, 7B-1, and stamenless-2.

Male sterility is a valuable trait for hybrid seed production in tomato (Solanum lycopersicum). The mutants male sterile-30 (ms-30) and ms-33 of tomato exhibit twisted stamens, exposed stigmas, and complete male sterility, thus holding potential for application in hybrid seed production. In this study, the ms-30 and ms-33 loci were fine-mapped to 53.3 kb and 111.2 kb intervals, respectively. Tomato PISTILLATA (TPI, syn. SlGLO2), a B-class MADS-box transcription factor gene, was identified as the most likely candidate gene for both loci. TPI is also the candidate gene of tomato male sterile mutant 7B-1 and sl-2. Allelism tests revealed that ms-30, ms-33, 7B-1, and sl-2 were allelic. Sequencing analysis showed sequence alterations in the TPI gene in all these mutants, with ms-30 exhibiting a transversion (G to T) that resulted in a missense mutation (S to I); ms-33 showing a transition (A to T) that led to alternative splicing, resulting in a loss of 46 amino acids in protein; and 7B-1 and sl-2 mutants showing the insertion of an approximately 4.8 kb retrotransposon. On the basis of these sequence alterations, a Kompetitive Allele Specific PCR marker, a sequencing marker, and an Insertion/Deletion marker were developed. Phenotypic analysis of the TPI gene-edited mutants and allelism tests indicated that the gene TPI is responsible for ms-30 and its alleles. Transcriptome analysis of ms-30 and quantitative RT-PCR revealed some differentially expressed genes associated with stamen and carpel development. These findings will aid in the marker-assisted selection for ms-30 and its alleles in tomato breeding and support the functional analysis of the TPI gene.

Acyl-CoA synthetase 1 plays an important role on pollen development and male fertility in tomato.

The development of pollen is critical to male reproduction in flowering plants. Acyl-CoA synthetase (ACOS) genes play conserved functions in regulating pollen development in various plants. Our previous work found that knockout of the SlACOS1 gene in tomato might decrease fruit setting. The current study further revealed that SlACOS1 was important to pollen development and male fertility. The SlACOS1 gene was preferentially expressed in the stamen of the flower with the highest expression at the tetrad stage of anther development. Mutation of the SlACOS1 gene by the CRISPR/Cas9-editing system reduced pollen number and viability as well as fruit setting. The tapetum layer exhibited premature degradation and the pollen showed abnormal development appearing irregular, shriveled, or anucleate in Slacos1 mutants at the tetrad stage. The fatty acid metabolism in anthers was significantly impacted by mutation of the SlACOS1 gene. Furthermore, targeted fatty acids profiling using GC-MS found that contents of most fatty acids except C18:1 and C18:2 were reduced. Yeast complementation assay demonstrated that the substrate preferences of SlACOS1 were C16:0 and C18:0 fatty acids. Male fertility of Slacos1 mutant could be slightly restored by applying exogenous palmitic acid, a type of C16:0 fatty acid. Taken together, SlACOS1 played important roles on pollen development and male fertility by regulating the fatty acid metabolism and the development of tapetum and tetrad. Our findings will facilitate unraveling the mechanism of pollen development and male fertility in tomato.

Optimized carbonization of coffee shell via response surface methodology: A circular economy approach for environmental remediation.

The disposal of coffee shell waste on farmland, is a common practice that can causing the environmental and waste valuable resources. Carbonization has been identified as an effective method for transforming coffee shells into useful products that mitigate environmental pollution. Through the response surface methodology, the carbonization conditions of the coffee shells were optimized and its potential as a biochar-based slow-release urea fertilizer was explored. Experiments were conducted on coffee shell performance under varying carbonization conditions such as temperature (600-1000 °C), time (1-5 h), and heating rate (5-20 °C/min). The results indicated that the ideal urea adsorption was 56.3 mg/g, achieved under carbonization conditions of 2.83 h, 809 °C, and 15.3 °C/min. The optimal nutrient release rate within seven days was 45.4% under carbonization conditions of 3.19 h, 813 °C, and 15.0 °C/min. The infrared spectroscopy analysis indicates that carbonization conditions influenced the absorption peak intensity of coffee shell biochar, while the functional group types remain unchanged. The biochar exhibits diverse functional groups and abundant pores, making it a promising candidate for use as a biochar-based fertilizer material. Overall, the findings demonstrate an effective waste management approach that significantly reduces environmental pollutants while remediating pollution.

Southern Tibetan rifting since late Miocene enabled by basal shear of the underthrusting Indian lithosphere.

Syncontractional extension is prominent in present-day Tibet, but its origin remains vigorously debated. Several deep-seated geodynamic processes (e.g., Indian underthrusting, horizontal flow, and mantle upwelling) have been linked to Tibetan rifting. Indian underthrusting is a good candidate because it can well explain why surface rifts are more prominent south of the Bangong-Nujiang suture; however, how Indian underthrusting causes extension is not well understood and lacks observational constraints. Seismic anisotropy, measured by exploiting the birefringence effect of shear waves, can be indicative of the deformation styles within the crust. Here, we unveil the dominant convergence-parallel alignment of anisotropic fabrics in the deep crust of the southern Tibetan rifts using seismic recordings collected from our recently deployed and existing seismic stations. This finding suggests that the strong north-directed shearing exerted by the underthrusting Indian plate is key to enabling present-day extension in southern Tibet.

Neuroprotective and antioxidant activities of different polarity parts of the extracts of the Ginkgo biloba leaf and Zingiber officinale rhizome from Yongzhou.

In order to make better use of the two local dominant plant resources of Ginkgo biloba and Zingiber officinale from Yongzhou in Hunan province, the in vitro neuroprotective and antioxidant activities of extracts from the G. biloba leaf and Z. officinale rhizome, and the correlation between these two kinds of activities, were analyzed. The in vivo effects of these two plant extracts on aged mice blood physiology and central neuron cell activity were then determined after continuous gavage with the best polarity part at different concentrations (2, 4, 8 mg/ml). The results showed that the cell survival rate and superoxide dismutase (SOD) activity of the induced injury central neurons increased, although the malondialdehyde (MDA) content decreased gradually with the extract concentrations increasing in a certain range. Different polarity parts performed differently, even though they had the same concentration, with G. biloba always performing better than the Z. officinale rhizome at the same concentration and polarity. The order of G. biloba extract from superior to inferior was ethanol, ethyl acetate, n-butanol, chloroform, water, and petroleum ether (except that the petroleum ether part performed slightly better than the water part at 0.4 and 0.5 mg/ml), while the order of Z. officinale rhizome extract from superior to inferior was ethanol, chloroform, n-butanol, ethyl acetate, water, and petroleum ether. These two plant extracts demonstrated good in vitro effect against oxygen free radicals; the scavenging rate of superoxide free radicals had a significant positive correlation with the cell survival rate. The in vivo central nerve cell activity and SOD, glutathione peroxidase (GSH-PX) activity in aged mice blood serum increased while the MDA content decreased with treatment with these two extracts (p < 0.05). There were no significant changes in the number of leukocytes, lymphocytes, red blood cells, hemoglobin content, blood urine nitrogen, uric acid, creatinine, and the enzyme activity of glutamic oxaloacetic transaminase (GOT) and glutamic pyruvic transaminase (GPT) (p > 0.05). G. biloba had a better in vivo effect than Z. officinale rhizome even though their concentration and polarity part were same. These results could provide some references for better development of these two plant extracts from Yongzhou in the field of neuroprotection.

Vascular Disruptive Hydrogel Platform for Enhanced Chemotherapy and Anti-Angiogenesis through Alleviation of Immune Surveillance.

Patients undergoing immunotherapy always exhibit a low-response rate due to tumor heterogeneity and immune surveillance in the tumor. Angiogenesis plays an important role in affecting the status of tumor-infiltrated lymphocytes by inducing hypoxia and acidosis microenvironment, suggesting its synergistic potential in immunotherapy. However, the antitumor efficacy of singular anti-angiogenesis therapy often suffers from failure in the clinic due to the compensatory pro-angiogenesis signaling pathway. In this work, classic injectable thermosensitive PLGA-PEG-PLGA copolymer was used to construct a platform to co-deliver CA4P (vascular disruptive agent) and EPI for inducing immunogenic cell death of cancer cells by targeting the tumor immune microenvironment. Investigation of 4T1 tumor-bearing mouse models suggests that local administration of injectable V+E@Gel could significantly inhibit the proliferation of cancer cells and prolong the survival rate of 4T1 tumor-bearing mouse models. Histological analysis further indicates that V+E@Gel could effectively inhibit tumor angiogenesis and metastasis by down-regulating the expression of CD34, CD31, MTA1 and TGF-ß. Moreover, due to the sustained release kinetics of V+E@Gel, its local administration relieves the immune surveillance in tumor tissues and thus induces a robust and long-lasting specific antitumor immune response. Overall, this work provides a new treatment strategy through the mediation of the tumor immune microenvironment by vascular disruption to fulfill enhanced chemotherapy and immunotherapy.

Spatiotemporal Pattern of Urban-Rural Integration Development and Its Driving Mechanism Analysis in Hangzhou Bay Urban Agglomeration.

The quantitative analysis of the urban-rural integration development (URID) level and its driving factors is of great significance for the new-type urbanization of urban agglomerations. This study constructed a multidimensional framework in the perspective of a population-space-economy-society-ecology framework to measure the URID level from 2000 to 2020 and further explored the driving mechanism of the URID changes by a geographical detector model in the Hangzhou Bay urban agglomeration (HBUA). The results showed that the land-use change in the HBUA from 2000 to 2020 showed a typical characteristic of the transition between cultivated and construction land. The URID level in the HBUA improved from 0.294 in 2000 to 0.563 in 2020, and the year 2005 may have been the inflection point of URID in the HBUA. The URID level showed a significant spatial aggregation with high values. Hangzhou, Jiaxing, and Ningbo were hot spots since 2015, and the cold spots were Huzhou and Shaoxing. The population and spatial integration had more important impacts on URID levels in 2000, 2005, and 2020, while economic and social integration had more significant impacts on URID levels in 2010 and 2015. This study provided a deeper understanding of the evolution of URID in an urban agglomeration and could be used as a reference for decision makers.

Loci underlying leaf agronomic traits identified by re-sequencing celery accessions based on an assembled genome.

Celery is one of the most popular vegetables in the world. The main edible parts of celery are the leaf blade and petiole. The celery petiole is usually green, red, or white, with a hollow or solid pith. However, the loci/genes controlling these petiole-related traits have not been reported. In this study, we present a chromosome-level celery genome assembly with a total size of 3.339 Gb. Simultaneous bursts of long-terminal repeats (78.43%) contributed greatly to the large genome size. Re-sequencing and population structure analysis of 79 celery accessions revealed that they could be divided into Chinese celery and Western celery. By combining genome-wide association studies (GWAS) and mapping data, we located the hollow petiole (hp) loci in an 807.6-kb region on chromosome 11. This study provides valuable resources for genetic research on celery and is also helpful for the identification and cloning of genes controlling leaf agronomic traits in celery.

Does Non-Food Cultivation of Cropland Increase Farmers' Income?

The production of cash crops is often regarded as an effective way to increase farmers' income. This study evaluates the impact of non-food cultivation of cropland on farmers' income by using the least-squares (OLS) model in Zhejiang Province, eastern China. Farmers are further divided into different groups according to their income levels to analyze the different impacts of non-food cultivation on their household income. The result shows that non-food cultivation has a significant negative effect on farmers' income, with a more pronounced effect on farmers with a relatively low income. Accordingly, the increase in the proportion of cash crops that are grown does not increase the income of farmers in Zhejiang; instead, this harms their income. Therefore, farmers in Zhejiang should not rely on the cultivation of cash crops for their prosperity but must focus on participating in non-farm employment to increase their household income.

Mapping and characterization of the Rx3 gene for resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 in tomato.

KEY MESSAGE: Rx3 encodes a typical CC-NBS-LRR resistance protein and confers the resistance to Xanthomonas euvesicatoria pv. euvesicatoria race T1 causing bacterial spot in tomato. Bacterial spot caused by at least four species of Xanthomonas is an epidemic disease severely affecting tomato production worldwide. The use of resistant cultivars is an economical and effective approach to control the disease. An unimproved tomato breeding line Hawaii 7988 has been considered as the most reliable source for resistance to X. euvesicatoria pv. euvesicatoria race T1, and the Rx3 locus located at a 4.53-Mb region on chromosome 5 (SL4.0) is the major locus for resistance to race T1 in this line. In the current study, the Rx3 locus was firstly located to a 1.05-Mb region based on comparisons of marker polymorphisms between the susceptible line Ohio 88119 and resistant lines Hawaii 7998, Ohio 9834 and FG02-7530. Using recombinant inbred lines (F5:6, F6:7, and F7:8) derived from a cross between Ohio 88119 and Ohio 9834, the Rx3 locus was finally mapped to a 64.3-kb interval between markers MG-Rx3-4 and MG-Rx3-A6. The Solyc05g053980 gene, designated as Rx3, encoding a coiled-coil nucleotide-binding leucine-rich repeat protein was considered as the candidate for the Rx3 locus. Expression of the gene could be induced by the infection of race T1 strain. Knockout of the Solyc05g053980 gene through CRISPR/Cas9 editing system in the resistant line FG02-7530 decreased resistance to race T1 strain. These results provide a close step for understanding the resistance mechanism to race T1 in Hawaii 7998 and guide tomato breeders accordingly to improve bacterial spot disease resistance in tomato.

Mapping of CaPP2C35 involved in the formation of light-green immature pepper (Capsicum annuum L.) fruits via GWAS and BSA.

KEY MESSAGE: Genome-wide association study, bulked segregant analysis, and genetic analysis delimited the LG locus controlling light-green immature pepper fruits into a 35.07 kbp region on chromosome 10. A strong candidate gene, CaPP2C35, was identified in this region. In pepper (Capsicum annuum L.), the common colors of immature fruits are yellowish white, milky yellow, green, purple, and purplish black. Genes related to dark green, white, and purple immature fruits have been cloned; however, only a few studies have investigated light-green immature fruits. Here, we performed a genetic study using light-green (17C827) and green (17C658) immature fruits. The light-green color of immature fruits was controlled by a single locus-dominant genetic trait compared with the green color of immature fruits. We also performed a genome-wide association study and bulked segregant analysis of immature-fruit color and mapped the LG locus to a 35.07 kbp region on chromosome 10. Only one gene, Capana10g001710, was found in this region. A G-A substitution occurred at the 313th base of the Capana10g001710 coding sequence in 17C827, resulting in the conversion of the α-helix of its encoded PP2C35 protein into a ß-fold. The expression of Capana10g001710 (termed CaPP2C35) in 17C827 was significantly higher than in 17C658. Silencing CaPP2C35 in 17C827 resulted in an increase in chlorophyll content in the exocarp and the appearance of green stripes on the surface of the fruit. These results indicate that CaPP2C35 may be involved in the formation of light-green immature fruits by regulating the accumulation of chlorophyll content in the exocarp. Thus, these findings lay the foundation for further studies and genetic improvement of immature-fruit color in pepper.

A high-continuity and annotated tomato reference genome.

BACKGROUND: Genetic and functional genomics studies require a high-quality genome assembly. Tomato (Solanum lycopersicum), an important horticultural crop, is an ideal model species for the study of fruit development. RESULTS: Here, we assembled an updated reference genome of S. lycopersicum cv. Heinz 1706 that was 799.09 Mb in length, containing 34,384 predicted protein-coding genes and 65.66% repetitive sequences. By comparing the genomes of S. lycopersicum and S. pimpinellifolium LA2093, we found a large number of genomic fragments probably associated with human selection, which may have had crucial roles in the domestication of tomato. We also used a recombinant inbred line (RIL) population to generate a high-density genetic map with high resolution and accuracy. Using these resources, we identified a number of candidate genes that were likely to be related to important agronomic traits in tomato. CONCLUSION: Our results offer opportunities for understanding the evolution of the tomato genome and will facilitate the study of genetic mechanisms in tomato biology.

Auxin Metabolism Is Involved in Fruit Set and Early Fruit Development in the Parthenocarpic Tomato "R35-P".

Parthenocarpic tomato can set fruit and develop without pollination and exogenous hormone treatments under unfavorable environmental conditions, which is beneficial to tomato production from late fall to early spring in greenhouses. In this study, the endogenous hormones in the ovaries of the parthenocarpic tomato line "R35-P" (stigma removed or self-pollination) and the non-parthenocarpic tomato line "R35-N" (self-pollination) at four stages between preanthesis and postanthesis investigated, using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). A nearly twofold IAA (indoleacetic acid) content was found in "R35-P" rather than in "R35-N" at -2 and 0 days after anthesis (DAA). Except at -2 DAA, a lower ABA (abscisic acid) content was observed in Pe (stigma removed in "R35-P") compared to that in Ps (self-pollination in "R35-P") or CK (self-pollination in "R35-N"). After pollination, although the content of GA1 (gibberellins acid 1) in CK increased, the levels of GAs (gibberellins acids) were notably low. At all four stages, a lower SA (salicylic acid) content was found in Ps and CK than in Pe, while the content and the change trend were similar in Ps and CK. The variation tendencies of JA (jasmonic acid) varied among Pe, Ps, and CK at the studied periods. Furthermore, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses of transcriptomic data identified 175 differentially expressed genes (DEGs) related to plant hormone signal transduction, including 63 auxin-related genes, 27 abscisic acid-related genes, 22 ethylene-related genes, 16 cytokinin-related genes, 16 salicylic acid-related genes, 14 brassinosteroid-related genes, 13 jasmonic acid-related genes, and 4 gibberellin-related genes at -2 DAA and 0 DAA. Our results suggest that the fate of a fruit set or degeneration occurred before anthesis in tomato. Auxins, whose levels were independent of pollination and fertilization, play prominent roles in controlling a fruit set in "R35-P," and other hormones are integrated in a synergistic or antagonistic way.

Tomato SlPUB24 enhances resistance to Xanthomonas euvesicatoria pv. perforans race T3.

Solanum lycopersicum var. cerasiforme accession PI 114490 has broad-spectrum resistance to bacterial spot caused by several species of Xanthomonas. Resistance is quantitatively inherited, and a common quantitative trait locus QTL-11B on chromosome 11 has been identified previously. In this study, the SlPub24 gene was characterized in QTL-11B. SlPub24 in PI 114490 was upregulated by infection with X. euvesicatoria pv. perforans race T3, but its transcription was low in the susceptible line OH 88119 whether or not it was infected by the pathogen. The differential expression of SlPub24 between PI 114490 and OH 88119 was due to great sequence variation in the promoter region. The promoter of SlPub24 in OH 88119 had very low activity and did not respond to pathogen infection. Transgenic lines of OH 88119 overexpressing SlPub24 isolated from PI 114490 showed significantly enhanced resistance, while mutants of Slpub24 generated by CRISPR/Cas9 editing showed more susceptibility to race T3 and to other races. The mutants also showed spontaneous cell death in leaves. The expression of the salicylic acid (SA) pathway gene phenylalanine ammonia-lyase (PAL) and signaling-related genes pathogenesis-related (PR1) and nonexpresser of PR1 (NPR1) were influenced by SlPub24. The content of SA in tomato plants was consistent with the level of SlPub24 expression. Furthermore, SlPUB24 interacted with the cell wall protein SlCWP and could regulate the degradation of SlCWP. The expression levels of SlCWP and SlCWINV1, a cell wall invertase gene, showed opposite patterns during pathogen infection. The activity of SlCWINV1 was lower in mutants than in PI 114490. The results are discussed in terms of the roles of the abovementioned genes, and a potential model for SlPUB24-mediated resistance to bacterial spot is proposed.

Tomato protein Rx4 mediates the hypersensitive response to Xanthomonas euvesicatoria pv. perforans race T3.

Bacterial spot, which is caused by several Xanthomonas species, is an economically important disease in tomato (Solanum lycopersicum). Great efforts have been made for the identification of resistant sources and the genetic analysis of resistance. However, the development of resistant commercial varieties is slow due to the existence of multiple species of the pathogen and a poor understanding of the resistance mechanism in tomato. The current study revealed that the Rx4 gene encodes a nucleotide-binding leucine-rich repeat protein in the wild tomato species Solanum pimpinellifolium and specifically recognizes and confers a hypersensitive response (HR) to Xanthomonas euvesicatoria pv. perforans race T3 expressing the AvrXv3 avirulence protein. Complementation of the Rx4 gene in the susceptible tomato line Ohio 88119 using a transgenic approach resulted in HR, whereas knockout of the gene through CRISPR/Cas9 editing in resistant lines Hawaii 7981 and PI 128216 led to non-HR to race T3. Transcription of Rx4 was not induced by the presence of race T3. Furthermore, the Rx4 protein did not show physical interaction with AvrXv3 but interacted with SGT1-1 and RAR1. Virus-induced gene silencing of SGT1-1 and RAR1 in the resistant line PI128216 suppressed the HR to race T3. Taken together, our study confirms Rx4 is the gene conferring the HR to bacterial spot race T3 and reveals the potential roles of SGT1-1 and RAR1 as signals in the Rx4-mediated HR. This discovery represents a step forward in our understanding of the mechanism of resistance to bacterial spot in tomato and may have important implications for understanding plant-bacterial interactions.

SlGID1a Is a Putative Candidate Gene for qtph1.1, a Major-Effect Quantitative Trait Locus Controlling Tomato Plant Height.

Plant height is an important agronomic trait in crops. Several genes underlying tomato (Solanum lycopersicum) plant height mutants have been cloned. However, few quantitative trait genes for plant height have been identified in tomato. In this study, seven quantitative trait loci (QTLs) controlling plant height were identified in tomato. Of which, qtph1.1 (QTL for tomato plant height 1.1), qtph3.1 and qtph12.1 were major QTLs and explained 15, 16, and 12% of phenotypic variation (R2), respectively. The qtph1.1 was further mapped to an 18.9-kb interval on chromosome 1. Based on the annotated tomato genome (version SL2.50, annotation ITAG2.40), Solyc01g098390 encoding GA receptor SlGID1a was the putative candidate gene. The SlGID1a gene underlying the qtph1.1 locus contained a single nucleotide polymorphism (SNP) that resulted in an amino acid alteration in protein sequence. The near-isogenic line containing the qtph1.1 locus (NIL-qtph1.1) exhibited shorter internode length and cell length than the wild type (NIL-WT). The dwarf phenotype of NIL-qtph1.1 could not be rescued by exogenous GA3 treatment. Transcriptome analysis and real-time quantitative reverse transcription PCR (qPCR) showed that several genes related to biosynthesis and signaling of GA and auxin were differentially expressed in stems between NIL-qtph1.1 and NIL-WT. These findings might pave the road for understanding the molecular regulation mechanism of tomato plant height.

Transcription of lncRNA ACoS-AS1 is essential to trans-splicing between SlPsy1 and ACoS-AS1 that causes yellow fruit in tomato.

Phytoene synthase (PSY) has been considered as an important regulatory enzyme in carotenoids biosynthesis pathway. Previous study finds that the yellow fruit in Solanum lycopersicum var. cerasiforme accession PI 114490 is caused by loss-of-function of SlPSY1 due to trans-splicing between SlPsy1 and an unknown gene transcribed from neighbour opposite strand DNA of SlPsy1. The genomic DNA sequences of SlPsy1 between red and yellow-fruited tomato lines have one single-nucleotide polymorphism (SNP) in the fourth intron and one SSR in the intergenic region. In the current study, the cause of trans-splicing event was further investigated. The data showed that the previously defined unknown gene was a putative long non-coding RNA ACoS-AS1 with three variants in many yellow-fruited tomato lines. The intronic SNP and intergenic SSR were tightly associated with trans-splicing event SlPsy1-ACoS-AS1. However, transgenic tomato lines carrying the genomic DNA of SlPsy1 from PI 114490 did not generate transcripts of ACoS-AS1and SlPsy1-ACoS-AS1 suggesting that only the intronic SNP could not cause the trans-splicing event. Over-expression of SlPsy1-ACoS-AS1 in red-fruited tomato line M82 did not have any phenotype change while over-expression of wild type SlPsy1 resulted in altered leaf colour. Sub-cellular localization analysis showed that SlPSY1-ACoS-AS1 could not enter plastids where SlPSY1 has its enzyme activity. Mutation of ACoS-AS1 in PI 114490 generated by CRISPR/Cas9 techniques resulted in red fruits implying that ACoS-AS1 was essential to trans-splicing event SlPsy1-ACoS-AS1. The results obtained here will extend knowledge to understand the mechanism of trans-splicing event SlPsy1-ACoS-AS1 and provide additional information for the regulation of carotenoids biosynthesis.

Erratum: Author Correction: Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies.

[This corrects the article DOI: 10.1038/s41438-018-0071-9.].

Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper (Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS.

There are many agronomic traits of pepper (Capsicum L.) with abundant phenotypes that can benefit pepper growth. Using specific-locus amplified fragment sequencing (SLAF-seq), a genome-wide association study (GWAS) of 36 agronomic traits was carried out for 287 representative pepper accessions. To ensure the accuracy and reliability of the GWAS results, we analyzed the genetic diversity, distribution of labels (SLAF tags and single nucleotide polymorphisms (SNPs)) and population differentiation and determined the optimal statistical model. In our study, 1487 SNPs were highly significantly associated with 26 agronomic traits, and 2126 candidate genes were detected in the 100-kb region up- and down-stream near these SNPs. Furthermore, 13 major association peaks were identified for 11 key agronomic traits. Then we examined the correlations among the 36 agronomic traits and analyzed SNP distribution and found 37 SNP polymerization regions (total size: 264.69 Mbp) that could be selected areas in pepper breeding. We found that the stronger the correlation between the two traits, the greater the possibility of them being in more than one polymerization region, suggesting that they may be linked or that one pleiotropic gene controls them. These results provide a theoretical foundation for future multi-trait pyramid breeding of pepper. Finally, we found that the GWAS signals were highly consistent with those from the nuclear restorer-of-fertility (Rf) gene for cytoplasmic male sterility (CMS), verifying their reliability. We further identified Capana06g002967 and Capana06g002969 as Rf candidate genes by functional annotation and expression analysis, which provided a reference for the study of cytoplasmic male sterility in Capsicum.