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Holmes A, Humphris S, Jones S. Total mRNA sequence dataset from Pectobacterium atrosepticum colonising potato or radish roots. Data Brief 2024; 54:110372. [PMID: 38623551 PMCID: PMC11016960 DOI: 10.1016/j.dib.2024.110372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Pectobacterium atrosepticum (Pba) is a gram-negative bacterium that causes blackleg and tuber soft rot of potato but can also asymptomatically colonise other (non-host) plant species. The aim of this study was to investigate the molecular processes and responses involved in Pba-host (potato) and Pba-non-host (radish) interactions, under laboratory conditions. To achieve this, we used total mRNA-sequencing to measure the gene expression patterns from all three species: Pba, potato and radish. We employed an end-point dual transcriptome approach. We used hydroponically grown potato (Solanum tuberosum var. Estima) and oil radish (Raphanus sativa var. Bento) roots inoculated with Pba SCRI1039 for 14 days compared to un-inoculated control plants or cultured bacteria. Total RNA was extracted from replicates of the two plant species and the bacterium using a Macherey-Nagel Nucleospin Plant RNA kit. The RNA from the 17 samples was then subjected to total mRNA-sequencing (paired-end) on an Illumina NovaSeq 6000™ sequencing platform. This gave between 39.2-58.1M reads per sample. The high-quality reads obtained were mapped to the corresponding reference genomes using Bowtie2 and the percentages of bacterium and plant transcripts calculated. This dataset constitutes the raw read fastq files and can be used to inform on genes active in plant rhizosphere-microbe interactions.
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Affiliation(s)
- Ashleigh Holmes
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, United Kingdom
| | - Sonia Humphris
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, United Kingdom
| | - Susan Jones
- Information and Computer Sciences, The James Hutton Institute, Dundee, DD2 5DA, United Kingdom
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2
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Sood S, Bhardwaj V, Mangal V, Kardile H, Dipta B, Kumar A, Singh B, Siddappa S, Sharma AK, Dalamu, Buckseth T, Chaudhary B, Kumar V, Pandey N. Development of near homozygous lines for diploid hybrid TPS breeding in potatoes. Heliyon 2024; 10:e31507. [PMID: 38831819 PMCID: PMC11145485 DOI: 10.1016/j.heliyon.2024.e31507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Diploid inbred-based F1 hybrid True Potato Seed (DHTPS) breeding is a novel technique to transform potato breeding and cultivation across the globe. Significant efforts are being made to identify elite diploids, dihaploids and develop diploid inbred lines for heterosis exploitation in potatoes. Self-incompatibility is the first obstacle for developing inbred lines in diploid potatoes, which necessitates the introgression of a dominant S locus inhibitor gene (Sli) for switching self-incompatibility to self-compatibility. We evaluated a set of 357 diploid clones in different selfing generations for self-compatibility and degree of homozygosity using Kompetitive Allele Specific PCR (KASP) Single Nucleotide Polymorphism (SNP) markers. A subset of 10 KASP markers of the Sli candidate region on chromosome 12 showed an association with the phenotype for self-compatibility. The results revealed that the selected 10 KASP markers for the Sli gene genotype could be deployed for high throughput rapid screening of self-compatibility in diploid populations and to identify new sources of self-compatibility. The homozygosity assessed through 99 KASP markers distributed across all the chromosomes of the potato genome was 20-78 % in founder diploid clones, while different selfing generations, i.e., S0, S1, S2 and S3 observed 36.1-80.4, 56.9-82.8, 59.5-85.4 and 73.7-87.8 % average homozygosity, respectively. The diploid plants with ∼80 % homozygosity were also observed in the first selfing generation, which inferred that homozygosity assessment in the early generations itself could identify the best plants with high homozygosity to speed up the generation of diploid inbred lines.
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Affiliation(s)
- Salej Sood
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Hemant Kardile
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | | | | | - Dalamu
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Babita Chaudhary
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, UP, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - N.K. Pandey
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
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Achakkagari SR, Bozan I, Camargo-Tavares JC, McCoy HJ, Portal L, Soto J, Bizimungu B, Anglin NL, Manrique-Carpintero N, Lindqvist-Kreuze H, Tai HH, Strömvik MV. The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids. Sci Data 2024; 11:454. [PMID: 38704417 PMCID: PMC11069515 DOI: 10.1038/s41597-024-03300-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/23/2024] [Indexed: 05/06/2024] Open
Abstract
Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.
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Affiliation(s)
- S R Achakkagari
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - I Bozan
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - J C Camargo-Tavares
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - H J McCoy
- Department of Chemistry, University of New Brunswick, Fredericton, NB, Canada
| | - L Portal
- International Potato Center (CIP), Lima, Peru
| | - J Soto
- International Potato Center (CIP), Lima, Peru
| | - B Bizimungu
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB, Canada
| | - N L Anglin
- International Potato Center (CIP), Lima, Peru
- USDA ARS Small Grains and Potato Germplasm Research, Aberdeen, ID, USA
| | - N Manrique-Carpintero
- International Potato Center (CIP), Lima, Peru
- Alliance of Bioversity International and International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - H H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB, Canada
| | - M V Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada.
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Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
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Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
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Zhu X, Chen A, Butler NM, Zeng Z, Xin H, Wang L, Lv Z, Eshel D, Douches DS, Jiang J. Molecular dissection of an intronic enhancer governing cold-induced expression of the vacuolar invertase gene in potato. THE PLANT CELL 2024; 36:1985-1999. [PMID: 38374801 PMCID: PMC11062429 DOI: 10.1093/plcell/koae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
Potato (Solanum tuberosum) is the third most important food crop in the world. Potato tubers must be stored at cold temperatures to minimize sprouting and losses due to disease. However, cold temperatures strongly induce the expression of the potato vacuolar invertase gene (VInv) and cause reducing sugar accumulation. This process, referred to as "cold-induced sweetening," is a major postharvest problem for the potato industry. We discovered that the cold-induced expression of VInv is controlled by a 200 bp enhancer, VInvIn2En, located in its second intron. We identified several DNA motifs in VInvIn2En that bind transcription factors involved in the plant cold stress response. Mutation of these DNA motifs abolished VInvIn2En function as a transcriptional enhancer. We developed VInvIn2En deletion lines in both diploid and tetraploid potato using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9)-mediated gene editing. VInv transcription in cold-stored tubers was significantly reduced in the deletion lines. Interestingly, the VInvIn2En sequence is highly conserved among distantly related Solanum species, including tomato (Solanum lycopersicum) and other non-tuber-bearing species. We conclude that the VInv gene and the VInvIn2En enhancer have adopted distinct roles in the cold stress response in tubers of tuber-bearing Solanum species.
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Affiliation(s)
- Xiaobiao Zhu
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Airu Chen
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Nathaniel M Butler
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Madison, WI 53706, USA
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan Province, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan Province, China
| | - Haoyang Xin
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Lixia Wang
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Zhaoyan Lv
- Anhui Province Key Laboratory of Horticultural Crop Quality Biology, School of Horticulture, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Dani Eshel
- Department of Postharvest Science, The Volcani Institute, ARO, Rishon LeZion 50250, Israel
| | - David S Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI 48824, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
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Ames M, Hamernik A, Behling W, Douches DS, Halterman DA, Bethke PC. A survey of the Sli gene in wild and cultivated potato. PLANT DIRECT 2024; 8:e589. [PMID: 38766508 PMCID: PMC11099725 DOI: 10.1002/pld3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.
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Affiliation(s)
- Mercedes Ames
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Andy Hamernik
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - William Behling
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - David S. Douches
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Dennis A. Halterman
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Paul C. Bethke
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
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Gartner U, Armstrong MR, Sharma SK, Jones JT, Blok VC, Hein I, Bryan GJ. Characterisation and mapping of a Globodera pallida resistance derived from the wild potato species Solanum spegazzinii. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:106. [PMID: 38622441 PMCID: PMC11018675 DOI: 10.1007/s00122-024-04605-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE A new resistance locus acting against the potato cyst nematode Globodera pallida was mapped to chromosome VI in the diploid wild potato species Solanum spegazzinii CPC 7195. The potato cyst nematodes (PCN) Globodera pallida and Globodera rostochiensis are economically important potato pests in almost all regions where potato is grown. One important management strategy involves deployment through introgression breeding into modern cultivars of new sources of naturally occurring resistance from wild potato species. We describe a new source of resistance to G. pallida from wild potato germplasm. The diploid species Solanum spegazzinii Bitter accession CPC 7195 shows resistance to G. pallida pathotypes Pa1 and Pa2/3. A cross and first backcross of S. spegazzinii with Solanum tuberosum Group Phureja cultivar Mayan Gold were performed, and the level of resistance to G. pallida Pa2/3 was determined in progeny clones. Bulk-segregant analysis (BSA) using generic mapping enrichment sequencing (GenSeq) and genotyping-by-sequencing were performed to identify single-nucleotide polymorphisms (SNPs) that are genetically linked to the resistance, using S. tuberosum Group Phureja clone DM1-3 516 R44 as a reference genome. These SNPs were converted into allele-specific PCR assays, and the resistance was mapped to an interval of roughly 118 kb on chromosome VI. This newly identified resistance, which we call Gpa VIlspg, can be used in future efforts to produce modern cultivars with enhanced and broad-spectrum resistances to the major pests and pathogens of potato.
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Affiliation(s)
- Ulrike Gartner
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, St Andrews, KY16 9, UK
| | | | - Sanjeev K Sharma
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John T Jones
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Biology, University of St Andrews, St Andrews, KY16 9, UK
| | - Vivian C Blok
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
- School of Life Sciences, University of Dundee, Dundee, UK.
| | - Glenn J Bryan
- Cell and Molecular Sciences Department, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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Bonthala VS, Stich B. StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes. PLANT CELL REPORTS 2024; 43:117. [PMID: 38622429 PMCID: PMC11018665 DOI: 10.1007/s00299-024-03201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
KEY MESSAGE We constructed a gene expression atlas and co-expression network for potatoes and identified several novel genes associated with various agronomic traits. This resource will accelerate potato genetics and genomics research. Potato (Solanum tuberosum L.) is the world's most crucial non-cereal food crop and ranks third in food production after wheat and rice. Despite the availability of several potato transcriptome datasets at public databases like NCBI SRA, an effort has yet to be put into developing a global transcriptome atlas and a co-expression network for potatoes. The objectives of our study were to construct a global expression atlas for potatoes using publicly available transcriptome datasets, identify housekeeping and tissue-specific genes, construct a global co-expression network and identify co-expression clusters, investigate the transcriptional complexity of genes involved in various essential biological processes related to agronomic traits, and provide a web server (StCoExpNet) to easily access the newly constructed expression atlas and co-expression network to investigate the expression and co-expression of genes of interest. In this study, we used data from 2299 publicly available potato transcriptome samples obtained from 15 different tissues to construct a global transcriptome atlas. We found that roughly 87% of the annotated genes exhibited detectable expression in at least one sample. Among these, we identified 281 genes with consistent and stable expression levels, indicating their role as housekeeping genes. Conversely, 308 genes exhibited marked tissue-specific expression patterns. We exemplarily linked some co-expression clusters to important agronomic traits of potatoes, such as self-incompatibility, anthocyanin biosynthesis, tuberization, and defense responses against multiple pathogens. The dataset compiled here constitutes a new resource (StCoExpNet), which can be accessed at https://stcoexpnet.julius-kuehn.de . This transcriptome atlas and the co-expression network will accelerate potato genetics and genomics research.
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Affiliation(s)
- Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, 18190, Sanitz, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Düsseldorf, Germany
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Shirani-Bidabadi M, Nazarian-Firouzabadi F, Sorkheh K, Ismaili A. Transcriptomic analysis of potato (Solanum tuberosum L.) tuber development reveals new insights into starch biosynthesis. PLoS One 2024; 19:e0297334. [PMID: 38574179 PMCID: PMC10994339 DOI: 10.1371/journal.pone.0297334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/03/2024] [Indexed: 04/06/2024] Open
Abstract
Potato tubers are rich sources of various nutrients and unique sources of starch. Many genes play major roles in different pathways, including carbohydrate metabolism during the potato tuber's life cycle. Despite substantial scientific evidence about the physiological and morphological development of potato tubers, the molecular genetic aspects of mechanisms underlying tuber formation have not yet been fully understood. In this study, for the first time, RNA-seq analysis was performed to shed light on the expression of genes involved in starch biosynthesis during potato tuber development. To this end, samples were collected at the hook-like stolon (Stage I), swollen tips stolon (Stage II), and tuber initiation (Stage III) stages of tuber formation. Overall, 23 GB of raw data were generated and assembled. There were more than 20000 differentially expressed genes (DEGs); the expression of 73 genes involved in starch metabolism was further studied. Moreover, qRT-PCR analysis revealed that the expression profile of the starch biosynthesis DEGs was consistent with that of the RNA-seq data, which further supported the role of the DEGs in starch biosynthesis. This study provides substantial resources on potato tuber development and several starch synthesis isoforms associated with starch biosynthesis.
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Affiliation(s)
- Maryam Shirani-Bidabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian-Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Karim Sorkheh
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Ahmad Ismaili
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
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Tumas H, Ilska JJ, Gérardi S, Laroche J, A’Hara S, Boyle B, Janes M, McLean P, Lopez G, Lee SJ, Cottrell J, Gorjanc G, Bousquet J, Woolliams JA, MacKay JJ. High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers. G3 (BETHESDA, MD.) 2024; 14:jkae020. [PMID: 38366548 PMCID: PMC10989875 DOI: 10.1093/g3journal/jkae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/03/2024] [Indexed: 02/18/2024]
Abstract
In species with large and complex genomes such as conifers, dense linkage maps are a useful resource for supporting genome assembly and laying the genomic groundwork at the structural, populational, and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 single nucleotide polymorphism (SNP) markers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-seq and genotyping array SNP data for 528 individuals from 2 full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and Picea glauca based on 27,052 markers and 11,609 gene sequences. Altogether, these 2 linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed, herein, open new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.
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Affiliation(s)
- Hayley Tumas
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
| | - Joana J Ilska
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Sebastien Gérardi
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Jerome Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Stuart A’Hara
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - Mateja Janes
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Paul McLean
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gustavo Lopez
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Steve J Lee
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Joan Cottrell
- Forest Research, Northern Research Station, Midlothian EH25 9SY, UK
| | - Gregor Gorjanc
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC GIV 0A6, Canada
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC GIV 0A6, Canada
| | - John A Woolliams
- The Roslin Institute, Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, UK
| | - John J MacKay
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK
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11
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Visser N, Herreman LCM, Vandooren J, Pereira RVS, Opdenakker G, Spelbrink REJ, Wilbrink MH, Bremer E, Gosens R, Nawijn MC, van der Ende-Metselaar HH, Smit JM, Laus MC, Laman JD. Novel high-yield potato protease inhibitor panels block a wide array of proteases involved in viral infection and crucial tissue damage. J Mol Med (Berl) 2024; 102:521-536. [PMID: 38381158 PMCID: PMC10963447 DOI: 10.1007/s00109-024-02423-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/22/2024]
Abstract
Viruses critically rely on various proteases to ensure host cell entry and replication. In response to viral infection, the host will induce acute tissue inflammation pulled by granulocytes. Upon hyperactivation, neutrophil granulocytes may cause undue tissue damage through proteolytic degradation of the extracellular matrix. Here, we assess the potential of protease inhibitors (PI) derived from potatoes in inhibiting viral infection and reducing tissue damage. The original full spectrum of potato PI was developed into five fractions by means of chromatography and hydrolysis. Individual fractions showed varying inhibitory efficacy towards a panel of proteases including trypsin, chymotrypsin, ACE2, elastase, and cathepsins B and L. The fractions did not interfere with SARS-CoV-2 infection of Vero E6 cells in vitro. Importantly, two of the fractions fully inhibited elastin-degrading activity of complete primary human neutrophil degranulate. These data warrant further development of potato PI fractions for biomedical purposes, including tissue damage crucial to SARS-CoV-2 pathogenesis. KEY MESSAGES: Protease inhibitor fractions from potato differentially inhibit a series of human proteases involved in viral replication and in tissue damage by overshoot inflammation. Protease inhibition of cell surface receptors such as ACE2 does not prevent virus infection of Vero cells in vitro. Protease inhibitors derived from potato can fully inhibit elastin-degrading primary human neutrophil proteases. Protease inhibitor fractions can be produced at high scale (hundreds of thousands of kilograms, i.e., tons) allowing economically feasible application in lower and higher income countries.
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Affiliation(s)
- Nienke Visser
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | | | - Jennifer Vandooren
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Rafaela Vaz Sousa Pereira
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Louvain, Belgium
| | | | | | - Edwin Bremer
- Department of Hematology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC) Research Institute, University of Groningen, 9713 GZ, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Heidi H van der Ende-Metselaar
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9713 GZ, Groningen, The Netherlands
| | - Marc C Laus
- Avebe Innovation Center Groningen, 9747 AW, Groningen, The Netherlands
| | - Jon D Laman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands.
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12
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Zinta R, Tiwari JK, Buckseth T, Goutam U, Singh RK, Kumar V, Thakur AK. Transcriptome profiling and characterization of genes associated with tuberization under high temperature in aeroponics in potato cv. Kufri Anand. Genes Genomics 2024; 46:409-421. [PMID: 38381322 DOI: 10.1007/s13258-024-01503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND High temperature stress is an important abiotic factor, which affects tuberization and ultimately causes heavy yield reduction in potato. OBJECTIVES Identification and characterization of genes associated with tuberization under high temperature stress is essential for future management through biotechnology. METHODOLOGY Two contrasting potato varieties Kufri Anand (profuse tuber-bearing) versus Kufri Frysona (very less/scanty tuber-bearing, control) were cultivated in aeroponics under high temperature stress, and transcriptomes were analyzed. RESULTS Potato cv. Kufri Anand was found superior over control (Kufri Frysona) for tuber yield and its component traits along with root morphology under aeroponics. Transcriptomes of tuber and leaf tissues were analyzed. Statistically significant (p < 0.05) differentially expressed genes (DEGs) were categorised into up-regulated (> 2 log2 fold change, FC) and down-regulated (< -2 log2 FC) genes. DEGs were annotated by gene ontology and KEGG pathways. A few selected up-regulated genes of both tissues were identified, and phylogeny tree and motif analysis were analysed based on 36 peptide sequences representing 15 selected DEGs in this study. Further, gene expression markers were developed and validated by real time qPCR analysis for the identification of high temperature tolerant genotypes. CONCLUSION A few key genes associated in tuberization under high temperature conditions were heat shock proteins (e.g. 18.5 kDa class I heat shock protein), sugar metabolism (e.g. glucosyltransferase), transcription factor (e.g. WRKY), and phytohormones (e.g. auxin-induced beta-glucosidase). Our study provides an overview of key genes involved in tuberization under high temperature stress in potato cv. Kufri Anand under aeroponics.
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Affiliation(s)
- Rasna Zinta
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Jagesh Kumar Tiwari
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research Institute, Varanasi, Uttar Pradesh, India.
| | - Tanuja Buckseth
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar Singh
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Indian Council of Agricultural Research-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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13
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Wang H, Yu R, Zhu Q, Tian Z, Li F. A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:263-276. [PMID: 38078656 DOI: 10.1111/tpj.16585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 04/02/2024]
Abstract
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as 32P-labeled probe in dot blot and small RNA northern blot experiments. Addition of locked nucleic acids in T4BC33 probe further enhanced its sensitivity in detecting low-abundance miRNAs. With newly developed northern blot method, expression of miR6027 and miR6149 family members was validated. Northern blot analysis also confirmed the successful application of virus-based miRNA silencing in pepper, knocking down accumulation of Can-miR6027a and Can-miR6149L. Importantly, further analysis showed that knocking-down Can-miR6027a led to upregulation of a nucleotide binding-leucine rich repeat domain protein coding gene (CaRLb1) and increased immunity against Phytophthora capsici in pepper leaves. Our study provided a highly sensitive and convenient method for sRNA research and identified new targets for genetic improvement of pepper immunity against P. capsici.
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Affiliation(s)
- Hongzheng Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ruimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, 430070, China
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14
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Gurina AA, Gancheva MS, Alpatieva NV, Rogozina EV. In silico search for and analysis of R gene variation in primitive cultivated potato species. Vavilovskii Zhurnal Genet Selektsii 2024; 28:175-184. [PMID: 38680181 PMCID: PMC11043503 DOI: 10.18699/vjgb-24-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 05/01/2024] Open
Abstract
Pathogen recognition receptors encoded by R genes play a key role in plant protection. Nowadays, R genes are a basis for breeding many crops, including potato. Many potato R genes have been discovered and found suitable for breeding thanks to the studies of a wide variety of wild potato species. The use of primitive cultivated potato species (PCPS) as representatives of the primary gene pool can also be promising in this respect. PCPS are the closest to the early domesticated forms of potato; therefore, their investigation could help understand the evolution of R genes. The present study was aimed at identifying and analyzing R genes in PCPS listed in the open database of NCBI and Solomics DB. In total, the study involved 27 accessions belonging to three species: Solanum phureja Juz. & Bukasov, S. stenotomum Juz. & Bukasov and S. goniocalyx Juz. & Bukasov Materials for the analysis were the sequencing data for the said three species from the PRJNA394943 and PRJCA006011 projects. An in silico search was carried out for sequences homologous to 26 R genes identified in potato species differing in phylogenetic distance from PCPS, namely nightshade (S. americanum), North- (S. bulbocastanum, S. demissum) and South-American (S. venturii, S. berthaultii) wild potato species, as well as the cultivated potato species S. tuberosum and S. andigenum. Homologs of all investigated protein-coding sequences were discovered in PCPS with a relatively high degree of similarity (85-100 %). Homologs of the Rpi-R3b, Rpi-amr3 and Rpi-ber1 genes have been identified in PCPS for the first time. An analysis of polymorphism of nucleotide and amino acid sequences has been carried out for 15 R genes. The differences in frequencies of substitutions in PCPS have been demonstrated by analysis of R genes, the reference sequences of which have been identified in different species. For all the studied NBS-LRR genes, the proportion of substituted amino acids in the LRR domain exceeds this figure for the NBS domain. The potential prospects of using PCPS as sources of resistance to Verticillium wilt have been shown.
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Affiliation(s)
- A A Gurina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - M S Gancheva
- St. Petersburg State University, St. Petersburg, Russia
| | - N V Alpatieva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - E V Rogozina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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15
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Park J, Whitworth J, Novy RG. QTL identified that influence tuber length-width ratio, degree of flatness, tuber size, and specific gravity in a russet-skinned, tetraploid mapping population. FRONTIERS IN PLANT SCIENCE 2024; 15:1343632. [PMID: 38584948 PMCID: PMC10996053 DOI: 10.3389/fpls.2024.1343632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/26/2024] [Indexed: 04/09/2024]
Abstract
Potato tuber shape, size, and specific gravity are important agronomic traits in the russet market class of potatoes with an impact on quality, consistency, and product recovery of processed foods such as French fries. Therefore, identifying genetic regions associated with the three traits through quantitative trait locus/loci (QTL) analysis is a crucial process in the subsequent development of marker-assisted selection for use in potato breeding programs. QTL analysis was conducted on a tetraploid mapping population consisting of 190 individuals derived from the cross between two russet-skinned parents, Palisade Russet and the breeding clone ND028673B-2Russ. Field data collected over a 2-year period and used in the QTL analyses included tuber length-width and width-depth ratios that were obtained using a digital caliper. The width-depth ratio provided an assessment of the "flatness" of a tuber, which is of importance in potato processing. To cross-validate the accuracy and differences among tuber shape measurement methods, a trained evaluator also assessed the identical tubers based on 1-5 scale (compressed to long) visual assessment method. Furthermore, the weights of analyzed tubers and specific gravities were also collected during the phenotyping process for each mapping clone. A major tuber shape QTL was consistently observed on chromosome 10 with both the length-width ratio and visual assessments. On chromosome 4, a significant QTL for tuber shape from the visual assessment phenotypic data was also detected. Additionally, a tuber shape-related QTL on chromosome 6 was also detected from the length-width ratio data from 2020. Chromosome 2 was also identified as having a significant QTL for the width-depth ratio, which is of importance in influencing the flatness of a tuber. One significant QTL for tuber weight (i.e., tuber size) was observed on chromosome 5, and a significant QTL for specific gravity was found on chromosome 3. These significant and major QTL should be useful for developing marker-assisted selection for more efficient potato breeding.
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Affiliation(s)
- Jaebum Park
- Small Grains and Potato Germplasm Research Station, United States Department of Agriculture—Agricultural Research Service, Aberdeen, ID, United States
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16
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Li H, Brouwer M, Pup ED, van Lieshout N, Finkers R, Bachem CWB, Visser RGF. Allelic variation in the autotetraploid potato: genes involved in starch and steroidal glycoalkaloid metabolism as a case study. BMC Genomics 2024; 25:274. [PMID: 38475714 DOI: 10.1186/s12864-024-10186-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Tuber starch and steroidal glycoalkaloid (SGA)-related traits have been consistently prioritized in potato breeding, while allelic variation pattern of genes that underlie these traits is less explored. RESULTS Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism and 38 in the biosynthesis of steroidal glycoalkaloids, and discovered 96,166 allelic variants among 2,169 gene haplotypes in six autotetraploid potato genomes. Comparative analyses revealed an uneven distribution of allelic variants among gene haplotypes and that the vast majority of deleterious mutations in these genes are retained in heterozygous state in the autotetraploid potato genomes. Leveraging full-length cDNA sequencing data, we find that approximately 70% of haplotypes of the 119 genes are transcribable. Population genetic analyses identify starch and SGA biosynthetic genes that are potentially conserved or diverged between potato varieties with varying starch or SGA content. CONCLUSIONS These results deepen the understanding of haplotypic diversity within functionally important genes in autotetraploid genomes and may facilitate functional characterization of genes or haplotypes contributing to traits related to starch and SGA in potato.
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Affiliation(s)
- Hongbo Li
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, Wageningen, the Netherlands
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
| | - Elena Del Pup
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
| | - Natascha van Lieshout
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
- , SURFsara, Science Park 140, Amsterdam, 1098 XG, the Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
- Gennovation B.V, Agro Business Park 10, Wageningen, 6708 PW, the Netherlands
| | - Christian W B Bachem
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, P. O. Box 386, Wageningen, 6700 AJ, the Netherlands.
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17
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Muñoz-Vargas MA, Taboada J, González-Gordo S, Palma JM, Corpas FJ. Characterization of leucine aminopeptidase (LAP) activity in sweet pepper fruits during ripening and its inhibition by nitration and reducing events. PLANT CELL REPORTS 2024; 43:92. [PMID: 38466441 PMCID: PMC10927865 DOI: 10.1007/s00299-024-03179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
KEY MESSAGE Pepper fruits contain two leucine aminopeptidase (LAP) genes which are differentially modulated during ripening and by nitric oxide. The LAP activity increases during ripening but is negatively modulated by nitration. Leucine aminopeptidase (LAP) is an essential metalloenzyme that cleaves N-terminal leucine residues from proteins but also metabolizes dipeptides and tripeptides. LAPs play a fundamental role in cell protein turnover and participate in physiological processes such as defense mechanisms against biotic and abiotic stresses, but little is known about their involvement in fruit physiology. This study aims to identify and characterize genes encoding LAP and evaluate their role during the ripening of pepper (Capsicum annuum L.) fruits and under a nitric oxide (NO)-enriched environment. Using a data-mining approach of the pepper plant genome and fruit transcriptome (RNA-seq), two LAP genes, designated CaLAP1 and CaLAP2, were identified. The time course expression analysis of these genes during different fruit ripening stages showed that whereas CaLAP1 decreased, CaLAP2 was upregulated. However, under an exogenous NO treatment of fruits, both genes were downregulated. On the contrary, it was shown that during fruit ripening LAP activity increased by 81%. An in vitro assay of the LAP activity in the presence of different modulating compounds including peroxynitrite (ONOO-), NO donors (S-nitrosoglutathione and nitrosocyteine), reducing agents such as reduced glutathione (GSH), L-cysteine (L-Cys), and cyanide triggered a differential response. Thus, peroxynitrite and reducing compounds provoked around 50% inhibition of the LAP activity in green immature fruits, whereas cyanide upregulated it 1.5 folds. To our knowledge, this is the first characterization of LAP in pepper fruits as well as of its regulation by diverse modulating compounds. Based on the capacity of LAP to metabolize dipeptides and tripeptides, it could be hypothesized that the LAP might be involved in the GSH recycling during the ripening process.
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Affiliation(s)
- María A Muñoz-Vargas
- Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín Spanish National Research Council, CSIC, C/Profesor Albareda, 1, 18008, Granada, Spain
| | - Jorge Taboada
- Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín Spanish National Research Council, CSIC, C/Profesor Albareda, 1, 18008, Granada, Spain
| | - Salvador González-Gordo
- Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín Spanish National Research Council, CSIC, C/Profesor Albareda, 1, 18008, Granada, Spain
| | - José M Palma
- Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín Spanish National Research Council, CSIC, C/Profesor Albareda, 1, 18008, Granada, Spain
| | - Francisco J Corpas
- Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estación Experimental del Zaidín Spanish National Research Council, CSIC, C/Profesor Albareda, 1, 18008, Granada, Spain.
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18
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Aalborg T, Sverrisdóttir E, Kristensen HT, Nielsen KL. The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1340189. [PMID: 38525152 PMCID: PMC10957621 DOI: 10.3389/fpls.2024.1340189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.
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Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Joshi JR, Paudel D, Eddy E, Charkowski AO, Heuberger AL. Plant necrotrophic bacterial disease resistance phenotypes, QTL, and metabolites identified through integrated genetic mapping and metabolomics in Solanum species. FRONTIERS IN PLANT SCIENCE 2024; 15:1336513. [PMID: 38504885 PMCID: PMC10949924 DOI: 10.3389/fpls.2024.1336513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/12/2024] [Indexed: 03/21/2024]
Abstract
Most food crops are susceptible to necrotrophic bacteria that cause rotting and wilting diseases in fleshy organs and foods. All varieties of cultivated potato (Solanum tuberosum L.) are susceptible to diseases caused by Pectobacterium species, but resistance has been demonstrated in wild potato relatives including S. chacoense. Previous studies demonstrated that resistance is in part mediated by antivirulence activity of phytochemicals in stems and tubers. Little is known about the genetic basis of antivirulence traits, and the potential for inheritance and introgression into cultivated potato is unclear. Here, the metabolites and genetic loci associated with antivirulence traits in S. chacoense were elucidated by screening a sequenced S. tuberosum x S. chacoense recombinant inbred line (RIL) population for antivirulence traits of its metabolite extracts. Metabolite extracts from the RILs exhibited a quantitative distribution for two antivirulence traits that were positively correlated: quorum sensing inhibition and exo-protease inhibition, with some evidence of transgressive segregation, supporting the role of multiple loci and metabolites regulating these resistance-associated systems. Metabolomics was performed on the highly resistant and susceptible RILs that revealed 30 metabolites associated with resistance, including several alkaloids and terpenes. Specifically, several prenylated metabolites were more abundant in resistant RILs. We constructed a high-density linkage map with 795 SNPs mapped to 12 linkage groups, spanning a length of 1,507 cM and a density of 1 marker per 1.89 cM. Genetic mapping of the antivirulence and metabolite data identified five quantitative trait loci (QTLs) related to quorum sensing inhibition that explained 8-28% of the phenotypic variation and two QTLs for protease activity inhibition that explained 14-19% of the phenotypic variation. Several candidate genes including alkaloid, and secondary metabolite biosynthesis that are related to disease resistance were identified within these QTLs. Taken together, these data support that quorum sensing inhibition and exo-protease inhibition assays may serve as breeding targets to improve resistance to nectrotrophic bacterial pathogens in potato and other plants. The identified candidate genes and metabolites can be utilized in marker assisted selection and genomic selection to improve soft- rot and blackleg disease resistance.
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Affiliation(s)
- Janak R. Joshi
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, United States
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Dev Paudel
- Department of Environmental Horticulture, University of Florida Gulf Coast Research and Education Center, Wimauma, FL, United States
| | - Ethan Eddy
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
| | - Amy O. Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Adam L. Heuberger
- Department of Horticulture & Landscape Architecture, Colorado State University, Fort Collins, CO, United States
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Schilling F, Schumacher C, Köhl K, Sprenger H, Kopka J, Peters R, Haas M, Zuther E, Horn R. Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance. Sci Rep 2024; 14:5476. [PMID: 38443466 PMCID: PMC10914802 DOI: 10.1038/s41598-024-55669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Climate changes leading to increasingly longer seasonal drought periods in large parts of the world increase the necessity for breeding drought-tolerant crops. Cultivated potato (Solanum tuberosum), the third most important vegetable crop worldwide, is regarded as drought-sensitive due to its shallow root architecture. Two German tetraploid potato cultivars differing in drought tolerance and their F1-progeny were evaluated under various drought scenarios. Bulked segregant analyses were combined with whole-genome sequencing (BSA-Seq) using contrasting bulks of drought-tolerant and drought-sensitive F1-clones. Applying QTLseqr, 15 QTLs comprising 588,983 single nucleotide polymorphisms (SNPs) in 2325 genes associated with drought stress tolerance were identified. SeqSNP analyses in an association panel of 34 mostly starch potato varieties using 1-8 SNPs for each of 188 selected genes narrowed the number of candidate genes down to 10. In addition, ent-kaurene synthase B was the only gene present under QTL 10. Eight of the identified genes (StABP1, StBRI1, StKS, StLEA, StPKSP1, StPKSP2, StYAB5, and StZOG1) address plant development, the other three genes (StFATA, StHGD and StSYP) contribute to plant protection under drought stress. Allelic variation in these genes might be explored in future breeding for drought-tolerant potato varieties.
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Affiliation(s)
- Florian Schilling
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Christina Schumacher
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany
| | - Karin Köhl
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Heike Sprenger
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Department of Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Rolf Peters
- Landwirtschaftskammer Niedersachsen, Dethlingen 14, 29633, Munster, Germany
- PotatoConsult UG, Hiddinger Straße 33, 27374, Visselhövede, Germany
| | - Manuela Haas
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Ministry of Agriculture, Environment and Climate Protection, Henning-Von-Tresckow-Straße 2-13, 14467, Potsdam, Germany
| | - Ellen Zuther
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Center of Artificial Intelligence in Public Health Research, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany
| | - Renate Horn
- Department of Plant Genetics, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Str. 3, 18059, Rostock, Germany.
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Liu C, Jiang X, Liu S, Liu Y, Li H, Wang Z, Kan J, Yang Q, Li X. Comprehensive Evolutionary Analysis of the SMXL Gene Family in Rosaceae: Further Insights into Its Origin, Expansion, Diversification, and Role in Regulating Pear Branching. Int J Mol Sci 2024; 25:2971. [PMID: 38474218 DOI: 10.3390/ijms25052971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
SMXL genes constitute a conserved gene family that is ubiquitous in angiosperms and involved in regulating various plant processes, including branching, leaf elongation, and anthocyanin biosynthesis, but little is known about their molecular functions in pear branching. Here, we performed genome-wide identification and investigation of the SMXL genes in 16 angiosperms and analyzed their phylogenetics, structural features, conserved motifs, and expression patterns. In total, 121 SMXLs genes were identified and were classified into four groups. The number of non-redundant SMXL genes in each species varied from 3 (Amborella trichopoda Baill.) to 18 (Glycine max Merr.) and revealed clear gene expansion events over evolutionary history. All the SMXL genes showed conserved structures, containing no more than two introns. Three-dimensional protein structure prediction revealed distinct structures between but similar structures within groups. A quantitative real-time PCR analysis revealed different expressions of 10 SMXL genes from pear branching induced by fruit-thinning treatment. Overall, our study provides a comprehensive investigation of SMXL genes in the Rosaceae family, especially pear. The results offer a reference for understanding the evolutionary history of SMXL genes and provide excellent candidates for studying fruit tree branching regulation, and in facilitating pear pruning and planting strategies.
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Affiliation(s)
- Chunxiao Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianda Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Susha Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yilong Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Hui Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhonghua Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jialiang Kan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Qingsong Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaogang Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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22
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Bilton TP, Sharma SK, Schofield MR, Black MA, Jacobs JME, Bryan GJ, Dodds KG. Construction of relatedness matrices in autopolyploid populations using low-depth high-throughput sequencing data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:64. [PMID: 38430392 PMCID: PMC10908621 DOI: 10.1007/s00122-024-04568-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/30/2024] [Indexed: 03/03/2024]
Abstract
KEY MESSAGE An improved estimator of genomic relatedness using low-depth high-throughput sequencing data for autopolyploids is developed. Its outputs strongly correlate with SNP array-based estimates and are available in the package GUSrelate. High-throughput sequencing (HTS) methods have reduced sequencing costs and resources compared to array-based tools, facilitating the investigation of many non-model polyploid species. One important quantity that can be computed from HTS data is the genetic relatedness between all individuals in a population. However, HTS data are often messy, with multiple sources of errors (i.e. sequencing errors or missing parental alleles) which, if not accounted for, can lead to bias in genomic relatedness estimates. We derive a new estimator for constructing a genomic relationship matrix (GRM) from HTS data for autopolyploid species that accounts for errors associated with low sequencing depths, implemented in the R package GUSrelate. Simulations revealed that GUSrelate performed similarly to existing GRM methods at high depth but reduced bias in self-relatedness estimates when the sequencing depth was low. Using a panel consisting of 351 tetraploid potato genotypes, we found that GUSrelate produced GRMs from genotyping-by-sequencing (GBS) data that were highly correlated with a GRM computed from SNP array data, and less biased than existing methods when benchmarking against the array-based GRM estimates. GUSrelate provides researchers with a tool to reliably construct GRMs from low-depth HTS data.
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Affiliation(s)
- Timothy P Bilton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.
| | - Sanjeev Kumar Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Matthew R Schofield
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, UK
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
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Wang Y, Sun Y, Li Y, Shao H, Cheng X, Wang X, Yong B, Tao X. Genome-wide identification and expression profiles of the Phytophthora infestans responsive CYPome (cytochrome P450 complement) in Solanum tuberosum. Biosci Biotechnol Biochem 2024; 88:283-293. [PMID: 38115610 DOI: 10.1093/bbb/zbad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Cytochrome P450s represent one of the largest protein families across all domains of life. In plants, biotic stress can regulate the expression of some P450 genes. However, the CYPome (cytochrome P450 complement) in Solanum tuberosum and its response to Phytophthora infestans infection remains unrevealed. In this study, 488 P450 genes were identified from potato genome, which can be divided into 41 families and 57 subfamilies. Responding to the infection of P. infestans, 375 potato P450 genes were expressed in late blight resistant or susceptible cultivars. A total of 14 P450 genes were identified as resistant related candidates, and 81 P450 genes were identified as late blight responsive candidates. Several phytohormone biosynthesis, brassinosteroid biosynthesis, and phenylpropanoid biosynthesis involved P450 genes were differentially expressed during the potato-pathogen interactions. This study firstly reported the CYPome in S. tuberosum, and characterized the expression patterns of these P450 genes during the infection of P. infestans.
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Affiliation(s)
- Yajie Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yining Sun
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yan Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Huanhuan Shao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiaojie Cheng
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiaoyang Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Bin Yong
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Xiang Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
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24
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Zarka KA, Jagd LM, Douches DS. T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop ® enrichment technology. FRONTIERS IN PLANT SCIENCE 2024; 15:1330429. [PMID: 38419775 PMCID: PMC10900525 DOI: 10.3389/fpls.2024.1330429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.
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Affiliation(s)
- Kelly A. Zarka
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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25
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Kaur G, Jain S, Bhushan S, Das N, Sharma M, Sharma D. Role of microRNAs and their putative mechanism in regulating potato (Solanum tuberosum L.) life cycle and response to various environmental stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108334. [PMID: 38219424 DOI: 10.1016/j.plaphy.2024.108334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024]
Abstract
The exponentially increasing population and the demand for food is inextricably linked. This has shifted global attention to improving crop plant traits to meet global food demands. Potato (Solanum tuberosum L.) is a major non-grain food crop that is grown all over the world. Currently, some of the major global potato research work focuses on the significance of microRNAs (miRNAs) in potato. miRNAs are a type of non-coding RNAs that regulate the gene expression of their target mRNA genes by cleavage and/or their translational inhibition. This suggests an essential role of miRNAs in a multitude of plant biological processes, including maintenance of genome integrity, plant growth, development and maturation, and initiation of responses to various stress conditions. Therefore, engineering miRNAs to generate stress-resistant varieties of potato may result in high yield and improved nutritional qualities. In this review, we discuss the potato miRNAs specifically known to play an essential role in the various stages of the potato life cycle, conferring stress-resistant characteristics, and modifying gene expression. This review highlights the significance of the miRNA machinery in plants, especially potato, encouraging further research into engineering miRNAs to boost crop yields and tolerance towards stress.
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Affiliation(s)
- Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu and Kashmir (UT), India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004, Punjab, India
| | - Munish Sharma
- Department of Plant Science, Central University of Himachal Pradesh, Shahpur Parisar, Kangra, Himachal Pradesh, India.
| | - Deepak Sharma
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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27
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Yang R, Sun Y, Zhu X, Jiao B, Sun S, Chen Y, Li L, Wang X, Zeng Q, Liang Q, Huang B. The tuber-specific StbHLH93 gene regulates proplastid-to-amyloplast development during stolon swelling in potato. THE NEW PHYTOLOGIST 2024; 241:1676-1689. [PMID: 38044709 DOI: 10.1111/nph.19426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/05/2023] [Indexed: 12/05/2023]
Abstract
In potato, stolon swelling is a complex and highly regulated process, and much more work is needed to fully understand the underlying mechanisms. We identified a novel tuber-specific basic helix-loop-helix (bHLH) transcription factor, StbHLH93, based on the high-resolution transcriptome of potato tuber development. StbHLH93 is predominantly expressed in the subapical and perimedullary region of the stolon and developing tubers. Knockdown of StbHLH93 significantly decreased tuber number and size, resulting from suppression of stolon swelling. Furthermore, we found that StbHLH93 directly binds to the plastid protein import system gene TIC56 promoter, activates its expression, and is involved in proplastid-to-amyloplast development during the stolon-to-tuber transition. Knockdown of the target TIC56 gene resulted in similarly problematic amyloplast biogenesis and tuberization. Taken together, StbHLH93 functions in the differentiation of proplastids to regulate stolon swelling. This study highlights the critical role of proplastid-to-amyloplast interconversion during potato tuberization.
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Affiliation(s)
- Rui Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yuan Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Xiaoling Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Baozhen Jiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Sifan Sun
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yun Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Lizhu Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Xue Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Qian Zeng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Qiqi Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Binquan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650500, China
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Nahirñak V, Almasia NI, Lia VV, Hopp HE, Vazquez Rovere C. Unveiling the defensive role of Snakin-3, a member of the subfamily III of Snakin/GASA peptides in potatoes. PLANT CELL REPORTS 2024; 43:47. [PMID: 38302779 DOI: 10.1007/s00299-023-03108-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/05/2023] [Indexed: 02/03/2024]
Abstract
KEY MESSAGE The first in-depth characterization of a subfamily III Snakin/GASA member was performed providing experimental evidence on promoter activity and subcellular localization and unveiling a role of potato Snakin-3 in defense Snakin/GASA proteins share 12 cysteines in conserved positions in the C-terminal region. Most of them were involved in different aspects of plant growth and development, while a small number of these peptides were reported to have antimicrobial activity or participate in abiotic stress tolerance. In potato, 18 Snakin/GASA genes were identified and classified into three groups based on phylogenetic analysis. Snakin-1 and Snakin-2 are members of subfamilies I and II, respectively, and were reported to be implicated not only in defense against pathogens but also in plant development. In this work, we present the first in-depth characterization of Snakin-3, a member of the subfamily III within the Snakin/GASA gene family of potato. Transient co-expression of Snakin-3 fused to the green fluorescent protein and organelle markers revealed that it is located in the endoplasmic reticulum. Furthermore, expression analyses via pSnakin-3::GUS transgenic plants showed GUS staining mainly in roots and vascular tissues of the stem. Moreover, GUS expression levels were increased after inoculation with Pseudomonas syringae pv. tabaci or Pectobacterium carotovorum subsp. carotovorum and also after auxin treatment mainly in roots and stems. To gain further insights into the function of Snakin-3 in planta, potato overexpressing lines were challenged against P. carotovorum subsp. carotovorum showing enhanced tolerance to this bacterial pathogen. In sum, here we report the first functional characterization of a Snakin/GASA gene from subfamily III in Solanaceae. Our findings provide experimental evidence on promoter activity and subcellular localization and reveal a role of potato Snakin-3 in plant defense.
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Affiliation(s)
- Vanesa Nahirñak
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
| | - Natalia Inés Almasia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
| | - Verónica Viviana Lia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repetto, Hurlingham, Argentina.
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Miao H, Wang L, Qu L, Liu H, Sun Y, Le M, Wang Q, Wei S, Zheng Y, Lin W, Duan Y, Cao H, Xiong S, Wang X, Wei L, Li C, Ma Q, Ju M, Zhao R, Li G, Mu C, Tian Q, Mei H, Zhang T, Gao T, Zhang H. Genomic evolution and insights into agronomic trait innovations of Sesamum species. PLANT COMMUNICATIONS 2024; 5:100729. [PMID: 37798879 PMCID: PMC10811377 DOI: 10.1016/j.xplc.2023.100729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
Sesame is an ancient oilseed crop with high oil content and quality. However, the evolutionary history and genetic mechanisms of its valuable agronomic traits remain unclear. Here, we report chromosome-scale genomes of cultivated sesame (Sesamum indicum L.) and six wild Sesamum species, representing all three karyotypes within this genus. Karyotyping and genome-based phylogenic analysis revealed the evolutionary route of Sesamum species from n = 13 to n = 16 and revealed that allotetraploidization occurred in the wild species Sesamum radiatum. Early divergence of the Sesamum genus (48.5-19.7 million years ago) during the Tertiary period and its ancient phylogenic position within eudicots were observed. Pan-genome analysis revealed 9164 core gene families in the 7 Sesamum species. These families are significantly enriched in various metabolic pathways, including fatty acid (FA) metabolism and FA biosynthesis. Structural variations in SiPT1 and SiDT1 within the phosphatidyl ethanolamine-binding protein gene family lead to the genomic evolution of plant-architecture and inflorescence-development phenotypes in Sesamum. A genome-wide association study (GWAS) of an interspecific population and genome comparisons revealed a long terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium and cultivated sesame, respectively; both variations independently cause high susceptibility to Fusarium wilt disease. A GWAS of 560 sesame accessions combined with an overexpression study confirmed that the NAC1 and PPO genes play an important role in upregulating oil content of sesame. Our study provides high-quality genomic resources for cultivated and wild Sesamum species and insights that can improve molecular breeding strategies for sesame and other oilseed crops.
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Affiliation(s)
- Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Lingbo Qu
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Hongyan Liu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yamin Sun
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Meiwang Le
- Crops Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qiang Wang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shuangling Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongzhan Zheng
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenchao Lin
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengchun Cao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Songjin Xiong
- TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin 300457, China
| | - Xuede Wang
- College of Food Science and Technology, Henan Technology University, Zhengzhou 450001, China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qin Ma
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Guiting Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Cong Mu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qiuzhen Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hongxian Mei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tide Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
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Zhou W, Wang C, Hao X, Chen F, Huang Q, Liu T, Xu J, Guo S, Liao B, Liu Z, Feng Y, Wang Y, Liao P, Xue J, Shi M, Maoz I, Kai G. A chromosome-level genome assembly of anesthetic drug-producing Anisodus acutangulus provides insights into its evolution and the biosynthesis of tropane alkaloids. PLANT COMMUNICATIONS 2024; 5:100680. [PMID: 37660252 PMCID: PMC10811374 DOI: 10.1016/j.xplc.2023.100680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 08/16/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Tropane alkaloids (TAs), which are anticholinergic agents, are an essential class of natural compounds, and there is a growing demand for TAs with anesthetic, analgesic, and spasmolytic effects. Anisodus acutangulus (Solanaceae) is a TA-producing plant that was used as an anesthetic in ancient China. In this study, we assembled a high-quality, chromosome-scale genome of A. acutangulus with a contig N50 of 7.4 Mb. A recent whole-genome duplication occurred in A. acutangulus after its divergence from other Solanaceae species, which resulted in the duplication of ADC1 and UGT genes involved in TA biosynthesis. The catalytic activities of H6H enzymes were determined for three Solanaceae plants. On the basis of evolution and co-expressed genes, AaWRKY11 was selected for further analyses, which revealed that its encoded transcription factor promotes TA biosynthesis by activating AaH6H1 expression. These findings provide useful insights into genome evolution related to TA biosynthesis and have potential implications for genetic manipulation of TA-producing plants.
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Affiliation(s)
- Wei Zhou
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Can Wang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Xiaolong Hao
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Fei Chen
- Sanya Nanfan Research Institute from Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Qikai Huang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Tingyao Liu
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhixiang Liu
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yue Feng
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yao Wang
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Pan Liao
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Jiayu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Min Shi
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Itay Maoz
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Guoyin Kai
- Zhejiang Provincial International S&T Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Zhejiang Provincial Key TCM Laboratory for Chinese Resource Innovation and Transformation, School of Pharmaceutical Sciences, Jinhua Academy, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China.
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Chen S, Tran TTT, Yeh AYC, Yang H, Chen J, Yang Y, Wang X. The Globodera rostochiensis Gr29D09 Effector with a Role in Defense Suppression Targets the Potato Hexokinase 1 Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:25-35. [PMID: 37717227 DOI: 10.1094/mpmi-07-23-0095-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
The potato cyst nematode (Globodera rostochiensis) is an obligate root pathogen of potatoes. G. rostochiensis encodes several highly expanded effector gene families, including the Gr4D06 family; however, little is known about the function of this effector family. We cloned four 29D09 genes from G. rostochiensis (named Gr29D09v1/v2/v3/v4) that share high sequence similarity and are homologous to the Hg29D09 and Hg4D06 effector genes from the soybean cyst nematode (Heterodera glycines). Phylogenetic analysis revealed that Gr29D09 genes belong to a subgroup of the Gr4D06 family. We showed that Gr29D09 genes are expressed exclusively within the nematode's dorsal gland cell and are dramatically upregulated in parasitic stages, indicating involvement of Gr29D09 effectors in nematode parasitism. Transgenic potato lines overexpressing Gr29D09 variants showed increased susceptibility to G. rostochiensis. Transient expression assays in Nicotiana benthamiana demonstrated that Gr29D09v3 could suppress reactive oxygen species (ROS) production and defense gene expression induced by flg22 and cell death mediated by immune receptors. These results suggest a critical role of Gr29D09 effectors in defense suppression. The use of affinity purification coupled with nanoliquid chromatography-tandem mass spectrometry identified potato hexokinase 1 (StHXK1) as a candidate target of Gr29D09. The Gr29D09-StHXK1 interaction was further confirmed using in planta protein-protein interaction assays. Plant HXKs have been implicated in defense regulation against pathogen infection. Interestingly, we found that StHXK1 could enhance flg22-induced ROS production, consistent with a positive role of plant HXKs in defense. Altogether, our results suggest that targeting StHXK1 by Gr29D09 effectors may impair the positive function of StHXK1 in plant immunity, thereby aiding nematode parasitism. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Shiyan Chen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Tien Thi Thuy Tran
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Athena Yi-Chun Yeh
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Huijun Yang
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
| | - Jiansong Chen
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
| | - Xiaohong Wang
- School of Integrative Plant Science, Cornell University, Ithaca, NY, U.S.A
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, U.S.A
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32
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Yang J, Wu Y, Zhang P, Ma J, Yao YJ, Ma YL, Zhang L, Yang Y, Zhao C, Wu J, Fang X, Liu J. Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family. Nat Commun 2023; 14:8457. [PMID: 38114555 PMCID: PMC10730914 DOI: 10.1038/s41467-023-44246-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Hyoscyamine and scopolamine (HS), two valuable tropane alkaloids of significant medicinal importance, are found in multiple distantly related lineages within the Solanaceae family. Here we sequence the genomes of three representative species that produce HS from these lineages, and one species that does not produce HS. Our analysis reveals a shared biosynthetic pathway responsible for HS production in the three HS-producing species. We observe a high level of gene collinearity related to HS synthesis across the family in both types of species. By introducing gain-of-function and loss-of-function mutations at key sites, we confirm the reduced/lost or re-activated functions of critical genes involved in HS synthesis in both types of species, respectively. These findings indicate independent and repeated losses of the HS biosynthesis pathway since its origin in the ancestral lineage. Our results hold promise for potential future applications in the artificial engineering of HS biosynthesis in Solanaceae crops.
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Affiliation(s)
- Jiao Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Jun Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yan Lin Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Lei Zhang
- Key Laboratory of Ecological Protection of Agro-Pastoral Ecotones in the Yellow River Basin, National Ethnic Affairs Commission of the People's Republic of China, College of Biological Science & Engineering, North Minzu University, Yinchuan, 750021, Ningxia, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Changmin Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jihua Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, China.
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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Lindqvist-Kreuze H, Bonierbale M, Grüneberg WJ, Mendes T, De Boeck B, Campos H. Potato and sweetpotato breeding at the international potato center: approaches, outcomes and the way forward. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:12. [PMID: 38112758 PMCID: PMC10730645 DOI: 10.1007/s00122-023-04515-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023]
Abstract
Root and tuber crop breeding is at the front and center of CIP's science program, which seeks to develop and disseminate sustainable agri-food technologies, information and practices to serve objectives including poverty alleviation, income generation, food security and the sustainable use of natural resources. CIP was established in 1971 in Peru, which is part of potato's center of origin and diversity, with an initial mandate on potato and expanding to include sweetpotato in 1986. Potato and sweetpotato are among the top 10 most consumed food staples globally and provide some of the most affordable sources of energy and vital nutrients. Sweetpotato plays a key role in securing food for many households in Africa and South Asia, while potato is important worldwide. Both crops grow in a range of conditions with relatively few inputs and simple agronomic techniques. Potato is adapted to the cooler environments, while sweetpotato grows well in hot climates, and hence, the two crops complement each other. Germplasm enhancement (pre-breeding), the development of new varieties and building capacity for breeding and variety testing in changing climates with emphasis on adaptation, resistance, nutritional quality and resource-use efficiency are CIP's central activities with significant benefits to the poor. Investments in potato and sweetpotato breeding and allied disciplines at CIP have resulted in the release of many varieties some of which have had documented impact in the release countries. Partnership with diverse types of organizations has been key to the centers way of working toward improving livelihoods through crop production in the global South.
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Affiliation(s)
| | - Merideth Bonierbale
- International Potato Center, Lima 12, 1558, Apartado, Peru
- Calle Bolivia, 12 Manilva, 29690, Malaga, Spain
| | | | - Thiago Mendes
- International Potato Center, Lima 12, 1558, Apartado, Peru
| | - Bert De Boeck
- International Potato Center, Lima 12, 1558, Apartado, Peru
| | - Hugo Campos
- International Potato Center, Lima 12, 1558, Apartado, Peru
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Zhang X, Fujino K, Shimura H. Transcriptomic Analyses Reveal the Role of Cytokinin and the Nodal Stem in Microtuber Sprouting in Potato ( Solanum tuberosum L.). Int J Mol Sci 2023; 24:17534. [PMID: 38139361 PMCID: PMC10743403 DOI: 10.3390/ijms242417534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
In potatoes, tuber secondary growth, especially sprouting, deforms the tubers and severely lowers their commercial value. Tuber sprouting is induced by signal substances, such as gibberellin (GA), which are transported to the tuber from the plant body. The molecular mechanism underlying GA-induced sprouting remains ambiguous. Here, we tried to recreate tuber secondary growth using in vitro stemmed microtubers (MTs) (with the nodal stem attached) and MT halves (with the nodal stem entirely removed). Our experiments showed that GA alone could initiate the sprouting of stemmed microtubers; however, GA failed to initiate MT halves unless 6-benzyladenine, a synthetic cytokinin CK, was co-applied. Here, we analyzed the transcriptional profiles of sprouting buds using these in vitro MTs. RNA-seq analysis revealed a downregulation of cytokinin-activated signaling but an upregulation of the "Zeatin biosynthesis" pathway, as shown by increased expression of CYP735A, CISZOG, and UGT85A1 in sprouting buds; additionally, the upregulation of genes, such as IAA15, IAA22, and SAUR50, associated with auxin-activated signaling and one abscisic acid (ABA) negative regulator, PLY4, plays a vital role during sprouting growth. Our findings indicate that the role of the nodal stem is synonymous with CK in sprouting growth, suggesting that CK signaling and homeostasis are critical to supporting GA-induced sprouting. To effectively control tuber sprouting, more effort is required to be devoted to these critical genes.
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Affiliation(s)
| | - Kaien Fujino
- Graduate School of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo 060-8589, Japan; (X.Z.)
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Xu Y, Yao Z, Cheng Y, Ruan M, Ye Q, Wang R, Zhou G, Liu J, Liu C, Wan H. Divergent Retention of Sucrose Metabolism Genes after Whole Genome Triplication in the Tomato ( Solanum lycopersicum). PLANTS (BASEL, SWITZERLAND) 2023; 12:4145. [PMID: 38140472 PMCID: PMC10747743 DOI: 10.3390/plants12244145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Sucrose, the primary carbon transport mode and vital carbohydrate for higher plants, significantly impacts plant growth, development, yield, and quality formation. Its metabolism involves three key steps: synthesis, transport, and degradation. Two genome triplication events have occurred in Solanaceae, which have resulted in massive gene loss. In this study, a total of 48 and 65 genes from seven sucrose metabolism gene families in Vitis vinifera and Solanum lycopersicum were identified, respectively. The number of members comprising the different gene families varied widely. And there were significant variations in the pattern of gene duplication and loss in the tomato following two WGD events. Tandem duplication is a major factor in the expansion of the SWEET and Acid INV gene families. All the genes are irregularly distributed on the chromosomes, with the majority of the genes showing collinearity with the grape, particularly the CIN family. And the seven gene families were subjected to a purifying selection. The expression patterns of the different gene families exhibited notable variations. This study presents basic information about the sucrose metabolism genes in the tomato and grape, and paves the way for further investigations into the impact of SCT events on the phylogeny, gene retention duplication, and function of sucrose metabolism gene families in the tomato or Solanaceae, and the adaptive evolution of the tomato.
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Affiliation(s)
- Yang Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Zhuping Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Yuan Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Meiying Ruan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Qingjing Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Rongqing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
| | - Jia Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
- Wulanchabu Academy of Agricultural and Forestry Sciences, Wulanchabu 012000, China
| | - Chaochao Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, China;
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.X.); (Z.Y.); (Y.C.); (M.R.); (Q.Y.); (R.W.); (G.Z.); (J.L.)
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Ortiz R. Challenges for crop improvement. Emerg Top Life Sci 2023; 7:197-205. [PMID: 37905719 DOI: 10.1042/etls20230106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
The genetic improvement of crops faces the significant challenge of feeding an ever-increasing population amidst a changing climate, and when governments are adopting a 'more with less' approach to reduce input use. Plant breeding has the potential to contribute to the United Nations Agenda 2030 by addressing various sustainable development goals (SDGs), with its most profound impact expected on SDG2 Zero Hunger. To expedite the time-consuming crossbreeding process, a genomic-led approach for predicting breeding values, targeted mutagenesis through gene editing, high-throughput phenomics for trait evaluation, enviromics for including characterization of the testing environments, machine learning for effective management of large datasets, and speed breeding techniques promoting early flowering and seed production are being incorporated into the plant breeding toolbox. These advancements are poised to enhance genetic gains through selection in the cultigen pools of various crops. Consequently, these knowledge-based breeding methods are pursued for trait introgression, population improvement, and cultivar development. This article uses the potato crop as an example to showcase the progress being made in both genomic-led approaches and gene editing for accelerating the delivery of genetic gains through the utilization of genetically enhanced elite germplasm. It also further underscores that access to technological advances in plant breeding may be influenced by regulations and intellectual property rights.
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Affiliation(s)
- Rodomiro Ortiz
- Department of Plant Breeding (VF), Swedish University of Agricultural Sciences (SLU), Box 190 Sundsvagen 10, SE 23422 Lomma, Sweden
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37
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Kaur Y, Das N. Molecular, in silico and expression studies on lipoxygenases (LOXs) in potato ( Solanum tuberosum L.). 3 Biotech 2023; 13:419. [PMID: 38037658 PMCID: PMC10684462 DOI: 10.1007/s13205-023-03839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Lipoxygenases (LOXs) namely 9-LOXs and 13-LOXs catalyse the oxygenation of polyunsaturated fatty acids to produce fatty acid hydroperoxides which are crucial in growth, development and stress responses in plants. Here, we isolated and characterized a 2723-bp cDNA encoding a distinct 861-aa 9-LOX form, designated StKCLX-1, using tuber total RNA from an Indian potato cultivar, Kufri Chipsona-1 through RT-PCR. A total of 17 LOX genes distributed in different chromosomes were identified and characterized in the potato genome. Multiple sequence alignment revealed highly conserved amino acids in the crucial domains, motifs and variable N-terminal regions between the LOX classes. A total of 36 LOXs from potato, tomato and Arabidopsis were used in phylogenetic analysis. A 3-D structure of StKCLX-1 was predicted by AlphaFold tool, validated through the predicted local-distance difference test (pLDDT) and Ramachandran Plot. Molecular docking predicted the nature of receptor-ligand interactions. STRING database was used to predict the protein-protein interactions. Expression patterns of the LOXs in the potato organs were examined by Expression Atlas and semi-quantitative RT-PCR. 9-LOX activity was noticed at early stages of tuberization, and significantly increased in the freshly-harvested mature tubers. This report would be useful in gaining insights into the structure-function relationships of the LOXs and corresponding multigene family-prerequisites for understanding tuber development in potato.
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Affiliation(s)
- Yadveer Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004 Punjab India
| | - Niranjan Das
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004 Punjab India
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38
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Wu Y, Liu J, Jiao B, Wang T, Sun S, Huang B. Genome-Wide Analysis of Family-1 UDP-Glycosyltransferases in Potato ( Solanum tuberosum L.): Identification, Phylogenetic Analysis and Determination of Response to Osmotic Stress. Genes (Basel) 2023; 14:2144. [PMID: 38136966 PMCID: PMC10742590 DOI: 10.3390/genes14122144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Family-1 UDP-glycosyltransferases (UGTs) are the most common and functional glycosyltransferases in the plant world. UGT is closely related to plant growth and the response to abiotic stress. However, despite systematic research, our understanding of potato UGT genes is still unclear. In this study, we identified 174 potato UGT proteins based on their conserved plant secondary product glycosyltransferase (PSPG) motifs. Phylogenetic analyses were used to compare these proteins with Arabidopsis UGTs and other plant UGTs, and it was found that they could be clustered into 18 distinct groups. Patterns of intron gain/loss and intron phases within potato UGTs revealed highly conserved intron insertion events. The promoter cis-elements of these 174 UGT genes were systematically investigated. The promoter regions of these UGT genes are known to contain various classes of cis-acting compounds. These include elements that are light-responsive, phytohormone-responsive, and stress-responsive. Transcriptome data analysis established that 25, 10, 6, and 4 of these 174 UGT genes were specifically expressed in leaves, roots, stolons, and young tubers, respectively. The mannitol-treated transcriptomic data showed thirty-eight UGT genes were significantly upregulated. The quantitative real-time PCR results showed that the four genes were all responsive to osmotic stress under a 10% PEG6000 treatment. The results of our study provide a basis for clarifying the molecular mechanism of potato osmotic stress resistance and better understanding its function in the future.
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Affiliation(s)
| | | | | | | | | | - Binquan Huang
- School of Agriculture, Yunnan University, Kunming 650504, China; (Y.W.); (J.L.); (B.J.); (T.W.); (S.S.)
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Zhang F, Jiang S, Li Q, Song Z, Yang Y, Yu S, Nie Z, Chu M, An Y. Identification of the ALMT gene family in the potato ( Solanum tuberosum L.) and analysis of the function of StALMT6/ 10 in response to aluminum toxicity. FRONTIERS IN PLANT SCIENCE 2023; 14:1274260. [PMID: 38053773 PMCID: PMC10694233 DOI: 10.3389/fpls.2023.1274260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Introduction Aluminum (Al)-activated malate transporters (ALMTs) play an important role in the response to Al toxicity, maintenance of ion homeostasis balance, mineral nutrient distribution, and fruit quality development in plants. However, the function of the StALMT gene family in potato remains unknown. Methods and results In this study, 14 StALMT genes were identified from the potato genome, unevenly distributed on seven different chromosomes. Collinearity and synteny analyses of ALMT genes showed that potatoes had 6 and 22 orthologous gene pairs with Arabidopsis and tomatoes, respectively, and more than one syntenic gene pair was identified for some StALMT gene family members. Real-time quantitative polymerase chain reaction (qPCR) results showed differential expression levels of StALMT gene family members in different tissues of the potato. Interestingly, StALMT1, StALMT6, StALMT8, StALMT10, and StALMT12 had higher expression in the root of the potato cultivar Qingshu No. 9. After being subjected to Al3+ stress for 24 h, the expression of StALMT6 and StALMT10 in roots was evidently increased, displaying their decisive role in Al3+ toxicity. Discussion In addition, overexpression of StALMT6 and StALMT10 in Arabidopsis enhanced its tolerance to Al toxicity. These results indicate that StALMT6 and StALMT10 impart Al3+ resistance in the potato, establishing the foundation for further studies of the biological functions of these genes.
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Affiliation(s)
- Feng Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Sixia Jiang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Qiong Li
- Department of Brewing Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Zhiying Song
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Ying Yang
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Shirui Yu
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
| | - Zongyue Nie
- Agriculture Science Institute of Bijie, Bijie, Guizhou, China
| | - Moli Chu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources/College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Yanlin An
- Department of Food Science and Engineering, Moutai Institute, Renhuai, Guizhou, China
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40
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Shang L, Zhou Y, Wen S, Wang K, Li Y, Zhang M, Jian H, Lyu D. Construction of heat stress regulation networks based on Illumina and SMRT sequencing data in potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1271084. [PMID: 38023929 PMCID: PMC10651764 DOI: 10.3389/fpls.2023.1271084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important tuber food crops in the world; however, the cultivated potatoes are susceptible to high temperature, by which potato production is adversely affected. Understanding the coping mechanism of potato to heat stress is essential to secure yield and expand adaptability under environmental conditions with rising temperature. However, the lack of heat-related information has significantly limited the identification and application of core genes. To gain deeper insights into heat tolerance genes, next-generation sequencing and single-molecule real-time sequencing were used to learn the transcriptional response of potato to heat stress and 13,159 differentially expressed genes (DEGs) were identified in this study. All DEGs were grouped into 12 clusters using the K-means clustering algorithm. Gene Ontology enrichment analysis revealed that they were involved in temperature signaling, phytohormone, and protein modification. Among them, there were 950 differentially expressed transcription factors (DETFs). According to the network analysis of DETFs at the sixth hour under heat stress, we found some genes that were previously reported to be associated with photoperiodic tuberization, StCO (CONSTANS), tuber formation, StBEL11 (BEL1-LIKE 11), and earliness in potato, StCDF1 (CYCLING DOF FACTOR 1) responding to temperature. Furthermore, we verified the relative expression levels using quantitative real-time polymerase chain reaction, and the results were consistent with the inferences from transcriptomes. In addition, there were 22,125 alternative splicing events and 2,048 long non-coding RNAs. The database and network established in this study will extend our understanding of potato response to heat stress. It ultimately provided valuable resources for molecular analysis of heat stress response in potato and cultivation of potato varieties with heat tolerance.
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Affiliation(s)
- Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yonghong Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ke Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Meihua Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Southwest University, Chongqing, China
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Wang Y, Brown LH, Adams TM, Cheung YW, Li J, Young V, Todd DT, Armstrong MR, Neugebauer K, Kaur A, Harrower B, Oome S, Wang X, Bayer M, Hein I. SMRT-AgRenSeq-d in potato ( Solanum tuberosum) as a method to identify candidates for the nematode resistance Gpa5. HORTICULTURE RESEARCH 2023; 10:uhad211. [PMID: 38023472 PMCID: PMC10681002 DOI: 10.1093/hr/uhad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Potato is the third most important food crop in the world. Diverse pathogens threaten sustainable crop production but can be controlled, in many cases, through the deployment of disease resistance genes belonging to the family of nucleotide-binding, leucine-rich-repeat (NLR) genes. To identify effective disease resistance genes in established varieties, we have successfully established SMRT-AgRenSeq in tetraploid potatoes and have further enhanced the methodology by including dRenSeq in an approach that we term SMR-AgRenSeq-d. The inclusion of dRenSeq enables the filtering of candidates after the association analysis by establishing a presence/absence matrix across resistant and susceptible varieties that is translated into an F1 score. Using a SMRT-RenSeq-based sequence representation of the NLRome from the cultivar Innovator, SMRT-AgRenSeq-d analyses reliably identified the late blight resistance benchmark genes Rpi-R1, Rpi-R2-like, Rpi-R3a, and Rpi-R3b in a panel of 117 varieties with variable phenotype penetrations. All benchmark genes were identified with an F1 score of 1, which indicates absolute linkage in the panel. This method also identified nine strong candidates for Gpa5 that controls the potato cyst nematode (PCN) species Globodera pallida (pathotypes Pa2/3). Assuming that NLRs are involved in controlling many types of resistances, SMRT-AgRenSeq-d can readily be applied to diverse crops and pathogen systems.
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Affiliation(s)
- Yuhan Wang
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Lynn H Brown
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Thomas M Adams
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Yuk Woon Cheung
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Jie Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Vanessa Young
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Drummond T Todd
- James Hutton Limited, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Miles R Armstrong
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Konrad Neugebauer
- Biomathematics and Statistics Scotland, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Amanpreet Kaur
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- Crop Research Centre, Teagasc, Oak Park, Carlow R93 XE12, Ireland
| | - Brian Harrower
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Stan Oome
- HZPC Research B.V. HZPC, Edisonweg 5, 8501 XG Joure, Netherlands
| | - Xiaodan Wang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
| | - Micha Bayer
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Ingo Hein
- Division of Plant Sciences at the Hutton, The University of Dundee, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100083, China
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Verbeecke V, Custódio L, Strobbe S, Van Der Straeten D. The role of orphan crops in the transition to nutritional quality-oriented crop improvement. Biotechnol Adv 2023; 68:108242. [PMID: 37640278 DOI: 10.1016/j.biotechadv.2023.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Micronutrient malnutrition is a persisting problem threatening global human health. Biofortification via metabolic engineering has been proposed as a cost-effective and short-term means to alleviate this burden. There has been a recent rise in the recognition of potential that underutilized, orphan crops can hold in decreasing malnutrition concerns. Here, we illustrate how orphan crops can serve as a medium to provide micronutrients to populations in need, whilst promoting and maintaining dietary diversity. We provide a roadmap, illustrating which aspects to be taken into consideration when evaluating orphan crops. Recent developments have shown successful biofortification via metabolic engineering in staple crops. This review provides guidance in the implementation of these successes to relevant orphan crop species, with a specific focus on the relevant micronutrients iron, zinc, provitamin A and folates.
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Affiliation(s)
- Vincent Verbeecke
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Laura Custódio
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Simon Strobbe
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium.
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von Dahlen JK, Schulz K, Nicolai J, Rose LE. Global expression patterns of R-genes in tomato and potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1216795. [PMID: 37965025 PMCID: PMC10641715 DOI: 10.3389/fpls.2023.1216795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023]
Abstract
Introduction As key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question. Methods In this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants. Results We found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes. Discussion These results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.
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Affiliation(s)
- Janina K. von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Kerstin Schulz
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Jessica Nicolai
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Laura E. Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
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Lu W, Wang Y, Shi Y, Liang Q, Lu X, Su D, Xu X, Pirrello J, Gao Y, Huang B, Li Z. Identification of SRS transcription factor family in Solanum lycopersicum, and functional characterization of their responses to hormones and abiotic stresses. BMC PLANT BIOLOGY 2023; 23:495. [PMID: 37833639 PMCID: PMC10576376 DOI: 10.1186/s12870-023-04506-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
The SHI RELATED SEQUENCE (SRS) family plays a vital role in the development of multiple plant organs such as floral meristem determinacy, organ morphogenesis, and signal transduction. Nevertheless, there is little understanding of the biological significance of tomato SRS family at this point. Our research identified eight SlSRS family members and classified them into three subfamilies based on phylogenetics, conserved motifs, and characteristic domain analysis. The intraspecies and interspecies collinearity analysis revealed clues of SRS family evolution. Many cis-elements related to hormones, stresses, and plant development can be found in the promoter region of SlSRS genes. All of eight SlSRS proteins were located in the nucleus and possessed transcriptional activity, half of which were transcriptional activators, and the other half were transcriptional repressors. Except for SlSRS1, which showed high transcript accumulation in vegetative organs, most SlSRS genes expressed ubiquitously in all flower organs. In addition, all SlSRS genes could significantly respond to at least four different plant hormones. Further, expression of SlSRS genes were regulated by various abiotic stress conditions. In summary, we systematically analyzed and characterized the SlSRS family, reviewed the expression patterns and preliminarily investigated the protein function, and provided essential information for further functional research of the tomato SRS genes in the determination of reproductive floral organs and the development of plants, and possibly other plants.
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Affiliation(s)
- Wang Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yan Wang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qin Liang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xiangyin Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Julien Pirrello
- Laboratory of Plant Science Research, Fruit Genomics and Biotechnology, UMR5546, University of Toulouse, CNRS, UPS, Toulouse-NP, Toulouse, France
| | - Ying Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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Park J, Sathuvalli V, Yilma S, Whitworth J, Novy RG. Identification of QTL associated with plant vine characteristics and infection response to late blight, early blight, and Verticillium wilt in a tetraploid potato population derived from late blight-resistant Palisade Russet. FRONTIERS IN PLANT SCIENCE 2023; 14:1222596. [PMID: 37900754 PMCID: PMC10600477 DOI: 10.3389/fpls.2023.1222596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
Potato late blight (causal agent Phytophthora infestans) is a disease of potatoes with economic importance worldwide. Control is primarily through field monitoring and the application of fungicides. Control of late blight with fungicides and host plant resistance is difficult, with documented cases of such control measures failing with the advent of new pathotypes of P. infestans. To better understand host plant resistance and to develop more durable late blight resistance, Quantitative Trait Locus/Loci (QTL) analysis was conducted on a tetraploid mapping population derived from late blight-resistant potato cultivar Palisade Russet. Additionally, QTL analyses for other traits such as Verticillium wilt and early blight resistance, vine size and maturity were performed to identify a potential relationship between multiple traits and prepare genetic resources for molecular markers useful in breeding programs. For this, one hundred ninety progenies from intercrossing Palisade Russet with a late blight susceptible breeding clone (ND028673B-2Russ) were assessed. Two parents and progenies were evaluated over a two-year period for response to infection by the US-8 genotype of P. infestans in inoculated field screenings in Corvallis, Oregon. In Aberdeen, Idaho, the same mapping population was also evaluated for phenotypic response to early blight and Verticillium wilt, and vine size and maturity in a field over a two-year period. After conducting QTL analyses with those collected phenotype data, it was observed that chromosome 5 has a significant QTL for all five traits. Verticillium wilt and vine maturity QTL were also observed on chromosome 1, and vine size QTL was also found on chromosomes 3 and 10. An early blight QTL was also detected on chromosome 2. The QTL identified in this study have the potential for converting into breeder-friendly molecular markers for marker-assisted selection.
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Affiliation(s)
- Jaebum Park
- Small Grains and Potato Germplasm Research Station, United States Department of Agriculture – Agricultural Research Service, Aberdeen, ID, United States
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Solomon Yilma
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Jonathan Whitworth
- Small Grains and Potato Germplasm Research Station, United States Department of Agriculture – Agricultural Research Service, Aberdeen, ID, United States
| | - Richard G. Novy
- Small Grains and Potato Germplasm Research Station, United States Department of Agriculture – Agricultural Research Service, Aberdeen, ID, United States
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46
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Wolters PJ, Wouters D, Tikunov YM, Ayilalath S, Kodde LP, Strijker MF, Caarls L, Visser RGF, Vleeshouwers VGAA. Tetraose steroidal glycoalkaloids from potato provide resistance against Alternaria solani and Colorado potato beetle. eLife 2023; 12:RP87135. [PMID: 37751372 PMCID: PMC10522338 DOI: 10.7554/elife.87135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023] Open
Abstract
Plants with innate disease and pest resistance can contribute to more sustainable agriculture. Natural defence compounds produced by plants have the potential to provide a general protective effect against pathogens and pests, but they are not a primary target in resistance breeding. Here, we identified a wild relative of potato, Solanum commersonii, that provides us with unique insight in the role of glycoalkaloids in plant immunity. We cloned two atypical resistance genes that provide resistance to Alternaria solani and Colorado potato beetle through the production of tetraose steroidal glycoalkaloids (SGA). Moreover, we provide in vitro evidence to show that these compounds have potential against a range of different (potato pathogenic) fungi. This research links structural variation in SGAs to resistance against potato diseases and pests. Further research on the biosynthesis of plant defence compounds in different tissues, their toxicity, and the mechanisms for detoxification, can aid the effective use of such compounds to improve sustainability of our food production.
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Affiliation(s)
| | - Doret Wouters
- Wageningen University and ResearchWageningenNetherlands
| | | | | | - Linda P Kodde
- Wageningen University and ResearchWageningenNetherlands
| | | | - Lotte Caarls
- Wageningen University and ResearchWageningenNetherlands
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47
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De la Cruz G, Blas R, Pérez W, Neyra E, Ortiz R. Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group. FRONTIERS IN PLANT SCIENCE 2023; 14:1210046. [PMID: 37780511 PMCID: PMC10535101 DOI: 10.3389/fpls.2023.1210046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/10/2023] [Indexed: 10/03/2023]
Abstract
Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.
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Affiliation(s)
- Germán De la Cruz
- Laboratorio de Genética y Biotecnología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de San Cristóbal de Huamanga (UNSCH), Ayacucho, Peru
| | - Raúl Blas
- Instituto de Biotecnologia (IBT), Facultad de Agronomia, Universidad Nacional Agraria La Molina (UNALM), Lima, Peru
| | - Willmer Pérez
- Plant Pathology Laboratory, Crop and Systems Sciences Division, International Potato Center, Lima, Peru
| | - Edgar Neyra
- Unidad de Genómica, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento Académico de Tecnología Médica, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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Xia D, Guan L, Yin Y, Wang Y, Shi H, Li W, Zhang D, Song R, Hu T, Zhan X. Genome-Wide Analysis of MBF1 Family Genes in Five Solanaceous Plants and Functional Analysis of SlER24 in Salt Stress. Int J Mol Sci 2023; 24:13965. [PMID: 37762268 PMCID: PMC10531278 DOI: 10.3390/ijms241813965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Multiprotein bridging factor 1 (MBF1) is an ancient family of transcription coactivators that play a crucial role in the response of plants to abiotic stress. In this study, we analyzed the genomic data of five Solanaceae plants and identified a total of 21 MBF1 genes. The expansion of MBF1a and MBF1b subfamilies was attributed to whole-genome duplication (WGD), and the expansion of the MBF1c subfamily occurred through transposed duplication (TRD). Collinearity analysis within Solanaceae species revealed collinearity between members of the MBF1a and MBF1b subfamilies, whereas the MBF1c subfamily showed relative independence. The gene expression of SlER24 was induced by sodium chloride (NaCl), polyethylene glycol (PEG), ABA (abscisic acid), and ethrel treatments, with the highest expression observed under NaCl treatment. The overexpression of SlER24 significantly enhanced the salt tolerance of tomato, and the functional deficiency of SlER24 decreased the tolerance of tomato to salt stress. SlER24 enhanced antioxidant enzyme activity to reduce the accumulation of reactive oxygen species (ROS) and alleviated plasma membrane damage under salt stress. SlER24 upregulated the expression levels of salt stress-related genes to enhance salt tolerance in tomato. In conclusion, this study provides basic information for the study of the MBF1 family of Solanaceae under abiotic stress, as well as a reference for the study of other plants.
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Affiliation(s)
- Dongnan Xia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Lulu Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Yue Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Yixi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Hongyan Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Wenyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Dekai Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Ran Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Tixu Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Xianyang 712100, China; (D.X.); (Y.Y.); (Y.W.); (H.S.); (W.L.); (D.Z.); (R.S.)
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49
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Lin X, Jia Y, Heal R, Prokchorchik M, Sindalovskaya M, Olave-Achury A, Makechemu M, Fairhead S, Noureen A, Heo J, Witek K, Smoker M, Taylor J, Shrestha RK, Lee Y, Zhang C, Park SJ, Sohn KH, Huang S, Jones JDG. Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors. Nat Genet 2023; 55:1579-1588. [PMID: 37640880 PMCID: PMC10484786 DOI: 10.1038/s41588-023-01486-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 07/21/2023] [Indexed: 08/31/2023]
Abstract
Potato (Solanum tuberosum) and tomato (Solanum lycopersicon) crops suffer severe losses to late blight caused by the oomycete pathogen Phytophthora infestans. Solanum americanum, a relative of potato and tomato, is globally distributed and most accessions are highly blight resistant. We generated high-quality reference genomes of four S. americanum accessions, resequenced 52 accessions, and defined a pan-NLRome of S. americanum immune receptor genes. We further screened for variation in recognition of 315P. infestans RXLR effectors in 52 S. americanum accessions. Using these genomic and phenotypic data, we cloned three NLR-encoding genes, Rpi-amr4, R02860 and R04373, that recognize cognate P. infestans RXLR effectors PITG_22825 (AVRamr4), PITG_02860 and PITG_04373. These genomic resources and methodologies will support efforts to engineer potatoes with durable late blight resistance and can be applied to diseases of other crops.
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Affiliation(s)
- Xiao Lin
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yuxin Jia
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming, China
| | - Robert Heal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Maxim Prokchorchik
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- Plant Pathology Group, The Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Maria Sindalovskaya
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Andrea Olave-Achury
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Moffat Makechemu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Azka Noureen
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jung Heo
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Smoker
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jodie Taylor
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yoonyoung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Soon Ju Park
- Department of Biological Science and Institute of Basic Science, Wonkwang University, Iksan, Republic of Korea
- Division of Applied Life Sciences and Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea.
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea.
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Area, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
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50
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Bvindi C, Howe K, Wang Y, Mullen RT, Rogan CJ, Anderson JC, Goyer A. Potato Non-Specific Lipid Transfer Protein StnsLTPI.33 Is Associated with the Production of Reactive Oxygen Species, Plant Growth, and Susceptibility to Alternaria solani. PLANTS (BASEL, SWITZERLAND) 2023; 12:3129. [PMID: 37687375 PMCID: PMC10490331 DOI: 10.3390/plants12173129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023]
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) are small proteins capable of transferring phospholipids between membranes and binding non-specifically fatty acids in vitro. They constitute large gene families in plants, e.g., 83 in potato (Solanum tuberosum). Despite their recognition decades ago, very few have been functionally characterized. Here, we set out to better understand the function of one of the potato members, StnsLTPI.33. Using quantitative polymerase chain reaction, we show that StnsLTPI.33 is expressed throughout the potato plant, but at relatively higher levels in roots and leaves compared to petals, anthers, and the ovary. We also show that ectopically-expressed StnsLTPI.33 fused to green fluorescent protein colocalized with an apoplastic marker in Nicotiana benthamiana leaves, indicating that StnsLTPI.33 is targeted to the apoplast. Constitutive overexpression of the StnsLTPI.33 gene in potato led to increased levels of superoxide anions and reduced plant growth, particularly under salt stress conditions, and enhanced susceptibility to Alternaria solani. In addition, StnsLTPI.33-overexpressing plants had a depleted leaf pool of pipecolic acid, threonic acid, and glycine, while they accumulated putrescine. To our knowledge, this is the first report of an nsLTP that is associated with enhanced susceptibility to a pathogen in potato.
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Affiliation(s)
- Carol Bvindi
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (C.B.); (K.H.); (C.J.R.); (J.C.A.)
| | - Kate Howe
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (C.B.); (K.H.); (C.J.R.); (J.C.A.)
| | - You Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.W.); (R.T.M.)
| | - Robert T. Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (Y.W.); (R.T.M.)
| | - Conner J. Rogan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (C.B.); (K.H.); (C.J.R.); (J.C.A.)
| | - Jeffrey C. Anderson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (C.B.); (K.H.); (C.J.R.); (J.C.A.)
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; (C.B.); (K.H.); (C.J.R.); (J.C.A.)
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