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Hosaka AJ, Sanetomo R, Hosaka K. A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes. G3 (BETHESDA, MD.) 2024; 14:jkae080. [PMID: 38608140 DOI: 10.1093/g3journal/jkae080] [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: 02/04/2024] [Revised: 03/23/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E-genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.
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Affiliation(s)
- Awie J Hosaka
- Nihon BioData Corporation, Takatsu, Kawasaki, Kanagawa 213-0012, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan
| | - Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Kazuyoshi Hosaka
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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2
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Shi L, de Biolley L, Shaikh MA, de Vries ME, Mittmann SU, Visser RGF, Prat S, Bachem CWB. Aging later but faster: how StCDF1 regulates senescence in Solanum tuberosum. THE NEW PHYTOLOGIST 2024; 242:2541-2554. [PMID: 38197194 DOI: 10.1111/nph.19525] [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: 10/13/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024]
Abstract
In potato, maturity is assessed by leaf senescence, which, in turn, affects yield and tuber quality traits. Previously, we showed that the CYCLING DOF FACTOR1 (StCDF1) locus controls leaf maturity in addition to the timing of tuberization. Here, we provide evidence that StCDF1 controls senescence onset separately from senescence progression and the total life cycle duration. We used molecular-biological approaches (DNA-Affinity Purification Sequencing) to identify a direct downstream target of StCDF1, named ORESARA1 (StORE1S02), which is a NAC transcription factor acting as a positive senescence regulator. By overexpressing StORE1S02 in the long life cycle genotype, early onset of senescence was shown, but the total life cycle remained long. At the same time, StORE1S02 knockdown lines have a delayed senescence onset. Furthermore, we show that StORE1 proteins play an indirect role in sugar transport from source to sink by regulating expression of SWEET sugar efflux transporters during leaf senescence. This study clarifies the important link between tuber formation and senescence and provides insight into the molecular regulatory network of potato leaf senescence onset. We propose a complex role of StCDF1 in the regulation of potato plant senescence.
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Affiliation(s)
- Li Shi
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700 AJ, the Netherlands
| | - Laura de Biolley
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700 AJ, the Netherlands
| | | | | | | | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700 AJ, the Netherlands
| | - Salome Prat
- Center for Research in Agriculture Genomics (CRAG), Barcelona, 08193, Spain
| | - Christian W B Bachem
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700 AJ, the Netherlands
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Tai HH. Insights into the molecular regulation of source-sink relations in potato. THE NEW PHYTOLOGIST 2024; 242:2385-2387. [PMID: 38523243 DOI: 10.1111/nph.19705] [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: 03/26/2024]
Abstract
This article is a Commentary on Shi et al. (2024), 242: 2541–2554.
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Affiliation(s)
- Helen H Tai
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, PO Box 20280, 95 Innovation Rd, Fredericton, NB, E3B 4Z7, Canada
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Hajibarat Z, Saidi A, Zeinalabedini M, Mousapour Gorji A, Ghaffari MR, Shariati V, Ahmadvand R. Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars. PLoS One 2024; 19:e0303783. [PMID: 38787845 PMCID: PMC11125566 DOI: 10.1371/journal.pone.0303783] [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: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.
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Affiliation(s)
- Zahra Hajibarat
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Mousapour Gorji
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology, NIGEB Genome Center, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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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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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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Manasseh R, Sathuvalli V, Pappu HR. Transcriptional and functional predictors of potato virus Y-induced tuber necrosis in potato ( Solanum tuberosum). FRONTIERS IN PLANT SCIENCE 2024; 15:1369846. [PMID: 38638354 PMCID: PMC11024271 DOI: 10.3389/fpls.2024.1369846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/26/2024] [Indexed: 04/20/2024]
Abstract
Introduction Potato (Solanum tuberosum L.), the fourth most important food crop in the world, is affected by several viral pathogens with potato virus Y (PVY) having the greatest economic impact. At least nine biologically distinct variants of PVY are known to infect potato. These include the relatively new recombinant types named PVY-NTN and PVYN-Wi, which induce tuber necrosis in susceptible cultivars. To date, the molecular plant-virus interactions underlying this pathogenicity have not been fully characterized. We hypothesized that this necrotic behavior is supported by transcriptional and functional signatures that are unique to PVY-NTN and PVYN-Wi. Methods To test this hypothesis, transcriptional responses of cv. Russet Burbank, a PVY susceptible cultivar, to three PVY strains PVY-O, PVY-NTN, and PVYN-Wi were studied using mRNA-Seq. A haploid-resolved genome assembly for tetraploid potato was used for bioinformatics analysis. Results The study revealed 36 GO terms and nine KEGG 24 pathways that overlapped across the three PVY strains, making them generic features of PVY susceptibility in potato. Ten GO terms and three KEGG pathways enriched for PVY-NTN and PVYN-Wi only, which made them candidate functional signatures associated with PVY-induced tuber necrosis in potato. In addition, five other pathways were enriched for PVYNTN or PVYN-Wi. One carbon pool by folate was enriched exclusively in response to PVY-NTN infection; PVYN-Wi infection specifically impacted cutin, suberine and wax biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and monoterpenoid biosynthesis. Discussion Results suggest that PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVY-NTN. Our study provides a basis for understanding the mechanism underlying the development of PVY-induced tuber necrosis in potato.
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Affiliation(s)
- Richard Manasseh
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Vidyasagar Sathuvalli
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR, United States
| | - Hanu R. Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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8
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Yu H, Li Y, Han W, Bao L, Liu F, Ma Y, Pu Z, Zeng Q, Zhang L, Bao Z, Wang S. Pan-evolutionary and regulatory genome architecture delineated by an integrated macro- and microsynteny approach. Nat Protoc 2024:10.1038/s41596-024-00966-4. [PMID: 38514839 DOI: 10.1038/s41596-024-00966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/20/2023] [Indexed: 03/23/2024]
Abstract
The forthcoming massive genome data generated by the Earth BioGenome Project will open up a new era of comparative genomics, for which genome synteny analysis provides an important framework. Profiling genome synteny represents an essential step in elucidating genome architecture, regulatory blocks/elements and their evolutionary history. Here we describe PanSyn, ( https://github.com/yhw320/PanSyn ), the most comprehensive and up-to-date genome synteny pipeline, providing step-by-step instructions and application examples to demonstrate its usage. PanSyn inherits both basic and advanced functions from existing popular tools, offering a user-friendly, highly customized approach for genome macrosynteny analysis and integrated pan-evolutionary and regulatory analysis of genome architecture, which are not yet available in public synteny software or tools. The advantages of PanSyn include: (i) advanced microsynteny analysis by functional profiling of microsynteny genes and associated regulatory elements; (ii) comprehensive macrosynteny analysis, including the inference of karyotype evolution from ancestors to extant species; and (iii) functional integration of microsynteny and macrosynteny for pan-evolutionary profiling of genome architecture and regulatory blocks, as well as integration with external functional genomics datasets from three- or four-dimensional genome and ENCODE projects. PanSyn requires basic knowledge of the Linux environment and Perl programming language and the ability to access a computer cluster, especially for large-scale genomic comparisons. Our protocol can be easily implemented by a competent graduate student or postdoc and takes several days to weeks to execute for dozens to hundreds of genomes. PanSyn provides yet the most comprehensive and powerful tool for integrated evolutionary and functional genomics.
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Affiliation(s)
- Hongwei Yu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuli Li
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
| | - Wentao Han
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lisui Bao
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Fuyun Liu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yuanting Ma
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhongqi Pu
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qifan Zeng
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lingling Zhang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China
| | - Zhenmin Bao
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
- Laboratory for Marine Fisheries and Aquaculture, Laoshan Laboratory, Qingdao, China
| | - Shi Wang
- Fang Zongxi Center for Marine Evo-Devo & MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China.
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9
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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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10
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Clot CR, Vexler L, de La O Leyva-Perez M, Bourke PM, Engelen CJM, Hutten RCB, van de Belt J, Wijnker E, Milbourne D, Visser RGF, Juranić M, van Eck HJ. Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:79. [PMID: 38472376 PMCID: PMC10933213 DOI: 10.1007/s00122-024-04563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/24/2024] [Indexed: 03/14/2024]
Abstract
KEY MESSAGE Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker-assisted selection for this trait.
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Affiliation(s)
- Corentin R Clot
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Lea Vexler
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
- Teagasc, Crops Research, Oak Park, Carlow, R93 XE12, Ireland
| | | | - Peter M Bourke
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Christel J M Engelen
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Ronald C B Hutten
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - José van de Belt
- Laboratory of Genetics, Wageningen University and Research, Po Box 16, 6700 AA, Wageningen, The Netherlands
| | - Erik Wijnker
- Laboratory of Genetics, Wageningen University and Research, Po Box 16, 6700 AA, Wageningen, The Netherlands
| | - Dan Milbourne
- Teagasc, Crops Research, Oak Park, Carlow, R93 XE12, Ireland
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Martina Juranić
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University and Research, Po Box 386, 6700 AJ, Wageningen, The Netherlands.
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11
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Schreiber M, Jayakodi M, Stein N, Mascher M. Plant pangenomes for crop improvement, biodiversity and evolution. Nat Rev Genet 2024:10.1038/s41576-024-00691-4. [PMID: 38378816 DOI: 10.1038/s41576-024-00691-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 02/22/2024]
Abstract
Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.
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Affiliation(s)
- Mona Schreiber
- Department of Biology, University of Marburg, Marburg, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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12
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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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13
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Qi T, He F, Zhang X, Wang J, Zhang Z, Jiang H, Zhao B, Du C, Che Y, Feng X, Wang Y, Li F. Genome-Wide Identification and Expression Profiling of Potato ( Solanum tuberosum L.) Universal Stress Proteins Reveal Essential Roles in Mechanical Damage and Deoxynivalenol Stress. Int J Mol Sci 2024; 25:1341. [PMID: 38279341 PMCID: PMC10816615 DOI: 10.3390/ijms25021341] [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: 12/12/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Universal stress proteins (USPs) play an important regulatory role in responses to abiotic stress. Most of the research related to USPs so far has been conducted on plant models such as Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa L.), and cotton (Gossypium hirsutum L.). The potato (Solanum tuberosum L.) is one of the four major food crops in the world. The potato is susceptible to mechanical damage and infection by pathogenic fungi during transport and storage. Deoxynivalenol (DON) released by Fusarium can seriously degrade the quality of potatoes. As a result, it is of great significance to study the expression pattern of the potato StUSP gene family under abiotic stress conditions. In this study, a total of 108 USP genes were identified from the genome of the Atlantic potato, divided into four subgroups. Based on their genetic structure, the physical and chemical properties of their proteins and other aspects of their biological characteristics are comprehensively analyzed. Collinear analysis showed that the homologous genes of StUSPs and four other representative species (Solanum lycopersicum, Arabidopsis, Oryza sativa L., and Nicotiana attenuata) were highly conserved. The cis-regulatory elements of the StUSPs promoter are involved in plant hormones, environmental stress, mechanical damage, and light response. RNA-seq analysis showed that there are differences in the expression patterns of members of each subgroup under different abiotic stresses. A Weighted Gene Coexpression Network Analysis (WGCNA) of the central gene showed that the differential coexpression gene is mainly involved in the plant-pathogen response process, plant hormone signal transduction, and the biosynthesis process of secondary metabolites. Through qRT-PCR analysis, it was confirmed that StUSP13, StUSP14, StUSP15, and StUSP41 may be important candidate genes involved in the response to adversity stress in potatoes. The results of this study provide a basis for further research on the functional analysis of StUSPs in the response of potatoes to adversity stress.
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Affiliation(s)
- Tianshuai Qi
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Fumeng He
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Xinqi Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Jiaqi Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Zengli Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Heran Jiang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China;
| | - Biao Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Chong Du
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Yunzhu Che
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Xu Feng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Yingnan Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
| | - Fenglan Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China; (T.Q.); (F.H.); (X.Z.); (J.W.); (Z.Z.); (B.Z.); (C.D.); (Y.C.); (X.F.)
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14
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Hu J, Duan Y, Hu J, Zhang S, Li G. Phylogenetic and Expression Analysis of the Sucrose Synthase and Sucrose Phosphate Synthase Gene Family in Potatoes. Metabolites 2024; 14:70. [PMID: 38276305 PMCID: PMC10820854 DOI: 10.3390/metabo14010070] [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: 12/12/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/27/2024] Open
Abstract
Sucrose synthase (SUS) and sucrose phosphate synthase (SPS) are essential in plant sucrose metabolism. The potato is an important crop worldwide, but systematic analyses of the StSUS and StSPS gene families in potatoes are still lacking. Ten sucrose metabolism-related genes were identified in this study. The SUSs and SPSs could each be split into three subgroups through phylogenetic analysis. StSUSIc was the most highly expressed gene in different developmental tissues. Ka/Ks analysis showed that StSUSIb and StSUSIc were subjected to more-significant homozygous selection pressure. Our cis-acting element analysis of the StSUS and StSPS promoter sequences showed four elements: defense- and stress-responsive, hormone-responsive, light-responsive, and transcription factor elements. The expression of StSUS and StSPS genes was found to be regulated by circadian rhythm. In the treatments of 1% to 5% sucrose, glucose, and fructose, the expression of StSUS and StSPS family genes was enhanced by sucrose, but inhibited at high-glucose and fructose concentrations. This study identified six StSUS and four StSPS genes and analyzed their gene structure, conserved motifs, chromosome position, promoter elements, phylogenetic tree, and tissue-specific expression patterns. Our results will motivate more research into the biological process underlying the genes of sucrose metabolism in potatoes.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.)
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.)
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinxue Hu
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Shuqing Zhang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Guangcun Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.)
- Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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15
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Serra Mari R, Schrinner S, Finkers R, Ziegler FMR, Arens P, Schmidt MHW, Usadel B, Klau GW, Marschall T. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data. Genome Biol 2024; 25:26. [PMID: 38243222 PMCID: PMC10797741 DOI: 10.1186/s13059-023-03160-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/27/2023] [Indexed: 01/21/2024] Open
Abstract
Potato is one of the world's major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. We introduce a novel strategy for the assembly of polyploid genomes and present an assembly of the autotetraploid potato cultivar Altus. Our method uses low-depth sequencing data from an offspring population to achieve chromosomal clustering and haplotype phasing on the assembly graph. Our approach generates high-quality assemblies of individual chromosomes with haplotype-specific sequence resolution of whole chromosome arms and can be applied in common breeding scenarios where collections of offspring are available.
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Affiliation(s)
- Rebecca Serra Mari
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven Schrinner
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Richard Finkers
- Gennovation B.V., Agro Business Park 10, 6708, PW, Wageningen, The Netherlands
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Freya Maria Rosemarie Ziegler
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Forschungszentrum Jülich, Institute of Bio and Geosciences, Bioinformatics (IBG-4), Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich, Jülich, Germany
- Biological Data Science, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - Maximilian H-W Schmidt
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Forschungszentrum Jülich, Institute of Bio and Geosciences, Bioinformatics (IBG-4), Jülich, Germany
| | - Björn Usadel
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Forschungszentrum Jülich, Institute of Bio and Geosciences, Bioinformatics (IBG-4), Jülich, Germany.
- Bioeconomy Science Center, c/o Forschungszentrum Jülich, Jülich, Germany.
- Biological Data Science, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Gunnar W Klau
- Algorithmic Bioinformatics, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Center for Digital Medicine, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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16
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Clot CR, Klein D, Koopman J, Schuit C, Engelen CJM, Hutten RCB, Brouwer M, Visser RGF, Jurani M, van Eck HJ. Crossover shortage in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility. Genetics 2024; 226:iyad194. [PMID: 37943687 PMCID: PMC10763545 DOI: 10.1093/genetics/iyad194] [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: 09/04/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes. However, if CO shortage is combined with another meiotic alteration that restitutes the first meiotic division, then uniform and balanced unreduced male gametes, essentially composed of nonrecombinant homologs, are produced. This mitosis-like division is of interest to breeders because it transmits most of the parental heterozygosity to the gametes. In potato, CO shortage, a recessive trait previously referred to as desynapsis, was tentatively mapped to chromosome 8. In this article, we have fine-mapped the position of the CO shortage locus and identified StMSH4, an essential component of the class I CO pathway, as the most likely candidate gene. A 7 base-pair insertion in the second exon of StMSH4 was found to be associated with CO shortage in our mapping population. We also identified a second allele with a 3,820 base-pair insertion and confirmed that both alleles cannot complement each other. Such nonfunctional alleles appear to be common in potato cultivars. More than half of the varieties we tested are carriers of mutational load at the StMSH4 locus. With this new information, breeders can choose to remove alleles associated with CO shortage from their germplasm to improve fertility or to use them to produce highly uniform unreduced male gametes in alternative breeding schemes.
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Affiliation(s)
- Corentin R Clot
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, 6708 PB, The Netherlands
| | - Dennis Klein
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Joey Koopman
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Cees Schuit
- Bejo Zaden B.V., Warmenhuizen, 1749 CZ, The Netherlands
| | - Christel J M Engelen
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Ronald C B Hutten
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Matthijs Brouwer
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Martina Jurani
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
| | - Herman J van Eck
- Plant Breeding, Wageningen University & Research, Wageningen, 6700 AJ, The Netherlands
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17
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Švara A, Sun H, Fei Z, Khan A. Chromosome-level phased genome assembly of "Antonovka" identified candidate apple scab-resistance genes highly homologous to HcrVf2 and HcrVf1 on linkage group 1. G3 (BETHESDA, MD.) 2023; 14:jkad253. [PMID: 37936323 PMCID: PMC10755186 DOI: 10.1093/g3journal/jkad253] [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: 08/07/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Apple scab, a fungal disease caused by Venturia inaequalis, leads to losses in both yield and fruit quality of apples (Malus domestica Borkh.). Most commercial apple cultivars, including those containing the well-characterized Rvi6-scab-resistance locus on linkage group (LG) 1, are susceptible to scab. HcrVf2 and HcrVf1 are considered the main paralogs of the Rvi6 locus. The major apple scab-resistance loci Vhc1 in "Honeycrisp" and Rvi17 in "Antonovka," were identified in close proximity to HcrVf2. In this study, we used long-read sequencing and in silico gene sequence characterization to identify candidate resistance genes homologous to HcrVf2 and HcrVf1 in Honeycrisp and Antonovka. Previously published chromosome-scale phased assembly of Honeycrisp and a newly assembled phased genome of Antonovka 172670-B were used to identify HcrVf2 and HcrVf1 homologs spanning Vhc1 and Rvi17 loci. In combination with 8 available Malus assemblies, 43 and 46 DNA sequences highly homologous to HcrVf2 and HcrVf1, respectively, were identified on LG 1 and 6, with identity and coverage ranging between 87-95 and 81-95%, respectively. Among these homologs, 2 candidate genes in Antonovka and Honeycrisp haplome A are located in close physical proximity to the scab-resistance marker Ch-Vf1 on LG 1. They showed the highest identity and coverage (95%) of HcrVf2 and only minor changes in the protein motifs. They were identical by state between each other, but not with HcrVf2. This study offers novel genomic resources and insights into the Vhc1 and Rvi17 loci on LG 1 and identifies candidate genes for further resistance characterization.
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Affiliation(s)
- Anže Švara
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
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18
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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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19
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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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20
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Tang X, Sun F, Zhang N, Rana BB, Kharel R, Luo P, Si H. RNA-seq provides insights into potato deubiquitinase responses to drought stress in seedling stage. FRONTIERS IN PLANT SCIENCE 2023; 14:1268448. [PMID: 37780518 PMCID: PMC10539648 DOI: 10.3389/fpls.2023.1268448] [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: 07/28/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023]
Abstract
Ubiquitination is a specific protein degradation and reversible post-translational modification process that can be reversed by deubiquitinase (DUBs). DUBs can hydrolyze and release ubiquitin in the substrate protein so that the substrate can avoid degradation or change its activity, and it has an impact on plant growth and development, cell cycle, abiotic stress response, and other biological processes. Transcript sequences of potato varieties "DM1-3", "Atlantic" and "Cooperation-88" downloaded from Potato Genome Resources were used for genome-wide identification of the DUB gene family using Hidden Markov Models and verified in the NCBI CD-Search tool. The characteristics of DUB genes from different potato varieties were analyzed including subcellular localization, gene structural motifs, phylogenetic tree, and sequence homology. Polyethylene glycol 6000 (PEG6000) induced drought stress transcriptome analysis was performed on the "Atlantic", and differentially expressed genes were screened, with emphasis on the characterization of deubiquitinase. DUB genes have a complex gene structure, often with a large number of exons and alternative splicing. Their promoters contain abundant abiotic stress-responsive elements, such as 425 MYC, 325 ABRE, and 320 MYB. There are also a large number of orthologous genes in the DUBs of the three potato varieties, and these genes are often clustered in similar regions on the genome. We performed transcriptome sequencing of the potato under PEG-induced drought stress and analyzed it for the first time using the Atlantic as a reference genome. We identified a total of 6067 down-regulated differentially expressed genes (DEGs) and 4950 up-regulated DEGs under PEG-induced drought stress. We screened the expression of DUBs and observed that 120 DUBs were up-regulated where most of them functioned in the nucleus, and the interacting proteins of DUBs were also localized in the nucleus. We have comprehensively identified and analyzed potato DUBs, and the accurately aligned transcriptome data which will further deepen the understanding of DUBs involved in the regulation of osmotic stress.
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Affiliation(s)
- Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fujun Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ning Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Birendra Bahadur Rana
- Nepal Agricultural Research Council, National Potato Research Program, Lalitpur, Nepal
| | - Raju Kharel
- Department of Genetics and Plant Breeding, Agricultural and Forestry University, Chitwan, Nepal
| | - Pan Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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21
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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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22
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Yasumoto S, Muranaka T. Foreign DNA detection in genome-edited potatoes by high-throughput sequencing. Sci Rep 2023; 13:12246. [PMID: 37558681 PMCID: PMC10412624 DOI: 10.1038/s41598-023-38897-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: 03/29/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Genome editing is a powerful breeding technique that introduces mutations into specific gene sequences in genomes. For genome editing in higher plants, nucleotides for artificial nuclease (e.g. TALEN or CRISPR-Cas9) are transiently or stably introduced into the plant cells. After the introduction of mutations by artificial nucleases, it is necessary to select lines that do not contain the foreign nucleotides to overcome GMO regulation; however, there is still no widely legally authorized and approved method for detecting foreign genes in genome-edited crops. Recently, k-mer analysis based on next-generation sequencing (NGS) was proposed as a new method for detecting foreign DNA in genome-edited agricultural products. Compared to conventional methods, such as PCR and Southern hybridization, in principle, this method can detect short DNA fragments with high accuracy. However, this method has not yet been applied to genome-edited potatoes. In this study, we evaluated the feasibility of k-mer analysis in tetraploid potatoes by computer simulation, and also evaluated whether the k-mer method can detect foreign genes with high accuracy by analyzing samples of genome-edited potatoes. We show that when NGS data (at a depth of × 30 the genome size) are used, the k-mer method can correctly detect foreign genes in the potato genome even with the insertion of DNA fragments of 20 nt in length. Based on these findings, we expect that k-mer analysis will be one of the main methods for detecting foreign genes in genome-edited potatoes.
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Affiliation(s)
- Shuhei Yasumoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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23
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Lomin SN, Kolachevskaya OO, Arkhipov DV, Romanov GA. Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes. Int J Mol Sci 2023; 24:11408. [PMID: 37511169 PMCID: PMC10380454 DOI: 10.3390/ijms241411408] [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: 04/21/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific.
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Affiliation(s)
- Sergey N Lomin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Oksana O Kolachevskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Dmitry V Arkhipov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
| | - Georgy A Romanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya 35, 127276 Moscow, Russia
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24
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Chen Q, Song Y, Liu K, Su C, Yu R, Li Y, Yang Y, Zhou B, Wang J, Hu G. Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE ( FRS) Family Members in Potato ( Solanum tuberosum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2575. [PMID: 37447143 DOI: 10.3390/plants12132575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar "Xisen 6", which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yang Song
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Chen Su
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Ying Li
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Yi Yang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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25
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Agha HI, Shannon LM, Morrell PL. Unloading potatoes: Potato breeding moves forward with only half the genome. CELL GENOMICS 2023; 3:100343. [PMID: 37388910 PMCID: PMC10300581 DOI: 10.1016/j.xgen.2023.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]
Abstract
Potato is one of the most important food crops in the world and, in contrast to other staples, has not seen large improvements in yield. Agha, Shannon, and Morrell preview an article recently published in Cell, "Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding," which advances potato breeding strategies via a genetic approach.
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Affiliation(s)
- Husain I. Agha
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55018, USA
| | - Laura M. Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55018, USA
| | - Peter L. Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
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26
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Kong W, Wang Y, Zhang S, Yu J, Zhang X. Recent Advances in Assembly of Complex Plant Genomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:427-439. [PMID: 37100237 PMCID: PMC10787022 DOI: 10.1016/j.gpb.2023.04.004] [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: 03/18/2023] [Revised: 03/18/2023] [Accepted: 04/07/2023] [Indexed: 04/28/2023]
Abstract
Over the past 20 years, tremendous advances in sequencing technologies and computational algorithms have spurred plant genomic research into a thriving era with hundreds of genomes decoded already, ranging from those of nonvascular plants to those of flowering plants. However, complex plant genome assembly is still challenging and remains difficult to fully resolve with conventional sequencing and assembly methods due to high heterozygosity, highly repetitive sequences, or high ploidy characteristics of complex genomes. Herein, we summarize the challenges of and advances in complex plant genome assembly, including feasible experimental strategies, upgrades to sequencing technology, existing assembly methods, and different phasing algorithms. Moreover, we list actual cases of complex genome projects for readers to refer to and draw upon to solve future problems related to complex genomes. Finally, we expect that the accurate, gapless, telomere-to-telomere, and fully phased assembly of complex plant genomes could soon become routine.
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Affiliation(s)
- Weilong Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yibin Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shengcheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jiaxin Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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27
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Xiao XO, Zhang N, Jin H, Si H. Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091895. [PMID: 37176953 PMCID: PMC10181131 DOI: 10.3390/plants12091895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The autotetraploid potato (Solanum tuberosum L.) is an important crop in China, and it is widely cultivated from Northeast China to South China. Thousands of varieties are bred by breeding institutions or companies, and distinguishing the different varieties based on morphological characteristics is difficult. Using DNA fingerprints is an efficient method to identify varieties that plays an increasingly important role in germplasm identification and property rights protection. In this study, the genetic diversity and population structure of 135 autotetraploid potatoes were evaluated using specific-locus amplified fragment sequencing (SLAF-seq) methods. A total of 3,397,137 high-quality single-nucleotide polymorphisms (SNPs), which were distributed across 12 chromosomes, were obtained. Principal component analysis (PCA), neighbour-joining genetic trees, and model-based structure analysis showed that these autotetraploid potato subpopulations, classified by their SNPs, were not consistent with their geographical origins. On the basis of the obtained 3,397,137 SNPs, 160 perfect SNPs were selected, and 71 SNPs were successfully converted to penta-primer amplification refractory mutation (PARMS-SNP) markers. Additionally, 190 autotetraploid potato varieties were analysed using these 71 PARMS-SNP markers. The PCA results show that the accessions were not completely classified on the basis of their geographical origins. The SNP DNA fingerprints of the 190 autotetraploid potato varieties were also constructed. The SNP fingerprint results show that both synonyms and homonyms were present amongst the 190 autotetraploid potatoes. Above all, these novel SNP markers can lay a good foundation for the analysis of potato genetic diversity, DUS (distinctness, uniformity, and stability) testing, and plant variety protection.
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Affiliation(s)
- Xi-Ou Xiao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- South Subtropical Crop Research Institution, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Ning Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hui Jin
- South Subtropical Crop Research Institution, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Huaijun Si
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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28
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Wu Y, Li D, Hu Y, Li H, Ramstein GP, Zhou S, Zhang X, Bao Z, Zhang Y, Song B, Zhou Y, Zhou Y, Gagnon E, Särkinen T, Knapp S, Zhang C, Städler T, Buckler ES, Huang S. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding. Cell 2023; 186:2313-2328.e15. [PMID: 37146612 DOI: 10.1016/j.cell.2023.04.008] [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: 08/24/2022] [Revised: 02/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.
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Affiliation(s)
- Yaoyao Wu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Dawei Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yong Hu
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
| | - Hongbo Li
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Guillaume P Ramstein
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus 8000, Denmark
| | - Shaoqun Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xinyan Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Zhigui Bao
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Yu Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; School of Agriculture, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261000, China
| | - Yao Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100094, China
| | - Yongfeng Zhou
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Edeline Gagnon
- Technische Universität München, TUM School of Life Sciences, Emil-Ramann-Strasse 2, 85354 Freising, Germany
| | - Tiina Särkinen
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Chunzhi Zhang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Thomas Städler
- Institute of Integrative Biology and Zurich-Basel Plant Science Center, ETH Zurich, 8092 Zurich, Switzerland
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; USDA-ARS, Ithaca, NY 14853, USA
| | - Sanwen Huang
- State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China; State Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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Zhao B, Yu H, Liu D, Wang J, Feng X, He F, Qi T, Du C, Wang L, Wang H, Li F. Combined Transcriptome and Metabolome Analysis Reveals Adaptive Defense Responses to DON Induction in Potato. Int J Mol Sci 2023; 24:ijms24098054. [PMID: 37175760 PMCID: PMC10179060 DOI: 10.3390/ijms24098054] [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: 03/23/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Phytophthora infestans poses a serious threat to potato production, storage, and processing. Understanding plant immunity triggered by fungal elicitors is important for the effective control of plant diseases. However, the role of the potato stress response to Fusarium toxin deoxynivalenol (DON)-induced stress is still not fully understood. In this study, the metabolites of DON-treated potato tubers were studied for four time intervals using UPLC-MS/MS. We identified 676 metabolites, and differential accumulation metabolite analysis showed that alkaloids, phenolic acids, and flavonoids were the major differential metabolites that directly determined defense response. Transcriptome data showed that differentially expressed genes (DEGs) were significantly enriched in phenylpropane and flavonoid metabolic pathways. Weighted gene co-expression network analysis (WGCNA) identified many hub genes, some of which modulate plant immune responses. This study is important for understanding the metabolic changes, transcriptional regulation, and physiological responses of active and signaling substances during DON induction, and it will help to design defense strategies against Phytophthora infestans in potato.
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Affiliation(s)
- Biao Zhao
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Dan Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Jiaqi Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Xu Feng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fumeng He
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Tianshuai Qi
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Chong Du
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Linlin Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530005, China
| | - Fenglan Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
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30
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Song L, Endelman JB. Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding. THE PLANT GENOME 2023:e20339. [PMID: 37063052 DOI: 10.1002/tpg2.20339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/16/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
At present, the potato (Solanum tuberosum L.) of international commerce is autotetraploid, and the complexity of this genetic system creates limitations for breeding. Diploid potato breeding has long been used for population improvement, and because of an improved understanding of the genetics of gametophytic self-incompatibility, there is now sustained interest in the development of uniform F1 hybrid varieties based on inbred parents. We report here on the use of haplotype and quantitative trait locus (QTL) analysis in a modified backcrossing (BC) scheme, using primary dihaploids of S. tuberosum as the recurrent parental background. In Cycle 1, we selected XD3-36, a self-fertile F2 individual homozygous for the self-compatibility gene Sli (S-locus inhibitor). Signatures of gametic and zygotic selection were observed at multiple loci in the F2 generation, including Sli. In the BC1 cycle, an F1 population derived from XD3-36 showed a bimodal response for vine maturity, which led to the identification of late versus early alleles in XD3-36 for the gene CDF1 (Cycling DOF Factor 1). Greenhouse phenotypes and haplotype analysis were used to select a vigorous and self-fertile F2 individual with 43% homozygosity, including for Sli and the early-maturing allele CDF1.3. Partially inbred lines from the BC1 and BC2 cycles have been used to initiate new cycles of selection, with the goal of reaching higher homozygosity while maintaining plant vigor, fertility, and yield.
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Affiliation(s)
- Lin Song
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin, USA
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31
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Zhao L, Zou M, Deng K, Xia C, Jiang S, Zhang C, Ma Y, Dong X, He M, Na T, Wang J, Xia Z, Wang F. Insights into the genetic determination of tuber shape and eye depth in potato natural population based on autotetraploid potato genome. FRONTIERS IN PLANT SCIENCE 2023; 14:1080666. [PMID: 37056497 PMCID: PMC10086151 DOI: 10.3389/fpls.2023.1080666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Potato is one of the world's most important food crops, with a time-consuming breeding process. In this study, we performed a genome-wide association (GWAS) analysis of the two important traits of potato tuber shape and eye depth, using the tetraploid potato genome (2n=4x=48) as a reference. A total of 370 potatoes were divided into three subgroups based on the principal component analysis and evolutionary tree analysis. The genetic diversity within subgroups is low (5.18×10-5, 4.36×10-5 and 4.24×10-5). Genome-wide linkage disequilibrium (LD) analysis showed that their LD is about 60 Kb. GWAS analysis identified that 146 significant single nucleotide polymorphism (SNP) loci at Chr01A1:34.44-35.25 Mb and Chr02A1:28.35-28.54 Mb regions are significantly associated with potato tuber shape, and that three candidate genes that might be related to potato tuber traits, PLATZ transcription factor, UTP-glucose-1-phosphate uridylyltransferase and FAR1 DNA-binding domain, are in the association region of Chr02A1. GWAS analysis identified 53 significant SNP loci at Chr05A2: 49.644-50.146 Mb and Chr06A2: 25.866-26.384 Mb regions with robust associations with potato tuber eye depth. Hydrolase and methyltransferases are present in the association region of Chr05A2, and three CYPs are present in the association region of Chr06A2. Our findings suggested that these genes are closely associated with potato tuber shape and eye depth. Our study identified molecular markers and candidate genes for improving tetraploid potato tuber shape and eye depth and provided ideas and insights for tetraploid potato breeding.
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Affiliation(s)
- Long Zhao
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Meiling Zou
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Ke Deng
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chengcai Xia
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Sirong Jiang
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Chenji Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yongzhen Ma
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xiaorui Dong
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Miaohua He
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Tiancang Na
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
| | - Zhiqiang Xia
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Fang Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, China
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Key Laboratory of Qinghai-Tibet Plateau Biotechnology Ministry of Education, Qinghai University, Xining, China
- Qinghai Provincial Key Laboratory of Potato Breeding, Qinghai University, Xining, China
- Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Qinghai University, Xining, China
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32
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Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia. Int J Mol Sci 2023; 24:ijms24065713. [PMID: 36982787 PMCID: PMC10059000 DOI: 10.3390/ijms24065713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.
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Yang X, Zhang L, Guo X, Xu J, Zhang K, Yang Y, Yang Y, Jian Y, Dong D, Huang S, Cheng F, Li G. The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions. MOLECULAR PLANT 2023; 16:314-317. [PMID: 36528795 DOI: 10.1016/j.molp.2022.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan 250100, China; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xiao Guo
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan 250100, China
| | - Jianfei Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yinqing Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yu Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan 250100, China
| | - Yinqiao Jian
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Daofeng Dong
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan 250100, China
| | - Sanwen Huang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences/State Key Laboratory of Vegetable Biobreeding/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Beijing 100081, China.
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34
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Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:446-459. [PMID: 36534120 DOI: 10.1111/tpj.16070] [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: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghui Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, BioSc, 52428, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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35
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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36
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Rogozina EV, Gurina AA, Chalaya NA, Zoteyeva NM, Kuznetsova MA, Beketova MP, Muratova OA, Sokolova EA, Drobyazina PE, Khavkin EE. Diversity of Late Blight Resistance Genes in the VIR Potato Collection. PLANTS (BASEL, SWITZERLAND) 2023; 12:273. [PMID: 36678985 PMCID: PMC9862067 DOI: 10.3390/plants12020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Late blight (LB) caused by the oomycete Phytophthora infestans (Mont.) de Bary is the greatest threat to potato production worldwide. Current potato breeding for LB resistance heavily depends on the introduction of new genes for resistance to P. infestans (Rpi genes). Such genes have been discovered in highly diverse wild, primitive, and cultivated species of tuber-bearing potatoes (Solanum L. section Petota Dumort.) and introgressed into the elite potato cultivars by hybridization and transgenic complementation. Unfortunately, even the most resistant potato varieties have been overcome by LB due to the arrival of new pathogen strains and their rapid evolution. Therefore, novel sources for germplasm enhancement comprising the broad-spectrum Rpi genes are in high demand with breeders who aim to provide durable LB resistance. The Genbank of the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg harbors one of the world's largest collections of potato and potato relatives. In this study, LB resistance was evaluated in a core selection representing 20 species of seven Petota series according to the Hawkes (1990) classification: Bulbocastana (Rydb.) Hawkes, Demissa Buk., Longipedicellata Buk., Maglia Bitt., Pinnatisecta (Rydb.) Hawkes, Tuberosa (Rydb.) Hawkes (wild and cultivated species), and Yungasensa Corr. LB resistance was assessed in 96 accessions representing 18 species in the laboratory test with detached leaves using a highly virulent and aggressive isolate of P. infestans. The Petota species notably differed in their LB resistance: S. bulbocastanum Dun., S. demissum Lindl., S. cardiophyllum Lindl., and S. berthaultii Hawkes stood out at a high frequency of resistant accessions (7-9 points on a 9-point scale). Well-established specific SCAR markers of ten Rpi genes-Rpi-R1, Rpi-R2/Rpi-blb3, Rpi-R3a, Rpi-R3b, Rpi-R8, Rpi-blb1/Rpi-sto1, Rpi-blb2, and Rpi-vnt1-were used to mine 117 accessions representing 20 species from seven Petota series. In particular, our evidence confirmed the diverse Rpi gene location in two American continents. The structural homologs of the Rpi-R2, Rpi-R3a, Rpi-R3b, and Rpi-R8 genes were found in the North American species other than S. demissum, the species that was the original source of these genes for early potato breeding, and in some cases, in the South American Tuberosa species. The Rpi-blb1/Rpi-sto1 orthologs from S. bulbocastanum and S. stoloniferum Schlechtd et Bché were restricted to genome B in the Mesoamerican series Bulbocastana, Pinnatisecta, and Longipedicellata. The structural homologs of the Rpi-vnt1 gene that were initially identified in the South American species S. venturii Hawkes and Hjert. were reported, for the first time, in the North American series of Petota species.
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Affiliation(s)
- Elena V. Rogozina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Alyona A. Gurina
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda A. Chalaya
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | - Nadezhda M. Zoteyeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), St. Petersburg 190000, Russia
| | | | | | | | | | | | - Emil E. Khavkin
- Institute of Agricultural Biotechnology, Moscow 127550, Russia
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37
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de Vries ME, Adams JR, Eggers EJ, Ying S, Stockem JE, Kacheyo OC, van Dijk LCM, Khera P, Bachem CW, Lindhout P, van der Vossen EAG. Converting Hybrid Potato Breeding Science into Practice. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020230. [PMID: 36678942 PMCID: PMC9861226 DOI: 10.3390/plants12020230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 05/27/2023]
Abstract
Research on diploid hybrid potato has made fast advances in recent years. In this review we give an overview of the most recent and relevant research outcomes. We define different components needed for a complete hybrid program: inbred line development, hybrid evaluation, cropping systems and variety registration. For each of these components the important research results are discussed and the outcomes and issues that merit further study are identified. We connect fundamental and applied research to application in a breeding program, based on the experiences at the breeding company Solynta. In the concluding remarks, we set hybrid breeding in a societal perspective, and we identify bottlenecks that need to be overcome to allow successful adoption of hybrid potato.
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Affiliation(s)
| | - James R. Adams
- Solynta, Wageningen 6703 HA, The Netherlands
- Institute of Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Ernst-jan Eggers
- Solynta, Wageningen 6703 HA, The Netherlands
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
| | - Su Ying
- Solynta, Wageningen 6703 HA, The Netherlands
| | - Julia E. Stockem
- Solynta, Wageningen 6703 HA, The Netherlands
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen 6700 AK, The Netherlands
| | - Olivia C. Kacheyo
- Solynta, Wageningen 6703 HA, The Netherlands
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen 6700 AK, The Netherlands
| | - Luuk C. M. van Dijk
- Solynta, Wageningen 6703 HA, The Netherlands
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen 6700 AK, The Netherlands
| | - Pawan Khera
- Solynta, Wageningen 6703 HA, The Netherlands
| | - Christian W. Bachem
- Solynta, Wageningen 6703 HA, The Netherlands
- Laboratory of Plant Breeding, Wageningen University & Research, Wageningen 6708 PB, The Netherlands
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38
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Shi J, Tian Z, Lai J, Huang X. Plant pan-genomics and its applications. MOLECULAR PLANT 2023; 16:168-186. [PMID: 36523157 DOI: 10.1016/j.molp.2022.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.
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Affiliation(s)
- Junpeng Shi
- State Key Laboratory of Biocontrol, School of Agriculture, Sun Yat-sen University, Shenzhen 518107, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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Usadel B. Solanaceae pangenomes are coming of graphical age to bring heritability back. ABIOTECH 2022; 3:233-236. [PMID: 36533266 PMCID: PMC9755766 DOI: 10.1007/s42994-022-00087-0] [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: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.
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Affiliation(s)
- Björn Usadel
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, Düsseldorf, Germany
- IBG-4 Bioinformatics, BioSC, Forschungszentrum Jülich, Jülich, Germany
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Herath V, Verchot J. Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato ( Solanum tuberosum L.). Int J Mol Sci 2022; 23:ijms232213795. [PMID: 36430273 PMCID: PMC9696714 DOI: 10.3390/ijms232213795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
We treated potato (Solanum tuberosum L.) plantlets with TM and performed gene expression studies to identify genome-wide changes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). An extensive network of responses was identified, including chromatin remodeling, transcriptional reprogramming, as well as changes in the structural components of the endomembrane network system. Limited genome-wide changes in alternative RNA splicing patterns of protein-coding transcripts were also discovered. Significant changes in RNA metabolism, components of the translation machinery, as well as factors involved in protein folding and maturation occurred, which included a broader set of genes than expected based on Arabidopsis research. Antioxidant defenses and oxygen metabolic enzymes are differentially regulated, which is expected of cells that may be experiencing oxidative stress or adapting to protect proteins from oxidation. Surges in protein kinase expression indicated early signal transduction events. This study shows early genomic responses including an array of differentially expressed genes that have not been reported in Arabidopsis. These data describe novel ER stress responses in a solanaceous host.
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Affiliation(s)
- Venura Herath
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA
- Correspondence: ; Tel.: +1-979-568-6369
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Chen W, Achakkagari SR, Strömvik M. Plastaumatic: Automating plastome assembly and annotation. FRONTIERS IN PLANT SCIENCE 2022; 13:1011948. [PMID: 36407635 PMCID: PMC9669643 DOI: 10.3389/fpls.2022.1011948] [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: 08/04/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Plastome sequence data is most often extracted from plant whole genome sequencing data and need to be assembled and annotated separately from the nuclear genome sequence. In projects comprising multiple genomes, it is labour intense to individually process the plastomes as it requires many steps and software. This study developed Plastaumatic - an automated pipeline for both assembly and annotation of plastomes, with the scope of the researcher being able to load whole genome sequence data with minimal manual input, and therefore a faster runtime. The main structure of the current automated pipeline includes trimming of adaptor and low-quality sequences using fastp, de novo plastome assembly using NOVOPlasty, standardization and quality checking of the assembled genomes through a custom script utilizing BLAST+ and SAMtools, annotation of the assembled genomes using AnnoPlast, and finally generating the required files for NCBI GenBank submissions. The pipeline is demonstrated with 12 potato accessions and three soybean accessions.
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42
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Solanum tuberosum (potato). Trends Genet 2022; 38:1193-1195. [PMID: 35820968 DOI: 10.1016/j.tig.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 01/24/2023]
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Wang F, Xia Z, Zou M, Zhao L, Jiang S, Zhou Y, Zhang C, Ma Y, Bao Y, Sun H, Wang W, Wang J. The autotetraploid potato genome provides insights into highly heterozygous species. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1996-2005. [PMID: 35767385 PMCID: PMC9491450 DOI: 10.1111/pbi.13883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 05/19/2023]
Abstract
Potato (Solanum tuberosum L.) originated in the Andes and evolved its vegetative propagation strategy through short day-dependent tuber development. Herein, we present a high-quality, chromosome-scale reference genome sequence of a tetraploid potato cultivar. The total length of this genome assembly was 2.67 Gb, with scaffold N50 and contig N50 sizes of 46.24 and 2.19 Mb, respectively. In total, 1.69 Gb repetitive sequences were obtained through de novo annotation, and long terminal repeats were the main transposable elements. A total of 126 070 protein-coding genes were annotated, of which 125 077 (99.21%) were located on chromosomes. The 48 chromosomes were classified into four haplotypes. We annotated 31 506 homologous genes, including 5913 (18.77%) genes with four homologues, 11 103 (35.24%) with three homologues, 12 177 (38.65%) with two homologues and 2313 (7.34%) with one homologue. MLH3, MSH6/7 and RFC3, which are the genes involved in the mismatch repair pathway, were found to be significantly expanded in the tetraploid potato genome relative to the diploid potato genome. Genome-wide association analysis revealed that cytochrome P450, flavonoid synthesis, chalcone enzyme, glycosyl hydrolase and glycosyl transferase genes were significantly correlated with the flesh colours of potato tuber in 150 tetraploid potatoes. This study provides valuable insights into the highly heterozygous autotetraploid potato genome and may facilitate the development of tools for potato cultivar breeding and further studies on autotetraploid crops.
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Affiliation(s)
- Fang Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Meiling Zou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Long Zhao
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
| | - Sirong Jiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yun Zhou
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Chenji Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Yongzhen Ma
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
| | - Yuting Bao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed LaboratorySanyaChina
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Haihong Sun
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
| | - Wenquan Wang
- College of Tropical Crops Hainan University, Hainan UniversityHaikouChina
| | - Jian Wang
- Academy of Agriculture and Forestry SciencesQinghai UniversityXiningChina
- National Key Laboratory of Sanjiangyuan Ecology and Plateau Agriculture and Animal HusbandryQinghai UniversityXiningChina
- Key Laboratory of Qinghai‐Tibet Plateau Biotechnology Ministry of EducationXiningChina
- Qinghai Provincial Key Laboratory of Potato BreedingXiningChina
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Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids. Int J Mol Sci 2022; 23:ijms231911406. [PMID: 36232706 PMCID: PMC9570356 DOI: 10.3390/ijms231911406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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Caraza-Harter MV, Endelman JB. The genetic architectures of vine and skin maturity in tetraploid potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2943-2951. [PMID: 35804168 DOI: 10.1007/s00122-022-04159-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The genetic architectures of potato vine and skin maturity, as well as the correlation between the traits, were investigated using multiple techniques from quantitative genetics and genomics. Potato vine and skin maturity, which refer to foliar senescence and adherence of the tuber periderm, respectively, are both important to production and therefore breeding. Our objective was to investigate the genetic architectures of these traits in a genome-wide association panel of 586 genotypes, and through joint linkage mapping in a half-diallel subset (N = 397). Skin maturity was measured by image analysis after mechanized harvest 120 days after planting. To correct for the influence of vine maturity on skin maturity under these conditions, the former was used as a covariate in the analysis. The genomic heritability based on a 10 K SNP array was 0.33 for skin maturity vs. 0.46 for vine maturity. Only minor QTLs were detected for skin maturity, the largest being on chromosome 9 and explaining 8% of the variation. As in many previous studies, S. tuberosum Cycling DOF Factor 1 (CDF1) had a large influence on vine maturity, explaining 33% of the variation in the panel as a bi-allelic SNP and 44% in the half-diallel as a multi-allelic QTL. From the estimated effects of the parental haplotypes in the half-diallel and prior knowledge of the allelic series for CDF1, the CDF1 allele for each haplotype was predicted and ultimately confirmed through whole-genome sequencing. The ability to connect statistical alleles from QTL models with biological alleles based on DNA sequencing represents a new milestone in genomics-assisted breeding for tetraploid species.
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Affiliation(s)
- Maria V Caraza-Harter
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Achakkagari SR, Kyriakidou M, Gardner KM, De Koeyer D, De Jong H, Strömvik MV, Tai HH. Genome sequencing of adapted diploid potato clones. FRONTIERS IN PLANT SCIENCE 2022; 13:954933. [PMID: 36003817 PMCID: PMC9394749 DOI: 10.3389/fpls.2022.954933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.
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Affiliation(s)
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Kyle M. Gardner
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - David De Koeyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Hielke De Jong
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Martina V. Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
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Jian H, Sun H, Liu R, Zhang W, Shang L, Wang J, Khassanov V, Lyu D. Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data. BMC PLANT BIOLOGY 2022; 22:381. [PMID: 35909124 PMCID: PMC9341072 DOI: 10.1186/s12870-022-03758-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Potato (Solanum tuberosum) is the fourth most important food crop in the world and plays an important role in food security. Drought stress has a significantly negative impact on potato growth and production. There are several publications involved drought stress in potato, this research contributes to enrich the knowledge. RESULTS In this study, next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technology were used to study the transcription profiles in potato in response to 20%PEG6000 simulates drought stress. The leaves of the variety "Désirée" from in vitro plantlets after drought stress at six time points from 0 to 48 hours were used to perform NGS and SMRT sequencing. According to the sequencing data, a total of 12,798 differentially expressed genes (DEGs) were identified in six time points. The real-time (RT)-PCR results are significantly correlated with the sequencing data, confirming the accuracy of the sequencing data. Gene ontology and KEGG analysis show that these DEGs participate in response to drought stress through galactose metabolism, fatty acid metabolism, plant-pathogen interaction, glutathione metabolism and other pathways. Through the analysis of alternative splicing of 66,888 transcripts, the functional pathways of these transcripts were enriched, and 51,098 transcripts were newly discovered from alternative splicing events and 47,994 transcripts were functionally annotated. Moreover, 3445 lncRNAs were predicted and enrichment analysis of corresponding target genes was also performed. Additionally, Alternative polyadenylation was analyzed by TADIS, and 26,153 poly (A) sites from 13,010 genes were detected in the Iso-Seq data. CONCLUSION Our research greatly enhanced potato drought-induced gene annotations and provides transcriptome-wide insights into the molecular basis of potato drought resistance.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715 China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, 400715 China
| | - Haonan Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Rongrong Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Wenzhe Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Lina Shang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715 China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, 400715 China
| | - Vadim Khassanov
- S. Seifullin Kazakh Agrotechnical University, Zhenis Avenue, 010011 Astana, Republic of Kazakhstan
| | - Dianqiu Lyu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing, 400715 China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing, 400715 China
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Rabanus-Wallace MT, Stein N. Why 2022 is a revolutionary year for potato genomics. MOLECULAR PLANT 2022; 15:1257-1259. [PMID: 35780297 DOI: 10.1016/j.molp.2022.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/19/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Affiliation(s)
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany; Center for Integrated Breeding Research, Georg-August-University Göttingen, 37075 Göttingen, Germany.
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Hosaka AJ, Sanetomo R, Hosaka K. A de novo genome assembly of Solanum verrucosum Schlechtendal, a Mexican diploid species geographically isolated from other diploid A-genome species of potato relatives. G3 GENES|GENOMES|GENETICS 2022; 12:6625657. [PMID: 35775942 PMCID: PMC9339273 DOI: 10.1093/g3journal/jkac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]
Abstract
There are over 100 known species of cultivated potatoes and their wild relatives. Many of these species, including cultivated potatoes, share the A genome; these species are mainly distributed in South America and are reproductively isolated from Mexican diploid species. The only diploid A-genome species distributed in Mexico is Solanum verrucosum Schlechtendal, which is also a maternal progenitor of Mexican polyploid species. In this study, we constructed a high-quality de novo assembly of the S. verrucosum genome using PacBio long-read sequencing and Hi-C scaffolding technologies. A monohaploid clone (2n = x = 12) of S. verrucosum was used to reduce assembly difficulty due to the heterozygous nature of the species. The final sequence assembly consisted of 780.2 Mb of sequence, 684.0 Mb of which were anchored to the 12 chromosomes, with a scaffold N50 of 55.2 Mb. Putative centromeres were identified using publicly available data obtained via chromatin immunoprecipitation sequencing against a centromere-specific histone 3 protein. Transposable elements accounted for approximately 61.8% (482.1 Mb) of the genome, and 46,904 genes were functionally annotated. High gene synteny and similarity were revealed among the genomes of S. verrucosum, Solanum commersonii, Solanum chacoense, Solanum phureja, Solanum tuberosum, and Solanum lycopersicum. The reference-quality S. verrucosum genome will provide new insights into the evolution of Mexican polyploid species and contribute to potato breeding programs.
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Affiliation(s)
| | - Rena Sanetomo
- Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Kazuyoshi Hosaka
- Corresponding author: Potato Germplasm Enhancement Laboratory, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan.
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50
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Bao Z, Li C, Li G, Wang P, Peng Z, Cheng L, Li H, Zhang Z, Li Y, Huang W, Ye M, Dong D, Cheng Z, VanderZaag P, Jacobsen E, Bachem CWB, Dong S, Zhang C, Huang S, Zhou Q. Genome architecture and tetrasomic inheritance of autotetraploid potato. MOLECULAR PLANT 2022; 15:1211-1226. [PMID: 35733345 DOI: 10.1016/j.molp.2022.06.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging the state-of-the-art sequencing technologies and polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting a distinct evolutionary trajectory of potato homologous centromeres. Furthermore, we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny, a feature of autopolyploid inheritance. By distinguishing maternal and paternal haplotype sets in C88, we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations, which were masked in the heterozygous condition by two parents. This study provides insights into the genomic architecture of autopolyploids and will guide their breeding.
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Affiliation(s)
- Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Canhui Li
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming 650500, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhen Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lin Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Zhiyang Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yuying Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wu Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingwang Ye
- Key Laboratory for Potato Biology of Yunnan Province, The CAAS-YNNU-YINMORE Joint Academy of Potato Science, Yunnan Normal University, Kunming 650500, China
| | - Daofeng Dong
- Vegetable Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Evert Jacobsen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Suomeng Dong
- Department of Plant Pathology and Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Qian Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Peng Cheng Laboratory, Shenzhen 518055, China.
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