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Tuttle HK, Del Rio AH, Bamberg JB, Shannon LM. Potato soup: analysis of cultivated potato gene bank populations reveals high diversity and little structure. FRONTIERS IN PLANT SCIENCE 2024; 15:1429279. [PMID: 39091313 PMCID: PMC11291250 DOI: 10.3389/fpls.2024.1429279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024]
Abstract
Cultivated potatoes are incredibly diverse, ranging from diploid to pentaploid and encompass four different species. They are adapted to disparate environments and conditions and carry unique alleles for resistance to pests and pathogens. Describing how diversity is partitioned within and among these populations is essential to understanding the potato genome and effectively utilizing landraces in breeding. This task is complicated by the difficulty of making comparisons across cytotypes and extensive admixture within section petota. We genotyped 730 accessions from the US Potato genebank including wild diploids and cultivated diploids and tetraploids using Genotype-by-sequencing. This data set allowed us to interrogate population structure and diversity as well as generate core subsets which will support breeders in efficiently screening genebank material for biotic and abiotic stress resistance alleles. We found that even controlling for ploidy, tetraploid material exhibited higher observed and expected heterozygosity than diploid accessions. In particular group chilotanum material was the most heterozygous and the only taxa not to exhibit any inbreeding. This may in part be because group chilotanum has a history of introgression not just from wild species, but landraces as well. All group chilotanum, exhibits introgression from group andigenum except clones from Southern South America near its origin, where the two groups are not highly differentiated. Moving north, we do not observe evidence for the same level of admixture back into group andigenum. This suggests that extensive history of admixture is a particular characteristic of chilotanum.
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Affiliation(s)
- Heather K. Tuttle
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Alfonso H. Del Rio
- U.S. Department of Agriculture (USDA)/Agricultural Research Service, Potato Genebank, Sturgeon Bay, WI, United States
| | - John B. Bamberg
- U.S. Department of Agriculture (USDA)/Agricultural Research Service, Potato Genebank, Sturgeon Bay, WI, United States
| | - Laura M. Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
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2
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Aalborg T, Sverrisdóttir E, Kristensen HT, Nielsen KL. The effect of marker types and density on genomic prediction and GWAS of key performance traits in tetraploid potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1340189. [PMID: 38525152 PMCID: PMC10957621 DOI: 10.3389/fpls.2024.1340189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Genomic prediction and genome-wide association studies are becoming widely employed in potato key performance trait QTL identifications and to support potato breeding using genomic selection. Elite cultivars are tetraploid and highly heterozygous but also share many common ancestors and generation-spanning inbreeding events, resulting from the clonal propagation of potatoes through seed potatoes. Consequentially, many SNP markers are not in a 1:1 relationship with a single allele variant but shared over several alleles that might exert varying effects on a given trait. The impact of such redundant "diluted" predictors on the statistical models underpinning genome-wide association studies (GWAS) and genomic prediction has scarcely been evaluated despite the potential impact on model accuracy and performance. We evaluated the impact of marker location, marker type, and marker density on the genomic prediction and GWAS of five key performance traits in tetraploid potato (chipping quality, dry matter content, length/width ratio, senescence, and yield). A 762-offspring panel of a diallel cross of 18 elite cultivars was genotyped by sequencing, and markers were annotated according to a reference genome. Genomic prediction models (GBLUP) were trained on four marker subsets [non-synonymous (29,553 SNPs), synonymous (31,229), non-coding (32,388), and a combination], and robustness to marker reduction was investigated. Single-marker regression GWAS was performed for each trait and marker subset. The best cross-validated prediction correlation coefficients of 0.54, 0.75, 0.49, 0.35, and 0.28 were obtained for chipping quality, dry matter content, length/width ratio, senescence, and yield, respectively. The trait prediction abilities were similar across all marker types, with only non-synonymous variants improving yield predictive ability by 16%. Marker reduction response did not depend on marker type but rather on trait. Traits with high predictive abilities, e.g., dry matter content, reached a plateau using fewer markers than traits with intermediate-low correlations, such as yield. The predictions were unbiased across all traits, marker types, and all marker densities >100 SNPs. Our results suggest that using non-synonymous variants does not enhance the performance of genomic prediction of most traits. The major known QTLs were identified by GWAS and were reproducible across exonic and whole-genome variant sets for dry matter content, length/width ratio, and senescence. In contrast, minor QTL detection was marker type dependent.
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Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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3
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Xie WZ, Zheng YY, He W, Bi F, Li Y, Dou T, Zhou R, Guo YX, Deng G, Zhang W, Yuan MH, Sanz-Jimenez P, Zhu XT, Xu XD, Zhou ZW, Zhou ZW, Feng JW, Liu S, Li C, Yang Q, Hu C, Gao H, Dong T, Dang J, Guo Q, Cai W, Zhang J, Yi G, Song JM, Sheng O, Chen LL. Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control. PLANT COMMUNICATIONS 2024; 5:100766. [PMID: 37974402 PMCID: PMC10873913 DOI: 10.1016/j.xplc.2023.100766] [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: 05/21/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Bananas (Musa spp.) are one of the world's most important fruit crops and play a vital role in food security for many developing countries. Most banana cultivars are triploids derived from inter- and intraspecific hybridizations between the wild diploid ancestor species Musa acuminate (AA) and M. balbisiana (BB). We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types, Plantain and Silk, and precisely characterize ancestral contributions by examining ancestry mosaics across the genome. Widespread asymmetric evolution is observed in their subgenomes, which can be linked to frequent homologous exchange events. We reveal the genetic makeup of triploid banana cultivars and verify that subgenome B is a rich source of disease resistance genes. Only 58.5% and 59.4% of Plantain and Silk genes, respectively, are present in all three haplotypes, with >50% of genes being differentially expressed alleles in different subgenomes. We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4 (Foc TR4), which confirms that Plantain can initiate defense responses faster than Silk. Additionally, we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk. Our study provides resources for better understanding the genomic architecture of cultivated bananas and has important implications for Musa genetics and breeding.
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Affiliation(s)
- Wen-Zhao Xie
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China; College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yu-Yu Zheng
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Weidi He
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Fangcheng Bi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Yaoyao Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tongxin Dou
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Run Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xiong Guo
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Wenhui Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Pablo Sanz-Jimenez
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Xin-Dong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zu-Wen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhi-Wei Zhou
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Wu Feng
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Siwen Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Qiaosong Yang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Chunhua Hu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Huijun Gao
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Tao Dong
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Jiangbo Dang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Qigao Guo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Jianwei Zhang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China.
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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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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5
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Noureen A, Khan MZ, Amin I, Zainab T, Mansoor S. CRISPR/Cas9-Mediated Targeting of Susceptibility Factor eIF4E-Enhanced Resistance Against Potato Virus Y. Front Genet 2022; 13:922019. [PMID: 35910230 PMCID: PMC9326172 DOI: 10.3389/fgene.2022.922019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important staple food around the world, and potato virus Y (PVY) is a major constraint for potato production. The VPg protein of PVY interacts with the translation initiation factor eIF4E of the host that works as a susceptibility factor during infection. The interaction between eIF4E and VPg was disrupted by CRISPR/Cas9. The homozygous conserved region of eIF4E of the potato variety “Kruda” was mutated by CRISPR/Cas9. Tracking of insertion, deletion, and conversion events was performed by Sanger sequencing with ∼15% editing efficiency. Truncated and mutated eIF4E proteins were unable to interact with VPg, and the virus was not able to exploit the host machinery for replication and systemic spreading. Mutated eIF4E lines showed enhanced resistance to PVYO strain. DAS-ELISA and RT-PCR were used for validation of the observed resistance. PVY resistance in tetraploid lines via CRISPR/Cas9 provides a route to develop novel resistant potato cultivars.
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Affiliation(s)
- Azka Noureen
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Tayyaba Zainab
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
- National Centre of Industrial Biotechnology (NCIB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
- *Correspondence: Tayyaba Zainab, ; Shahid Mansoor,
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- *Correspondence: Tayyaba Zainab, ; Shahid Mansoor,
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6
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Correr FH, Furtado A, Franco Garcia AA, Henry RJ, Rodrigues Alves Margarido G. Allele expression biases in mixed-ploid sugarcane accessions. Sci Rep 2022; 12:8778. [PMID: 35610293 PMCID: PMC9130122 DOI: 10.1038/s41598-022-12725-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Allele-specific expression (ASE) represents differences in the magnitude of expression between alleles of the same gene. This is not straightforward for polyploids, especially autopolyploids, as knowledge about the dose of each allele is required for accurate estimation of ASE. This is the case for the genomically complex Saccharum species, characterized by high levels of ploidy and aneuploidy. We used a Beta-Binomial model to test for allelic imbalance in Saccharum, with adaptations for mixed-ploid organisms. The hierarchical Beta-Binomial model was used to test if allele expression followed the expectation based on genomic allele dosage. The highest frequencies of ASE occurred in sugarcane hybrids, suggesting a possible influence of interspecific hybridization in these genotypes. For all accessions, genes showing ASE (ASEGs) were less frequent than those with balanced allelic expression. These genes were related to a broad range of processes, mostly associated with general metabolism, organelles, responses to stress and responses to stimuli. In addition, the frequency of ASEGs in high-level functional terms was similar among the genotypes, with a few genes associated with more specific biological processes. We hypothesize that ASE in Saccharum is largely a genotype-specific phenomenon, as a large number of ASEGs were exclusive to individual accessions.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil.,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Antonio Augusto Franco Garcia
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13418-900, Brazil. .,Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
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7
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Hoopes G, Meng X, Hamilton JP, Achakkagari SR, de Alves Freitas Guesdes F, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bornowski N, Bourke P, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, De Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursum RA, Vales MI, Vining K, Visser RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Strömvik MV, Tai HH, Usadel B, Buell CR, Finkers R. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. MOLECULAR PLANT 2022; 15:520-536. [PMID: 35026436 DOI: 10.1016/j.molp.2022.01.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/19/2021] [Accepted: 01/07/2022] [Indexed: 05/11/2023]
Abstract
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.
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Affiliation(s)
- Genevieve Hoopes
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Sai Reddy Achakkagari
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | | | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany
| | - Joseph J Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Danny Esselink
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natalie R Kaiser
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Bayer Crop Science, Woodland, CA 95695, USA
| | - Linda Kodde
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Brian Lavrijssen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natascha van Lieshout
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Rachel Shereda
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Heather K Tuttle
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Joshua C Wood
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Peter Bourke
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - David Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Herman J van Eck
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Dave Ellis
- International Potato Center, 1895 Avenida La Molina, Lima, Peru
| | | | - Kyle M Gardner
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Walter S De Jong
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1901, USA
| | - Joseph C Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Richard G Novy
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Stan Oome
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - Vidyasagar Sathuvalli
- Department of Crop and Soil Science, Oregon State University, Hermiston, OR 97838, USA
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall Orono, ME 04469, USA
| | - Remco A Ursum
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA
| | - Kelly Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jack Vossen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA
| | - Noelle L Anglin
- International Potato Center, 1895 Avenida La Molina, Lima, Peru; USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Christian W B Bachem
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura M Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - Martina V Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany; Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, 40225 Düsseldorf, Germany
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA.
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands.
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8
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Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar. Nat Genet 2022; 54:342-348. [PMID: 35241824 PMCID: PMC8920897 DOI: 10.1038/s41588-022-01015-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
Abstract
Potato is the most widely produced tuber crop worldwide. However, reconstructing the four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly of the potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing of 717 pollen genomes and Hi-C data. Unexpectedly, ~50% of the genome was identical-by-descent due to recent inbreeding, which was contrasted by highly abundant structural rearrangements involving ~20% of the genome. Among 38,214 genes, only 54% were present in all four haplotypes with an average of 3.2 copies per gene. Taking the leaf transcriptome as an example, 11% of the genes were differently expressed in at least one haplotype, where 25% of them were likely regulated through allele-specific DNA methylation. Our work sheds light on the recent breeding history of potato, the functional organization of its tetraploid genome and has the potential to strengthen the future of genomics-assisted breeding. Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the tetraploid genome and provides the potential for genomics-assisted breeding.
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9
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Margarido GRA, Correr FH, Furtado A, Botha FC, Henry RJ. Limited allele-specific gene expression in highly polyploid sugarcane. Genome Res 2022; 32:297-308. [PMID: 34949669 PMCID: PMC8805727 DOI: 10.1101/gr.275904.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/19/2021] [Indexed: 12/04/2022]
Abstract
Polyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole-genome level in the highly polyploid sugarcane genome. Very high depth whole-genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single-copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.
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Affiliation(s)
- Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
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10
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Amundson KR, Ordoñez B, Santayana M, Nganga ML, Henry IM, Bonierbale M, Khan A, Tan EH, Comai L. Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability. THE PLANT CELL 2021; 33:2149-2163. [PMID: 33792719 PMCID: PMC8364225 DOI: 10.1093/plcell/koab100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/26/2021] [Indexed: 05/03/2023]
Abstract
In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.
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Affiliation(s)
- Kirk R. Amundson
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- International Potato Center (CIP), Lima 15024, Peru
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, California 95616
| | | | - Mwaura Livingstone Nganga
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Isabelle M. Henry
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Merideth Bonierbale
- International Potato Center (CIP), Lima 15024, Peru
- Duquesa Business Centre, Malaga 29692, Spain
| | - Awais Khan
- International Potato Center (CIP), Lima 15024, Peru
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York 14456
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Luca Comai
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- Author for correspondence:
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11
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Modern Approaches for Transcriptome Analyses in Plants. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:11-50. [DOI: 10.1007/978-3-030-80352-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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Picart-Picolo A, Grob S, Picault N, Franek M, Llauro C, Halter T, Maier TR, Jobet E, Descombin J, Zhang P, Paramasivan V, Baum TJ, Navarro L, Dvořáčková M, Mirouze M, Pontvianne F. Large tandem duplications affect gene expression, 3D organization, and plant-pathogen response. Genome Res 2020; 30:1583-1592. [PMID: 33033057 PMCID: PMC7605254 DOI: 10.1101/gr.261586.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.
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Affiliation(s)
- Ariadna Picart-Picolo
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Stefan Grob
- Institute of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Nathalie Picault
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Christel Llauro
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Thierry Halter
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Tom R Maier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Edouard Jobet
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Julie Descombin
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
| | - Panpan Zhang
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | | | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Lionel Navarro
- ENS, IBENS, CNRS/INSERM, PSL Research University, 75005 Paris, France
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, 625 00 Brno, Czech Republic
| | - Marie Mirouze
- UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,IRD, UMR232 DIADE, 34394 Montpellier, France
| | - Frédéric Pontvianne
- CNRS, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France.,UPVD, LGDP UMR5096, Université de Perpignan, 66860 Perpignan, France
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13
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Pham GM, Hamilton JP, Wood JC, Burke JT, Zhao H, Vaillancourt B, Ou S, Jiang J, Buell CR. Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience 2020; 9:giaa100. [PMID: 32964225 PMCID: PMC7509475 DOI: 10.1093/gigascience/giaa100] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/26/2020] [Accepted: 09/05/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. FINDINGS Here, we present an updated version of the DM1-3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. CONCLUSIONS Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.
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Affiliation(s)
- Gina M Pham
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Joshua C Wood
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Joseph T Burke
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 2200 Osborne Dr, Ames, IA 50011, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 W. Circle Drive, East Lansing, MI 48824, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
- MSU AgBioResearch, Michigan State University, 446 W. Circle Drive, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
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14
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Su D, Chen L, Sun J, Zhang L, Gao R, Li Q, Han Y, Li Z. Comparative Chromosomal Localization of 45S and 5S rDNA Sites in 76 Purple-Fleshed Sweet Potato Cultivars. PLANTS 2020; 9:plants9070865. [PMID: 32650507 PMCID: PMC7412053 DOI: 10.3390/plants9070865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022]
Abstract
In recent years, the purple-fleshed sweet potato has attracted more attention because of its high nutritional value. The cytogenetics of this crop is relatively unexplored, limiting our knowledge on its genetic diversity. Therefore, we conducted cytogenetic analysis of 76 purple-fleshed sweet potato cultivars to analyze the chromosome structure and distribution of 45S and 5S rDNA. We noted that only 62 cultivars had 90 chromosomes, and the others were aneuploid with 88, 89, 91, or 92 chromosomes. The number of 45S rDNA in the 76 cultivars varied from 16 to 21; these sites showed different signal sizes and intensities and were localized at the chromosomal termini or satellite. The number of 5S rDNA was relatively stable; 74 cultivars showed six sites located at the chromosomal sub-terminal or near the centromere. Only the ‘Quanzishu 96’ and ‘Yuzixiang 10’ showed seven and five 5S rDNA sites, respectively. Additionally, both parent cultivars of ‘Quanzishu 96’ showed 18 45S and six 5S rDNA sites. Overall, our results indicate a moderate diversity in the distribution pattern of rDNAs. Our findings provide comprehensive cytogenetic information for the identification of sweet potato chromosomes, which can be useful for developing a high-quality germplasm resource.
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Affiliation(s)
- Dan Su
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Lei Chen
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Jianying Sun
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Luyue Zhang
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
| | - Runfei Gao
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Qiang Li
- Jiangsu Xuhuai Regional Xuzhou Institute of Agricultural Sciences/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences, Xuzhou 221100, China; (R.G.); (Q.L.)
| | - Yonghua Han
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
| | - Zongyun Li
- Institute of Integrative Plant Biology, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou 221100, China; (D.S.); (L.C.); (J.S.); (L.Z.)
- Correspondence: (Y.H.); (Z.L.); Tel.: +86-0516-8350-0083 (Y.H. & Z.L.)
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15
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Amundson KR, Ordoñez B, Santayana M, Tan EH, Henry IM, Mihovilovich E, Bonierbale M, Comai L. Genomic Outcomes of Haploid Induction Crosses in Potato ( Solanum tuberosum L.). Genetics 2020; 214:369-380. [PMID: 31871130 PMCID: PMC7017018 DOI: 10.1534/genetics.119.302843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/09/2019] [Indexed: 01/12/2023] Open
Abstract
The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.
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Affiliation(s)
- Kirk R Amundson
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology and Genome Center, University of California, Davis, California 95616
- International Potato Center (CIP), Lima 12, Peru
| | | | - Ek Han Tan
- Plant Biology and Genome Center, University of California, Davis, California 95616
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Isabelle M Henry
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | | | | | - Luca Comai
- Plant Biology and Genome Center, University of California, Davis, California 95616
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16
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Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes (Basel) 2019; 10:E671. [PMID: 31480756 PMCID: PMC6770967 DOI: 10.3390/genes10090671] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 01/16/2023] Open
Abstract
Arabidopsis thaliana is one of the best studied plant model organisms. Besides cultivation in greenhouses, cells of this plant can also be propagated in suspension cell culture. At7 is one such cell line that was established about 25 years ago. Here, we report the sequencing and the analysis of the At7 genome. Large scale duplications and deletions compared to the Columbia-0 (Col-0) reference sequence were detected. The number of deletions exceeds the number of insertions, thus indicating that a haploid genome size reduction is ongoing. Patterns of small sequence variants differ from the ones observed between A. thaliana accessions, e.g., the number of single nucleotide variants matches the number of insertions/deletions. RNA-Seq analysis reveals that disrupted alleles are less frequent in the transcriptome than the native ones.
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Affiliation(s)
- Boas Pucker
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany.
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Ralf Stracke
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Sequenz 1, 33615 Bielefeld, NRW, Germany
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17
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Lauer S, Gresham D. An evolving view of copy number variants. Curr Genet 2019; 65:1287-1295. [PMID: 31076843 DOI: 10.1007/s00294-019-00980-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 01/08/2023]
Abstract
Copy number variants (CNVs) are regions of the genome that vary in integer copy number. CNVs, which comprise both amplifications and deletions of DNA sequence, have been identified across all domains of life, from bacteria and archaea to plants and animals. CNVs are an important source of genetic diversity, and can drive rapid adaptive evolution and progression of heritable and somatic human diseases, such as cancer. However, despite their evolutionary importance and clinical relevance, CNVs remain understudied compared to single-nucleotide variants (SNVs). This is a consequence of the inherent difficulties in detecting CNVs at low-to-intermediate frequencies in heterogeneous populations of cells. Here, we discuss molecular methods used to detect CNVs, the limitations associated with using these techniques, and the application of new and emerging technologies that present solutions to these challenges. The goal of this short review and perspective is to highlight aspects of CNV biology that are understudied and define avenues for further research that address specific gaps in our knowledge of these complex alleles. We describe our recently developed method for CNV detection in which a fluorescent gene functions as a single-cell CNV reporter and present key findings from our evolution experiments in Saccharomyces cerevisiae. Using a CNV reporter, we found that CNVs are generated at a high rate and undergo selection with predictable dynamics across independently evolving replicate populations. Many CNVs appear to be generated through DNA replication-based processes that are mediated by the presence of short, interrupted, inverted-repeat sequences. Our results have important implications for the role of CNVs in evolutionary processes and the molecular mechanisms that underlie CNV formation. We discuss the possible extension of our method to other applications, including tracking the dynamics of CNVs in models of human tumors.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - David Gresham
- Center for Genomics and System Biology, Department of Biology, New York University, New York, NY, USA.
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18
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Nadakuduti SS, Starker CG, Voytas DF, Buell CR, Douches DS. Genome Editing in Potato with CRISPR/Cas9. Methods Mol Biol 2019; 1917:183-201. [PMID: 30610637 DOI: 10.1007/978-1-4939-8991-1_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cultivated potato, Solanum tuberosum Group Tuberosum L. (2n = 4x = 48) is a heterozygous tetraploid crop that is clonally propagated, thereby resulting in identical genotypes. Due to the lack of sexual reproduction and its concomitant segregation of alleles, genetic engineering is an efficient way of introducing crop improvement traits in potato. In recent years, genome-editing via the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system for targeted genome modifications has emerged as the most powerful method due to the ease in designing and construction of gene-specific single guide RNA (sgRNA) vectors. These sgRNA vectors are easily reprogrammable to direct Streptococcus pyogenes Cas9 (SpCas9) to generate double stranded breaks (DSBs) in the target genomes that are then repaired by the cell via the error-prone non-homologous end-joining (NHEJ) pathway or by precise homologous recombination (HR) pathway. CRISPR/Cas9 technology has been successfully implemented in potato for targeted mutagenesis to generate knockout mutations (by means of NHEJ) as well as gene targeting to edit an endogenous gene (by HR). In this chapter, we describe procedures for designing sgRNAs, protocols to clone sgRNAs for CRISPR/Cas9 constructs to generate knockouts, design of donor repair templates and use geminivirus replicons (GVRs) to facilitate gene-editing by HR in potato. We also describe tissue culture procedures in potato for Agrobacterium-mediated transformation to generate gene-edited events along with their molecular characterization.
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Affiliation(s)
- Satya Swathi Nadakuduti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Michigan State University AgBioResearch, Michigan State University, East Lansing, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, USA
| | - David S Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
- Michigan State University AgBioResearch, Michigan State University, East Lansing, MI, USA
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19
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Tengkun N, Dongdong W, Xiaohui M, Yue C, Qin C. Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data. FRONTIERS IN PLANT SCIENCE 2019; 10:603. [PMID: 31156673 PMCID: PMC6527903 DOI: 10.3389/fpls.2019.00603] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/24/2019] [Indexed: 05/18/2023]
Abstract
The accumulation of secondary metabolites, such as anthocyanins, in cells plays an important role in colored plants. The synthesis and accumulation of anthocyanins are regulated by multiple genes, of which the R2R3-MYB transcription factor gene family plays an important role. Based on the genomic data in the Potato Genome Sequencing Consortium database (PGSC) and the transcriptome data in the SRA, this study used potato as a model plant to comprehensively analyze the plant anthocyanin accumulation process. The results indicated that the most critical step in the synthesis of potato anthocyanins was the formation of p-coumaroyl-CoA to enter the flavonoid biosynthetic pathway. The up-regulated expression of the CHS gene and the down-regulated expression of HCT significantly promoted this process. At the same time, the anthocyanins in the potato were gradually synthesized during the process from leaf transport to tubers. New transcripts of stAN1 and PAL were cloned and named stAN1-like and PAL-like, respectively, but the functions of these two new transcripts still need further study. In addition, the sequence characteristics of amino acids in the R2-MYB and R3-MYB domains of potato were preliminarily identified. The aims of this study are to identify the crucial major genes that affect anthocyanin biosynthesis through multi-omics joint analysis and to transform quantitative traits into quality traits, which provides a basis and reference for the regulation of plant anthocyanin biosynthesis. Simultaneously, this study provides the basis for improving the anthocyanin content in potato tubers and the cultivation of new potato varieties with high anthocyanin content.
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Affiliation(s)
- Nie Tengkun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Nie Tengkun, Chen Yue, Chen Qin,
| | - Wang Dongdong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ma Xiaohui
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Chen Yue
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Nie Tengkun, Chen Yue, Chen Qin,
| | - Chen Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Food Science and Engineering, Northwest A&F University, Yangling, China
- *Correspondence: Nie Tengkun, Chen Yue, Chen Qin,
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20
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Wu S, Lau KH, Cao Q, Hamilton JP, Sun H, Zhou C, Eserman L, Gemenet DC, Olukolu BA, Wang H, Crisovan E, Godden GT, Jiao C, Wang X, Kitavi M, Manrique-Carpintero N, Vaillancourt B, Wiegert-Rininger K, Yang X, Bao K, Schaff J, Kreuze J, Gruneberg W, Khan A, Ghislain M, Ma D, Jiang J, Mwanga ROM, Leebens-Mack J, Coin LJM, Yencho GC, Buell CR, Fei Z. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nat Commun 2018; 9:4580. [PMID: 30389915 PMCID: PMC6214957 DOI: 10.1038/s41467-018-06983-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/05/2018] [Indexed: 02/08/2023] Open
Abstract
Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops due to a lack of genomic and genetic resources and inherent challenges in breeding a heterozygous, clonally propagated polyploid. Here, we report the genome sequences of its two diploid relatives, I. trifida and I. triloba, and show that these high-quality genome assemblies are robust references for hexaploid sweetpotato. Comparative and phylogenetic analyses reveal insights into the ancient whole-genome triplication history of Ipomoea and evolutionary relationships within the Batatas complex. Using resequencing data from 16 genotypes widely used in African breeding programs, genes and alleles associated with carotenoid biosynthesis in storage roots are identified, which may enable efficient breeding of varieties with high provitamin A content. These resources will facilitate genome-enabled breeding in this important food security crop.
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Affiliation(s)
- Shan Wu
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Kin H Lau
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Qinghe Cao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, Jiangsu, 221131, China
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Honghe Sun
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chenxi Zhou
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Lauren Eserman
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Department of Conservation and Research, Atlanta Botanical Garden, Atlanta, GA, 30309, USA
| | | | - Bode A Olukolu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Haiyan Wang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Grant T Godden
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chen Jiao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Mercy Kitavi
- International Potato Center, Nairobi, 00603, Kenya
| | | | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Xinsun Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer Schaff
- Genomic Sciences Laboratory, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jan Kreuze
- International Potato Center, Lima 12, Peru
| | | | - Awais Khan
- International Potato Center, Lima 12, Peru
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY, 14456, USA
| | | | - Daifu Ma
- Jiangsu Xuzhou Sweetpotato Research Center, Xuzhou, Jiangsu, 221131, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, 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.
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21
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Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L, Pham GM, Jiang J, Douches DS, Jansky SH, Buell CR. Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:562-570. [PMID: 29405524 DOI: 10.1111/tpj.13857] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 05/21/2023]
Abstract
Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.
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Affiliation(s)
- Courtney P Leisner
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Emily Crisovan
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Norma C Manrique-Carpintero
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Alexandre P Marand
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gina M Pham
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David S Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Shelley H Jansky
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- United States Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI, 53706, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
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22
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Manrique-Carpintero NC, Coombs JJ, Pham GM, Laimbeer FPE, Braz GT, Jiang J, Veilleux RE, Buell CR, Douches DS. Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2018; 9:944. [PMID: 30018631 PMCID: PMC6037889 DOI: 10.3389/fpls.2018.00944] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/12/2018] [Indexed: 05/18/2023]
Abstract
The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance.
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Affiliation(s)
- Norma C. Manrique-Carpintero
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Joseph J. Coombs
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Gina M. Pham
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | | | - Guilherme T. Braz
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | | | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
| | - David S. Douches
- Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- *Correspondence: David S. Douches
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