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Mascher M, Jayakodi M, Shim H, Stein N. Promises and challenges of crop translational genomics. Nature 2024:10.1038/s41586-024-07713-5. [PMID: 39313530 DOI: 10.1038/s41586-024-07713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/13/2024] [Indexed: 09/25/2024]
Abstract
Crop translational genomics applies breeding techniques based on genomic datasets to improve crops. Technological breakthroughs in the past ten years have made it possible to sequence the genomes of increasing numbers of crop varieties and have assisted in the genetic dissection of crop performance. However, translating research findings to breeding applications remains challenging. Here we review recent progress and future prospects for crop translational genomics in bringing results from the laboratory to the field. Genetic mapping, genomic selection and sequence-assisted characterization and deployment of plant genetic resources utilize rapid genotyping of large populations. These approaches have all had an impact on breeding for qualitative traits, where single genes with large phenotypic effects exert their influence. Characterization of the complex genetic architectures that underlie quantitative traits such as yield and flowering time, especially in newly domesticated crops, will require further basic research, including research into regulation and interactions of genes and the integration of genomic approaches and high-throughput phenotyping, before targeted interventions can be designed. Future priorities for translation include supporting genomics-assisted breeding in low-income countries and adaptation of crops to changing environments.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle, Germany.
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2
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Qu L, Huang X, Su X, Zhu G, Zheng L, Lin J, Wang J, Xue H. Potato: from functional genomics to genetic improvement. MOLECULAR HORTICULTURE 2024; 4:34. [PMID: 39160633 PMCID: PMC11331666 DOI: 10.1186/s43897-024-00105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024]
Abstract
Potato is the most widely grown non-grain crop and ranks as the third most significant global food crop following rice and wheat. Despite its long history of cultivation over vast areas, slow breeding progress and environmental stress have led to a scarcity of high-yielding potato varieties. Enhancing the quality and yield of potato tubers remains the ultimate objective of potato breeding. However, conventional breeding has faced challenges due to tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression. Recent advancements in molecular biology and functional genomic studies of potato have provided valuable insights into the regulatory network of physiological processes and facilitated trait improvement. In this review, we present a summary of identified factors and genes governing potato growth and development, along with progress in potato genomics and the adoption of new breeding technologies for improvement. Additionally, we explore the opportunities and challenges in potato improvement, offering insights into future avenues for potato research.
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Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xueqing Huang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Su
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guoqing Zhu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Lin
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiawen Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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Chen G, Shi G, Dai Y, Zhao R, Wu Q. Graph-Based Pan-Genome Reveals the Pattern of Deleterious Mutations during the Domestication of Saccharomyces cerevisiae. J Fungi (Basel) 2024; 10:575. [PMID: 39194902 DOI: 10.3390/jof10080575] [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: 04/29/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 08/29/2024] Open
Abstract
The "cost of domestication" hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used Saccharomyces cerevisiae, the world's oldest domesticated fungus, as a model to investigate the genomic characteristics of deleterious variants arising from fungal domestication. Employing a graph-based pan-genome approach, we identified 1,297,761 single nucleotide polymorphisms (SNPs), 278,147 insertion/deletion events (indels; <30 bp), and 19,967 non-redundant structural variants (SVs; ≥30 bp) across 687 S. cerevisiae isolates. Comparing these variants with synonymous SNPs (sSNPs) as neutral controls, we found that the majority of the derived nonsynonymous SNPs (nSNPs), indels, and SVs were deleterious. Heterozygosity was positively correlated with the impact of deleterious SNPs, suggesting a role of genetic diversity in mitigating their effects. The domesticated isolates exhibited a higher additive burden of deleterious SNPs (dSNPs) than the wild isolates, but a lower burden of indels and SVs. Moreover, the domesticated S. cerevisiae showed reduced rates of adaptive evolution relative to the wild S. cerevisiae. In summary, deleterious variants tend to be heterozygous, which may mitigate their harmful effects, but they also constrain breeding potential. Addressing deleterious alleles and minimizing the genetic load are crucial considerations for future S. cerevisiae breeding efforts.
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Affiliation(s)
- Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guohui Shi
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Dai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruilin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Xu X, Xu Y, Che J, Han X, Wang Z, Wang X, Zhang Q, Li X, Zhang Q, Xiao J, Li X, Zhang Q, Ouyang Y. The genetic basis and process of inbreeding depression in an elite hybrid rice. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1727-1738. [PMID: 38679669 DOI: 10.1007/s11427-023-2547-2] [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: 12/15/2023] [Accepted: 02/02/2024] [Indexed: 05/01/2024]
Abstract
Inbreeding depression refers to the reduced performance arising from increased homozygosity, a phenomenon that is the reverse of heterosis and exists among plants and animals. As a natural self-pollinated crop with strong heterosis, the mechanism of inbreeding depression in rice is largely unknown. To understand the genetic basis of inbreeding depression, we constructed a successive inbreeding population from the F2 to F4 generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each generation. The expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle, 11 for primary branches, and 12 for secondary branches, and these loci constitute the main correlation between heterosis and inbreeding depression. However, the genetic basis of inbreeding depression is also distinct from that of heterosis, such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected depression. Noticeably, two-locus interactions may change the extent and direction of the depression effects of the target loci, and overall interactions would promote inbreeding depression among generations. Using an F2:3 variation population, the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after inbreeding. We found inconsistent or various degrees of background depression from the F2 to F3 generation assuming different genotypes of the target locus, which may affect the actual depression effect of the locus due to epistasis. The results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms, which expand our understanding of the whole-genome architecture of inbreeding depression.
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Affiliation(s)
- Xiaodong Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yawen Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Che
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Han
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhengji Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianmeng Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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Aalborg T, Nielsen KL. To be or not to be tetraploid-the impact of marker ploidy on genomic prediction and GWAS of potato. FRONTIERS IN PLANT SCIENCE 2024; 15:1386837. [PMID: 39139728 PMCID: PMC11319270 DOI: 10.3389/fpls.2024.1386837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/10/2024] [Indexed: 08/15/2024]
Abstract
Cultivated potato, Solanum tuberosum L., is considered an autotetraploid with 12 chromosomes with four homologous phases. However, recent evidence found that, due to frequent large phase deletions in the genome, gene ploidy is not constant across the genome. The elite cultivar "Otava" was found to have an average gene copy number of 3.2 across all loci. Breeding programs for elite potato cultivars rely increasingly on genomic prediction tools for selection breeding and elucidation of quantitative trait loci underpinning trait genetic variance. These are typically based on anonymous single nucleotide polymorphism (SNP) markers, which are usually called from, for example, SNP array or sequencing data using a tetraploid model. In this study, we analyzed the impact of using whole genome markers genotyped as either tetraploid or observed allele frequencies from genotype-by-sequencing data on single-trait additive genomic best linear unbiased prediction (GBLUP) genomic prediction (GP) models and single-marker regression genome-wide association studies of potato to evaluate the implications of capturing varying ploidy on the statistical models employed in genomic breeding. A panel of 762 offspring of a diallel cross of 18 parents of elite breeding material was used for modeling. These were genotyped by sequencing and phenotyped for five key performance traits: chipping quality, length/width ratio, senescence, dry matter content, and yield. We also estimated the read coverage required to confidently discriminate between a heterozygous triploid and tetraploid state from simulated data. It was found that using a tetraploid model neither impaired nor improved genomic predictions compared to using the observed allele frequencies that account for true marker ploidy. In genome-wide associations studies (GWAS), very minor variations of both signal amplitude and number of SNPs supporting both minor and major quantitative trait loci (QTLs) were observed between the two data sets. However, all major QTLs were reproducible using both data sets.
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Affiliation(s)
- Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kåre Lehmann Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Research and Development, Kartoffelmelcentralen (KMC) Amba, Brande, Denmark
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Eggers EJ, Su Y, van der Poel E, Flipsen M, de Vries ME, Bachem CWB, Visser RGF, Lindhout P. Identification, Elucidation and Deployment of a Cytoplasmic Male Sterility System for Hybrid Potato. BIOLOGY 2024; 13:447. [PMID: 38927327 PMCID: PMC11200408 DOI: 10.3390/biology13060447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Recent advances in diploid F1 hybrid potato breeding rely on the production of inbred lines using the S-locus inhibitor (Sli) gene. As a result of this method, female parent lines are self-fertile and require emasculation before hybrid seed production. The resulting F1 hybrids are self-fertile as well and produce many undesirable berries in the field. Utilization of cytoplasmic male sterility would eliminate the need for emasculation, resulting in more efficient hybrid seed production and male sterile F1 hybrids. We observed plants that completely lacked anthers in an F2 population derived from an interspecific cross between diploid S. tuberosum and S. microdontum. We studied the antherless trait to determine its suitability for use in hybrid potato breeding. We mapped the causal locus to the short arm of Chromosome 6, developed KASP markers for the antherless (al) locus and introduced it into lines with T and A cytoplasm. We found that antherless type male sterility is not expressed in T and A cytoplasm, proving that it is a form of CMS. We hybridized male sterile al/al plants with P cytoplasm with pollen from al/al plants with T and A cytoplasm and we show that the resulting hybrids set significantly fewer berries in the field. Here, we show that the antherless CMS system can be readily deployed in diploid F1 hybrid potato breeding to improve hybridization efficiency and reduce berry set in the field.
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Affiliation(s)
- Ernst-Jan Eggers
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
- Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Ying Su
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
| | - Esmee van der Poel
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Martijn Flipsen
- Hogeschool Arnhem Nijmegen, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands
| | | | - Christian W. B. Bachem
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Pim Lindhout
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
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Sood S, Bhardwaj V, Mangal V, Kardile H, Dipta B, Kumar A, Singh B, Siddappa S, Sharma AK, Dalamu, Buckseth T, Chaudhary B, Kumar V, Pandey N. Development of near homozygous lines for diploid hybrid TPS breeding in potatoes. Heliyon 2024; 10:e31507. [PMID: 38831819 PMCID: PMC11145485 DOI: 10.1016/j.heliyon.2024.e31507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Diploid inbred-based F1 hybrid True Potato Seed (DHTPS) breeding is a novel technique to transform potato breeding and cultivation across the globe. Significant efforts are being made to identify elite diploids, dihaploids and develop diploid inbred lines for heterosis exploitation in potatoes. Self-incompatibility is the first obstacle for developing inbred lines in diploid potatoes, which necessitates the introgression of a dominant S locus inhibitor gene (Sli) for switching self-incompatibility to self-compatibility. We evaluated a set of 357 diploid clones in different selfing generations for self-compatibility and degree of homozygosity using Kompetitive Allele Specific PCR (KASP) Single Nucleotide Polymorphism (SNP) markers. A subset of 10 KASP markers of the Sli candidate region on chromosome 12 showed an association with the phenotype for self-compatibility. The results revealed that the selected 10 KASP markers for the Sli gene genotype could be deployed for high throughput rapid screening of self-compatibility in diploid populations and to identify new sources of self-compatibility. The homozygosity assessed through 99 KASP markers distributed across all the chromosomes of the potato genome was 20-78 % in founder diploid clones, while different selfing generations, i.e., S0, S1, S2 and S3 observed 36.1-80.4, 56.9-82.8, 59.5-85.4 and 73.7-87.8 % average homozygosity, respectively. The diploid plants with ∼80 % homozygosity were also observed in the first selfing generation, which inferred that homozygosity assessment in the early generations itself could identify the best plants with high homozygosity to speed up the generation of diploid inbred lines.
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Affiliation(s)
- Salej Sood
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Hemant Kardile
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Ashwani Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Baljeet Singh
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | | | | | - Dalamu
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - Babita Chaudhary
- ICAR-Central Potato Research Institute, Regional Station, Modipuram, UP, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
| | - N.K. Pandey
- ICAR-Central Potato Research Institute, Shimla, HP, 171001, India
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Lavanchy E, Weir BS, Goudet J. Detecting inbreeding depression in structured populations. Proc Natl Acad Sci U S A 2024; 121:e2315780121. [PMID: 38687793 PMCID: PMC11087799 DOI: 10.1073/pnas.2315780121] [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: 09/13/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024] Open
Abstract
Measuring inbreeding and its consequences on fitness is central for many areas in biology including human genetics and the conservation of endangered species. However, there is no consensus on the best method, neither for quantification of inbreeding itself nor for the model to estimate its effect on specific traits. We simulated traits based on simulated genomes from a large pedigree and empirical whole-genome sequences of human data from populations with various sizes and structures (from the 1,000 Genomes project). We compare the ability of various inbreeding coefficients ([Formula: see text]) to quantify the strength of inbreeding depression: allele-sharing, two versions of the correlation of uniting gametes which differ in the weight they attribute to each locus and two identical-by-descent segments-based estimators. We also compare two models: the standard linear model and a linear mixed model (LMM) including a genetic relatedness matrix (GRM) as random effect to account for the nonindependence of observations. We find LMMs give better results in scenarios with population or family structure. Within the LMM, we compare three different GRMs and show that in homogeneous populations, there is little difference among the different [Formula: see text] and GRM for inbreeding depression quantification. However, as soon as a strong population or family structure is present, the strength of inbreeding depression can be most efficiently estimated only if i) the phenotypes are regressed on [Formula: see text] based on a weighted version of the correlation of uniting gametes, giving more weight to common alleles and ii) with the GRM obtained from an allele-sharing relatedness estimator.
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Affiliation(s)
- Eléonore Lavanchy
- Department of Ecology and Evolution, University of Lausanne, Lausanne1015, Switzerland
- Population Genetics and Genomics group, Swiss Institute of Bioinformatics, University of Lausanne, LausanneCH-1015, Switzerland
| | - Bruce S. Weir
- Department of Biostatistics, University of Washington, SeattleWA98195
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne1015, Switzerland
- Population Genetics and Genomics group, Swiss Institute of Bioinformatics, University of Lausanne, LausanneCH-1015, Switzerland
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9
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Ames M, Hamernik A, Behling W, Douches DS, Halterman DA, Bethke PC. A survey of the Sli gene in wild and cultivated potato. PLANT DIRECT 2024; 8:e589. [PMID: 38766508 PMCID: PMC11099725 DOI: 10.1002/pld3.589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/27/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Inbred-hybrid breeding of diploid potatoes necessitates breeding lines that are self-compatible. One way of incorporating self-compatibility into incompatible cultivated potato (Solanum tuberosum) germplasm is to introduce the S-locus inhibitor gene (Sli), which functions as a dominant inhibitor of gametophytic self-incompatibility. To learn more about Sli diversity and function in wild species relatives of cultivated potato, we obtained Sli gene sequences that extended from the 5'UTR to the 3'UTR from 133 individuals from 22 wild species relatives of potato and eight diverse cultivated potato clones. DNA sequence alignment and phylogenetic trees based on genomic and protein sequences show that there are two highly conserved groups of Sli sequences. DNA sequences in one group contain the 533 bp insertion upstream of the start codon identified previously in self-compatible potato. The second group lacks the insertion. Three diploid and four polyploid individuals of wild species collected from geographically disjointed localities contained Sli with the 533 bp insertion. For most of the wild species clones examined, however, Sli did not have the insertion. Phylogenetic analysis indicated that Sli sequences with the insertion, in wild species and in cultivated clones, trace back to a single origin. Some diploid wild potatoes that have Sli with the insertion were self-incompatible and some wild potatoes that lack the insertion were self-compatible. Although there is evidence of positive selection for some codon positions in Sli, there is no evidence of diversifying selection at the gene level. In silico analysis of Sli protein structure did not support the hypothesis that amino acid changes from wild-type (no insertion) to insertion-type account for changes in protein function. Our study demonstrated that genetic factors besides the Sli gene must be important for conditioning a switch in the mating system from self-incompatible to self-compatible in wild potatoes.
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Affiliation(s)
- Mercedes Ames
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Andy Hamernik
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - William Behling
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - David S. Douches
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Dennis A. Halterman
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
| | - Paul C. Bethke
- US Department of Agriculture, Agricultural Research Service, Vegetable Crops Research Unit, Department of HorticultureUniversity of WisconsinMadisonWisconsinUSA
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10
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Zhang L, Duan Y, Zhang Z, Zhang L, Chen S, Cai C, Duan S, Zhang K, Li G, Cheng F. OcBSA: An NGS-based bulk segregant analysis tool for outcross populations. MOLECULAR PLANT 2024; 17:648-657. [PMID: 38369755 DOI: 10.1016/j.molp.2024.02.011] [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: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.
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Affiliation(s)
- Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zewei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoguang Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangcun Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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11
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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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12
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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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13
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Barragan AC, Collenberg M, Schwab R, Kersten S, Kerstens MHL, Požárová D, Bezrukov I, Bemm F, Kolár F, Weigel D. Deleterious phenotypes in wild Arabidopsis arenosa populations are common and linked to runs of homozygosity. G3 (BETHESDA, MD.) 2024; 14:jkad290. [PMID: 38124484 PMCID: PMC10917499 DOI: 10.1093/g3journal/jkad290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
In this study, we aimed to systematically assess the frequency at which potentially deleterious phenotypes appear in natural populations of the outcrossing model plant Arabidopsis arenosa, and to establish their underlying genetics. For this purpose, we collected seeds from wild A. arenosa populations and screened over 2,500 plants for unusual phenotypes in the greenhouse. We repeatedly found plants with obvious phenotypic defects, such as small stature and necrotic or chlorotic leaves, among first-generation progeny of wild A. arenosa plants. Such abnormal plants were present in about 10% of maternal sibships, with multiple plants with similar phenotypes in each of these sibships, pointing to a genetic basis of the observed defects. A combination of transcriptome profiling, linkage mapping and genome-wide runs of homozygosity patterns using a newly assembled reference genome indicated a range of underlying genetic architectures associated with phenotypic abnormalities. This included evidence for homozygosity of certain genomic regions, consistent with alleles that are identical by descent being responsible for these defects. Our observations suggest that deleterious alleles with different genetic architectures are segregating at appreciable frequencies in wild A. arenosa populations.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- The Sainsbury Laboratory, Norwich NR4 7UH, UK
| | - Maximilian Collenberg
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Catalent, 73614 Schorndorf, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Institute of Plant Breeding, University of Hohenheim, 70599 Stuttgart, Germany
| | - Merijn H L Kerstens
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Department of Plant Developmental Biology, Wageningen University and Research, 6708 PB, Wageningen, Netherlands
| | - Doubravka Požárová
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
- The MAMA AI, 100 00 Prague, Czech Republic
| | - Ilja Bezrukov
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Felix Bemm
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
- KWS Saat, 37574 Einbeck, Germany
| | - Filip Kolár
- Department of Botany, Faculty of Science, Charles University, 128 01 Prague, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
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14
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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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15
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Zhu L, Li F, Xie T, Li Z, Tian T, An X, Wei X, Long Y, Jiao Z, Wan X. Receptor-like kinases and their signaling cascades for plant male fertility: loyal messengers. THE NEW PHYTOLOGIST 2024; 241:1421-1434. [PMID: 38174365 DOI: 10.1111/nph.19527] [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: 10/01/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
Receptor-like kinases (RLKs) are evolved for plant cell-cell communications. The typical RLK protein contains an extracellular and hypervariable N-terminus to perceive various signals, a transmembrane domain to anchor into plasma membrane, and a cytoplasmic, highly conserved kinase domain to phosphorylate target proteins. To date, RLKs have manifested their significance in a myriad of biological processes during plant reproductive growth, especially in male fertility. This review first summarizes a recent update on RLKs and their interacting protein partners controlling anther and pollen development, pollen release from dehisced anther, and pollen function during pollination and fertilization. Then, regulatory networks of RLK signaling pathways are proposed. In addition, we predict RLKs in maize and rice genome, obtain homologs of well-studied RLKs from phylogeny of three subfamilies and then analyze their expression patterns in developing anthers of maize and rice to excavate potential RLKs regulating male fertility in crops. Finally, current challenges and future prospects regarding RLKs are discussed. This review will contribute to a better understanding of plant male fertility control by RLKs, creating potential male sterile lines, and inspiring innovative crop breeding methods.
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Affiliation(s)
- Lei Zhu
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Fan Li
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tianle Xie
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Ziwen Li
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Tian Tian
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
| | - Xueli An
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Yan Long
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
| | - Ziwei Jiao
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Zhongzhi International Institute of Agricultural Biosciences, Shunde Innovation School, University of Science and Technology Beijing, Beijing, 100083, China
- Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining, 835000, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Beijing Solidwill Sci-Tech Co. Ltd, Beijing, 100192, China
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16
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Li D, Lu X, Qian D, Wang P, Tang D, Zhong Y, Shang Y, Guo H, Wang Z, Zhu G, Zhang C. Dissected Leaf 1 encodes an MYB transcription factor that controls leaf morphology in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:183. [PMID: 37555965 DOI: 10.1007/s00122-023-04430-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE The transcription factor StDL1 regulates dissected leaf formation in potato and the genotype frequency of recessive Stdl1/Stdl1, which results in non-dissected leaves, has increased in cultivated potatoes. Leaf morphology is a key trait of plants, influencing plant architecture, photosynthetic efficiency and yield. Potato (Solanum tuberosum L.), the third most important food crop worldwide, has a diverse leaf morphology. However, despite the recent identification of several genes regulating leaf formation in other plants, few genes involved in potato leaf development have been reported. In this study, we identified an R2R3 MYB transcription factor, Dissected Leaf 1 (StDL1), regulating dissected leaf formation in potato. A naturally occurring allele of this gene, Stdl1, confers non-dissected leaves in young seedlings. Knockout of StDL1 in a diploid potato changes the leaf morphology from dissected to non-dissected. Experiments in N. benthamiana and yeast show that StDL1 is a transcriptional activator. Notably, by calculating the genotype frequency of the Stdl1/Stdl1 in 373-potato accessions, we found that it increases significantly in cultivated potatoes. This work reveals the genetic basis of dissected leaf formation in potato and provides insights into plant leaf morphology.
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Affiliation(s)
- Dawei Li
- 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
| | - Xiaoyue Lu
- 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
| | - Duoduo Qian
- 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
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518120, China
| | - Pei Wang
- 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
| | - Dié Tang
- 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
| | - Yang Zhong
- 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
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhen Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Chunzhi Zhang
- 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.
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17
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Sun S, Wang B, Li C, Xu G, Yang J, Hufford MB, Ross-Ibarra J, Wang H, Wang L. Unraveling Prevalence and Effects of Deleterious Mutations in Maize Elite Lines across Decades of Modern Breeding. Mol Biol Evol 2023; 40:msad170. [PMID: 37494285 PMCID: PMC10414807 DOI: 10.1093/molbev/msad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Future breeding is likely to involve the detection and removal of deleterious alleles, which are mutations that negatively affect crop fitness. However, little is known about the prevalence of such mutations and their effects on phenotypic traits in the context of modern crop breeding. To address this, we examined the number and frequency of deleterious mutations in 350 elite maize inbred lines developed over the past few decades in China and the United States. Our findings reveal an accumulation of weakly deleterious mutations and a decrease in strongly deleterious mutations, indicating the dominant effects of genetic drift and purifying selection for the two types of mutations, respectively. We also discovered that slightly deleterious mutations, when at lower frequencies, were more likely to be heterozygous in the developed hybrids. This is consistent with complementation as a potential explanation for heterosis. Subsequently, we found that deleterious mutations accounted for more of the variation in phenotypic traits than nondeleterious mutations with matched minor allele frequencies, especially for traits related to leaf angle and flowering time. Moreover, we detected fewer deleterious mutations in the promoter and gene body regions of differentially expressed genes across breeding eras than in nondifferentially expressed genes. Overall, our results provide a comprehensive assessment of the prevalence and impact of deleterious mutations in modern maize breeding and establish a useful baseline for future maize improvement efforts.
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Affiliation(s)
- Shichao Sun
- 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, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Li 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, China
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, China
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18
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Ortiz R, Reslow F, Vetukuri R, García-Gil MR, Pérez-Rodríguez P, Crossa J. Inbreeding Effects on the Performance and Genomic Prediction for Polysomic Tetraploid Potato Offspring Grown at High Nordic Latitudes. Genes (Basel) 2023; 14:1302. [PMID: 37372482 DOI: 10.3390/genes14061302] [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: 05/27/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
Inbreeding depression (ID) is caused by increased homozygosity in the offspring after selfing. Although the self-compatible, highly heterozygous, tetrasomic polyploid potato (Solanum tuberosum L.) suffers from ID, some argue that the potential genetic gains from using inbred lines in a sexual propagation system of potato are too large to be ignored. The aim of this research was to assess the effects of inbreeding on potato offspring performance under a high latitude and the accuracy of the genomic prediction of breeding values (GEBVs) for further use in selection. Four inbred (S1) and two hybrid (F1) offspring and their parents (S0) were used in the experiment, with a field layout of an augmented design with the four S0 replicated in nine incomplete blocks comprising 100, four-plant plots at Umeå (63°49'30″ N 20°15'50″ E), Sweden. S0 was significantly (p < 0.01) better than both S1 and F1 offspring for tuber weight (total and according to five grading sizes), tuber shape and size uniformity, tuber eye depth and reducing sugars in the tuber flesh, while F1 was significantly (p < 0.01) better than S1 for all tuber weight and uniformity traits. Some F1 hybrid offspring (15-19%) had better total tuber yield than the best-performing parent. The GEBV accuracy ranged from -0.3928 to 0.4436. Overall, tuber shape uniformity had the highest GEBV accuracy, while tuber weight traits exhibited the lowest accuracy. The F1 full sib's GEBV accuracy was higher, on average, than that of S1. Genomic prediction may facilitate eliminating undesired inbred or hybrid offspring for further use in the genetic betterment of potato.
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Affiliation(s)
- Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE 23436 Lomma, Sweden
- Umeå Plant Science Center, SLU Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE 90183 Umeå, Sweden
| | - Fredrik Reslow
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE 23436 Lomma, Sweden
| | - Ramesh Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), SE 23436 Lomma, Sweden
| | - M Rosario García-Gil
- Umeå Plant Science Center, SLU Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), SE 90183 Umeå, Sweden
| | | | - José Crossa
- Colegio de Postgraduados (COLPOS), Montecillos 56230, Edo. de México, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco 56237, Edo. de México, Mexico
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Jiang X, Li D, Du H, Wang P, Guo L, Zhu G, Zhang C. Genomic features of meiotic crossovers in diploid potato. HORTICULTURE RESEARCH 2023; 10:uhad079. [PMID: 37323232 PMCID: PMC10261879 DOI: 10.1093/hr/uhad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Meiotic recombination plays an important role in genome evolution and crop improvement. Potato (Solanum tuberosum L.) is the most important tuber crop in the world, but research about meiotic recombination in potato is limited. Here, we resequenced 2163 F2 clones derived from five different genetic backgrounds and identified 41 945 meiotic crossovers. Some recombination suppression in euchromatin regions was associated with large structural variants. We also detected five shared crossover hotspots. The number of crossovers in each F2 individual from the accession Upotato 1 varied from 9 to 27, with an average of 15.5, 78.25% of which were mapped within 5 kb of their presumed location. We show that 57.1% of the crossovers occurred in gene regions, with poly-A/T, poly-AG, AT-rich, and CCN repeats enriched in the crossover intervals. The recombination rate is positively related with gene density, SNP density, Class II transposon, and negatively related with GC density, repeat sequence density and Class I transposon. This study deepens our understanding of meiotic crossovers in potato and provides useful information for diploid potato breeding.
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Affiliation(s)
- Xiuhan Jiang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- 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
| | - Dawei 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, Guangdong 518120, China
| | - Hui Du
- 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
| | - 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, Guangdong 518120, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, Yunnan 650500, China
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20
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Lee S, Enciso-Rodriguez FE, Behling W, Jayakody T, Panicucci K, Zarka D, Nadakuduti SS, Buell CR, Manrique-Carpintero NC, Douches DS. HT-B and S-RNase CRISPR-Cas9 double knockouts show enhanced self-fertility in diploid Solanum tuberosum. FRONTIERS IN PLANT SCIENCE 2023; 14:1151347. [PMID: 37324668 PMCID: PMC10264808 DOI: 10.3389/fpls.2023.1151347] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023]
Abstract
The Gametophytic Self-Incompatibility (GSI) system in diploid potato (Solanum tuberosum L.) poses a substantial barrier in diploid potato breeding by hindering the generation of inbred lines. One solution is gene editing to generate self-compatible diploid potatoes which will allow for the generation of elite inbred lines with fixed favorable alleles and heterotic potential. The S-RNase and HT genes have been shown previously to contribute to GSI in the Solanaceae family and self-compatible S. tuberosum lines have been generated by knocking out S-RNase gene with CRISPR-Cas9 gene editing. This study employed CRISPR-Cas9 to knockout HT-B either individually or in concert with S-RNase in the diploid self-incompatible S. tuberosum clone DRH-195. Using mature seed formation from self-pollinated fruit as the defining characteristic of self-compatibility, HT-B-only knockouts produced little or no seed. In contrast, double knockout lines of HT-B and S-RNase displayed levels of seed production that were up to three times higher than observed in the S-RNase-only knockout, indicating a synergistic effect between HT-B and S-RNase in self-compatibility in diploid potato. This contrasts with compatible cross-pollinations, where S-RNase and HT-B did not have a significant effect on seed set. Contradictory to the traditional GSI model, self-incompatible lines displayed pollen tube growth reaching the ovary, yet ovules failed to develop into seeds indicating a potential late-acting self-incompatibility in DRH-195. Germplasm generated from this study will serve as a valuable resource for diploid potato breeding.
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Affiliation(s)
- Sarah Lee
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - William Behling
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Thilani Jayakody
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Kaela Panicucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Daniel Zarka
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | | | - C. Robin Buell
- Department of Crop and Soil Sciences, Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Norma C. Manrique-Carpintero
- Alliance of Bioversity International and The International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - David S. Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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21
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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: 15] [Impact Index Per Article: 15.0] [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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22
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Forbes E, Wulff-Vester AK, Hvoslef-Eide T(A. Will genetically modified late blight resistant potatoes be the first GM crops to be approved for commercial growing in Norway? FRONTIERS IN PLANT SCIENCE 2023; 14:1137598. [PMID: 36938038 PMCID: PMC10014530 DOI: 10.3389/fpls.2023.1137598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Last decade's advances in biotechnology, with the introduction of CRISPR, have challenged the regulatory framework for competent authorities all over the world. Hence, regulatory issues related to gene editing are currently high on the agenda both in the EU and in the European Economic Area (EEA) Agreement country of Norway, particularly with regards to sustainable agriculture. During the negotiations on the EEA Agreement, Norway was allowed to retain three extra aims in the Gene Technology Act: "That the production and use of GMO happens in an ethical way, is beneficial to society and is in accordance with the principle of sustainable development". We argue the case that taking sustainability into the decisions on regulating gene edited products could be easier in Norway than in the EU because of these extra aims. Late blight is our chosen example, as a devastating disease in potato that is controlled in Norway primarily by high levels of fungicide use. Also, many of these fungicides are being banned due to negative environmental and health effects. The costs of controlling late blight in Norway were calculated in 2006, and since then there have been new cultivars developed, inflation and an outbreak of war in Europe increasing farm input costs. A genetically modified (GM) cisgenic late blight resistant (LBR) potato presents a possible solution that could reduce fungicide use, but this could still be controversial. This paper aims to discuss the advantages and disadvantages of approving the commercial use of a GM LBR potato cultivar in Norway and compare these against currently used late blight management methods and conventional potato resistance breeding. We argue that a possible route for future regulatory framework could build upon the proposal by the Norwegian Biotechnology Advisory Board from 2019, also taking sustainability goals into account. This could favour a positive response from the Competent Authorities without breeching the European Economic Area (EEA) Agreement. Perhaps the EU could adopt a similar approach to fulfil their obligations towards a more sustainable agriculture?
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Nicolao R, Gaiero P, Castro CM, Heiden G. Solanum malmeanum, a promising wild relative for potato breeding. FRONTIERS IN PLANT SCIENCE 2023; 13:1046702. [PMID: 36891130 PMCID: PMC9986444 DOI: 10.3389/fpls.2022.1046702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Crop wild relatives are gaining increasing attention. Their use in plant breeding is essential to broaden the genetic basis of crops as well as to meet industrial demands, for global food security and sustainable production. Solanum malmeanum (Solanum sect. Petota, Solanaceae) is a wild relative of potatoes (S. tuberosum) from Southern South America, occurring in Argentina, Brazil, Paraguay and Uruguay. This wild potato has been largely mistaken for or historically considered as conspecific with S. commersonii. Recently, it was reinstated at the species level. Retrieving information on its traits and applied uses is challenging, because the species name has not always been applied correctly and also because species circumscriptions and morphological criteria applied to recognize it have not been consistent. To overcome these difficulties, we performed a thorough literature reference survey, herbaria specimens' identification revision and genebank database queries to review and update the information available on this potato wild relative, contributing to an increase in research on it to fully understand and explore its potential for potato breeding. Scarce studies have been carried out concerning its reproductive biology, resistance against pests and diseases as well as tolerance to abiotic stresses and evaluation of quality traits. The scattered information available makes it less represented in genebanks and genetic studies are missing. We compile, update and present available information for S. malmeanum on taxonomy, geographical distribution, ecology, reproductive biology, relationship with its closest relatives, biotic and abiotic stresses resistance and quality traits and discuss ways to overcome sexual barriers of hybridization and future perspectives for its use in potato breeding. As a final remark, we highlight that this species' potential uses have been neglected and must be unlocked. Thus, further studies on morphological and genetic variability with molecular tools are fundamental for an efficient conservation and applied use of this promising genetic resource.
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Affiliation(s)
- Rodrigo Nicolao
- Programa de Pós-Graduação em Agronomia/Fitomelhoramento - Universidade Federal de Pelotas (UFPel), Pelotas, RS, Brazil
| | - Paola Gaiero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Caroline M. Castro
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
| | - Gustavo Heiden
- Laboratório de Recursos Genéticos, Embrapa Clima Temperado, Pelotas, RS, Brazil
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Li C, Long Y, Lu M, Zhou J, Wang S, Xu Y, Tan X. Gene coexpression analysis reveals key pathways and hub genes related to late-acting self-incompatibility in Camellia oleifera. FRONTIERS IN PLANT SCIENCE 2023; 13:1065872. [PMID: 36762174 PMCID: PMC9902722 DOI: 10.3389/fpls.2022.1065872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Self-incompatibility (SI) is an important strategy for plants to maintain abundant variation to enhance their adaptability to the environment. Camellia oleifera is one of the most important woody oil plants and is widely cultivated in China. Late acting self-incompatibility (LSI) in C. oleifera results in a relatively poor fruit yield in the natural state, and understanding of the LSI mechanism remains limited. METHODS To better understand the molecular expression and gene coexpression network in the LSI reaction in C. oleifera, we conducted self- and cross-pollination experiments at two different flower bud developmental stages (3-4 d before flowering and 1 d before flowering), and cytological observation, fruit setting rate (FSR) investigation and RNA-Seq analysis were performed to investigate the mechanism of the male -female interaction and identify hub genes responsible for the LSI in C. oleifera. RESULTS Based on the 21 ovary transcriptomes, a total of 7669 DEGs were identified after filtering out low-expression genes. Weighted gene coexpression network analysis (WGCNA) divided the DEGs into 15 modules. Genes in the blue module (1163 genes) were positively correlated with FSR, and genes in the pink module (339 genes) were negatively correlated with FSR. KEGG analysis indicated that flavonoid biosynthesis, plant MAPK signaling pathways, ubiquitin-mediated proteolysis, and plant-pathogen interaction were the crucial pathways for the LSI reaction. Fifty four transcription factors (TFs) were obtained in the two key modules, and WRKY and MYB were potentially involved in the LSI reaction in C. oleifera. Network establishment indicated that genes encoding G-type lectin S-receptor-like serine (lecRLK), isoflavone 3'-hydroxylase-like (CYP81Q32), cytochrome P450 87A3-like (CYP87A3), and probable calcium-binding protein (CML41) were the hub genes that positively responded to the LSI reaction. The other DEGs inside the two modules, including protein RALF-like 10 (RALF), F-box and pectin acetylesterase (MTERF5), might also play vital roles in the LSI reaction in C. oleifera. DISCUSSION Overall, our study provides a meaningful resource for gene network studies of the LSI reaction process and subsequent analyses of pollen-pistil interactions and TF roles in the LSI reaction, and it also provides new insights for exploring the mechanisms of the LSI response.
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Affiliation(s)
- Chang Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
| | - Yi Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
| | - Mengqi Lu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
| | - Junqin Zhou
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
| | - Sen Wang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- The Belt and Road International Union Research Center for Tropical Arid Non-wood Forest in Hunan Province, Changsha, China
| | - Yan Xu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
| | - Xiaofeng Tan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, China
- Academy of Camellia Oil Tree, Central South University of Forestry and Technology, Changsha, China
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25
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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: 6] [Impact Index Per Article: 6.0] [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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Identification of quantitative trait loci for growth traits in red swamp crayfish (Procambarus clarkii). AQUACULTURE AND FISHERIES 2023. [DOI: 10.1016/j.aaf.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Tuncel A, Qi Y. CRISPR/Cas mediated genome editing in potato: Past achievements and future directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111474. [PMID: 36174801 DOI: 10.1016/j.plantsci.2022.111474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/29/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Genome engineering has been re-shaping plant biotechnology and agriculture. Crop improvement using the recently developed gene editing techniques is now easier, faster, and more precise than ever. Although considered to be a global food security crop, potato has not benefitted enough from diverse collection of these techniques. Unique genetic features of cultivated potatoes such as tetrasomic inheritance, high genomic heterozygosity, and inbreeding depression hamper conventional breeding of this important crop. Therefore, genome editing provides an excellent arsenal of tools for trait improvement in potato. Moreover, using specific transformation protocols, it is possible to engineer transgene free commercial varieties. In this review we first describe the past achievements in potato genome editing and highlight some of the missing aspects of these efforts. Then, we discuss about technical challenges of genome editing in potato and present approaches to overcome these difficulties. Finally, we talk about genome editing applications that have not been explored in potato and point out some of the missing venues in literature.
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Affiliation(s)
- Aytug Tuncel
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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28
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Wang N, Song X, Ye J, Zhang S, Cao Z, Zhu C, Hu J, Zhou Y, Huang Y, Cao S, Liu Z, Wu X, Chai L, Guo W, Xu Q, Gaut BS, Koltunow AMG, Zhou Y, Deng X. Structural variation and parallel evolution of apomixis in citrus during domestication and diversification. Natl Sci Rev 2022; 9:nwac114. [PMID: 36415319 PMCID: PMC9671666 DOI: 10.1093/nsr/nwac114] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 09/02/2023] Open
Abstract
Apomixis, or asexual seed formation, is prevalent in Citrinae via a mechanism termed nucellar or adventitious embryony. Here, multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for growth. Whilst nucellar embryony enables the propagation of clonal plants of maternal genetic constitution, it is also a barrier to effective breeding through hybridization. To address the genetics and evolution of apomixis in Citrinae, a chromosome-level genome of the Hongkong kumquat (Fortunella hindsii) was assembled following a genome-wide variation map including structural variants (SVs) based on 234 Citrinae accessions. This map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection, which may explain the capability of nucellar embryony in most cultivars during Citrinae diversification. Analyses revealed that parallel evolution may explain the repeated origin of apomixis in different genera of Citrinae. Within Fortunella, we found that apomixis of some varieties originated via introgression. In apomictic Fortunella, the locus associated with apomixis contains the FhRWP gene, encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in Citrus. We found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus and Fortunella, due to either two or three miniature inverted transposon element (MITE) insertions. A transcription factor, FhARID, encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties, which facilitates induction of nucellar embryogenesis. This study provides evolutionary genomic and molecular insights into apomixis in Citrinae and has potential ramifications for citrus breeding.
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Affiliation(s)
- Nan Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xietian Song
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Siqi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhen Cao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Chenqiao Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Jianbing Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Yin Zhou
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Shuo Cao
- 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 518124, China
| | - Zhongjie Liu
- 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 518124, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Anna M G Koltunow
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Yongfeng 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 518124, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
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29
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Li N, Zhang X, Sun X, Zhu S, Cheng Y, Liu M, Gao S, Zhang J, Wang Y, Yang X, Chen J, Li F, He Q, Zeng Z, Yuan X, Zhou Z, Ma L, Wang T, Li X, Liu H, Pan Y, Zhou M, Gao C, Zhou G, Han Z, Liu S, Su J, Cheng Z, Tian S, Liu T. Genomic insights into the evolutionary history and diversification of bulb traits in garlic. Genome Biol 2022; 23:188. [PMID: 36071507 PMCID: PMC9450234 DOI: 10.1186/s13059-022-02756-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown. Results Here we report a comprehensive map of garlic genomic variation, consisting of amazingly 129.4 million variations. Evolutionary analysis indicates that the garlic population diverged at least 100,000 years ago, and the two groups cultivated in China were domesticated from two independent routes. Consequently, 15.0 and 17.5% of genes underwent an expression change in two cultivated groups, causing a reshaping of their transcriptomic architecture. Furthermore, we find independent domestication leads to few overlaps of deleterious substitutions in these two groups due to separate accumulation and selection-based removal. By analysis of selective sweeps, genome-wide trait associations and associated transcriptomic analysis, we uncover differential selections for the bulb traits in these two garlic groups during their domestication. Conclusions This study provides valuable resources for garlic genomics-based breeding, and comprehensive insights into the evolutionary history of this clonal-propagated crop. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02756-1.
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Affiliation(s)
- Ningyang Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Shandong Agricultural University, Tai'an, 271018, China
| | - Xueyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiudong Sun
- Shandong Agricultural University, Tai'an, 271018, China
| | - Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yi Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Meng Liu
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Song Gao
- Shandong Agricultural University, Tai'an, 271018, China.,Yangzhou University, Yangzhou, 225009, China
| | - Jiangjiang Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China
| | | | - Fu Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zheng Zeng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaoge Yuan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Zhiman Zhou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Longchuan Ma
- Shandong Dongyun Research Center of garlic Engineering, JinXiang, 272200, China
| | - Taotao Wang
- Shandong Dongyun Research Center of garlic Engineering, JinXiang, 272200, China
| | - Xiang Li
- Shandong Agricultural University, Tai'an, 271018, China
| | - Hanqiang Liu
- Northwest A&F University, Yangling, 712100, China
| | - Yupeng Pan
- Northwest A&F University, Yangling, 712100, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Chunsheng Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Zhenlin Han
- University of Hawaii at Manoa, Honolulu, 96822, USA
| | - Shiqi Liu
- Shandong Agricultural University, Tai'an, 271018, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Zhihui Cheng
- Northwest A&F University, Yangling, 712100, China.
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, 100083, China.
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China. .,Industrial Research Institute of garlic (IBFC-Jinxiang), Jinxiang, 272200, China.
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30
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Construction of homozygous diploid potato through maternal haploid induction. ABIOTECH 2022; 3:163-168. [PMID: 36304841 PMCID: PMC9590536 DOI: 10.1007/s42994-022-00080-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/25/2022] [Indexed: 11/02/2022]
Abstract
Reinventing the tetraploid potato into a seed-propagated, diploid, hybrid potato would significantly accelerate potato breeding. In this regard, the development of highly homozygous inbred lines is a prerequisite for breeding hybrid potatoes, but self-incompatibility and inbreeding depression present challenges for developing pure inbred lines. To resolve this impediment, we developed a doubled haploid (DH) technology, based on mutagenesis of the potato DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (StDMP) gene. Here, we show that a deficiency in StDMP allows the generation of maternal haploids for generating diploid potato lines. An exercisable protocol, involving hybridization, fluorescent marker screening, molecular and flow cytometric identification, and doubling with colchicine generates nearly 100% homozygous diploid potato lines. This dmp-triggered haploid induction (HI) system greatly shortens the breeding process and offers a robust method for generating diploid potato inbred lines with high purity. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-022-00080-7.
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31
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Zheng H, Ma J, Huang W, Di H, Xia X, Ma W, Ma J, Yang J, Li X, Lian H, Huang Z, Tang Y, Zheng Y, Li H, Zhang F, Sun B. Physiological and Comparative Transcriptome Analysis Reveals the Mechanism by Which Exogenous 24-Epibrassinolide Application Enhances Drought Resistance in Potato (Solanum tuberosum L.). Antioxidants (Basel) 2022; 11:antiox11091701. [PMID: 36139774 PMCID: PMC9495798 DOI: 10.3390/antiox11091701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
Drought stress is a key factor limiting the growth and tuber yield of potatoes (Solanum tuberosum L.). Brassinosteroids (BRs) have been shown to alleviate drought stress in several plant species; however, little is known about the physiological and molecular mechanisms by which BRs enhance drought resistance in potatoes. Here, we characterized changes in the physiology and transcriptome of the tetraploid potato variety ‘Xuanshu-2′ in response to drought stress after 24-epibrassinolide (EBR) pretreatment. The abscisic acid (ABA) content, photosynthetic capacity, and the activities of antioxidant enzymes were increased; the intercellular CO2 concentration, relative conductivity, reactive oxygen species, malondialdehyde, proline, and soluble sugar content were decreased after EBR pretreatment compared with plants under drought stress. Transcriptome analysis revealed 1330 differently expressed genes (DEGs) involved in the response to drought stress after EBR pretreatment. DEGs were enriched in plant hormone signal transduction, starch and sucrose metabolism, circadian rhythm, flavonoid biosynthesis, and carotenoid biosynthesis. DEGs associated with the BR signaling and biosynthesis pathways, as well as ABA metabolic pathways were identified. Our findings provide new insights into the mechanisms by which BRs enhance the drought resistance of potatoes.
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Affiliation(s)
- Hao Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Ma
- Bijie lnstitution of Agricultural Science, Bijie 551700, China
| | - Wenli Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongmei Di
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xue Xia
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Ma
- Bijie lnstitution of Agricultural Science, Bijie 551700, China
| | - Jun Ma
- Bijie lnstitution of Agricultural Science, Bijie 551700, China
| | - Jiao Yang
- Bijie lnstitution of Agricultural Science, Bijie 551700, China
| | - Xiaomei Li
- Rice and Sorghum Research Institue, Sichuan Academy of Agricultural Sciences, Deyang 618000, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan, Chengdu 610300, China
| | - Huashan Lian
- School of Agriculture and Horticulture, Chengdu Agricultural College, Chengdu 611130, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (F.Z.); (B.S.); Tel.: +86-28-86291840 (F.Z.); +86-28-86291848 (B.S.)
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (F.Z.); (B.S.); Tel.: +86-28-86291840 (F.Z.); +86-28-86291848 (B.S.)
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32
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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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33
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Tang D, Jia Y, Zhang J, Li H, Cheng L, Wang P, Bao Z, Liu Z, Feng S, Zhu X, Li D, Zhu G, Wang H, Zhou Y, Zhou Y, Bryan GJ, Buell CR, Zhang C, Huang S. Genome evolution and diversity of wild and cultivated potatoes. Nature 2022; 606:535-541. [PMID: 35676481 PMCID: PMC9200641 DOI: 10.1038/s41586-022-04822-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/28/2022] [Indexed: 12/21/2022]
Abstract
Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and the vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have the potential to revolutionize future potato breeding and production1-4. So far, relatively few studies have examined the genome evolution and diversity of wild and cultivated landrace potatoes, which limits the application of their diversity in potato breeding. Here we assemble 44 high-quality diploid potato genomes from 24 wild and 20 cultivated accessions that are representative of Solanum section Petota, the tuber-bearing clade, as well as 2 genomes from the neighbouring section, Etuberosum. Extensive discordance of phylogenomic relationships suggests the complexity of potato evolution. We find that the potato genome substantially expanded its repertoire of disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative of the effect of tuber-based propagation strategies on the evolution of the potato genome. We discover a transcription factor that determines tuber identity and interacts with the mobile tuberization inductive signal SP6A. We also identify 561,433 high-confidence structural variants and construct a map of large inversions, which provides insights for improving inbred lines and precluding potential linkage drag, as exemplified by a 5.8-Mb inversion that is associated with carotenoid content in tubers. This study will accelerate hybrid potato breeding and enrich our understanding of the evolution and biology of potato as a global staple food crop.
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Affiliation(s)
- Dié Tang
- 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, China
| | - Yuxin Jia
- 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, China
| | - Jinzhe Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 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, China.,Graduate School Experimental Plant Sciences, Laboratory of Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - 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, 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, China
| | - 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, China
| | - Zhihong Liu
- 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, China
| | - Shuangshuang Feng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijian Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Dawei 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, China
| | - Guangtao Zhu
- The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, China
| | - Hongru Wang
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Yao 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, China
| | - Yongfeng 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, China
| | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, UK
| | - C Robin Buell
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - 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, 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, China.
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34
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Huang X, Huang S, Han B, Li J. The integrated genomics of crop domestication and breeding. Cell 2022; 185:2828-2839. [PMID: 35643084 DOI: 10.1016/j.cell.2022.04.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 12/13/2022]
Abstract
As a major event in human civilization, wild plants were successfully domesticated to be crops, largely owing to continuing artificial selection. Here, we summarize new discoveries made during the past decade in crop domestication and breeding. The construction of crop genome maps and the functional characterization of numerous trait genes provide foundational information. Approaches to read, interpret, and write complex genetic information are being leveraged in many plants for highly efficient de novo or re-domestication. Understanding the underlying mechanisms of crop microevolution and applying the knowledge to agricultural productions will give possible solutions for future challenges in food security.
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Affiliation(s)
- Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - 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, Guangdong 518120, China.
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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35
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Kardile HB, Yilma S, Sathuvalli V. Molecular Approaches to Overcome Self-Incompatibility in Diploid Potatoes. PLANTS 2022; 11:plants11101328. [PMID: 35631752 PMCID: PMC9143039 DOI: 10.3390/plants11101328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
There has been an increased interest in true potato seeds (TPS) as planting material because of their advantages over seed tubers. TPS produced from a tetraploid heterozygous bi-parental population produces non-uniform segregating progenies, which have had limited uniformity in yield and quality in commercial cultivation, and, thus, limited success. Inbreeding depression and self-incompatibility hamper the development of inbred lines in both tetraploid and diploid potatoes, impeding hybrid development efforts. Diploid potatoes have gametophytic self-incompatibility (SI) controlled by S-locus, harboring the male-dependent S-locus F-box (SLF/SFB) and female-dependent Stylar-RNase (S-RNase). Manipulation of these genes using biotechnological tools may lead to loss of self-incompatibility. Self-compatibility can also be achieved by the introgression of S-locus inhibitor (Sli) found in the self-compatible (SC) natural mutants of Solanum chacoense. The introgression of Sli through conventional breeding methods has gained much success. Recently, the Sli gene has been cloned from diverse SC diploid potato lines. It is expressed gametophytically and can overcome the SI in different diploid potato genotypes through conventional breeding or transgenic approaches. Interestingly, it has a 533 bp insertion in its promoter elements, a MITE transposon, making it a SC allele. Sli gene encodes an F-box protein PP2-B10, which consists of an F-box domain linked to a lectin domain. Interaction studies have revealed that the C-terminal region of Sli interacts with most of the StS-RNases, except StS-RNase 3, 9, 10, and 13, while full-length Sli cannot interact with StS-RNase 3, 9, 11, 13, and 14. Thus, Sli may play an essential role in mediating the interactions between pollen and stigma and function like SLFs to interact with and detoxify the S-RNases during pollen tube elongation to confer SC to SI lines. These advancements have opened new avenues in the diploid potato hybrid.
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Affiliation(s)
- Hemant Balasaheb Kardile
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
- Division of Crop Improvement and Seed Technology, ICAR-Central Potato Research Institute, Shimla 171001, Himachal Pradesh, India
| | - Solomon Yilma
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
| | - Vidyasagar Sathuvalli
- Department of Crop and Soil Science, 109 Crop Science Building, Oregon State University, Corvallis, OR 97331, USA; (H.B.K.); (S.Y.)
- Hermiston Agricultural Research, and Extension Center, Hermiston, Department of Crop and Soil Science, Oregon State University, Hermiston, 2121 South 1st Street, Hermiston, OR 97838, USA
- Correspondence:
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Adams JR, de Vries ME, Zheng C, van Eeuwijk FA. Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop. G3 (BETHESDA, MD.) 2022; 12:6572814. [PMID: 35460241 PMCID: PMC9157145 DOI: 10.1093/g3journal/jkac076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/27/2022] [Indexed: 11/17/2022]
Abstract
Hybrid potato breeding has become a novel alternative to conventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigor. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a 2-step multivariate modeling approach to estimate the variance components to assess the magnitude of the general and specific combining abilities in diploid hybrid potato. Specific combining ability effects were identified for all yield components studied here warranting evidence of nonadditive genetic effects in hybrid potato yield. However, the estimated general combining ability effects were on average 2 times larger than their respective specific combining ability quantile across all yield phenotypes. Tuber number general combining abilities and specific combining abilities were found to be highly correlated with total yield's genetic components. Tuber volume was shown to have the largest proportion of additive and nonadditive genetic variation suggesting under-selection of this phenotype in this population. The prominence of additive effects found for all traits presents evidence that the mid-parent value alone is useful for hybrid potato evaluation. Heterotic vigor stands to be useful in bolstering simpler traits but this will be dependent on target phenotypes and market requirements. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding program.
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Affiliation(s)
- James R Adams
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands,Solynta, 6703 HA Wageningen, The Netherlands,Corresponding author: Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands.
| | | | - Chaozhi Zheng
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
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Bradshaw JE. Breeding Diploid F 1 Hybrid Potatoes for Propagation from Botanical Seed (TPS): Comparisons with Theory and Other Crops. PLANTS (BASEL, SWITZERLAND) 2022; 11:1121. [PMID: 35567122 PMCID: PMC9101707 DOI: 10.3390/plants11091121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 12/23/2022]
Abstract
This paper reviews the progress and the way ahead in diploid F1 hybrid potato breeding by comparisons with expectations from the theory of inbreeding and crossbreeding, and experiences from other diploid outbreeding crops. Diploid potatoes can be converted from an outbreeding species, in which self-pollination is prevented by a gametophytic self-incompatibility system, into one where self-pollination is possible, either through a dominant self-incompatibility inhibitor gene (Sli) or knockout mutations in the incompatibility locus. As a result, diploid F1 hybrid breeding can be used to produce genetically uniform potato cultivars for propagation from true potato seeds by crossing two near-homozygous inbred lines, derived from a number of generations of self-pollination despite inbreeding depression. Molecular markers can be used to detect and remove deleterious recessive mutations of large effect, including those in tight repulsion linkage. Improvements to the inbred lines can be made by introducing and stacking genes and chromosome segments of large desirable effect from wild relatives by backcrossing. Improvements in quantitative traits require a number of cycles of inbreeding and crossbreeding. Seed production can be achieved by hand pollinations. F1 hybrid planting material can be delivered to farmers as true seeds or young plants, and mini-tubers derived from true seeds.
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Affiliation(s)
- John E Bradshaw
- Honorary Associate, James Hutton Institute, Dundee DD2 5DA, UK
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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: 65] [Impact Index Per Article: 32.5] [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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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: 79] [Impact Index Per Article: 39.5] [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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Li D, Lu X, Zhu Y, Pan J, Zhou S, Zhang X, Zhu G, Shang Y, Huang S, Zhang C. The multi-omics basis of potato heterosis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:671-687. [PMID: 34963038 DOI: 10.1111/jipb.13211] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Heterosis is a fundamental biological phenomenon characterized by the superior performance of hybrids over their parents. Although tremendous progress has been reported in seed crops, the molecular mechanisms underlying heterosis in clonally propagated crops are largely unknown. Potato (Solanum tuberosum L.) is the most important tuber crop and an ongoing revolution is transforming potato from a clonally propagated tetraploid crop into a seed-propagated diploid hybrid potato. In our previous study, we developed the first generation of highly homozygous inbred lines of potato and hybrids with strong heterosis. Here, we integrated transcriptome, metabolome, and DNA methylation data to explore the genetic and molecular basis of potato heterosis at three developmental stages. We found that the initial establishment of heterosis in diploid potato was mainly due to dominant complementation. Flower color, male fertility, and starch and sucrose metabolism showed obvious gene dominant complementation in hybrids, and hybrids devoted more energy to primary metabolism for rapid growth. In addition, we identified ~2 700 allele-specific expression genes at each stage, which likely function in potato heterosis and might be regulated by CHH allele-specific methylation level. Our multi-omics analysis provides insight into heterosis in potato and facilitates the exploitation of heterosis in potato breeding.
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Affiliation(s)
- Dawei Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xiaoyue Lu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yanhui Zhu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Jun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Shaoqun Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Xinyan Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Sanwen Huang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
| | - Chunzhi Zhang
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518172, China
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Xu Y, Zhang Q, Zhang X, Wang J, Ayup M, Yang B, Guo C, Gong P, Dong W. The proteome reveals the involvement of serine/threonine kinase in the recognition of self- incompatibility in almond. J Proteomics 2022; 256:104505. [PMID: 35123051 DOI: 10.1016/j.jprot.2022.104505] [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: 11/04/2021] [Revised: 01/15/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
The self-incompatibility recognition mechanism determines whether the gametophyte is successfully fertilized between pollen tube SCF (SKP1-CUL1-F-box-RBX1) protein and pistil S-RNase protein during fertilization is unclear. In this study, the pistils of two almond cultivars 'Wanfeng' and 'Nonpareil' were used as the experimental materials after self- and nonself/cross-pollination, and pistils from the stamen-removed flowers were used as controls. We used fluorescence microscopy to observe the development of pollen tubes after pollination and 4D-LFQ to detect the protein expression profiles of 'Wanfeng' and 'Nonpareil' pistils and in controls. The results showed that it took 24-36 h for the development of the pollen tube to 1/3 of the pistil, and a total of 7684 differentially accumulated proteins (DAPs) were identified in the pistil after pollinating for 36 h, of which 7022 were quantifiable. Bioinformatics analysis based on the function of DAPs, identified RNA polymerases (4 DAPs), autophagy (3 DAPs), oxidative phosphorylation (3 DAPs), and homologous recombination (2 DAPs) pathways associated with the self-incompatibility process. These results were confirmed by parallel reaction monitoring (PRM), protein interaction and bioinformatics analysis. Taken together, these results provide the involvement of serine/threonine kinase protein in the reaction of pollen tube recognition the nonself- and the self-S-RNase protein. SIGNIFICANCE: Gametophytic self-incompatibility (GSI) is controlled by the highly polymorphic S locus or S haplotype, with two linked self-incompatibility genes, one encoding the S-RNase protein of the pistil S-determinant and the other encoding the F-box/SLF/SFB (S haplotype-specific F-box protein) protein of the pollen S-determinant. The recognition mechanism between pollen tube SCF protein and pistil S-RNase protein is divided into nonself- and self-recognition hypothesis mechanisms. At present, two hypothetical mechanisms cannot explain the recognition between pollen and pistil well, so the mechanism of gametophytic self-incompatibility recognition is still not fully revealed. In this experiment, we investigated the molecular mechanism of pollen-pistil recognition in self-incompatibility using self- and nonself-pollinated pistils of almond cultivars 'Wanfeng' and 'Nonpareil'. Based on our results, we proposed a potential involvement of the MARK2 (serine/threonine kinase) protein in the reaction of pollen tube recognition of the nonself- and the self-S-RNase protein. It provides a new way to reveal how almond pollen tubes recognize the self and nonself S-RNase enzyme protein.
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Affiliation(s)
- Yeting Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China; Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Qiuping Zhang
- Liaoning Institute of Pomology, Xiongyue 115009, Liaoning, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China
| | - Mubarek Ayup
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Bo Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Chunmiao Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Peng Gong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China.
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China.
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Zhu M, Cheng Y, Wu S, Huang X, Qiu J. Deleterious mutations are characterized by higher genomic heterozygosity than other genic variants in plant genomes. Genomics 2022; 114:110290. [DOI: 10.1016/j.ygeno.2022.110290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/08/2021] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
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Fumia N, Pironon S, Rubinoff D, Khoury CK, Gore MA, Kantar MB. Wild relatives of potato may bolster its adaptation to new niches under future climate scenarios. Food Energy Secur 2022. [DOI: 10.1002/fes3.360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Nathan Fumia
- Department of Tropical Plant and Soil Science University of Hawaii at Manoa Honolulu Hawaii USA
| | | | - Daniel Rubinoff
- Department of Plant and Environmental Protection Sciences University of Hawaii at Manoa Honolulu Hawaii USA
| | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- San Diego Botanic Garden Encinitas California USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section School of Integrative Plant Science Cornell University Ithaca New York USA
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Science University of Hawaii at Manoa Honolulu Hawaii USA
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Samayoa LF, Olukolu BA, Yang CJ, Chen Q, Stetter MG, York AM, Sanchez-Gonzalez JDJ, Glaubitz JC, Bradbury PJ, Romay MC, Sun Q, Yang J, Ross-Ibarra J, Buckler ES, Doebley JF, Holland JB. Domestication reshaped the genetic basis of inbreeding depression in a maize landrace compared to its wild relative, teosinte. PLoS Genet 2021; 17:e1009797. [PMID: 34928949 PMCID: PMC8722731 DOI: 10.1371/journal.pgen.1009797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/03/2022] [Accepted: 12/03/2021] [Indexed: 12/29/2022] Open
Abstract
Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte. Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. Mating of close relatives increases the probability that an individual inherits two non-functioning mutations at the same gene, resulting in lower fitness of such matings. We do not know the extent to which inbreeding depression is due to mutations with large-effects versus small-effect polygenic variants. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits and we found that this was consistent with higher predicted ‘genetic load’ in maize based solely on the evolutionary conservation of the sequence variants observed in the population. We also mapped genome positions associated with inbreeding depression, identifying more and larger-effect genetic variants in teosinte than maize. These results suggest that during domestication, some of the rare large-effect variants in teosinte were bred out, but many genetic variants of small effects on inbreeding depression increased in frequency maize.
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Affiliation(s)
- Luis Fernando Samayoa
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Qiuyue Chen
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Markus G. Stetter
- Institute for Plant Sciences and Center of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Alessandra M. York
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | | | - Jeffrey C. Glaubitz
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Peter J. Bradbury
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - Maria Cinta Romay
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, California, United States of America
| | - Edward S. Buckler
- US Department of Agriculture–Agricultural Research Service, Cornell University, Ithaca, New York, United States of America
| | - John F. Doebley
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - James B. Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
- United States Department of Agriculture–Agriculture Research Service, Raleigh, North Carolina, United States of America
- * E-mail:
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Beumer K, Stemerding D. A breeding consortium to realize the potential of hybrid diploid potato for food security. NATURE PLANTS 2021; 7:1530-1532. [PMID: 34815537 DOI: 10.1038/s41477-021-01035-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Koen Beumer
- Copernicus Institute of Sustainable Development, Utrecht University, Utrecht, the Netherlands.
| | - Dirk Stemerding
- Independent researcher in biotechnology and society, Enschede, the Netherlands
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Affiliation(s)
- 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.
| | - 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.
- Center for Integrated Breeding Research (CiBreed), Georg-August-University Göttingen, Göttingen, Germany.
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Freire R, Weisweiler M, Guerreiro R, Baig N, Hüttel B, Obeng-Hinneh E, Renner J, Hartje S, Muders K, Truberg B, Rosen A, Prigge V, Bruckmüller J, Lübeck J, Stich B. Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety. G3-GENES GENOMES GENETICS 2021; 11:6371871. [PMID: 34534288 PMCID: PMC8664475 DOI: 10.1093/g3journal/jkab330] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/08/2021] [Indexed: 01/27/2023]
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops with a worldwide production of 370 million metric tons. The objectives of this study were (1) to create a high-quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (2) to evaluate the new assembly’s usefulness for various genomic methods; and (3) to assess the performance of phasing in diploid and tetraploid clones, using linked-read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.
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Affiliation(s)
- Ruth Freire
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ricardo Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Nadia Baig
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Bruno Hüttel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding, Carl-von-Linne-Weg 10, 50829 Köln, Germany
| | - Evelyn Obeng-Hinneh
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Juliane Renner
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Stefanie Hartje
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Strehlow 19, 17111 Hohenmocker, Germany
| | - Katja Muders
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Bernd Truberg
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Arne Rosen
- Nordring- Kartoffelzucht- und Vermehrungs- GmbH, Parkweg 4, 18190 Sanitz, Germany
| | - Vanessa Prigge
- SaKa Pflanzenzucht GmbH & Co. KG, Zuchtstation Windeby, Eichenallee 9, 24340 Windeby, Germany
| | | | - Jens Lübeck
- Solana Research GmbH, Eichenallee 9, 24340 Windeby, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Universitätsstraße 1, 40225 Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences, From Complex Traits towards Synthetic Modules, Universitätsstraße 1, 40225 Düsseldorf, Germany
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48
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Yengo L, Yang J, Keller MC, Goddard ME, Wray NR, Visscher PM. Genomic partitioning of inbreeding depression in humans. Am J Hum Genet 2021; 108:1488-1501. [PMID: 34214457 DOI: 10.1016/j.ajhg.2021.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Across species, offspring of related individuals often exhibit significant reduction in fitness-related traits, known as inbreeding depression (ID), yet the genetic and molecular basis for ID remains elusive. Here, we develop a method to quantify enrichment of ID within specific genomic annotations and apply it to human data. We analyzed the phenomes and genomes of ∼350,000 unrelated participants of the UK Biobank and found, on average of over 11 traits, significant enrichment of ID within genomic regions with high recombination rates (>21-fold; p < 10-5), with conserved function across species (>19-fold; p < 10-4), and within regulatory elements such as DNase I hypersensitive sites (∼5-fold; p = 8.9 × 10-7). We also quantified enrichment of ID within trait-associated regions and found suggestive evidence that genomic regions contributing to additive genetic variance in the population are enriched for ID signal. We find strong correlations between functional enrichment of SNP-based heritability and that of ID (r = 0.8, standard error: 0.1). These findings provide empirical evidence that ID is most likely due to many partially recessive deleterious alleles in low linkage disequilibrium regions of the genome. Our study suggests that functional characterization of ID may further elucidate the genetic architectures and biological mechanisms underlying complex traits and diseases.
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Huang X, Han B. The magic of genomics in creating hybrid potato. MOLECULAR PLANT 2021; 14:1237-1238. [PMID: 34166848 DOI: 10.1016/j.molp.2021.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/19/2021] [Accepted: 06/20/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Bin Han
- National Center for Gene Research, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
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50
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Han T, Wang F, Song Q, Ye W, Liu T, Wang L, Chen ZJ. An epigenetic basis of inbreeding depression in maize. SCIENCE ADVANCES 2021; 7:7/35/eabg5442. [PMID: 34452913 PMCID: PMC8397266 DOI: 10.1126/sciadv.abg5442] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/07/2021] [Indexed: 05/12/2023]
Abstract
Inbreeding depression is widespread across plant and animal kingdoms and may arise from the exposure of deleterious alleles and/or loss of overdominant alleles resulting from increased homozygosity, but these genetic models cannot fully explain the phenomenon. Here, we report epigenetic links to inbreeding depression in maize. Teosinte branched1/cycloidea/proliferating cell factor (TCP) transcription factors control plant development. During successive inbreeding among inbred lines, thousands of genomic regions across TCP-binding sites (TBS) are hypermethylated through the H3K9me2-mediated pathway. These hypermethylated regions are accompanied by decreased chromatin accessibility, increased levels of the repressive histone marks H3K27me2 and H3K27me3, and reduced binding affinity of maize TCP-proteins to TBS. Consequently, hundreds of TCP-target genes involved in mitochondrion, chloroplast, and ribosome functions are down-regulated, leading to reduced growth vigor. Conversely, random mating can reverse corresponding hypermethylation sites and TCP-target gene expression, restoring growth vigor. These results support a unique role of reversible epigenetic modifications in inbreeding depression.
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Affiliation(s)
- Tongwen Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Fang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Tieshan Liu
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Wang
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
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