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Maistriaux LC, Laurent MJ, Jeanguenin L, Prado SA, Nader J, Welcker C, Charcosset A, Tardieu F, Nicolas SD, Chaumont F. Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression. PLANT PHYSIOLOGY 2024; 196:368-384. [PMID: 38839061 PMCID: PMC11376376 DOI: 10.1093/plphys/kiae326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024]
Abstract
Plant aquaporins are involved in numerous physiological processes, such as cellular homeostasis, tissue hydraulics, transpiration, and nutrient supply, and are key players of the response to environmental cues. While varying expression patterns of aquaporin genes have been described across organs, developmental stages, and stress conditions, the underlying regulation mechanisms remain elusive. Hence, this work aimed to shed light on the expression variability of 4 plasma membrane intrinsic protein (PIP) genes in maize (Zea mays) leaves, and its genetic causes, through expression quantitative trait locus (eQTL) mapping across a 252-hybrid diversity panel. Significant genetic variability in PIP transcript abundance was observed to different extents depending on the isoforms. The genome-wide association study mapped numerous eQTLs, both local and distant, thus emphasizing the existing natural diversity of PIP gene expression across the studied panel and the potential to reveal regulatory actors and mechanisms. One eQTL associated with PIP2;5 expression variation was characterized. Genomic sequence comparison and in vivo reporter assay attributed, at least partly, the local eQTL to a transposon-containing polymorphism in the PIP2;5 promoter. This work paves the way to the molecular understanding of PIP gene regulation and its possible integration into larger networks regulating physiological and stress adaptation processes.
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Affiliation(s)
- Laurie C Maistriaux
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Maxime J Laurent
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Linda Jeanguenin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | | | - Joseph Nader
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
| | - Claude Welcker
- INRAE, LEPSE, Université de Montpellier, 34060 Montpellier, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - François Tardieu
- INRAE, LEPSE, Université de Montpellier, 34060 Montpellier, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE-Le Moulon, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - François Chaumont
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, 1348 Louvain-la-Neuve, Belgium
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Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
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Canaguier A, Guilbaud R, Denis E, Magdelenat G, Belser C, Istace B, Cruaud C, Wincker P, Le Paslier MC, Faivre-Rampant P, Barbe V. Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection. BMC Genomics 2022; 23:317. [PMID: 35448948 PMCID: PMC9026655 DOI: 10.1186/s12864-022-08499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection. This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1). RESULTS We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. CONCLUSIONS Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.
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Affiliation(s)
- Aurélie Canaguier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Romane Guilbaud
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Erwan Denis
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Ghislaine Magdelenat
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique CEA, Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marie-Christine Le Paslier
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Patricia Faivre-Rampant
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux EPGV, 91000 Evry-Courcouronnes, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Pook T, Nemri A, Gonzalez Segovia EG, Valle Torres D, Simianer H, Schoen CC. Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks. PLoS Genet 2021; 17:e1009944. [PMID: 34941872 PMCID: PMC8699914 DOI: 10.1371/journal.pgen.1009944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 11/13/2021] [Indexed: 01/16/2023] Open
Abstract
High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline (“HBimpute”) that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced at 0.5X read-depth. The overall imputing error rates are cut in half compared to state-of-the-art software like BEAGLE and STITCH, while the average read-depth is increased to 83X, thus enabling the calling of copy number variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance of sequence data in common breeding applications to that of genomic data generated with a genotyping array. For both genome-wide association studies and genomic prediction, results are on par or even slightly better than results obtained with high-density array data (600k). In particular for genomic prediction, we observe slightly higher data quality for the sequence data compared to the 600k array in the form of higher prediction accuracies. This occurred specifically when reducing the data panel to the set of overlapping markers between sequence and array, indicating that sequencing data can benefit from the same marker ascertainment as used in the array process to increase the quality and usability of genomic data. High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics and breeding. Cost, precision, and throughput must be balanced to achieve optimal efficiency given available technologies and finite resources. Although genotyping arrays are still considered the gold standard in high-throughput quantitative genetics, recent advances in sequencing provide new opportunities. Both the quality and cost of genomic data generated based on sequencing are highly dependent on the used read-depth. In this work, we propose a new imputation pipeline (“HBimpute”) that uses haplotype blocks to detect individuals of the same genetic origin and subsequently uses all reads of those individuals in the variant calling. Thus, the obtained virtual read-depth is artificially increased, leading to higher calling accuracy, coverage, and the ability to call copy number variation based on low read-depth sequencing data. To conclude, our approach makes sequencing a cost-competitive alternative to genotyping arrays with the added benefit of allowing the calling of structural variation.
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Affiliation(s)
- Torsten Pook
- Center for Integrated Breeding Research, Animal Breeding and Genetics Group, University of Goettingen, Goettingen, Germany
- * E-mail:
| | | | | | - Daniel Valle Torres
- Plant Breeding, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
| | - Henner Simianer
- Center for Integrated Breeding Research, Animal Breeding and Genetics Group, University of Goettingen, Goettingen, Germany
| | - Chris-Carolin Schoen
- Plant Breeding, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
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Liang S, Lin F, Qian Y, Zhang T, Wu Y, Qi Y, Ren S, Ruan L, Zhao H. A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers. PLANT METHODS 2020; 16:101. [PMID: 32742299 PMCID: PMC7391534 DOI: 10.1186/s13007-020-00644-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/22/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Maize is one of the most important cereal crop all over the world with a complex genome of about 2.3 gigabase, and exhibits tremendous phenotypic and molecular diversity among different germplasms. Along with the phenotype identification, molecular markers have been accepted extensively as an alternative tool to discriminate different genotypes. RESULTS By using previous re-sequencing data of 205 lines, bi-allelic insertions and deletions (InDels) all over maize genome were screened, and a barcode system was constructed consisting of 37 bi-allelic insertion-deletion markers with high polymorphism information content (PIC) values, large discriminative size among varieties. The barcode system was measured and determined, different maize hybrids and inbreds were clearly discriminated efficiently with these markers, and hybrids responding parents were accurately determined. Compared with microarray data of more than 200 maize lines, the barcode system can discriminate maize varieties with 1.57% of different loci as a threshold. The barcode system can be used in standardized easy and quick operation with very low cost and minimum equipment requirements. CONCLUSION A barcode system was constructed for genetic discrimination of maize lines, including 37 InDel markers with high PIC values and user-friendly. The barcode system was measured and determined for efficient identification of maize lines.
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Affiliation(s)
- Shuaiqiang Liang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Feng Lin
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yiliang Qian
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tifu Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yibo Wu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yaocheng Qi
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Sihai Ren
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Long Ruan
- Anhui Academy of Agricultural Sciences, Hefei, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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