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Aguirre NC, Villalba PV, García MN, Filippi CV, Rivas JG, Martínez MC, Acuña CV, López AJ, López JA, Pathauer P, Palazzini D, Harrand L, Oberschelp J, Marcó MA, Cisneros EF, Carreras R, Martins Alves AM, Rodrigues JC, Hopp HE, Grattapaglia D, Cappa EP, Paniego NB, Marcucci Poltri SN. Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden). Front Genet 2024; 15:1361418. [PMID: 38606359 PMCID: PMC11008695 DOI: 10.3389/fgene.2024.1361418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/19/2024] [Indexed: 04/13/2024] Open
Abstract
Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.
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Affiliation(s)
| | | | - Martín Nahuel García
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Carla Valeria Filippi
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Juan Gabriel Rivas
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - María Carolina Martínez
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Cintia Vanesa Acuña
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Augusto J. López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Juan Adolfo López
- Estación Experimental Agropecuaria de Bella Vista, Instituto Nacional de Tecnología Agropecuaria, Bella Vista, Argentina
| | - Pablo Pathauer
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Dino Palazzini
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Leonel Harrand
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Javier Oberschelp
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Martín Alberto Marcó
- Estación Experimental Agropecuaria de Concordia, Instituto Nacional de Tecnología Agropecuaria, Concordia, Argentina
| | - Esteban Felipe Cisneros
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Rocío Carreras
- Facultad de Ciencias Forestales, Universidad Nacional de Santiago del Estero (UNSE), Santiago del Estero, Argentina
| | - Ana Maria Martins Alves
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - José Carlos Rodrigues
- Centro de Estudos Florestais e Laboratório Associado TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, Portugal
| | - H. Esteban Hopp
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
| | - Dario Grattapaglia
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Recursos Genéticos e Biotecnologia, Brasilia, Brazil
| | - Eduardo Pablo Cappa
- Instituto de Recursos Biológicos, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Norma Beatriz Paniego
- Instituto de Agrobiotecnología y Biología Molecular, UEDD INTA-CONICET, Hurlingham, Argentina
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Degen B, Müller NA. A simulation study comparing advanced marker-assisted selection with genomic selection in tree breeding programs. G3 (BETHESDA, MD.) 2023; 13:jkad164. [PMID: 37494068 PMCID: PMC10542556 DOI: 10.1093/g3journal/jkad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023]
Abstract
Advances in DNA sequencing technologies allow the sequencing of whole genomes of thousands of individuals and provide several million single nucleotide polymorphisms (SNPs) per individual. These data combined with precise and high-throughput phenotyping enable genome-wide association studies (GWAS) and the identification of SNPs underlying traits with complex genetic architectures. The identified causal SNPs and estimated allelic effects could then be used for advanced marker-assisted selection (MAS) in breeding programs. But could such MAS compete with the broadly used genomic selection (GS)? This question is of particular interest for the lengthy tree breeding strategies. Here, with our new software "SNPscan breeder," we simulated a simple tree breeding program and compared the impact of different selection criteria on genetic gain and inbreeding. Further, we assessed different genetic architectures and different levels of kinship among individuals of the breeding population. Interestingly, apart from progeny testing, GS using gBLUP performed best under almost all simulated scenarios. MAS based on GWAS results outperformed GS only if the allelic effects were estimated in large populations (ca. 10,000 individuals) of unrelated individuals. Notably, GWAS using 3,000 extreme phenotypes performed as good as the use of 10,000 phenotypes. GS increased inbreeding and thus reduced genetic diversity more strongly compared to progeny testing and GWAS-based selection. We discuss the practical implications for tree breeding programs. In conclusion, our analyses further support the potential of GS for forest tree breeding and improvement, although MAS may gain relevance with decreasing sequencing costs in the future.
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Affiliation(s)
- Bernd Degen
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Schleswig-Holstein, Germany
| | - Niels A Müller
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Schleswig-Holstein, Germany
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Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA. Genes (Basel) 2021; 12:genes12081240. [PMID: 34440416 PMCID: PMC8391649 DOI: 10.3390/genes12081240] [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: 07/06/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022] Open
Abstract
Prairie cordgrass (Spartina pectinata Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.
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Pirrello C, Zeilmaker T, Bianco L, Giacomelli L, Moser C, Vezzulli S. Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing. Biomolecules 2021; 11:181. [PMID: 33525704 PMCID: PMC7912118 DOI: 10.3390/biom11020181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes-namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2-in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Silvia Vezzulli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
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Physical mapping and InDel marker development for the restorer gene Rf 2 in cytoplasmic male sterile CMS-D8 cotton. BMC Genomics 2021; 22:24. [PMID: 33407111 PMCID: PMC7789476 DOI: 10.1186/s12864-020-07342-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07342-y.
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Zou C, Karn A, Reisch B, Nguyen A, Sun Y, Bao Y, Campbell MS, Church D, Williams S, Xu X, Ledbetter CA, Patel S, Fennell A, Glaubitz JC, Clark M, Ware D, Londo JP, Sun Q, Cadle-Davidson L. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nat Commun 2020; 11:413. [PMID: 31964885 PMCID: PMC6972940 DOI: 10.1038/s41467-019-14280-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.
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Affiliation(s)
- Cheng Zou
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Bruce Reisch
- School of Integrative Plant Science, Cornell AgriTech, Cornell University, Geneva, NY, 14456, USA
| | - Allen Nguyen
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yongming Sun
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | - Yun Bao
- Integrated DNA Technologies, Redwood City, CA, 94063, USA
| | | | | | | | - Xia Xu
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Craig A Ledbetter
- USDA-ARS, Crop Diseases, Pests and Genetics Research, Parlier, CA, 93648, USA
| | - Sagar Patel
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Anne Fennell
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, 57007, USA
| | - Jeffrey C Glaubitz
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Jason P Londo
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, 14456, USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
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Duzlu O, Yildirim A, Yetismis G, Onder Z, Simsek E, Ciloglu A, Demirpolat GS, Inci A. Development and field evaluation of a species-specific mt-COI targeted SYBR-Green Real Time PCR for detection and quantification of Haemonchus contortus in cattle in Turkey. Vet Parasitol 2019; 277:109020. [PMID: 31896019 DOI: 10.1016/j.vetpar.2019.109020] [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: 10/31/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022]
Abstract
Haemonchus contortus is one of the most important gastrointestinal nematodes (GINs) infecting sheep, goats, and cattle worldwide. We developed a SYBR Green real-time PCR (qPCR) assay for detection and quantification of H. contortus by using specific primers based on a conserved region of the mitochondrial cytochrome oxidase subunit I (mt-COI) gene, and evaluated this technique in the detection of H. contortus infections in cattle in Central Anatolia Region of Turkey. The newly developed qPCR assay successfully discriminated H. contortus from other GIN species infecting cattle in the specificity evaluations, with a specific melt peak of 77.5 °C. Our results revealed the efficient amplification of the proposed target COI region within the range of plasmid copies, from 2 × 106 to 2 × 101 per μl, with 96.9 % efficiency, R² value of 0.999, and a slope of -3.398. Among the 920 cattle fecal samples from the field, 58 samples (6.3 %) were positive with qPCR assay, whereas 45 samples (4.9 %) were positive, as determined by larval culture, suggesting the utility of SYBR Green qPCR. Phylogenetic characterization of the partial COI gene of H. contortus isolates was also evaluated for 100 eggs and third stage larvae recovered from positive cattle faecal samples, which were verified with the qPCR assay prior to analyses. COI sequences were classified into three haplotypes (THC1 to THC3) with intraspecific nucleotide differences of 0.50 to 0.76 %. Phylogenetic analyses revealed that the haplotypes grouped with H. contortus isolates from several countries in a monophyletic cluster, with evidence of at least two main haplogroups. Overall, the SYBR Green qPCR assay was highly specific and sensitive, suggesting that it can be used for screening of H. contortus infections in livestock populations in epidemiological studies and the control of this important parasite.
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Affiliation(s)
- Onder Duzlu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey.
| | - Alparslan Yildirim
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Gamze Yetismis
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Zuhal Onder
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Emrah Simsek
- Preclinical Sciences, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Arif Ciloglu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | | | - Abdullah Inci
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
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Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC Genomics 2019; 20:331. [PMID: 31046664 PMCID: PMC6498479 DOI: 10.1186/s12864-019-5712-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus. Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Montanari
- Department of Plant Sciences, University of California, Davis, CA, USA.
| | - Luca Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Nahla V Bassil
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Joseph Postman
- USDA Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, USA
| | - Mareike Knäbel
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Biff Kitson
- Motueka Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Motueka, New Zealand
| | - Cecilia H Deng
- Auckland Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - David Chagné
- Palmerston North Research Centre, The New Zealand Institute for Plant & Food Research Limited (PFR), Palmerston North, New Zealand
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Kate Evans
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, USA
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Fresnedo-Ramírez J, Yang S, Sun Q, Karn A, Reisch BI, Cadle-Davidson L. Computational Analysis of AmpSeq Data for Targeted, High-Throughput Genotyping of Amplicons. FRONTIERS IN PLANT SCIENCE 2019; 10:599. [PMID: 31156670 PMCID: PMC6528068 DOI: 10.3389/fpls.2019.00599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 04/24/2019] [Indexed: 05/11/2023]
Abstract
Amplicon sequencing (AmpSeq) is a practical, intuitive strategy with a semi-automated computational pipeline for analysis of highly multiplexed PCR-derived sequences. This genotyping platform is particularly cost-effective when multiplexing 96 or more samples with a few amplicons up to thousands of amplicons. Amplicons can target from a single nucleotide to the upper limit of the sequencing platform. The flexibility of AmpSeq's wet lab methods make it a tool of broad interest for diverse species, and AmpSeq excels in flexibility, high-throughput, low-cost, accuracy, and semi-automated analysis. Here we provide an open science framework procedure to output data out of an AmpSeq project, with an emphasis on the bioinformatics pipeline to generate SNPs, haplotypes and presence/absence variants in a set of diverse genotypes. Open-access tutorial datasets with actual data and a containerization open source software instance are provided to enable training in each of these genotyping applications. The pipelines presented here should be applicable to the analysis of various target-enriched (e.g., amplicon or sequence capture) Illumina sequence data.
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Affiliation(s)
| | - Shanshan Yang
- School of Integrative Plant Science, Cornell AgriTech, Geneva, NY, United States
| | - Qi Sun
- Biotechnology Resource Center, Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, United States
| | - Avinash Karn
- School of Integrative Plant Science, Cornell AgriTech, Geneva, NY, United States
| | - Bruce I. Reisch
- School of Integrative Plant Science, Cornell AgriTech, Geneva, NY, United States
| | - Lance Cadle-Davidson
- School of Integrative Plant Science, Cornell AgriTech, Geneva, NY, United States
- United States Department of Agriculture – Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, United States
- *Correspondence: Lance Cadle-Davidson,
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10
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Pichler R, Silbermayr K, Periasamy K. A novel snapback primer probe assay for the detection and discrimination of sympatric Haemonchus species using DNA melting analysis. Vet Parasitol 2017; 237:94-103. [PMID: 28242041 DOI: 10.1016/j.vetpar.2017.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
Abstract
Different sympatric species of Haemonchus parasites infecting ruminants and camels can be distinguished morphologically, but involves tedious microscopic examinations, measurements and several other limitations. Information on internal transcribed spacer-2 (ITS-2) sequence provides confirmatory differentiation of sympatric Haemonchus species. The present study introduces a novel, snapback primer probe based, real time PCR assay for the differentiation of three sympatric Haemonchus species, H. contortus (Hco), H. placei (Hpl) and H. longistipes (Hlo). The assay was designed to amplify a region of 130bp within the ITS-2 gene that included three diagnostic mutational sites capable of discriminating Hco, Hpl and Hlo. Following melt curve analysis, species-specific diagnostic melt peaks were obtained for Hco, Hpl and Hlo with a mean melting temperature of 56.6±0.3°C, 64.4±0.1°C and 54.4±0.1°C respectively. The test for analytical sensitivity revealed the ability of the assay to detect up to 5 copies per reaction. To evaluate the discriminating power of the assay, 174 samples from adult worms and 3rd stage larvae belonging to different Haemonchus species and various other nematode species including Cooperia curticei, Trichostrongylus axei, Trichostrongylus colubriformis, and Teladorsagia circumcincta were tested. Additionally, DNA extracted from 25 fecal egg samples was also tested and the specificity of the assay was verified by sequencing the ITS-2 gene of all the Haemonchus positive and non-Haemonchus samples. The assay worked accurately with 100% specificity in at least three real time PCR platforms. The assay is an effective alternative to the sequencing approach and is expected to be helpful for the screening of individual adult and larval Haemonchus parasites. However, caution needs to be applied while interpreting the results from fecal egg samples due to varying levels of sympatric co-infections from different Haemonchus species. The present study is the first report on the application of snapback primer probe methodology for the differentiation of nematode parasites.
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Affiliation(s)
- Rudolf Pichler
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.
| | - Katja Silbermayr
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria; Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine, Vienna, Austria.
| | - Kathiravan Periasamy
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria.
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11
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He X, Johansson ML, Heath DD. Role of genomics and transcriptomics in selection of reintroduction source populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:1010-1018. [PMID: 26756292 DOI: 10.1111/cobi.12674] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 01/02/2016] [Accepted: 01/05/2016] [Indexed: 06/05/2023]
Abstract
The use and importance of reintroduction as a conservation tool to return a species to its historical range from which it has been extirpated will increase as climate change and human development accelerate habitat loss and population extinctions. Although the number of reintroduction attempts has increased rapidly over the past 2 decades, the success rate is generally low. As a result of population differences in fitness-related traits and divergent responses to environmental stresses, population performance upon reintroduction is highly variable, and it is generally agreed that selecting an appropriate source population is a critical component of a successful reintroduction. Conservation genomics is an emerging field that addresses long-standing challenges in conservation, and the potential for using novel molecular genetic approaches to inform and improve conservation efforts is high. Because the successful establishment and persistence of reintroduced populations is highly dependent on the functional genetic variation and environmental stress tolerance of the source population, we propose the application of conservation genomics and transcriptomics to guide reintroduction practices. Specifically, we propose using genome-wide functional loci to estimate genetic variation of source populations. This estimate can then be used to predict the potential for adaptation. We also propose using transcriptional profiling to measure the expression response of fitness-related genes to environmental stresses as a proxy for acclimation (tolerance) capacity. Appropriate application of conservation genomics and transcriptomics has the potential to dramatically enhance reintroduction success in a time of rapidly declining biodiversity and accelerating environmental change.
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Affiliation(s)
- Xiaoping He
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Mattias L Johansson
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada.
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12
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Ribeiro T, Barrela RM, Bergès H, Marques C, Loureiro J, Morais-Cecílio L, Paiva JAP. Advancing Eucalyptus Genomics: Cytogenomics Reveals Conservation of Eucalyptus Genomes. FRONTIERS IN PLANT SCIENCE 2016; 7:510. [PMID: 27148332 PMCID: PMC4840385 DOI: 10.3389/fpls.2016.00510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/31/2016] [Indexed: 05/30/2023]
Abstract
The genus Eucalyptus encloses several species with high ecological and economic value, being the subgenus Symphyomyrtus one of the most important. Species such as E. grandis and E. globulus are well characterized at the molecular level but knowledge regarding genome and chromosome organization is very scarce. Here we characterized and compared the karyotypes of three economically important species, E. grandis, E. globulus, and E. calmadulensis, and three with ecological relevance, E. pulverulenta, E. cornuta, and E. occidentalis, through an integrative approach including genome size estimation, fluorochrome banding, rDNA FISH, and BAC landing comprising genes involved in lignin biosynthesis. All karyotypes show a high degree of conservation with pericentromeric 35S and 5S rDNA loci in the first and third pairs, respectively. GC-rich heterochromatin was restricted to the 35S rDNA locus while the AT-rich heterochromatin pattern was species-specific. The slight differences in karyotype formulas and distribution of AT-rich heterochromatin, along with genome sizes estimations, support the idea of Eucalyptus genome evolution by local expansions of heterochromatin clusters. The unusual co-localization of both rDNA with AT-rich heterochromatin was attributed mainly to the presence of silent transposable elements in those loci. The cinnamoyl CoA reductase gene (CCR1) previously assessed to linkage group 10 (LG10) was clearly localized distally at the long arm of chromosome 9 establishing an unexpected correlation between the cytogenetic chromosome 9 and the LG10. Our work is novel and contributes to the understanding of Eucalyptus genome organization which is essential to develop successful advanced breeding strategies for this genus.
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Affiliation(s)
- Teresa Ribeiro
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Ricardo M. Barrela
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
| | - Hélène Bergès
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomiques VégétalesCastanet-Tolosan, France
| | - Cristina Marques
- RAIZ, Instituto de Investigação da Floresta e PapelAveiro, Portugal
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of CoimbraCoimbra, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of LisbonLisboa, Portugal
| | - Jorge A. P. Paiva
- Plant Cell Biotechnology Laboratory, Instituto de Biologia Experimental e TecnológicaOeiras, Portugal
- Department of Integrative Plant Biology, Instytut Genetyki Roślin, Polskiej Akademii NaukPoznań, Poland
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13
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Faivre-Rampant P, Zaina G, Jorge V, Giacomello S, Segura V, Scalabrin S, Guérin V, De Paoli E, Aluome C, Viger M, Cattonaro F, Payne A, PaulStephenRaj P, Le Paslier MC, Berard A, Allwright MR, Villar M, Taylor G, Bastien C, Morgante M. New resources for genetic studies in Populus nigra: genome-wide SNP discovery and development of a 12k Infinium array. Mol Ecol Resour 2016; 16:1023-36. [PMID: 26929265 DOI: 10.1111/1755-0998.12513] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022]
Abstract
Whole genome resequencing of 51 Populus nigra (L.) individuals from across Western Europe was performed using Illumina platforms. A total number of 1 878 727 SNPs distributed along the P. nigra reference sequence were identified. The SNP calling accuracy was validated with Sanger sequencing. SNPs were selected within 14 previously identified QTL regions, 2916 expressional candidate genes related to rust resistance, wood properties, water-use efficiency and bud phenology and 1732 genes randomly spread across the genome. Over 10 000 SNPs were selected for the construction of a 12k Infinium Bead-Chip array dedicated to association mapping. The SNP genotyping assay was performed with 888 P. nigra individuals. The genotyping success rate was 91%. Our high success rate was due to the discovery panel design and the stringent parameters applied for SNP calling and selection. In the same set of P. nigra genotypes, linkage disequilibrium throughout the genome decayed on average within 5-7 kb to half of its maximum value. As an application test, ADMIXTURE analysis was performed with a selection of 600 SNPs spread throughout the genome and 706 individuals collected along 12 river basins. The admixture pattern was consistent with genetic diversity revealed by neutral markers and the geographical distribution of the populations. These newly developed SNP resources and genotyping array provide a valuable tool for population genetic studies and identification of QTLs through natural-population based genetic association studies in P. nigra.
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Affiliation(s)
| | - G Zaina
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy
| | - V Jorge
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Giacomello
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Segura
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - S Scalabrin
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - V Guérin
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - E De Paoli
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - C Aluome
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.,INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Viger
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - F Cattonaro
- IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
| | - A Payne
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | | | | | - A Berard
- INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France
| | - M R Allwright
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - M Villar
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - G Taylor
- Centre For Biological Sciences, University of Southampton, Life Sciences, SO17 1BJ, Southampton, UK
| | - C Bastien
- INRA, UR 0588 AGPF, Centre INRA Val de Loire, 2163 avenue de la Pomme de Pin, CS 40001 - Ardon, 45075, Orléans, France
| | - M Morgante
- DI4A, University of Udine, via delle Scienze 206, 33100, Udine, Italy.,IGA, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy
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14
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Valdisser PAMR, Pappas GJ, de Menezes IPP, Müller BSF, Pereira WJ, Narciso MG, Brondani C, Souza TLPO, Borba TCO, Vianello RP. SNP discovery in common bean by restriction-associated DNA (RAD) sequencing for genetic diversity and population structure analysis. Mol Genet Genomics 2016; 291:1277-91. [PMID: 26932372 DOI: 10.1007/s00438-016-1182-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 02/12/2016] [Indexed: 11/28/2022]
Abstract
Researchers have made great advances into the development and application of genomic approaches for common beans, creating opportunities to driving more real and applicable strategies for sustainable management of the genetic resource towards plant breeding. This work provides useful polymorphic single-nucleotide polymorphisms (SNPs) for high-throughput common bean genotyping developed by RAD (restriction site-associated DNA) sequencing. The RAD tags were generated from DNA pooled from 12 common bean genotypes, including breeding lines of different gene pools and market classes. The aligned sequences identified 23,748 putative RAD-SNPs, of which 3357 were adequate for genotyping; 1032 RAD-SNPs with the highest ADT (assay design tool) score are presented in this article. The RAD-SNPs were structurally annotated in different coding (47.00 %) and non-coding (53.00 %) sequence components of genes. A subset of 384 RAD-SNPs with broad genome distribution was used to genotype a diverse panel of 95 common bean germplasms and revealed a successful amplification rate of 96.6 %, showing 73 % of polymorphic SNPs within the Andean group and 83 % in the Mesoamerican group. A slightly increased He (0.161, n = 21) value was estimated for the Andean gene pool, compared to the Mesoamerican group (0.156, n = 74). For the linkage disequilibrium (LD) analysis, from a group of 580 SNPs (289 RAD-SNPs and 291 BARC-SNPs) genotyped for the same set of genotypes, 70.2 % were in LD, decreasing to 0.10 %in the Andean group and 0.77 % in the Mesoamerican group. Haplotype patterns spanning 310 Mb of the genome (60 %) were characterized in samples from different origins. However, the haplotype frameworks were under-represented for the Andean (7.85 %) and Mesoamerican (5.55 %) gene pools separately. In conclusion, RAD sequencing allowed the discovery of hundreds of useful SNPs for broad genetic analysis of common bean germplasm. From now, this approach provides an excellent panel of molecular tools for whole genome analysis, allowing integrating and better exploring the common bean breeding practices.
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Affiliation(s)
| | - Georgios J Pappas
- Laboratório de Biologia Molecular, Departamento de Biologia Celular, Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Ivandilson P P de Menezes
- Laboratório de Genética e Biologia Molecular, Departamento de Biologia, Instituto Federal Goiano (IF Goiano), Urutaí, GO, Brazil
| | - Bárbara S F Müller
- Programa de Pós-Graduação em Biologia Molecular, Universidade de Brasília (UnB), Brasilia, DF, Brazil
| | - Wendell J Pereira
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | - Marcelo G Narciso
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Claudio Brondani
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Thiago L P O Souza
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Tereza C O Borba
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil
| | - Rosana P Vianello
- Laboratório de Biotecnologia, Embrapa Arroz e Feijão, Santo Antônio de Goiás, GO, Brazil.
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15
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Yang S, Fresnedo-Ramírez J, Wang M, Cote L, Schweitzer P, Barba P, Takacs EM, Clark M, Luby J, Manns DC, Sacks G, Mansfield AK, Londo J, Fennell A, Gadoury D, Reisch B, Cadle-Davidson L, Sun Q. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine. HORTICULTURE RESEARCH 2016; 3:16002. [PMID: 27257505 PMCID: PMC4879517 DOI: 10.1038/hortres.2016.2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 05/07/2023]
Abstract
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.
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Affiliation(s)
- Shanshan Yang
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Minghui Wang
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
| | - Linda Cote
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Schweitzer
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elizabeth M Takacs
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Matthew Clark
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - James Luby
- Department of Horticultural Science, University of Minnesota, St Paul, MN 55108, USA
| | - David C Manns
- Department of Food Science, Cornell University, Geneva, NY 14456, USA
| | - Gavin Sacks
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | | | - Jason Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, NY 14456, USA
| | - Anne Fennell
- Plant Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - David Gadoury
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Qi Sun
- Bioinformatics Facility, Cornell University, Ithaca, NY 14853, USA
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16
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Klocko AL, Ma C, Robertson S, Esfandiari E, Nilsson O, Strauss SH. FT overexpression induces precocious flowering and normal reproductive development in Eucalyptus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:808-19. [PMID: 26132805 DOI: 10.1111/pbi.12431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 05/29/2015] [Accepted: 06/10/2015] [Indexed: 05/18/2023]
Abstract
Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1-5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat-shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT-induced flowers were morphologically normal and produced viable pollen grains and viable self- and cross-pollinated seeds. Many self-seedlings inherited AtFT and flowered early. FT overexpression-induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.
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Affiliation(s)
- Amy L Klocko
- Department Forest Ecosystems & Society, Oregon State University, Corvallis, OR, USA
| | - Cathleen Ma
- Department Forest Ecosystems & Society, Oregon State University, Corvallis, OR, USA
| | - Sarah Robertson
- Department Forest Ecosystems & Society, Oregon State University, Corvallis, OR, USA
| | - Elahe Esfandiari
- Department Forest Ecosystems & Society, Oregon State University, Corvallis, OR, USA
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Steven H Strauss
- Department Forest Ecosystems & Society, Oregon State University, Corvallis, OR, USA
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17
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Telfer EJ, Stovold GT, Li Y, Silva-Junior OB, Grattapaglia DG, Dungey HS. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness. PLoS One 2015; 10:e0130601. [PMID: 26158446 PMCID: PMC4497620 DOI: 10.1371/journal.pone.0130601] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/21/2015] [Indexed: 12/28/2022] Open
Abstract
Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource available with the EuCHIP60k, opens a whole new array of opportunities for high-throughput, genome-wide or targeted genotyping in species of Eucalyptus.
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Affiliation(s)
- Emily J. Telfer
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Grahame T. Stovold
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Yongjun Li
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Orzenil B. Silva-Junior
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
| | - Dario G. Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, Brasília, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasilia, Brazil
| | - Heidi S. Dungey
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
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18
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Bartholomé J, Mandrou E, Mabiala A, Jenkins J, Nabihoudine I, Klopp C, Schmutz J, Plomion C, Gion JM. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. THE NEW PHYTOLOGIST 2015; 206:1283-96. [PMID: 25385325 DOI: 10.1111/nph.13150] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/29/2014] [Indexed: 05/21/2023]
Abstract
Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.
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Affiliation(s)
- Jérôme Bartholomé
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Eric Mandrou
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Ibouniyamine Nabihoudine
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Christophe Klopp
- Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
| | - Jean-Marc Gion
- CIRAD, UMR AGAP, F-33612, Cestas, France
- INRA, UMR1202 BIOGECO, F-33610, Cestas, France
- BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France
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Silva-Junior OB, Faria DA, Grattapaglia D. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species. THE NEW PHYTOLOGIST 2015; 206:1527-40. [PMID: 25684350 DOI: 10.1111/nph.13322] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/02/2015] [Indexed: 05/23/2023]
Abstract
We used whole genome resequencing of pooled individuals to develop a high-density single-nucleotide polymorphism (SNP) chip for Eucalyptus. Genomes of 240 trees of 12 species were sequenced at 3.5× each, and 46 997 586 raw SNP variants were subject to multivariable filtering metrics toward a multispecies, genome-wide distributed chip content. Of the 60 904 SNPs on the chip, 59 222 were genotyped and 51 204 were polymorphic across 14 Eucalyptus species, providing a 96% genome-wide coverage with 1 SNP/12-20 kb, and 47 069 SNPs at ≤ 10 kb from 30 444 of the 33 917 genes in the Eucalyptus genome. Given the EUChip60K multi-species genotyping flexibility, we show that both the sample size and taxonomic composition of cluster files impact heterozygous call specificity and sensitivity by benchmarking against 'gold standard' genotypes derived from deeply sequenced individual tree genomes. Thousands of SNPs were shared across species, likely representing ancient variants arisen before the split of these taxa, hinting to a recent eucalypt radiation. We show that the variable SNP filtering constraints allowed coverage of the entire site frequency spectrum, mitigating SNP ascertainment bias. The EUChip60K represents an outstanding tool with which to address population genomics questions in Eucalyptus and to empower genomic selection, GWAS and the broader study of complex trait variation in eucalypts.
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Affiliation(s)
- Orzenil B Silva-Junior
- Laboratório de Bioinformática, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
| | - Danielle A Faria
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
| | - Dario Grattapaglia
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, SGAN 916, 70790-160, Brasilia, DF, Brazil
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, 70770-970, Brasilia, DF, Brazil
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20
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Filippi CV, Aguirre N, Rivas JG, Zubrzycki J, Puebla A, Cordes D, Moreno MV, Fusari CM, Alvarez D, Heinz RA, Hopp HE, Paniego NB, Lia VV. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers. BMC PLANT BIOLOGY 2015; 15:52. [PMID: 25848813 PMCID: PMC4351844 DOI: 10.1186/s12870-014-0360-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 11/27/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. RESULTS The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. CONCLUSION The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent estimations of genetic diversity and population structure in sunflower breeding materials. The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation.
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Affiliation(s)
- Carla V Filippi
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia Aguirre
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Juan G Rivas
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Jeremias Zubrzycki
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Puebla
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Diego Cordes
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Maria V Moreno
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Corina M Fusari
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Currently at System Regulation Group, Metabolic Networks Department, Max Planck Institute of Molecular Plant Physiology, Am Mühlemberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Alvarez
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Ruth A Heinz
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Horacio E Hopp
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Norma B Paniego
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Veronica V Lia
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
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Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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22
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Karam MJ, Lefèvre F, Dagher-Kharrat MB, Pinosio S, Vendramin G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq. Mol Ecol Resour 2014; 15:601-12. [DOI: 10.1111/1755-0998.12329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 01/05/2023]
Affiliation(s)
- M.-J. Karam
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - F. Lefèvre
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - M. Bou Dagher-Kharrat
- Laboratoire Caractérisation Génomique des Plantes; Département Sciences de la Vie et de la Terre; Faculté des Sciences; Campus Sciences et Technologies; Université Saint-Joseph; Mar Roukos Mkalles Lebanon
| | - S. Pinosio
- Istituto di Genomica Applicata (IGA); Udine Italy
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
| | - G.G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
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23
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Grattapaglia D, Mamani EMC, Silva-Junior OB, Faria DA. A novel genome-wide microsatellite resource for species ofEucalyptuswith linkage-to-physical correspondence on the reference genome sequence. Mol Ecol Resour 2014; 15:437-48. [DOI: 10.1111/1755-0998.12317] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/05/2014] [Accepted: 08/13/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Dario Grattapaglia
- Laboratório de Genética Vegetal; EMBRAPA Recursos Genéticos e Biotecnologia; PqEB Brasilia DF 70770-970 Brazil
| | - Eva M. C. Mamani
- Laboratório de Genética Vegetal; EMBRAPA Recursos Genéticos e Biotecnologia; PqEB Brasilia DF 70770-970 Brazil
| | - Orzenil B. Silva-Junior
- Programa de Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; SGAN 916 Brasilia DF 70790-160 Brazil
- Laboratório de Bioinformática; EMBRAPA Recursos Genéticos e Biotecnologia; PqEB Brasilia DF 70770-970 Brazil
| | - Danielle A. Faria
- Laboratório de Genética Vegetal; EMBRAPA Recursos Genéticos e Biotecnologia; PqEB Brasilia DF 70770-970 Brazil
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24
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Lapègue S, Harrang E, Heurtebise S, Flahauw E, Donnadieu C, Gayral P, Ballenghien M, Genestout L, Barbotte L, Mahla R, Haffray P, Klopp C. Development of SNP-genotyping arrays in two shellfish species. Mol Ecol Resour 2014; 14:820-30. [DOI: 10.1111/1755-0998.12230] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/26/2013] [Accepted: 01/08/2014] [Indexed: 11/30/2022]
Affiliation(s)
- S. Lapègue
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - E. Harrang
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - S. Heurtebise
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - E. Flahauw
- Ifremer; SG2M-LGPMM; Laboratoire de Génétique et Pathologie des Mollusques Marins; La Tremblade France
| | - C. Donnadieu
- INRA UMR444; Laboratoire de Génétique Cellulaire; Plateforme GeT-PlaGe Genotoul; Castanet-Tolosan France
| | - P. Gayral
- CNRS UMR 5554; Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; Montpellier France
- CNRS UMR 7261; Institut de Recherche sur la Biologie de l'Insecte; Faculté des Sciences et Techniques; Université François Rabelais; Tours France
| | - M. Ballenghien
- CNRS UMR 5554; Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; Montpellier France
| | - L. Genestout
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - L. Barbotte
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - R. Mahla
- LABOGENA; Domaine de Vilvert; Jouy-en-Josas France
| | - P. Haffray
- SYSAAF; Station LPGP/INRA; Campus de Beaulieu; 35042 Rennes France
| | - C. Klopp
- INRA; Sigenae; UR875 Biométrie et Intelligence Artificielle; Castanet-Tolosan France
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25
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Wang JP, Naik PP, Chen HC, Shi R, Lin CY, Liu J, Shuford CM, Li Q, Sun YH, Tunlaya-Anukit S, Williams CM, Muddiman DC, Ducoste JJ, Sederoff RR, Chiang VL. Complete proteomic-based enzyme reaction and inhibition kinetics reveal how monolignol biosynthetic enzyme families affect metabolic flux and lignin in Populus trichocarpa. THE PLANT CELL 2014; 26:894-914. [PMID: 24619611 PMCID: PMC4001400 DOI: 10.1105/tpc.113.120881] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/12/2014] [Accepted: 02/12/2014] [Indexed: 05/17/2023]
Abstract
We established a predictive kinetic metabolic-flux model for the 21 enzymes and 24 metabolites of the monolignol biosynthetic pathway using Populus trichocarpa secondary differentiating xylem. To establish this model, a comprehensive study was performed to obtain the reaction and inhibition kinetic parameters of all 21 enzymes based on functional recombinant proteins. A total of 104 Michaelis-Menten kinetic parameters and 85 inhibition kinetic parameters were derived from these enzymes. Through mass spectrometry, we obtained the absolute quantities of all 21 pathway enzymes in the secondary differentiating xylem. This extensive experimental data set, generated from a single tissue specialized in wood formation, was used to construct the predictive kinetic metabolic-flux model to provide a comprehensive mathematical description of the monolignol biosynthetic pathway. The model was validated using experimental data from transgenic P. trichocarpa plants. The model predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis. This model provides an explanation of the effects of genetic and transgenic perturbations of the monolignol biosynthetic pathway in flowering plants.
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Affiliation(s)
- Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Punith P. Naik
- Civil, Construction, and Environmental Engineering, North
Carolina State University, Raleigh, North Carolina 27695
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Christopher M. Shuford
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- College of Forestry, Shandong Agricultural University,
Taian, Shandong 271018, China
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung-Hsing University,
Taichung, 40227, Taiwan
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Cranos M. Williams
- Electrical and Computer Engineering, North Carolina State
University, Raleigh, North Carolina 27695
| | - David C. Muddiman
- W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
| | - Joel J. Ducoste
- Civil, Construction, and Environmental Engineering, North
Carolina State University, Raleigh, North Carolina 27695
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding,
Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and
Environmental Resources, North Carolina State University, Raleigh, North Carolina
27695
- Department of Forest Biomaterials, North Carolina State
University, Raleigh, North Carolina 27695
- Address correspondence to
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26
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A high-density gene map of loblolly pine (Pinus taeda L.) based on exome sequence capture genotyping. G3-GENES GENOMES GENETICS 2014; 4:29-37. [PMID: 24192835 PMCID: PMC3887537 DOI: 10.1534/g3.113.008714] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Loblolly pine (Pinus taeda L.) is an economically and ecologically important conifer for which a suite of genomic resources is being generated. Despite recent attempts to sequence the large genome of conifers, their assembly and the positioning of genes remains largely incomplete. The interspecific synteny in pines suggests that a gene-based map would be useful to support genome assemblies and analysis of conifers. To establish a reference gene-based genetic map, we performed exome sequencing of 14729 genes on a mapping population of 72 haploid samples, generating a resource of 7434 sequence variants segregating for 3787 genes. Most markers are single-nucleotide polymorphisms, although short insertions/deletions and multiple nucleotide polymorphisms also were used. Marker segregation in the population was used to generate a high-density, gene-based genetic map. A total of 2841 genes were mapped to pine’s 12 linkage groups with an average of one marker every 0.58 cM. Capture data were used to detect gene presence/absence variations and position 65 genes on the map. We compared the marker order of genes previously mapped in loblolly pine and found high agreement. We estimated that 4123 genes had enough sequencing depth for reliable detection of markers, suggesting a high marker conversation rate of 92% (3787/4123). This is possible because a significant portion of the gene is captured and sequenced, increasing the chances of identifying a polymorphic site for characterization and mapping. This sub-centiMorgan genetic map provides a valuable resource for gene positioning on chromosomes and guide for the assembly of a reference pine genome.
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27
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Association genetics of chilling injury susceptibility in peach (Prunus persica (L.) Batsch) across multiple years. 3 Biotech 2013; 3:481-490. [PMID: 28324420 PMCID: PMC3824784 DOI: 10.1007/s13205-012-0109-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/13/2012] [Indexed: 11/22/2022] Open
Abstract
Peach and nectarine (Prunus persica L.) are highly perishable; they ripen and deteriorate quickly at ambient temperature. Storage at low temperature (0–5 °C) is a common strategy used to slow the ripening processes and to extend shelf life. However, if susceptible varieties are held too long at a low temperature, they will not ripen properly and will develop chilling injury (CI) symptoms like mealiness (M), flesh browning (FB), and flesh bleeding (FBL). Understanding the genetic control of these traits to produce CI resistant cultivars will greatly benefit producers, shippers and consumers. In this study, we evaluated a population of 51 individuals from Pop-DG across 4 years with CI traits observed in one or two time points to detect molecular marker association with selected 960 single-nucleotide polymorphisms (SNPs) from 1,536 SNPs chip. Genotypic and phenotypic data were analyzed by general linear model and mixed linear model to see comparative results from both analyses. Among 960 SNPs used, 22 SNPs were found associated with CI susceptibility traits like M, FB, and FBL. Many SNP markers were located in or close to previously reported quantitative trait loci mapped by linkage analysis.
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Montanari S, Saeed M, Knäbel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE, Perchepied L, Schaffer R, Wiedow C, Bus V, Brewer L, Gardiner SE, Crowhurst RN, Chagné D. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One 2013; 8:e77022. [PMID: 24155917 PMCID: PMC3796552 DOI: 10.1371/journal.pone.0077022] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/26/2013] [Indexed: 11/18/2022] Open
Abstract
We have used new generation sequencing (NGS) technologies to identify single nucleotide polymorphism (SNP) markers from three European pear (Pyrus communis L.) cultivars and subsequently developed a subset of 1096 pear SNPs into high throughput markers by combining them with the set of 7692 apple SNPs on the IRSC apple Infinium® II 8K array. We then evaluated this apple and pear Infinium® II 9K SNP array for large-scale genotyping in pear across several species, using both pear and apple SNPs. The segregating populations employed for array validation included a segregating population of European pear ('Old Home'×'Louise Bon Jersey') and four interspecific breeding families derived from Asian (P. pyrifolia Nakai and P. bretschneideri Rehd.) and European pear pedigrees. In total, we mapped 857 polymorphic pear markers to construct the first SNP-based genetic maps for pear, comprising 78% of the total pear SNPs included in the array. In addition, 1031 SNP markers derived from apple (13% of the total apple SNPs included in the array) were polymorphic and were mapped in one or more of the pear populations. These results are the first to demonstrate SNP transferability across the genera Malus and Pyrus. Our construction of high density SNP-based and gene-based genetic maps in pear represents an important step towards the identification of chromosomal regions associated with a range of horticultural characters, such as pest and disease resistance, orchard yield and fruit quality.
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Affiliation(s)
- Sara Montanari
- Istituto Agrario San Michele all'Adige Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy ; The New Zealand Institute for Plant & Food Research Limited (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand ; Institut National de la Recherche Agronomique (INRA), UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 Quasav, Pres L'UNAM, F-49071 Beaucouzé, France ; Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France ; AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045 Angers, France
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Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol 2013; 14:120. [PMID: 23796049 PMCID: PMC3706761 DOI: 10.1186/gb-2013-14-6-120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
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30
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Uitdewilligen JGAML, Wolters AMA, D’hoop BB, Borm TJA, Visser RGF, van Eck HJ. A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato. PLoS One 2013; 8:e62355. [PMID: 23667470 PMCID: PMC3648547 DOI: 10.1371/journal.pone.0062355] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 03/20/2013] [Indexed: 11/23/2022] Open
Abstract
Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1–3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60–80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
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Affiliation(s)
- Jan G. A. M. L. Uitdewilligen
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Anne-Marie A. Wolters
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Bjorn B. D’hoop
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
| | - Theo J. A. Borm
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
| | - Richard G. F. Visser
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
| | - Herman J. van Eck
- Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands
- The Graduate School for Experimental Plant Sciences, Wageningen, The Netherlands
- Centre for BioSystems Genomics, Wageningen, The Netherlands
- * E-mail:
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31
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Cardoso SD, Gonçalves D, Robalo JI, Almada VC, Canário AVM, Oliveira RF. Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats. Mar Genomics 2013; 11:11-6. [PMID: 23665344 DOI: 10.1016/j.margen.2013.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/17/2013] [Accepted: 04/18/2013] [Indexed: 12/12/2022]
Abstract
Transcriptome data are a good resource to develop microsatellites due to their potential in targeting candidate genes. However, developing microsatellites can be a time-consuming enterprise due to the numerous primer pairs to be tested. Therefore, the use of methodologies that make it efficient to identify polymorphic microsatellites is desirable. Here we used a 62,038 contigs transcriptome assembly, obtained from pyrosequencing a peacock blenny (Salaria pavo) multi-tissue cDNA library, to mine for microsatellites and in silico evaluation of their polymorphism. A total of 4190 microsatellites were identified in 3670 unique unigenes, and from these microsatellites, in silico polymorphism was detected in 733. We selected microsatellites based either on their in silico polymorphism and annotation results or based only on their number of repeats. Using these two approaches, 28 microsatellites were successfully amplified in twenty-six individuals, and all but 2 were found to be polymorphic, being the first genetic markers for this species. Our results showed that the strategy of selection based on number of repeats is more efficient in obtaining polymorphic microsatellites than the strategy of in silico polymorphism (allelic richness was 8.2±3.85 and 4.56±2.45 respectively). This study demonstrates that combining the knowledge of number of repeats with other predictors of variability, for example in silico microsatellite polymorphism, improves the rates of polymorphism, yielding microsatellites with higher allelic richness, and decreases the number of monomorphic microsatellites obtained.
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Affiliation(s)
- Sara D Cardoso
- Unidade de Investigação em Eco-Etologia, Instituto Superior de Psicologia Aplicada - Instituto Universitário, Rua Jardim do Tabaco, 34, 1149-041 Lisboa, Portugal.
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Pavy N, Gagnon F, Rigault P, Blais S, Deschênes A, Boyle B, Pelgas B, Deslauriers M, Clément S, Lavigne P, Lamothe M, Cooke JE, Jaramillo‐Correa JP, Beaulieu J, Isabel N, Mackay J, Bousquet J. Development of high‐density
SNP
genotyping arrays for white spruce (
P
icea glauca
) and transferability to subtropical and nordic congeners. Mol Ecol Resour 2013; 13:324-36. [DOI: 10.1111/1755-0998.12062] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 12/01/2012] [Accepted: 12/04/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - France Gagnon
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | | | - Sylvie Blais
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Astrid Deschênes
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Brian Boyle
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Betty Pelgas
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Marie Deslauriers
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Sébastien Clément
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Patricia Lavigne
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Manuel Lamothe
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - Janice E.K. Cooke
- Department of Biological Sciences CW405 Biological Sciences Building University of Alberta Edmonton Canada AB T6G 2E9
| | - Juan P. Jaramillo‐Correa
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Departamento de Ecología Evolutiva Instituto de Ecología Universidad Nacional Autónoma de México Apartado Postal 70‐275 México D.F. Mexico
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Wood Fibre Centre 1055 Rue du P.E.P.S., C.P. 10380 succ. Sainte‐Foy Québec Canada QC G1V 4C7
| | - Nathalie Isabel
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
- Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 Rue du P.E.P.S., C.P. 10380 succ, Sainte‐Foy Québec Canada QC G1V 4C7
| | - John Mackay
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics Centre for Forest Research and Institute for Systems and Integrative Biology Université Laval Québec Canada QC G1V 0A6
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Wong MML, Cannon CH, Wickneswari R. Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data. BMC Genomics 2012; 13:726. [PMID: 23265623 PMCID: PMC3556151 DOI: 10.1186/1471-2164-13-726] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 12/21/2012] [Indexed: 11/22/2022] Open
Abstract
Background Next Generation Sequencing has provided comprehensive, affordable and high-throughput DNA sequences for Single Nucleotide Polymorphism (SNP) discovery in Acacia auriculiformis and Acacia mangium. Like other non-model species, SNP detection and genotyping in Acacia are challenging due to lack of genome sequences. The main objective of this study is to develop the first high-throughput SNP genotyping assay for linkage map construction of A. auriculiformis x A. mangium hybrids. Results We identified a total of 37,786 putative SNPs by aligning short read transcriptome data from four parents of two Acacia hybrid mapping populations using Bowtie against 7,839 de novo transcriptome contigs. Given a set of 10 validated SNPs from two lignin genes, our in silico SNP detection approach is highly accurate (100%) compared to the traditional in vitro approach (44%). Further validation of 96 SNPs using Illumina GoldenGate Assay gave an overall assay success rate of 89.6% and conversion rate of 37.5%. We explored possible factors lowering assay success rate by predicting exon-intron boundaries and paralogous genes of Acacia contigs using Medicago truncatula genome as reference. This assessment revealed that presence of exon-intron boundary is the main cause (50%) of assay failure. Subsequent SNPs filtering and improved assay design resulted in assay success and conversion rate of 92.4% and 57.4%, respectively based on 768 SNPs genotyping. Analysis of clustering patterns revealed that 27.6% of the assays were not reproducible and flanking sequence might play a role in determining cluster compression. In addition, we identified a total of 258 and 319 polymorphic SNPs in A. auriculiformis and A. mangium natural germplasms, respectively. Conclusion We have successfully discovered a large number of SNP markers in A. auriculiformis x A. mangium hybrids using next generation transcriptome sequencing. By using a reference genome from the most closely related species, we converted most SNPs to successful assays. We also demonstrated that Illumina GoldenGate genotyping together with manual clustering can provide high quality genotypes for a non-model species like Acacia. These SNPs markers are not only important for linkage map construction, but will be very useful for hybrid discrimination and genetic diversity assessment of natural germplasms in the future.
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Affiliation(s)
- Melissa M L Wong
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi 43600, Selangor, Malaysia
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Shahin A, van Kaauwen M, Esselink D, Bargsten JW, van Tuyl JM, Visser RGF, Arens P. Generation and analysis of expressed sequence tags in the extreme large genomes Lilium and Tulipa. BMC Genomics 2012; 13:640. [PMID: 23167289 PMCID: PMC3576253 DOI: 10.1186/1471-2164-13-640] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Bulbous flowers such as lily and tulip (Liliaceae family) are monocot perennial herbs that are economically very important ornamental plants worldwide. However, there are hardly any genetic studies performed and genomic resources are lacking. To build genomic resources and develop tools to speed up the breeding in both crops, next generation sequencing was implemented. We sequenced and assembled transcriptomes of four lily and five tulip genotypes using 454 pyro-sequencing technology. RESULTS Successfully, we developed the first set of 81,791 contigs with an average length of 514 bp for tulip, and enriched the very limited number of 3,329 available ESTs (Expressed Sequence Tags) for lily with 52,172 contigs with an average length of 555 bp. The contigs together with singletons covered on average 37% of lily and 39% of tulip estimated transcriptome. Mining lily and tulip sequence data for SSRs (Simple Sequence Repeats) showed that di-nucleotide repeats were twice more abundant in UTRs (UnTranslated Regions) compared to coding regions, while tri-nucleotide repeats were equally spread over coding and UTR regions. Two sets of single nucleotide polymorphism (SNP) markers suitable for high throughput genotyping were developed. In the first set, no SNPs flanking the target SNP (50 bp on either side) were allowed. In the second set, one SNP in the flanking regions was allowed, which resulted in a 2 to 3 fold increase in SNP marker numbers compared with the first set. Orthologous groups between the two flower bulbs: lily and tulip (12,017 groups) and among the three monocot species: lily, tulip, and rice (6,900 groups) were determined using OrthoMCL. Orthologous groups were screened for common SNP markers and EST-SSRs to study synteny between lily and tulip, which resulted in 113 common SNP markers and 292 common EST-SSR. Lily and tulip contigs generated were annotated and described according to Gene Ontology terminology. CONCLUSIONS Two transcriptome sets were built that are valuable resources for marker development, comparative genomic studies and candidate gene approaches. Next generation sequencing of leaf transcriptome is very effective; however, deeper sequencing and using more tissues and stages is advisable for extended comparative studies.
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Affiliation(s)
- Arwa Shahin
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Martijn van Kaauwen
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Danny Esselink
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Joachim W Bargsten
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
- Netherlands Bioinformatics Centre, Geert Grooteplein 28, Nijmegen, 6525 GA, The Netherlands
- Applied Bioinformatics, Plant Research International, PO Box 619, Wageningen, 6700 AP, The Netherlands
| | - Jaap M van Tuyl
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Richard GF Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
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Loridon K, Burgarella C, Chantret N, Martins F, Gouzy J, Prospéri JM, Ronfort J. Single-nucleotide polymorphism discovery and diversity in the model legume Medicago truncatula. Mol Ecol Resour 2012; 13:84-95. [PMID: 23017123 DOI: 10.1111/1755-0998.12021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 08/16/2012] [Accepted: 08/20/2012] [Indexed: 01/09/2023]
Abstract
Extensive genomic resources are available in the model legume Medicago truncatula. Here, we present the discovery and design of the first array of single-nucleotide polymorphism (SNP) markers in M. truncatula through large-scale Sanger resequencing of genomic fragments spanning the genome, in a diverse panel of 16 M. truncatula accessions. Both anonymous fragments and fragments targeting candidate genes for flowering phenology and symbiosis were surveyed for nucleotide variation in almost 230 kb of unique genomic regions. A set of 384 SNP markers was designed for an Illumina's GoldenGate assay, genotyped on a collection of 192 inbred lines (CC192) representing the geographical range of the species and used to survey the diversity of two natural populations. Finally, 86% of the tested SNPs were of high quality and exhibited polymorphism in the CC192 collection. Even at the population level, we detected polymorphism for more than 50% of the selected SNPs. Analysis of the allele frequency spectrum in the CC192 showed a reduced ascertainment bias, mostly limited to very rare alleles (frequency <0.01). The substantial polymorphism detected at the species and population levels, the high marker quality and the potential to survey large samples of individuals make this set of SNP markers a valuable tool to improve our understanding of the effect of demographic and selective factors that shape the natural genetic diversity within the selfing species Medicago truncatula.
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Affiliation(s)
- Karine Loridon
- INRA, UMR AGAP, 2 place Pierre Viala, F-34060, Montpellier Cedex 1, France.
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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
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Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 2012; 19:357-73. [PMID: 22864163 PMCID: PMC3473369 DOI: 10.1093/dnares/dss018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
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Hendre PS, Kamalakannan R, Varghese M. High-throughput and parallel SNP discovery in selected candidate genes in Eucalyptus camaldulensis using Illumina NGS platform. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:646-56. [PMID: 22607345 DOI: 10.1111/j.1467-7652.2012.00699.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Next generation sequencing (NGS) technologies have revolutionized the pace and scale of genomics- and transcriptomics-based SNP discovery across different plant and animal species. Herein, 72-base paired-end Illumina sequencing was employed for high-throughput, parallel and large-scale SNP discovery in 41 growth-related candidate genes in Eucalyptus camaldulensis. Approximately 100 kb of genome from 96 individuals was amplified and sequenced using a hierarchical DNA/PCR pooling strategy and assembled over corresponding E. grandis reference. A total of 1191 SNPs (minimum 5% other allele frequency) were identified with an average frequency of 1 SNP/83.9 bp, whereas in exons and introns, it was 1 SNP/108.4 bp and 1 SNP/65.6 bp, respectively. A total of 75 insertions and 89 deletions were detected of which approximately 15% were exonic. Transitions (Tr) were in excess than transversions (Tv) (Tr/Tv: 1.89), but exceeded in exons (Tr/Tv: 2.73). In exons, synonymous SNPs (Ka) prevailed over the non-synonymous SNPs (Ks; average Ka/Ks ratio: 0.72, range: 0-3.00 across genes). Many of the exonic SNPs/indels had potential to change amino acid sequence of respective genes. Transcription factors appeared more conserved, whereas enzyme coding genes appeared under relaxed control. Further, 541 SNPs were classified into 196 'equal frequency' (EF) blocks with almost similar minor allele frequencies to facilitate selection of one tag-SNP/EF-block. There were 241 (approximately 20%) 'zero-SNP' blocks with absence of SNPs in surrounding ±60 bp windows. The data thus indicated enormous extant and unexplored diversity in E. camaldulensis in the studied genes with potential applications for marker-trait associations.
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Affiliation(s)
- Prasad S Hendre
- ITC R&D Centre, Peenya Industrial Area, Bangalore, Karnataka, India.
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Hoffman JI, Tucker R, Bridgett SJ, Clark MS, Forcada J, Slate J. Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Mol Ecol Resour 2012; 12:861-72. [PMID: 22727236 DOI: 10.1111/j.1755-0998.2012.03158.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although single nucleotide polymorphisms (SNPs) are increasingly being recognized as powerful molecular markers, their application to non-model organisms can bring significant challenges. Among these are imperfect conversion rates of assays designed from in silico resources and the enhanced potential for genotyping error relative to pre-validated, highly optimized human SNPs. To explore these issues, we used Illumina's GoldenGate assay to genotype 480 Antarctic fur seal (Arctocephalus gazella) individuals at 144 putative SNPs derived from a 454 transcriptome assembly. One hundred and thirty-five polymorphic SNPs (93.8%) were automatically validated by the program GenomeStudio, and the initial genotyping error rate, estimated from nine replicate samples, was 0.004 per reaction. However, an almost tenfold further reduction in the error rate was achieved by excluding 31 loci (21.5%) that exhibited unclear clustering patterns, manually editing clusters to allow rescoring of ambiguous or incorrect genotypes, and excluding 18 samples (3.8%) with unreliable genotypes. After stringent quality filtering, we also found a counter-intuitive negative relationship between in silico minor allele frequency and the conversion rate, suggesting that some of our assays may have been designed from paralogous loci. Nevertheless, we obtained over 45 000 individual SNP genotypes with a final error rate of 0.0005, indicating that the GoldenGate assay is eminently capable of generating large, high-quality data sets for non-model organisms. This has positive implications for future studies of the evolutionary, behavioural and conservation genetics of natural populations.
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Affiliation(s)
- J I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany.
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Hudson CJ, Freeman JS, Kullan ARK, Petroli CD, Sansaloni CP, Kilian A, Detering F, Grattapaglia D, Potts BM, Myburg AA, Vaillancourt RE. A reference linkage map for Eucalyptus. BMC Genomics 2012; 13:240. [PMID: 22702473 PMCID: PMC3436727 DOI: 10.1186/1471-2164-13-240] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 06/04/2012] [Indexed: 01/26/2023] Open
Abstract
Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.
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Affiliation(s)
- Corey J Hudson
- School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia.
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Hand ML, Cogan NOI, Forster JW. Genome-wide SNP identification in multiple morphotypes of allohexaploid tall fescue (Festuca arundinacea Schreb). BMC Genomics 2012; 13:219. [PMID: 22672128 PMCID: PMC3444928 DOI: 10.1186/1471-2164-13-219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/15/2012] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) provide essential tools for the advancement of research in plant genomics, and the development of SNP resources for many species has been accelerated by the capabilities of second-generation sequencing technologies. The current study aimed to develop and use a novel bioinformatic pipeline to generate a comprehensive collection of SNP markers within the agriculturally important pasture grass tall fescue; an outbreeding allopolyploid species displaying three distinct morphotypes: Continental, Mediterranean and rhizomatous. RESULTS A bioinformatic pipeline was developed that successfully identified SNPs within genotypes from distinct tall fescue morphotypes, following the sequencing of 414 polymerase chain reaction (PCR) - generated amplicons using 454 GS FLX technology. Equivalent amplicon sets were derived from representative genotypes of each morphotype, including six Continental, five Mediterranean and one rhizomatous. A total of 8,584 and 2,292 SNPs were identified with high confidence within the Continental and Mediterranean morphotypes respectively. The success of the bioinformatic approach was demonstrated through validation (at a rate of 70%) of a subset of 141 SNPs using both SNaPshot™ and GoldenGate™ assay chemistries. Furthermore, the quantitative genotyping capability of the GoldenGate™ assay revealed that approximately 30% of the putative SNPs were accessible to co-dominant scoring, despite the hexaploid genome structure. The sub-genome-specific origin of each SNP validated from Continental tall fescue was predicted using a phylogenetic approach based on comparison with orthologous sequences from predicted progenitor species. CONCLUSIONS Using the appropriate bioinformatic approach, amplicon resequencing based on 454 GS FLX technology is an effective method for the identification of polymorphic SNPs within the genomes of Continental and Mediterranean tall fescue. The GoldenGate™ assay is capable of high-throughput co-dominant SNP allele detection, and minimises the problems associated with SNP genotyping in a polyploid by effectively reducing the complexity to a diploid system. This SNP collection may now be refined and used in applications such as cultivar identification, genetic linkage map construction, genome-wide association studies and genomic selection in tall fescue. The bioinformatic pipeline described here represents an effective general method for SNP discovery within outbreeding allopolyploid species.
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Affiliation(s)
- Melanie L Hand
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, 1 Park Drive, La Trobe University Research and Development Park, Bundoora, VIC 3083, Australia
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Studer B, Byrne S, Nielsen RO, Panitz F, Bendixen C, Islam MS, Pfeifer M, Lübberstedt T, Asp T. A transcriptome map of perennial ryegrass (Lolium perenne L.). BMC Genomics 2012; 13:140. [PMID: 22513206 PMCID: PMC3483695 DOI: 10.1186/1471-2164-13-140] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/18/2012] [Indexed: 01/26/2023] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass. Results A perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome. Conclusions Here, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.
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Affiliation(s)
- Bruno Studer
- Department of Molecular Biology and Genetics, Faculty of Science and Technology, Research Centre Flakkebjerg, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
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Nieminen K, Robischon M, Immanen J, Helariutta Y. Towards optimizing wood development in bioenergy trees. THE NEW PHYTOLOGIST 2012; 194:46-53. [PMID: 22474686 DOI: 10.1111/j.1469-8137.2011.04011.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
To secure a sustainable energy source for the future, we need to develop an alternative to fossil fuels. Cellulose-based biofuel production has great potential for development into a sustainable and renewable energy source. The thick secondary walls of xylem cells provide a natural source of cellulose. As a result of the extensive production of wood through cambial activity, massive amounts of xylem cells can be harvested from trees. How can we obtain a maximal cellulose biomass yield from these trees? Thus far, tree breeding has been very challenging because of the long generation time. Currently, new breeding possibilities are emerging through the development of high-throughput technologies in molecular genetics. What potential does our current knowledge on the regulation of cambial activity provide for the domestication of optimal bioenergy trees? We examine the hormonal and molecular regulation of wood development with the aim of identifying the key regulatory aspects. We describe traits, including stem morphology and xylem cell dimensions, that could be modified to enhance wood production. Finally, we discuss the potential of novel marker-assisted tree breeding technologies.
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Affiliation(s)
- Kaisa Nieminen
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
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Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C. Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 2012; 7:e31745. [PMID: 22363718 PMCID: PMC3283661 DOI: 10.1371/journal.pone.0031745] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/12/2012] [Indexed: 01/07/2023] Open
Abstract
As high-throughput genetic marker screening systems are essential for a range of genetics studies and plant breeding applications, the International RosBREED SNP Consortium (IRSC) has utilized the Illumina Infinium® II system to develop a medium- to high-throughput SNP screening tool for genome-wide evaluation of allelic variation in apple (Malus×domestica) breeding germplasm. For genome-wide SNP discovery, 27 apple cultivars were chosen to represent worldwide breeding germplasm and re-sequenced at low coverage with the Illumina Genome Analyzer II. Following alignment of these sequences to the whole genome sequence of ‘Golden Delicious’, SNPs were identified using SoapSNP. A total of 2,113,120 SNPs were detected, corresponding to one SNP to every 288 bp of the genome. The Illumina GoldenGate® assay was then used to validate a subset of 144 SNPs with a range of characteristics, using a set of 160 apple accessions. This validation assay enabled fine-tuning of the final subset of SNPs for the Illumina Infinium® II system. The set of stringent filtering criteria developed allowed choice of a set of SNPs that not only exhibited an even distribution across the apple genome and a range of minor allele frequencies to ensure utility across germplasm, but also were located in putative exonic regions to maximize genotyping success rate. A total of 7867 apple SNPs was established for the IRSC apple 8K SNP array v1, of which 5554 were polymorphic after evaluation in segregating families and a germplasm collection. This publicly available genomics resource will provide an unprecedented resolution of SNP haplotypes, which will enable marker-locus-trait association discovery, description of the genetic architecture of quantitative traits, investigation of genetic variation (neutral and functional), and genomic selection in apple.
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Affiliation(s)
- David Chagné
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Ross N. Crowhurst
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Michela Troggio
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Mark W. Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Barbara Gilmore
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cindy Lawley
- Illumina Inc., Hayward, California, United States of America
| | - Stijn Vanderzande
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Heverlee, Leuven, Belgium
| | - Roger P. Hellens
- Plant and Food Research, Mount Albert Research Centre, Auckland, New Zealand
| | - Satish Kumar
- Plant and Food Research, Hawke's Bay Research Centre, Havelock North, New Zealand
| | - Alessandro Cestaro
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Riccardo Velasco
- IASMA Research and Innovation Centre, Foundation Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Dorrie Main
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
| | - Jasper D. Rees
- Agricultural Research Council, Onderstepoort, South Africa
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, Michigan, United States of America
| | - Todd Mockler
- The Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Larry Wilhelm
- Oregon Health Sciences University, Portland, Oregon, United States of America
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Susan E. Gardiner
- Plant and Food Research, Palmerston North Research Centre, Palmerston North, New Zealand
| | - Nahla Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, Oregon, United States of America
| | - Cameron Peace
- Department of Horticulture and Landscape Architecture, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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Abstract
More than 70 years after the first ex situ genebanks have been established, major efforts in this field are still concerned with issues related to further completion of individual collections and securing of their storage. Attempts regarding valorization of ex situ collections for plant breeders have been hampered by the limited availability of phenotypic and genotypic information. With the advent of molecular marker technologies first efforts were made to fingerprint genebank accessions, albeit on a very small scale and mostly based on inadequate DNA marker systems. Advances in DNA sequencing technology and the development of high-throughput systems for multiparallel interrogation of thousands of single nucleotide polymorphisms (SNPs) now provide a suite of technological platforms facilitating the analysis of several hundred of Gigabases per day using state-of-the-art sequencing technology or, at the same time, of thousands of SNPs. The present review summarizes recent developments regarding the deployment of these technologies for the analysis of plant genetic resources, in order to identify patterns of genetic diversity, map quantitative traits and mine novel alleles from the vast amount of genetic resources maintained in genebanks around the world. It also refers to the various shortcomings and bottlenecks that need to be overcome to leverage the full potential of high-throughput DNA analysis for the targeted utilization of plant genetic resources.
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Affiliation(s)
- Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Genebank/Genome Diversity, Corrensstrasse 3, 06466 Gatersleben, Germany.
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Sexton TR, Henry RJ, Harwood CE, Thomas DS, McManus LJ, Raymond C, Henson M, Shepherd M. Pectin Methylesterase genes influence solid wood properties of Eucalyptus pilularis. PLANT PHYSIOLOGY 2012; 158:531-41. [PMID: 22052017 PMCID: PMC3252102 DOI: 10.1104/pp.111.181602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/25/2011] [Indexed: 05/17/2023]
Abstract
This association study of Eucalyptus pilularis populations provides empirical evidence for the role of Pectin Methylesterase (PME) in influencing solid wood characteristics of Eucalyptus. PME6 was primarily associated with the shrinkage and collapse of drying timber, which are phenotypic traits consistent with the role of pectin as a hydrophilic polysaccharide. PME7 was primarily associated with cellulose and pulp yield traits and had an inverse correlation with lignin content. Selection of specific alleles in these genes may be important for improving trees as sources of high-quality wood products. A heterozygote advantage was postulated for the PME7 loci and, in combination with haplotype blocks, may explain the absence of a homozygous class at all single-nucleotide polymorphisms investigated in this gene.
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Affiliation(s)
- Timothy R Sexton
- Cooperative Research Centre for Forestry, Hobart, Tasmania 7001, Australia.
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Dal-Bianco M, Carneiro MS, Hotta CT, Chapola RG, Hoffmann HP, Garcia AAF, Souza GM. Sugarcane improvement: how far can we go? Curr Opin Biotechnol 2011; 23:265-70. [PMID: 21983270 DOI: 10.1016/j.copbio.2011.09.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/26/2011] [Accepted: 09/13/2011] [Indexed: 01/05/2023]
Abstract
In recent years, efforts to improve sugarcane have focused on the development of biotechnology for this crop. It has become clear that sugarcane lacks tools for the biotechnological route of improvement and that the initial efforts in sequencing ESTs had limited impact for breeding. Until recently, the models used by breeders in statistical genetics approaches have been developed for diploid organisms, which are not ideal for a polyploid genome such as that of sugarcane. Breeding programs are dealing with decreasing yield gains. The contribution of multiple alleles to complex traits such as yield is a basic question underlining the breeding efforts that could only be addressed by the development of specific tools for this grass. However, functional genomics has progressed and gene expression profiling is leading to the definition of gene networks. The sequencing of the sugarcane genome, which is underway, will greatly contribute to numerous aspects of research on grasses. We expect that both the transgenic and the marker-assisted route for sugarcane improvement will contribute to increased sugar, stress tolerance, and higher yield and that the industry for years to come will be able to rely on sugarcane as the most productive energy crop.
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Affiliation(s)
- Maximiller Dal-Bianco
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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Silva-Junior OB, Rosado TB, Laviola BG, Pappas MR, Pappas GJ, Grattapaglia D. Genome-wide SNP discovery from a pooled sample of accessions of the biofuel plant Jatropha curcasbased on whole-transcriptome Illumina resequencing. BMC Proc 2011. [PMCID: PMC3240079 DOI: 10.1186/1753-6561-5-s7-p57] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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Grattapaglia D, de Alencar S, Pappas G. Genome-wide genotyping and SNP discovery by ultra-deep Restriction-Associated DNA (RAD) tag sequencing of pooled samples of E. grandis and E. globulus. BMC Proc 2011. [PMCID: PMC3240066 DOI: 10.1186/1753-6561-5-s7-p45] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Correia L, Faria D, Grattapaglia D. Comparative assessment of SNPs and microsatellites for fingerprinting, parentage and assignment testing in species of Eucalyptus. BMC Proc 2011. [PMCID: PMC3240062 DOI: 10.1186/1753-6561-5-s7-p41] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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