Data and Resources
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Additional Info
| Field | Value |
|---|---|
| Title | Genotyping-by-sequencing of 103 Irish black alder trees |
| License | Licence Not Specified | Teagasc Department | Forestry Development |
| Teagasc Programme | Crops, Environment and Land Use |
| Description | This dataset has two linked parts from the Irish A. glutinosa breeding and improvement programme, begun in 2005. (1) Genotyping-by-sequencing (GBS) reads from 103 plus-trees held in the Teagasc Oak Park clonal gene-bank (NCBI SRA). After variant calling and filtering these yielded 95,139 SNPs, which were used to assess genetic diversity, population structure and genomic relatedness. (2) Height and diameter-at-breast-height (DBH) measurements, 2008-2020, from a replicated half-sib progeny trial at Corcovety, Co. Cavan, with R scripts for data processing and genomic prediction (Zenodo). The trial holds 88 open-pollinated half-sib families raised from plus-tree seed plus one commercial seed control. The plus-trees showed high genetic diversity and no evidence of inbreeding. Heritability of relative growth was 0.45-0.53 for height and 0.28-0.31 for DBH. Genomic prediction (GBLUP) gave low-to-moderate predictive ability for height and negligible predictive ability for DBH. |
| Language | English |
| Principal Investigator (PI) | Dr Dheeraj Singh Rathore |
| Principal Investigator (PI) email | dheeraj.rathore@teagasc.ie |
| Data creator(s) |
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| Citation | Huang, J., Byrne, S., Oliver, S., Byrne, T., Hodkinson, T., Kelleher, C., Barth, S., Nemesio Gorriz, M., & Rathore, D. S. (2025). Data related to: "Genetic diversity and genomic prediction in alder (Alnus glutinosa) to support seed orchard improvement and sustainable forestry" [Dataset]. Zenodo |
| Landing page | https://zenodo.org/records/17698837 |
| Project funders | Teagasc Walsh Scholarship programme (grant 2021036). The Department of Agriculture, Food and the Marine (DAFM) supported the underlying alder research programmes. |
| Related resources |
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| Equipment used | * Illumina NextSeq, 150 bp paired-end (LGC, Berlin); MslI restriction enzyme (NEB) * BWA; bcftools (mpileup, call); VCFtools; Beagle 5.5 (versions of the first three not reported) * R 4.5.2; packages lme4, emmeans 2.0.1, sommer, adegenet, hierfstat, rrBLUP, pheatmap 1.0.13 * Haglöf Vertex 5 hypsometer (height); DBH measuring tape, 2 m, circumference-to-diameter (Kestrel Forestry) * Standards and calibration information, if appropriate: Not reported * Environmental/experimental conditions: - Progeny trial, Corcovety, Co. Cavan: poorly drained clay loam; 80 m elevation; mean annual temperature 9.4 C; annual precipitation 976 mm (Met Éireann) - Gene-bank, Oak Park, Co. Carlow: well-drained grey brown podzolic soil; 59 m elevation; mean annual temperature 11.2 C; annual precipitation 936.4 mm - Ethics approval not applicable; plant collection under landowner consent, institutional permissions and a DAFM seed collection licence * Describe any quality-assurance procedures performed on the data: Expert confirmation of species identity and an archived voucher specimen; living clonal reference copies kept in the gene-bank; SNP quality filters as above; heritability adjusted for unbalanced data from mortality (adjusted trees per family per block); 500-iteration cross-validation of genomic prediction. |
| Provenance information | Plus-tree selection: from October 2005, 114 plus-trees (90 in 2005) were selected from wild and plantation stands across Ireland, in collaboration with Coillte and private landowners. Trees had to be mature, healthy, straight-stemmed, symmetrically branched and of high timber volume (13-23 m tall, DBH 30-99 cm), and were sampled at least 50 m apart to reduce relatedness. Species identity was confirmed by D. S. Rathore and O. Sheridan with T. R. Hodkinson (TCD) and C. Kelleher (National Botanic Gardens), using Parnell & Curtis (Webb's An Irish Flora). Progeny trial: open-pollinated seed was collected from plus-trees in 2006, under a DAFM seed collection licence, and sown in 2007. The trial at Corcovety, Co. Cavan was planted in spring 2008 on a strip-ploughed drumlin. Layout: RCBD, 3 blocks, 9-tree plots (3 x 3), 2 m x 2 m spacing, two guard rows per block, no thinning since planting. Height was measured with a Haglöf Vertex 5 hypsometer and DBH with a DBH tape. Clonal gene-bank: scion wood of 103 plus-trees was grafted in early spring 2014, grown in a glasshouse and planted at Teagasc Oak Park at 4 m x 3 m spacing. Genotyping: six 0.6 cm leaf discs per plus-tree were freeze-dried for 72 h and sent to LGC (Berlin) in BioArk leaf sampling kits. LGC carried out DNA extraction, GBS library construction (MslI restriction enzyme, NEB) and Illumina NextSeq sequencing, 150 bp paired-end. |