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Genotyping-by-sequencing of 103 Irish black alder trees

Published by: Teagasc
Licensed under: Licence Not Specified
Category: Agriculture
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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.

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Data Owner Dr Dheeraj Singh Rathore
Data Owner Email dheeraj.rathore@teagasc.ie
Theme Agriculture
Language English
Landing page https://zenodo.org/records/17698837
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.
High Value Dataset (HVD) No