Genetic diversity assessment and genomic prediction in alder (Alnus glutinosa) to support seed orchard improvement and sustainable forestry

Alnus glutinosa (L.) Gaertn (also known as common alder and black alder) is an important broadleaf species in Europe, valued for its ecological functions in riparian ecosystems and its versatile hardwood timber. Despite its importance, natural regeneration and productivity have declined due to habitat fragmentation and the spread of the pathogen Phytophthora alni . To support a sustainable supply of improved planting material, a national breeding programme was established in Ireland. In this study, we evaluated growth traits of 80 half-sib families derived from 103 selected plus-trees under field conditions and applied genome-wide single nucleotide polymorphism (SNP) markers to assess genetic diversity and perform genomic prediction of growth performance. The progeny trial revealed considerable variation in height and diameter-at-breast-height (DBH), with heritability estimates ranging from 0.45 to 0.53 for relative growth in height, and from 0.28 to 0.31 for DBH across different periods. Genotyping-by-sequencing (GBS) of 103 plus-trees genotyped identified 95,139 SNP markers, revealing high genetic diversity and no evidence of inbreeding, confirming the broad genetic base of the Irish breeding population. Genomic prediction using genome-wide markers provided low-to-moderate predictive ability for height and negligible predictive ability for DBH, reflecting the limitation of small training population size and relatedness. However, the markers demonstrated immediate value for diversity monitoring and seed orchard management. These findings identify superior A. glutinosa genotypes and provide a genomic framework for improving existing seed orchards and supporting sustainable forestry through enhanced A. glutinosa breeding.