Fricano, A. | Search bioRxiv

bioRxiv2026

Development of the 4TREE SNP array, a forest multispecies array to enhance European Breeding and conservation programs in pine, poplar and ash.

Within the framework of the European Adaptive BREEDING for Better FORESTs project (B4EST, https://b4est.eu/), we have developed genotyping tools for Poplar, Ash, and Pine forest tree species. SNP arrays are attractive genotyping tools because of the user-friendly genotype calling system and the robust transferability among laboratories. Here we describe the development of an Axiom SNP array for Pinus pinaster (13,407 SNPs), Pinus pinea (5,671 SNPs), Poplar spp. (13,408 SNPs), and Fraxinus spp. (13,407 SNPs) based on a two-step process. We first assembled a high-density (>100,000 SNPs/species) screening array that served to test a large panel of candidate SNPs on a diversity panel involving at least 120 individual trees per species or species group. In the second step, we selected and combined the most informative SNPs to build the final 50,000 SNP 4TREE array. This approach resulted in high genotyping success rates, including for species lacking previously validated high-quality SNP resources. The 4TREE SNP array provides a valuable and transferable genomic tool to support genomic prediction, breeding, and adaptive management of forest tree species.

genomics↗

bioRxiv2021

Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. We report the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. We show that the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group-, and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. We discuss the origin and domestication history of the GGAtAt lineages in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool. We provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

evolutionary biology↗