From Phenomics to Genomics: Macro-GWAS of Almond Morphology and Quality

Abstract

Abstract In plant breeding and genetics, recent advances in high-throughput phenotyping are beginning to meet the growing demand for large-scale, high-quality phenotypic data that emerged after the development of next-generation sequencing technologies. Recent developments in phenomics have been incorporated into almond breeding programs, facilitating the large-scale acquisition of quantitative phenotypes and the dissection of the genetic architecture underlying morphological and quality-related traits. The implementation of a high-throughput phenotyping platform integrating RGB and hyperspectral imaging with genotyping using the 60K almond SNP array enabled the large-scale characterization of almond populations and the identification of 567 robust marker–trait associations across 66 traits. These analyses revealed two major genomic hotspots on chromosomes 2 and 5 associated with morphological and quality-related traits. These regions harbored biologically relevant candidate genes, including genes associated with OVATE family proteins, brassinosteroid signaling, protein ubiquitination, and acyl-CoA metabolism, as well as other regulators of organ growth, cell proliferation, hormone signaling, and seed development. Furthermore, a novel candidate gene encoding a COMT-like O-methyltransferase involved in lignin biosynthesis was identified and proposed to contribute to shell hardness, a major genetically controlled trait in almond. Together, these findings demonstrate the potential of integrating high-throughput phenomics and genomics to dissect complex traits, identify candidate genes, and accelerate genomics-informed breeding in almond.

Plant phenotyping relevance

RGB・ハイパースペクトル画像を統合した高スループット表現型解析プラットフォームの実装と大規模形質取得が研究の主要部分であり、単なる形質のルーチン測定ではない。

Code and data availability

The supplied blocks describe the almond phenotyping/GWAS pipeline (RGB and hyperspectral imaging, EFA, PLS models, GWAS with supplementary tables) but contain no public deposit, availability statement, or URL for phenotype datasets, images, code, or models. Only the paper's own DOI appears; supplementary tables are not

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