Harnessing cytonuclear diversity to map barley spike traits using the Cytonuclear Multi-Parent Population.

作者：Schewach Bodenheimer, E. Bdolach, Avital Be'ery, L. D. Tiwari, R. S. Perez-Alfaro, Shengming Yang, Daniel Koenig, E. Fridman · 发表于：Genetics · 年份：2025 · DOI：10.1093/genetics/iyaf167 · 被引用次数：2 · 研究领域：Medicine

The interplay between nuclear and cytoplasmic genomes, collectively known as cytonuclear interactions (CNIs), is increasingly recognized as a key driver of phenotypic variation and adaptive potential across diverse organisms. Yet, leveraging cytoplasmic diversity and fully understanding the role of CNIs in agriculturally important traits remain major challenges in crop improvement. Here, we present the Cytonuclear Multi-Parent Population (CMPP), a novel interspecific resource comprising 951 doubled haploid lines, generated from two backcrosses between ten genetically diverse wild barley accessions (Hordeum vulgare ssp. spontaneum) used as female founders and the elite cultivar Noga (H. vulgare). Phenotyping across multiple environments revealed that up to 5% of variation in key spike and grain trait values are explained by cytoplasm (η² = 0.05). Notably, wild cytoplasms influenced trait stability, with the B1K-50-04 cytoplasm increasing grain weight stability based on Shukla's measure. Genome-wide association studies employing Nested Association Mapping (NAM), FASTmrMLM, and MatrixEpistasis (ME) identified 76 marker-trait associations (MTAs). The ME approach specifically uncovered 16 cytonuclear QTL (cnQTL) exhibiting cytoplasm-dependent effects. Furthermore, we developed a genomic prediction strategy incorporating interactions between significant MTAs and population structure variables (subfamily and cytoplasm), which achieved cross-validation accuracies comparable to, or ev...