Genome-wide Runs of Homozygosity Islands Uncover Candidate Genes Involved in Stress Response in Pistacia Vera

Document Type : Research Article

Authors

1 Department of Plant Genetics and Production Engineering, University of Mohaghegh Ardabili, Ardabil, Iran

2 Department of Animal Science, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran

3 Department of Animal Science Research, Ardabil Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Ardabil, Iran

4 Department of Agronomy and Plant Breeding, Agriculture Institute, Research Institute of Zabol, Zabol, Iran

Abstract

Pistacia vera L. is a perennial tree species of significant economic importance, exhibiting natural adaptation to arid and semi-arid environments. Elucidating the genomic underpinnings of this adaptation is crucial for enhancing stress resilience and facilitating breeding programs. This study employed whole-genome sequencing data from 31 Iranian pistachio samples to characterize runs of homozygosity (ROHs) and identify genomic regions potentially shaped by selective pressures. A total of 3597 ROHs were detected, predominantly comprising short segments (<200 kb), which reflect both the scaffold-level genome assembly and historical recombination patterns. The overall genomic inbreeding coefficient (FROH) was low (mean = 0.026), suggesting limited recent inbreeding within the studied accessions. Utilizing SNP frequency-based criteria, 48 ROH islands were identified across 44 scaffolds, representing localized regions of elevated homozygosity. Functional annotation of these regions revealed 589 protein-coding genes, many of which are associated with stress responses, hormonal regulation, metabolism, and development. Notably, genes such as HDAC9, implicated in epigenetic regulation under heat stress; NCED6 and PSY2, key components of abscisic acid and carotenoid biosynthesis pathways, respectively; AAE3, linked to oxalate metabolism and tolerance to biotic and abiotic stresses; TPR1, associated with drought response; and ATG5, a central regulator of autophagy under diverse stress conditions, were localized within ROH islands. Collectively, these findings indicate that ROH-based analyses can effectively delineate genomic regions and candidate genes potentially involved in environmental adaptation and trait optimization in pistachio. This study provides a genomic framework for comprehending selective processes in P. vera and offers valuable targets for future functional investigations and molecular breeding initiatives.

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Journal of Medicinal Plants and By-products
Volume 16, Issue 2
March and April 2027
Pages 161-168

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