Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut

Mohammad M Arab; Patrick J Brown; Rostam Abdollahi-Arpanahi; Seyed Sajad Sohrabi; Hossein Askari; Sasan Aliniaeifard; Ali Mokhtassi-Bidgoli; Mohsen B Mesgaran; Charles A Leslie; Annarita Marrano; David B Neale; Kourosh Vahdati

doi:10.1093/hr/uhac124

Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut

Hortic Res. 2022 Aug 1:9:uhac124. doi: 10.1093/hr/uhac124. eCollection 2022.

Affiliations

¹ Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran.
² Department of Plant Sciences, University of California, Davis, CA 95616.
³ Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
⁴ Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
⁵ Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
⁶ Photosynthesis laboratory, Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran.
⁷ Department of Agronomy, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

Abstract

Uncovering the genetic basis of photosynthetic trait variation under drought stress is essential for breeding climate-resilient walnut cultivars. To this end, we examined photosynthetic capacity in a diverse panel of 150 walnut families (1500 seedlings) from various agro-climatic zones in their habitats and grown in a common garden experiment. Photosynthetic traits were measured under well-watered (WW), water-stressed (WS) and recovery (WR) conditions. We performed genome-wide association studies (GWAS) using three genomic datasets: genotyping by sequencing data (∼43 K SNPs) on both mother trees (MGBS) and progeny (PGBS) and the Axiom™ Juglans regia 700 K SNP array data (∼295 K SNPs) on mother trees (MArray). We identified 578 unique genomic regions linked with at least one trait in a specific treatment, 874 predicted genes that fell within 20 kb of a significant or suggestive SNP in at least two of the three GWAS datasets (MArray, MGBS, and PGBS), and 67 genes that fell within 20 kb of a significant SNP in all three GWAS datasets. Functional annotation identified several candidate pathways and genes that play crucial roles in photosynthesis, amino acid and carbohydrate metabolism, and signal transduction. Further network analysis identified 15 hub genes under WW, WS and WR conditions including GAPB, PSAN, CRR1, NTRC, DGD1, CYP38, and PETC which are involved in the photosynthetic responses. These findings shed light on possible strategies for improving walnut productivity under drought stress.