Association Mapping of Phenological Traits and Major Regulatory Genes (Vrn and Ppd) in Iranian Wheat Germplasm

Sima Fatanatvash; Ehsan Rabieyan; Hadi Alipour

Just Accepted

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Association Mapping of Phenological Traits and Major Regulatory Genes (Vrn and Ppd) in Iranian Wheat Germplasm

Sima Fatanatvash, Ehsan Rabieyan, Hadi Alipour

Abstract

Context. Wheat (Triticum aestivum L.) is an important main crop widely cultivated in various environments. Since wheat phenology determines adaptation to different environments, it is important to understand the genes underlying developmental variation. Aims. Using Iranian wheat varieties and landraces characterized for GY and phenological traits, the study aimed to assess potential QTLs and gene. Methods. In this study, one single-locus genome-wide association studies (SL-GWAS) method (MLM) in conjunction with three multi-locus genome-wide association studies (ML-GWAS) approaches (mrMLM, pKWmEB, and 3VmrMLM) were performed using a set of 260 Iranian wheat landraces and cultivars, which were each genotyped for 44,044 single nucleotide polymorphism (SNP) markers. Key results. Three main SNPs with high pleiotropic effect (rs64682, rs27840, rs31006) were discovered along with the functional marker Ppd D1 D001- KASP, associated with days to booting (DB), days to flowering (DF), growing degree days (GDD) of days to booting (GDDDB), GDD of days to flowering (GDDDF), and grain filling period (GF) and mapped on chromosomes 2A, 2B and 5B by both two methods. Furthermore, two genes, SAUR50 (TraesCS3B02G471300) and alcohol dehydrogenase-like 7 (TraesCS7B02G046700) possibly involved in plant development, grain filling, and flowering are candidate genes for phenological traits. Conclusions. Our results identified markers that were significantly ‎associated with more than one phenological trait by both SL-GWAS and ML-GWAS methods and mapped at ‎genomic loci 2A, 2B, 5B, and 2D. Among them, a functional marker named Ppd-D1 associated with flowering ‎time was identified on chromosome 2D. Implications. Taken together, these novel significant ‎SNP markers and candidate genes identified in this study will contribute to the accuracy of future breeding ‎programs through marker-assisted selection.

CP25027 Accepted 12 June 2025