Genomic dissection of environmental responsiveness and cross-environment productivity in fenugreek
4 affiliations
- 1Department of Biology, Faculty of Science, Umm Al-Qura University, Makkah, Saudi Arabia.
- 2Department of Agronomy, Faculty of Agriculture, Cairo University, Giza, Egypt.
- 3Natural Resources Department, Faculty of African Postgraduate Studies, Cairo University, Giza, Egypt.
- 4Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
Abstract
Dissecting the genetic basis of genotype × environment interaction (G × E) is important for breeding crops with stable or responsive performance across production environments. Using previously published seed-yield data from 107 Egyptian fenugreek accessions evaluated under two contrasting field environments, we investigated whether yield potential and environmental responsiveness share a common genetic basis. Seed yield per plant was measured in Giza (SYP_G; reference environment) and Wadi El-Natrun (SYP_W; contrasting environment). Nine derived indices were calculated to characterize environmental responsiveness, productivity, and stability: relative performance index (RPI), yield plasticity index (YPI), stress tolerance index (STI), log response ratio (LRR), mean productivity (MP), harmonic mean (HM), tolerance index (TOL), stress susceptibility index (SSI), and AMMI stability value (ASV). The near-zero correlation between SYP_G and SYP_W (r = 0.107) indicated substantial genotype reranking across environments, while several response indices were closely related to SYP_W and therefore predominantly reflected environment-dependent yield expression. Phenotypic analyses also identified contrasting performance strategies, ranging from highly responsive accessions, such as G15 (RPI = 3.629), to highly stable accessions, such as G41 (YPI = 0.001). These phenotypes were integrated with 38,142 SNPs using univariate association-mapping approaches. In addition, SYP_G and SYP_W were subjected to multivariate association-mapping. Association mapping identified one genome-wide-significant SNP for STI and several suggestive loci showed concordant associations across mapping methods. Within the current panel, marker coverage, and significance thresholds, most adaptation-index associations did not overlap previously reported yield loci; however, dDocent_Contig_39939_66, previously associated with seed yield in this panel, also showed cross-method suggestive associations with RPI and TOL. Comparative genomic analysis of three legume reference genomes supported two gene-linked candidate loci associated with STI: a cation/H⁺ antiporter and an importin subunit beta-1. The same analysis classified two of the strongest statistical signals, including the sole genome-wide-significant locus, as repetitive or transposable-element sequences rather than single-copy genes. These findings demonstrate that statistical association strength does not necessarily establish a coding-gene basis for loci identified using reference-free ddRAD markers. Within the current population size and marker coverage, environmental responsiveness and productivity appeared partially distinct but biologically connected components of environment-dependent yield performance. The results provide a genomic and phenotypic framework for prioritizing fenugreek germplasm for further evaluation while emphasizing the need for independent-population, multi-season, and functional validation of the identified candidate loci.
Related
- Clinical and environmental impact of diagnostic endoscopic dissection strategy versus first-line surgery for colorectal lesions with focal deep invasion
- Optimizing nitrogen fertilization in mustard through GreenSeeker-based precision agriculture: Impacts on productivity, economics, and environmental sustainability
- Investigating effects of day-to-day variations in environmental exposure on the human brain: study protocol for the Day2Day Environment project
- Leveraging synthetic environmental covariates to explore crop genotype by environment interactions
- Integrative genotype-environment association and single-cell transcriptomic analyses identify candidate mechanisms of environmental adaptation in pigs.
BibTeX
@article{aljabri2026genomic,
title = {{Genomic dissection of environmental responsiveness and cross-environment productivity in fenugreek}},
author = {Maha Aljabri and Mustafa M H Abd El-Wahab and Amani Mahmoud Dobeie and Mohamed El-Soda},
journal = {PLOS One},
year = {2026},
month = oct,
doi = {10.1371/journal.pone.0361774},
url = {https://doi.org/10.1371/journal.pone.0361774},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genomic dissection of environmental responsiveness and cross-environment productivity in fenugreek
AU - Maha Aljabri
AU - Mustafa M H Abd El-Wahab
AU - Amani Mahmoud Dobeie
AU - Mohamed El-Soda
PY - 2026
DA - 2026/10/29
JO - PLOS One
DO - 10.1371/journal.pone.0361774
UR - https://doi.org/10.1371/journal.pone.0361774
AB - Dissecting the genetic basis of genotype × environment interaction (G × E) is important for breeding crops with stable or responsive performance across production environments. Using previously published seed-yield data from 107 Egyptian fenugreek accessions evaluated under two contrasting field environments, we investigated whether yield potential and environmental responsiveness share a common genetic basis. Seed yield per plant was measured in Giza (SYP_G; reference environment) and Wadi El-Natrun (SYP_W; contrasting environment). Nine derived indices were calculated to characterize environmental responsiveness, productivity, and stability: relative performance index (RPI), yield plasticity index (YPI), stress tolerance index (STI), log response ratio (LRR), mean productivity (MP), harmonic mean (HM), tolerance index (TOL), stress susceptibility index (SSI), and AMMI stability value (ASV). The near-zero correlation between SYP_G and SYP_W (r = 0.107) indicated substantial genotype reranking across environments, while several response indices were closely related to SYP_W and therefore predominantly reflected environment-dependent yield expression. Phenotypic analyses also identified contrasting performance strategies, ranging from highly responsive accessions, such as G15 (RPI = 3.629), to highly stable accessions, such as G41 (YPI = 0.001). These phenotypes were integrated with 38,142 SNPs using univariate association-mapping approaches. In addition, SYP_G and SYP_W were subjected to multivariate association-mapping. Association mapping identified one genome-wide-significant SNP for STI and several suggestive loci showed concordant associations across mapping methods. Within the current panel, marker coverage, and significance thresholds, most adaptation-index associations did not overlap previously reported yield loci; however, dDocent_Contig_39939_66, previously associated with seed yield in this panel, also showed cross-method suggestive associations with RPI and TOL. Comparative genomic analysis of three legume reference genomes supported two gene-linked candidate loci associated with STI: a cation/H⁺ antiporter and an importin subunit beta-1. The same analysis classified two of the strongest statistical signals, including the sole genome-wide-significant locus, as repetitive or transposable-element sequences rather than single-copy genes. These findings demonstrate that statistical association strength does not necessarily establish a coding-gene basis for loci identified using reference-free ddRAD markers. Within the current population size and marker coverage, environmental responsiveness and productivity appeared partially distinct but biologically connected components of environment-dependent yield performance. The results provide a genomic and phenotypic framework for prioritizing fenugreek germplasm for further evaluation while emphasizing the need for independent-population, multi-season, and functional validation of the identified candidate loci.
SN - 1932-6203
ER -