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An integrative RNA-Seq and whole-genome sequencing study of two Tunisian landraces — Chili and Mahmoudi — revealing transcriptional and genomic signatures of local adaptation.
How does a 10,000-year-old landrace adapt to its environment? We compared two divergent Tunisian durum wheat varieties across tissues and conditions.
Chili (humid northern and central Tunisia) and Mahmoudi (semi-arid to arid southern Tunisia, also grown in many other regions) are morphologically distinct landraces of T. turgidum still maintained by a limited number of traditional farmers.
RNA-Seq across root and leaf tissues identified thousands of differentially expressed genes — revealing that stress-response pathways are constitutively activated in Mahmoudi even under controlled conditions.
Whole-genome sequencing revealed 46 permutation-significant FST outlier windows (10 kb), marking regions of divergent selection — concentrated on chromosomes 1A, 2A, 5A, 6B, 1B, and 2B.
Cross-referencing DEGs with published stress QTLs identified 160+ validated candidate genes — potential targets for marker-assisted selection in Mediterranean wheat breeding programs.
Two ancient varieties, two strategies for survival. Here is what 10,000 years of selection has encoded in each genome — and what they offer the future of wheat breeding.
"I grew where the sea breeze tempers the heat and seasonal rains arrive reliably. My strategy is efficiency, not armament. I invest in growth, in photosynthetic gain, in reducing oxidative load. I carry the machinery for reactive oxygen scavenging and precise protein turnover. I am not built for crisis — I am built to thrive when conditions allow. In a changing world, I am what agriculture has cultivated: optimised productivity."
"I was forged in the harshest soils of the Tunisian south, where rain is a rumour and the sun shows no mercy. My roots learned to scavenge, my leaves learned to hold on. I do not wait for stress to respond — I am always ready. My NLR guards are perpetually awake, my dehydrins never fully sleep, and my ubiquitin machinery quietly prunes damaged proteins before they accumulate. I am expensive to run, but I do not break."
Browse and filter all differentially expressed genes. Click column headers to sort. Search by gene ID or product name.
| Gene ID ↕ | Product ↕ | Category ↕ | Comparison ↕ | Direction ↕ | log₂FC ↕ | adj. p-value ↕ |
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Per-chromosome population genomics. Click a chromosome bar to see details. Chromosomes with FST outliers indicate regions under divergent selection.
Biological pathway enrichment across 16 AHRD-curated functional categories. Toggle direction to explore what each landrace activates.
Cross-referenced DEGs validated against published stress QTLs in durum/bread wheat. These are priority candidates for marker-assisted selection.