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Researchers analyzed 197 date palm genomes to understand how the species developed exceptional salt tolerance, identifying selective sweeps in multiple genes of the Salt Overly Sensitive (SOS) pathway that manages sodium exclusion in plants. A dominant pdSOS1 gene variant shows very high frequency across both Eastern and Western date palm populations, with evidence suggesting it originated in the East and spread westward. The study also discovered unique transposable element insertions in salt tolerance genes and evidence of an ancient introgression event with a wild Phoenix species that predates the selective sweep.
Why it matters
Understanding the genetic basis of salt tolerance in date palms could inform breeding strategies for crops facing increasing soil salinity due to climate change, particularly in North Africa and South Asia where date palms are economically important and salinity is projected to worsen.
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⚠️ Preprint – Noch nicht peer-reviewed
Dieser Artikel wurde noch nicht von unabhängigen Experten begutachtet. Die Ergebnisse sind vorläufig und sollten mit Vorsicht interpretiert werden.
The date palm is a high salinity tolerant fruit tree grown mainly in the region spanning from North Africa to parts of South Asia. Climate change models of this region indicate the possibility of increasing salinity in the future. The Salt Overly Sensitive (SOS) pathway is crucial for salinity tolerance in plants, serving as a primary defense mechanism by facilitating sodium exclusion. To better understand date palms’ salt tolerance, we analyzed variation in SOS pathway genes in a set of 197 date palm genomes collected from across the range of cultivation. Here, we show evidence for selective sweeps in multiple SOS pathway genes. A single major pdSOS1 haplotype is at very high frequency in Eastern and Western subpopulations, with a minor, likely ancestral haplotype still present in both geographical locations. Allele-specific gene expression analysis showed differences in salt-treated roots between swept and ancestral haplotypes. Interestingly, sequence-based analysis of the pdSOS1 haplotype suggested a second, much earlier introgression event between P. theophrasti and date palm, though direction is unclear. This event happened before both the selective sweep and the previously reported recent introgression to date palm. We identified a MITE transposable element inserted into a pdSOS1 intron on the swept haplotype, and a similar insertion was found in an intron of the SOS2 paralog pdCIPK8. Both insertions are unique to date palm among Phoenix species. The pdCIPK8 haplotype containing the MITE is also at high frequency in both populations. Further analysis showed evidence for a selective sweep spanning the pdSOS3 region in the western population that shares similarity to an Eastern haplotype spanning the promoter region only. Slower extended haplotype homozygosity decay surrounding the genes in the western population suggests that the swept haplotype originated in the East and spread to the West in all cases. Altogether, our data provide evidence of selective sweeps in the date palm SOS pathway and may go to explaining how this species has developed such high salinity tolerance.