Biology subjects

Younuskunju, S.

Publications and source records attributed to Younuskunju, S..

5 recordsLinked to original sources

bioRxiv2026

Salinity adaptation in date palm (Phoenix dactylifera): evidence for selective sweeps at Salt Overly Sensitive (SOS) genes

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.

genomics↗

bioRxiv2025

Genomic Analysis of Date Palm Fruit Size Trait and Identification of Candidate Genes through GWAS

The commercial value of economically significant fruits, including date palm fruit (dates), is influenced by various factors, such as biochemical composition and morphological features like size, shape, and visual appearance, which are key determinants of their quality and market value. Dates are typically consumed at the dry stage (Tamar), during which they exhibit a wide range of physical characteristics, such as color, length, weight, and skin appearance. Understanding the genetic basis of these traits is crucial for improving crop quality and breeding new cultivars. In this study, we integrated a genome dataset from highly diverse date cultivars with phenotypes of dry fruit such as length, width, area, and weight, identifying multiple significant genetic loci (SNPs) associated with these traits. We also identified candidate genes located near the associated SNPs that are involved in biological processes such as cell differentiation, proliferation, growth, and the regulation of signalling pathways for growth regulators like auxin and abscisic acid, as observed in other plants. Gene expression analysis reveals that many of these genes are highly expressed in the early stage of fruit development when the fruit attains its maximum size and weight. These findings will enhance our understanding of genetic determinants of fruit size particularly at the commercially important Tamar stage.

genomics↗

bioRxiv2024

The genetics of fruit skin separation in date palm

The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. In this study, we show that there is both an environmental and genetic contribution to the fruit skin separation phenotype. We show that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. A genome-wide association study was conducted using genome data of 199 samples collected from 14 countries that identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.

bioinformatics↗

bioRxiv2022

Genome-wide analysis of dry (Tamar) Date palm fruit color

Date palm (Phoenix dactylifera) fruit are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some Date palm traits have been performed, including for date palm sex-determination, sugar content and fresh fruit colour. In this study, we used genome sequences and image data of 199 dry date fruit (Tamar) samples collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover the previously identified VIR genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of the date palm fruit color phenotype especially at the most commercially important tamar stage.

bioinformatics↗

bioRxiv2019

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future.

plant biology↗