Biology subjects

El-Walid, M. Z.

Publications and source records attributed to El-Walid, M. Z..

2 recordsLinked to original sources

bioRxiv2025

Identification of Freezing Tolerance QTLs in Tripsacum dactyloides Using Open-Pollinated Bulk Segregant Analysis

This study investigates the genetic basis of freezing tolerance in Tripsacum dactyloides and related subspecies as a potential source of valuable traits for improving maize agriculture. Recognizing the significant economic losses in corn yields due to frost damage, we hypothesized that northern populations of T. dactyloides are enriched for freezing tolerance alleles. 40 diverse Tripsacum accessions were collected from natural populations and long-established field collections and used to generate F1 hybrids and open-pollinated F2 families. F2 seedlings were germinated then screened within a growth chamber for freezing tolerance by exposure to freezing temperatures. Seedlings were then phenotyped by tissue survival, and extremes were pooled to create tolerant and susceptible bulks. DNA sequencing was performed on founders, F1s, and tolerant/susceptible F2 bulks. To overcome challenges in traditional SNP calling in bulked samples, we developed a regression-based approach to estimate gamete frequencies and impute allele frequencies in pooled populations. The results showed genetic diversity among Tripsacum accessions, with divergence between northern and southern populations. We tracked segregation of alleles across genomic loci, and performed a joint bulk segregant analysis, identifying 9 QTLs significantly associated with freezing tolerance. These findings highlight potential loci for freezing tolerance that could inform genetic engineering of maize. Central HypothesisNorthern populations of Tripsacum dactyloides, a wild relative of maize, are enriched for freezing tolerance alleles which can be identified by mapping.

genomics↗

bioRxiv2025

Extensive modulation of a conserved cis-regulatory code across 589 grass species

The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation through comparative genomics. While cis-regulatory regions drive much of phenotypic evolution, linking them to specific functions remains challenging. We identified 514 cis-regulatory motifs enriched in regulatory regions of five diverse grass species, with 73% consistently enriched across all, suggesting a deeply conserved regulatory code. We then quantified conservation of specific motif instances across 589 grass species, revealing widespread gain and loss over evolutionary time. Conservation declined rapidly over the first few million years of divergence, yet [~]50% of motif instances were conserved back to the origin of grasses [~]100 million years ago. Conservation patterns varied by gene class, with modestly higher conservation at transcription factor genes. To test for adaptive cis-regulatory changes, we used phylogenetic mixed models to identify motif gains and losses associated with ecological niche transitions. Our models revealed polygenic adaptation across 810 motif-orthogroup combinations, including convergent gains of HSF/GARP motifs at an Alpha-N-acetylglucosaminidase gene associated with adaptation to temperate environments. Our results support a "stable code, variable sites" model in which cis-regulatory evolution involves extensive turnover of individual binding site instances while largely preserving transcription factors binding preferences. Cis-regulatory changes at hundreds to thousands of genes appear to contribute to environmental adaptation. Our results highlight the potential of comparative genomics and phylogenetic mixed models to reveal the genetic basis of complex traits.

genomics↗