Hussain, B. | Search bioRxiv

bioRxiv2023

Genome-wide characterization of MLO family genes in bread wheat shed light on their role in powdery mildew, rusts, blight, abiotic stresses, and development

Powdery mildew (PM) is a notorious disease that causes up to 62% of yield losses in wheat. The 66 PM resistance quantitative trait loci (QTL)/genes (Pm1 - Pm66) break down when new pathogen races interact with plants. The knockout of three wheat Mildew resistance locus o (MLO) has conferred stable resistance against PM. However, only seven MLO genes are known in bread wheat, which has limited the development of PM-resistant cultivars. Taking advantage of IWGSC Ref-seq v2.1, we identified 47 MLO genes in wheat that were distributed on all 21 chromosomes in a non-random fashion. Phylogenetic analysis showed that MLOs are divided into four clades/subfamilies, while clades I, II, III, and IV harbored 6, 28, 6, and 7 MLO genes, respectively. The phylogenetic patterns were strongly supported by gene structure and motif distribution in different clades. Motif analysis found 16 conserved motifs in wheat MLOs. Comparative phylogenetic tree of wheat, Arabidopsis, and rice MLOs classified the genes into four clades. Evolution analysis showed that segmental duplications and purifying selection are prevalent in TaMLOs. Finally, nine MLOs showed in silico expression in different tissues during growth and development. Eight genes (TaMLO3/6-A2, TaMLO7-A1, TaMLO9-D1, TaMLO10-A2, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, and TaMLO10-D2) showed overlapping expression under cold, drought, heat stress, and phosphate starvation. Several MLOs showed differential in silico expression under PM (TaMLO10-A2, TaMLO3/6-A2, TaMLO7-A1, TaMLO10-D5), stripe rust (TaMLO9-D1), and head blight (TaMLO10-A2, TaMLO4-A1, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, TaMLO10-D2). The quantitative real-time polymerase chain reaction (qRT-PCR) showed that nine genes (TaMLO3/6-A2, TaMLO3/6-B2, TaMLO3/6-D2, TaMLO8-A1, TaMLO8-B1, TaMLO8-D1, TaMLO9-A1, TaMLO10-A1, and TaMLO10-D1) exhibited significant upregulation in PM-resistant line after 24, 48, and 72 hours of post-inoculation with the pathogen as compared with the susceptible cultivar. Whereas TaMLO9-D1 showed downregulation. Thus, these MLO genes have a potential role in wheat under these conditions. Therefore, we hope that the MLO genes identified in this study will be edited through CRISPR/Cas9 and/or will be overexpressed to develop PM and disease-resistant and abiotic stress-tolerant wheat.

bioinformatics↗

bioRxiv2020

MADS-box genes galore in wheat genome: phylogenomics, evolution and stress associated functions

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. However, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the latest publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies, without a single FLOWERING LOCUS C homolog present in the wheat genome. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more recent evolutionary origin was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that will accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

genomics↗