Genome-Wide Diversity of MADS-Box Genes in Bread Wheat is Associated with its Rapid Global Adaptability.

Qasim Raza,Ibrahim A Alaraidh,Iqrar Ahmad Rana,Rana Muhammad Atif,Zulfiqar Ali,Hikmet Budak,Awais Riaz,Babar Hussain

doi:10.3389/fgene.2021.818880

Abstract

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. Here, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more rapid evolution 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 could accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

Highlights

In the fight for global food security and safety, bread wheat represents one of the largest contributing grain crops
In this study, conserved domains and query search-based approaches identified a total of 300 high confidence and non-redundant MADS-box genes from the publicly available wheat genome (Figure 1A, Supplementary Table S2)
MIKC-type genes were the largest group of MADS-box genes in wheat

Summary

Introduction

In the fight for global food security and safety, bread wheat represents one of the largest contributing grain crops. Following the green revolution, improvement of wheat grain production has been hindered by various bottlenecks This includes, but is not limited to, the non-availability of a reliable and fully annotated reference genome (Brenchley et al, 2012; Lukaszewski et al, 2014; Chapman et al, 2015; Clavijo et al, 2017; Zimin et al, 2017). An alliance of geneticists combined resources over 13 years, to produce a fully annotated sequence of the wheat genome, which had a resultant size of ∼17 Gbps. This is the largest known genome among crop plants (Appels et al, 2018). The high-quality of the reference genome, together with large scale RNA-seq data and expression repositories (Borrill et al, 2016; Ramírez-González et al, 2018), provide a rich resource for studying evolutionary dynamics and functional characterization of important gene families, which in turn could facilitate crop improvement efforts

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Discussion

Conclusion