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

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.

Genome-Wide Identification and Expression of the Paulownia fortunei MADS-Box Gene Family in Response to Phytoplasma Infection

“…In particular, the SVP and SEP1/2/3 subclades were significantly expanded in P. fortunei (9 SVP and 9 SEP1/2/3 genes) compared with those in A. thaliana (4, 6) and O. sativa (3, 7). It is noteworthy that most of the genes in the largest subclade Mγ as well as the expanded SEP subclade, were located at the distal telomeric chromosomal regions, which was similar to the results in wheat [ 9 , 34 ].…”

Capturing Wheat Phenotypes at the Genome Level

“…For instance, in silico analyses of the published wheat reference genome, IWGSC RefSeq v1 ( Appels et al, 2018 ), have allowed the identification and characterization of the gene families. They include: (i) Domain of Unknown Function (DUF-966, TaDUF966 ) gene family, involved in salinity-stress tolerance ( Zhou et al, 2020 ); (ii) MADS-Box gene ( TaMADS -box) family members, involved in wheat growth, development, and abiotic stresses ( Raza et al, 2021 ); (iii) Gretchen Hagen3 ( TaGH3 ) gene family, important in various biological processes, including phytohormone responses, growth, development, metabolism, defense, and abiotic-stress tolerance, such as salinity and osmotic ones, with polyploidization contributing to their high number ( Jiang et al, 2020 ); (iv) superoxide dismutase (SOD) gene ( TaSOD ) family, encoding antioxidant enzymes scavenging reactive oxygen species (ROS), also involved in plant growth, development, and abiotic-stress tolerance, including drought and salinity ( Jiang et al, 2019 ); (v) non-specific lipid transfer proteins (nsLTP/LTP) gene ( TansLTP/TaLTP ) family, involved in transporting phospholipids across membranes, growth, development, and abiotic stresses, such as drought and salinity, showing high numbers, due to gene duplications ( Fang et al, 2020a ); (vi) REMorin (REM) gene ( TaREM ) family, involved in vernalization, plant-microbe interactions, hormonal regulation, development, and tolerance to biotic and abiotic stresses, including cold acclimation ( Badawi et al, 2019 ); (vii) S-phase Kinase-associated Protein 1 (SKP1) gene ( TaSKP1 ) family, encoding core subunits of the Ubiquitin Proteasome 26S (UPS) and have expanded through duplications, being involved in development and stress signaling ( El Beji et al, 2019 ); (viii) subtilase or subtilisin-like protease (SBT) genes ( TaSBT ), involved in many biological functions, such as defense and tolerance to biotic stresses caused by pathogens, among which are Puccinia striiformis f . sp.…”

Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena

“…They were divided into type II (MIKC C and MIKC * ) and type I (Mα, Mβ, and Mγ) subfamilies according to their phylogenetic relationships. The number of type II members is generally greater than the number of type I members [16,17,[33][34][35][36][37][38]; in this study, the number of type I members was greater than the number of type II members in eggplant. In addition, the structure of type II SmMADS-box genes was more complex than that of type I genes because type II genes contained more exons than type I genes.…”

“…The publication of a greater number of high-quality genomes has aided genome-wide analyses. Several MADS-box gene family members have been identified in various plants, including Arabidopsis (107) [16], rice (75) [17], tomato (131) [18], potato (153) [19], bread wheat (300) [33], cucumber (43) [20], Brassica rapa (167) [34], radish (144) [35], apple (146) [36], sesame (57) [37], chrysanthemum (108) [38], and watermelon (39) [39]. In this study, 120 SmMADS-box genes were identified in eggplant.…”