Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress.

Catalase (CAT, EC 1.11.1.6), one of the most important antioxidant enzymes, can control excess levels of H2O2 produced under oxidative stress in plants. In this study, 16, 8, and 7 CAT genes in the genome of Brassica napus, B. rapa, and B. oleracea were identified, respectively. Phylogenetic studies showed that CATs could be divided into two main groups, each containing specific monocotyledon and dicotyledon subgroups. Motifs, gene structure, and intron phase of CATs in B. napus, Brassica rapa, and Brassica oleracea are highly conserved. Analysis of codon usage bias showed the mutation pressure and natural selection of the codon usage of CATs. Segmental duplication and polyploid were major factors in the expansion of this gene family in B. napus, and genes have experienced  negative selection during evolution. Existence of hormones and stress-responsive cis-elements and identifying miRNA molecules affecting CATs showed that these genes are complexly regulated at the transcriptional and posttranscriptional levels. Based on RNA-seq data, CATs are divided into two groups; the first group has moderate and specific expression in flowers, leaves, stems, and roots, while the second group shows expression in most tissues. qRT-PCR analysis showed that the expression of these genes is dynamic and has a specific expression consistent with other CAT genes in response to salinity and cadmium (Cd) stresses. These results provide information for further investigation of the function of CAT genes in response to stresses and the development of tolerant  plants.

Meta-analysis of QTLs and candidate genes associated with seed germination in rice (Oryza sativa L.).

Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01232-1.

Mega Meta-QTLs: A Strategy for the Production of Golden Barley (Hordeum vulgare L.) Tolerant to Abiotic Stresses.

Abiotic stresses cause a significant decrease in productivity and growth in agricultural products, especially barley. Breeding has been considered to create resistance against abiotic stresses. Pyramiding genes for tolerance to abiotic stresses through selection based on molecular markers connected to Mega MQTLs of abiotic tolerance can be one of the ways to reach Golden Barley. In this study, 1162 original QTLs controlling 116 traits tolerant to abiotic stresses were gathered from previous research and mapped from various populations. A consensus genetic map was made, including AFLP, SSR, RFLP, RAPD, SAP, DArT, EST, CAPS, STS, RGA, IFLP, and SNP markers based on two genetic linkage maps and 26 individual linkage maps. Individual genetic maps were created by integrating individual QTL studies into the pre-consensus map. The consensus map covered a total length of 2124.43 cM with an average distance of 0.25 cM between markers. In this study, 585 QTLs and 191 effective genes related to tolerance to abiotic stresses were identified in MQTLs. The most overlapping QTLs related to tolerance to abiotic stresses were observed in MQTL6.3. Furthermore, three MegaMQTL were identified, which explained more than 30% of the phenotypic variation. MQTLs, candidate genes, and linked molecular markers identified are essential in barley breeding and breeding programs to develop produce cultivars resistant to abiotic stresses.

Analyses of Lysin-motif Receptor-like Kinase (LysM-RLK) Gene Family in Allotetraploid Brassica napus L. and Its Progenitor Species: An In Silico Study.

The LysM receptor-like kinases (LysM-RLKs) play a crucial role in plant symbiosis and response to environmental stresses. Brassica napus, B. rapa, and B. oleracea are utilized as valuable vegetables. Different biotic and abiotic stressors affect these crops, resulting in yield losses. Therefore, genome-wide analysis of the LysM-RLK gene family was conducted. From the genome of the examined species, 33 LysM-RLK have been found. The conserved domains of Brassica LysM-RLKs were divided into three groups: LYK, LYP, and LysMn. In the BrassicaLysM-RLK gene family, only segmental duplication has occurred. The Ka/Ks ratio for the duplicated pair of genes was less than one indicating that the genes' function had not changed over time. The BrassicaLysM-RLKs contain 70 cis-elements, indicating that they are involved in stress response. 39 miRNA molecules were responsible for the post-transcriptional regulation of 12 Brassica LysM-RLKs. A total of 22 SSR loci were discovered in 16 Brassica LysM-RLKs. According to RNA-seq data, the highest expression in response to biotic stresses was related to BnLYP6. According to the docking simulations, several residues in the active sites of BnLYP6 are in direct contact with the docked chitin and could be useful in future studies to develop pathogen-resistant B. napus. This research reveals comprehensive information that could lead to the identification of potential genes for Brassica species genetic manipulation.

Identification, evolution, expression, and docking studies of fatty acid desaturase genes in wheat (Triticum aestivum L.).

BACKGROUNDS: Fatty acid desaturases (FADs) introduce a double bond into the fatty acids acyl chain resulting in unsaturated fatty acids that have essential roles in plant development and response to biotic and abiotic stresses. Wheat germ oil, one of the important by-products of wheat, can be a good alternative for edible oils with clinical advantages due to the high amount of unsaturated fatty acids. Therefore, we performed a genome-wide analysis of the wheat FAD gene family (TaFADs). RESULTS: 68 FAD genes were identified from the wheat genome. Based on the phylogenetic analysis, wheat FADs clustered into five subfamilies, including FAB2, FAD2/FAD6, FAD4, DES/SLD, and FAD3/FAD7/FAD8. The TaFADs were distributed on chromosomes 2A-7B with 0 to 10 introns. The Ka/Ks ratio was less than one for most of the duplicated pair genes revealed that the function of the genes had been maintained during the evolution. Several cis-acting elements related to hormones and stresses in the TaFADs promoters indicated the role of these genes in plant development and responses to environmental stresses. Likewise, 72 SSRs and 91 miRNAs in 36 and 47 TaFADs have been identified. According to RNA-seq data analysis, the highest expression in all developmental stages and tissues was related to TaFAB2.5, TaFAB2.12, TaFAB2.15, TaFAB2.17, TaFAB2.20, TaFAD2.1, TaFAD2.6, and TaFAD2.8 genes while the highest expression in response to temperature stress was related to TaFAD2.6, TaFAD2.8, TaFAB2.15, TaFAB2.17, and TaFAB2.20. Furthermore, docking simulations revealed several residues in the active site of TaFAD2.6 and TaFAD2.8 in close contact with the docked oleic acid that could be useful in future site-directed mutagenesis studies to increase the catalytic efficiency of them and subsequently improve agronomic quality and tolerance of wheat against environmental stresses. CONCLUSIONS: This study provides comprehensive information that can lead to the detection of candidate genes for wheat genetic modification.

In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues.

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

Genome-wide identification and characterization of the metal tolerance protein (MTP) family in grape (Vitis vinifera L.).

Metal tolerance proteins (MTPs) play an important role in the transport of metals at the cellular, tissue and whole plant levels. In the present study, 11 MTP genes were identified and these clustered in three major sub-families Fe/Zn-MTP, Zn-MTP, and Mn-MTP, and seven groups, which are similar to the grouping of MTP genes in both Arabidopsis and rice. Vitis vinifera metal tolerance proteins (VvMTP) ranged from 366 to 1092 amino acids, were predicted to be located in the cell vacuole, and had four to six putative TMDs, except for VvtMTP12 and VvMTP1. The VvMTPs had putative cation diffusion facilitator (CDF) domains and the putative Mn-MTPs also had zinc transporter dimerization domains (ZD-domains). V. vinifera Mn-MTPs had gene structures and motif distributions similar to those of the Fe/Zn-MTP and Zn-MTP sub-families. The upstream regions of VvMTP genes had variable frequencies of cis-regulatory elements that could indicate regulation at different developmental stages and/or differential regulation in response to stress. Comparison of the VvMTP coding sequences with known miRNAs found in various plant species indicated the presence of 13 putative miRNAs, with 7 of these associated with VvMTPs. Temporal and spatial expression profiling indicates a potential role for VvMTP genes during growth and development in grape plants, as well as the involvement of these genes in plant responses to environmental stress, especially osmotic stress. The data generated from this study provides a basis for further investigation of the roles of MTP genes in grapes.

Innovative root-end filling materials based on calcium-silicates and calcium-phosphates.

This in vitro study evaluated the apical sealing ability, bioactivity and biocompatibility of an experimental calcium silicate-based and two light-curing calcium silicate/calcium-phosphate cements as potential root end filling materials. A calcium silicate Portland-based (Control PC), an experimental calcium silicate (Exp. PC) and two light-curing cements (LC-CaP; LC-Si/CaP) were assessed for their alkalinising activity (pH) and biocompatibility. Single-rooted human canines were endodontically treated, filled with gutta-percha and finally submitted to apicoectomy. Root end fillings were performed using all tested cements, and their apical sealing ability was evaluated up to 4 weeks of immersion in simulated body fluid (SBF). The mineral precipitation at the apical region and the cement adaptation to root dentine were also evaluated through non-destructive optical microscopy both at 24 h and after prolonged water storage (four week). LC-CaP and LC-Si/CaP had neutral pH, the greatest sealing ability (24 h) and excellent cytocompatibility. The Exp. PC cement presented sealing ability after two and four weeks, as well as biocompatibility after four and seven days, similar to LC-CaP and LC-Si/CaP. The control PC cement showed the lowest sealing ability and the greatest cytotoxicity. Mineral precipitation was observed in all groups, while some differences were seen in terms of cement adaptation along the root canal dentine walls. The experimental light-curable cements as well as the experimental PC might be suitable root end filling materials with appropriate (in vitro) sealing ability, biocompatibility and aptitude to induce mineral precipitation.