Development of Dof (DNA binding with one finger) transcription factor gene-specific primers through data mining as a functional marker and their use for genetic diversity study in barley (Hordeum vulgare L.) germplasm

Molecular and agro-morphological characterization of new barley genotypes in arid environments

BACKGROUND

Genetic diversity, population structure, agro-morphological traits, and molecular characteristics, are crucial for either preserving genetic resources or developing new cultivars. Due to climate change, water availability for agricultural use is progressively diminishing. This study used 100 molecular markers (25 TRAP, 22 SRAP, 23 ISTR, and 30 SSR). Additionally, 15 morphological characteristics were utilized to evaluate the optimal agronomic traits of 12 different barley genotypes under arid conditions.

RESULTS

Substantial variations, ranging from significant to highly significant, were observed in the 15 agromorphological parameters evaluated among the 12 genotypes. The KSU-B101 barley genotype demonstrated superior performance in five specific traits: spike number per plant, 100-grain weight, spike number per square meter, harvest index, and grain yield. These results indicate its potential for achieving high yields in arid regions. The Sahrawy barley genotype exhibited the highest values across five parameters, namely leaf area, spike weight per plant, spike length, spike weight per square meter, and biological yield, making it a promising candidate for animal feed. The KSU-B105 genotype exhibited early maturity and a high grain count per spike, which reflects its early maturity and ability to produce a high number of grains per spike. This suggests its suitability for both animal feed and human food in arid areas. Based on marker data, the molecular study found that the similarity coefficients between the barley genotypes ranged from 0.48 to 0.80, with an average of 0.64. The dendrogram constructed from these data revealed three distinct clusters with a similarity coefficient of 0.80. Notably, the correlation between the dendrogram and its similarity matrix was high (0.903), indicating its accuracy in depicting the genetic relationships. The combined analysis revealed a moderate correlation between the morphological and molecular analysis, suggesting alignment between the two characterization methods.

CONCLUSIONS

The morphological and molecular analyses of the 12 barley genotypes in this study effectively revealed the varied genetic characteristics of their agro-performance in arid conditions. KSU-B101, Sahrawy, and KSU-B105 have emerged as promising candidates for different agricultural applications in arid regions. Further research on these genotypes could reveal their full potential for breeding programs.

Retraction Note to: Elucidate genetic diversity and population structure of Olea europaea L. germplasm in Iran using AFLP and IRAP molecular markers

[This retracts the article DOI: 10.1007/s13205-017-0669-x.].

Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

Background

Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth.

Results

A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress.

Conclusions

Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08104-0.

Non-Invasive Phenotyping Reveals Genomic Regions Involved in Pre-Anthesis Drought Tolerance and Recovery in Spring Barley

With ongoing climate change, drought events are becoming more frequent and will affect biomass formation when occurring during pre-flowering stages. We explored growth over time under such a drought scenario, via non-invasive imaging and revealed the underlying key genetic factors in spring barley. By comparing with well-watered conditions investigated in an earlier study and including information on timing, QTL could be classified as constitutive, drought or recovery-adaptive. Drought-adaptive QTL were found in the vicinity of genes involved in dehydration tolerance such as dehydrins (Dhn4, Dhn7, Dhn8, and Dhn9) and aquaporins (e.g. HvPIP1;5, HvPIP2;7, and HvTIP2;1). The influence of phenology on biomass formation increased under drought. Accordingly, the main QTL during recovery was the region of HvPPD-H1. The most important constitutive QTL for late biomass was located in the vicinity of HvDIM, while the main locus for seedling biomass was the HvWAXY region. The disappearance of QTL marked the genetic architecture of tiller number. The most important constitutive QTL was located on 6HS in the region of 1-FEH. Stage and tolerance specific QTL might provide opportunities for genetic manipulation to stabilize biomass and tiller number under drought conditions and thereby also grain yield.

Identification of Dof transcription factors in ramie (Boehmeria nivea L. Gaud) and their expression in response to different nitrogen treatments

19 DNA binding with one finger (Dof) transcription factor genes were identified from genome and transcriptome data of ramie (Boehmeria nivea L. Gaud). Chemical character, subnuclear localization, motif analysis, phylogenetic analysis, and tissue-specific analysis were performed. To select BnDof genes participating in nitrogen metabolism, we analyzed the expression patterns of BnDof genes in different nitrogen conditions (N0, N4, N8, and N12) in different tissues. As a result, eight BnDof genes were identified. BnDof07 (stem) and BnDof14 (root) had higher expression levels in N0 and N4, and BnDof15 (stem and leaves) and BnDof18 (stem) both exhibited the highest expression level in N0, suggesting that these four genes may take part in nitrogen stress. In the leaves, BnDof01, BnDof06, BnDof09, and BnDof19 expression levels were higher in N8 and N12 but lower in N0 and N4. The present findings provide insights into nitrogen metabolism in ramie highlighting the need to investigate this aspect in further detail in future studies.