Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat.
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ABSTRACT:
SUBMITTER: Soriano JM
PROVIDER: S-EPMC8178383 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Drought and heat are the main abiotic constraints affecting durum wheat production. This study aimed to screen for tolerance to drought, heat, and combined stresses in durum wheat, at the juvenile stage under controlled conditions. Five durum wheat genotypes, including four landraces and one improved genotype, were used to test their tolerance to abiotic stress. After 15 days of growing, treatments were applied as three drought levels (100, 50, and 25% field capacity (FC)), three heat stress levels (24, 30, and 35°C), and three combined treatments (100% FC at 24°C, 50% FC at 30°C and 25% FC at 35°C). The screening was performed using a set of morpho-physiological, and biochemical traits. The results showed that the tested stresses significantly affect all measured parameters. The dry matter content (DM) decreased by 37.1% under heat stress (35°C), by 37.3% under severe drought stress (25% FC), and by 53.2% under severe combined stress (25% FC at 35°C). Correlation analyses of drought and heat stress confirmed that aerial part length, dry matter content, hydrogen peroxide content, catalase, and Glutathione peroxidase activities could be efficient screening criteria for both stresses. The principal component analysis (PCA) showed that only the landrace Aouija tolerated the three studied stresses, while Biskri and Hedhba genotypes were tolerant to drought and heat stresses and showed the same sensitivity under combined stress. Nevertheless, improved genotype Karim and the landrace Hmira were the most affected genotypes by drought, against a minimum growth for the Hmira genotype under heat stress. The results showed that combined drought and heat stresses had a more pronounced impact than simple effects. In addition, the tolerance of durum wheat to drought and heat stresses involves several adjustments of morpho-physiological and biochemical responses, which are proportional to the stress intensity.
| S-EPMC10994418 | biostudies-literature
Project description:A detailed study was made of changes in the plant development, morphology, physiology and yield biology of near-isogenic lines of spring durum wheat sown in the field with different plant densities in two consecutive years (2013-2014). An analysis was made of the drought tolerance of isogenic lines selected for yield QTLs (QYld.idw-2B and QYld.idw-3B), and the presence of QTL effects was examined in spring sowings. Comparisons were made of the traits of the isogenic pairs QYld.idw-3B++ and QYld.idw-3B-- both within and between the pairs. Changes in the polyamine content, antioxidant enzyme activity, chlorophyll content of the flag leaf and the normalized difference vegetation index (NDVI) of the plot were monitored in response to drought stress, and the relationship between these components and the yield was analyzed. In the case of moderate stress, differences between the NIL++ and NIL-- pairs appeared in the early dough stage, indicating that the QYld.idw-3B++ QTL region was able to maintain photosynthetic activity for a longer period, resulting in greater grain number and grain weight at the end of the growing period. The chlorophyll content of the flag leaf in phenophases Z77 and Z83 was significantly correlated with the grain number and grain weight of the main spike. The grain yield was greatly influenced by the treatment, while the genotype had a significant effect on the thousand-kernel weight and on the grain number and grain weight of the main spike. When the lines were compared in the non-irrigated treatment, significantly more grains and significantly higher grain weight were observed in the main spike in NIL++ lines, confirming the theory that the higher yields of the QYld.idw-3B++ lines when sown in spring and exposed to drought stress could be attributed to the positive effect of the "Kofa" QTL on chromosome 3B.
| S-EPMC7923076 | biostudies-literature
Project description:Sucrose non-fermenting-1-related protein kinases (SnRKs) play vital roles in plant growth and stress responses. However, little is known about the SnRK functions in wheat. In this study, 149 TaSnRKs (wheat SnRKs) were identified and were divided into three subfamilies. A combination of public transcriptome data and real-time reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed the distinct expression patterns of TaSnRKs under various abiotic and biotic stresses. TaSnRK2.4-B, a member of SnRK2s, has different expression patterns under polyethylene glycol (PEG), sodium chloride (NaCl) treatment, and high concentrations of abscisic acid (ABA) application. Yeast two-hybrid assay indicated that TaSnRK2.4-B could interact with the SnRK2-interacting calcium sensor (SCS) in wheat and play a role in the ABA-dependent pathway. Moreover, TaSnRK2.4-B might be a negative regulator in wheat against pathogen infection. The present study provides valuable information for understanding the functions of the TaSnRK family and provides recommendations for future genetic improvement in wheat stress resistance.
| S-EPMC9280681 | biostudies-literature
Project description:A wide range of biotic stresses (BS) and abiotic stresses (AS) adversely affect plant growth and productivity worldwide. The study of individual genes cannot be considered as an effective approach for the understanding of tolerance mechanisms, since these stresses are frequent and often in combination with each other, and a large number of genes are involved in these mechanisms. The availability of high-throughput genomic data has enabled the discovery of the role of transcription factors (TFs) in regulatory networks. A meta-analysis of BS and AS responses was performed by analyzing a total of 391 microarray samples from 23 different experiments and 2,336 differentially expressed genes (DEGs) involved in multiple stresses were identified. We identified 1,862 genes differentially regulated in response to BS was much greater than that regulated by AS, 835 genes, and found 15.4% or 361 DEGs with the conserved expression between AS and BS. The greatest percent of genes related to the cellular process (>76% genes), metabolic process (>76% genes) and response to stimulus (>50%). About 4.2% of genes involved in BS and AS responses belonged to the TF families. We identified several genes, which encode TFs that play an important role in AS and BS responses. These proteins included Jasmonate Ethylene Response Factor 1 (JERF1), SlGRAS6, MYB48, SlERF4, EIL2, protein LATE ELONGATED HYPOCOTYL (LHY), SlERF1, WRKY 26, basic leucine zipper TF, inducer of CBF expression 1-like, pti6, EIL3 and WRKY 11. Six of these proteins, JERF1, MYB48, protein LHY, EIL3, EIL2 and SlGRAS6, play central roles in these mechanisms. This research promoted a new approach to clarify the expression profiles of various genes under different conditions in plants, detected common genes from differentially regulated in response to these conditions and introduced them as candidate genes for improving plant tolerance through genetic engineering approach.
| S-EPMC6054068 | biostudies-literature
Project description:Plants have evolved with intricate mechanisms to cope with multiple environmental stresses. To adapt with biotic and abiotic stresses, plant responses involve changes at the cellular and molecular levels. The current study was designed to investigate the effects of combinations of different environmental stresses on the transcriptome level of Arabidopsis genome using public microarray databases. We investigated the role of cyclopentenones in mediating plant responses to environmental stress through TGA (TGACG motif-binding factor) transcription factor, independently from jasmonic acid. Candidate genes were identified by comparing plants inoculated with Botrytis cinerea or treated with heat, salt or osmotic stress with non-inoculated or non-treated tissues. About 2.5% heat-, 19% salinity- and 41% osmotic stress-induced genes were commonly upregulated by B. cinerea-treatment; and 7.6%, 19% and 48% of genes were commonly downregulated by B. cinerea-treatment, respectively. Our results indicate that plant responses to biotic and abiotic stresses are mediated by several common regulatory genes. Comparisons between transcriptome data from Arabidopsis stressed-plants support our hypothesis that some molecular and biological processes involved in biotic and abiotic stress response are conserved. Thirteen of the common regulated genes to abiotic and biotic stresses were studied in detail to determine their role in plant resistance to B. cinerea. Moreover, a T-DNA insertion mutant of the Responsive to Dehydration gene (rd20), encoding for a member of the caleosin (lipid surface protein) family, showed an enhanced sensitivity to B. cinerea infection and drought. Overall, the overlapping of plant responses to abiotic and biotic stresses, coupled with the sensitivity of the rd20 mutant, may provide new interesting programs for increased plant resistance to multiple environmental stresses, and ultimately increases its chances to survive. Future research directions towards a better dissection of the potential crosstalk between B. cinerea, abiotic stress, and oxylipin signaling are of our particular interest.
| S-EPMC4416716 | biostudies-literature
Project description:Certain plant growth promoting bacteria have ability to ameliorate abiotic and/or biotic stressors, which can be exploited to enhance plant growth and productivity of the plants under stress conditions. Therefore, the present study aimed to examine the role of a rhizospheric bacterial isolate SBP-9 isolated from Sorghum bicolor (i) in promoting the wheat plant growth under salinity stress, and (ii) in enhancing the defense response in wheat against fungal pathogen "Fusarium graminearum." The test isolate possessed plant growth promoting (PGP) traits including ACC deaminase (ACCD), gibberellic acid, indole acetic acid (IAA), siderophore, and inorganic phosphate solubilization. Under salt (NaCl) stress, inoculation of this isolate to wheat plant significantly increased plant growth in terms of various growth parameters such as shoot length/root length (20-39%), fresh weight/dry weight (28-42%), and chlorophyll content (24-56%) following inoculation of test isolate SBP-9. Bacterial inoculation decreased the level of proline, and malondialdehyde, whereas elevated the antioxidative enzymatic activities of superoxide-dismutase (SOD; 28-41%), catalase (CAT; 24-56%), and peroxidase (POX; 26-44%). Furthermore, it also significantly decreased the Na+ accumulation in both shoot and roots in the range of 25-32%, and increased the K+ uptake by 20-28%, thereby favoring the K+/Na+ ratio. On the other hand, the test isolate also enhanced the level of defense enzymes like ?-1, 3 glucanase, phenylalanine ammonia lyase (PAL), peroxidae (PO), and polyphenol oxidase (PPO), which can protect plants from the infection of pathogens. The result of colonization test showed an ability of the test isolate to successfully colonize the wheat plants. These results indicate that Stenotrophomonas maltophilia SBP-9 has potential to promote the wheat growth under biotic and abiotic (salt) stressors directly or indirectly and can be further tested at field level for exploitation as bioinoculant.
| S-EPMC5640710 | biostudies-literature
Project description:Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but for normalization of data requires the use of stable reference genes. However, suitable reference genes are still not known in the case of Phenacoccus solenopsis under variable experimental treatments. The present study focused on the identification of stable housekeeping genes as a reference for analysis under different abiotic and biotic factors in P. solenopsis. We analyzed the relative expression of six commonly used candidate reference genes in different developmental stages, host-feeding assay, temperature treatments and field distribution conditions. Expression stabilities were analyzed by geNorm, NormFinder, and RefFinder. Under developmental and field distribution conditions, β-Tubulin was found to be most stable reference genes followed by rpl32 and α-Tubulin. In the case host feeding treatment conditions, β-Tubulin and α-tubulin identified to be the most stable reference genes, while in temperature stress, a combination of α-Tubulin and rpl32 found to be suitable for normalizing the RT-qPCR data. Further, the above-identified genes were validated using RT-qPCR based gene expression analysis of four objective genes namely, Myoinhibitory peptides (MIPs), Zinc_metalloprotease (Zn_Mp), fatty acid synthase (fas) and alpha-glucosidase. Identified reference genes will facilitate gene expression studies in future under different stress treatments in P. solenopsis.
| S-EPMC5648885 | biostudies-literature
Project description:Carotenoid pigment content is an important quality trait as it confers a natural bright yellow color to pasta preferred by consumers (whiteness vs. yellowness) and nutrients, such as provitamin A and antioxidants, essential for human diet. The main goal of the present review is to summarize the knowledge about the genetic regulation of the accumulation of pigment content in durum wheat grain and describe the genetic improvements obtained by using breeding approaches in the last two decades. Although carotenoid pigment content is a quantitative character regulated by various genes with additive effects, its high heritability has facilitated the durum breeding progress for this quality trait. Mapping research for yellow index and yellow pigment content has identified quantitative trait loci (QTL) on all wheat chromosomes. The major QTL, accounting for up to 60%, were mapped on 7L homoeologous chromosome arms, and they are explained by allelic variations of the phytoene synthase (PSY) genes. Minor QTL were detected on all chromosomes and associated to significant molecular markers, indicating the complexity of the trait. Despite there being currently a better knowledge of the mechanisms controlling carotenoid content and composition, there are gaps that require further investigation and bridging to better understand the genetic architecture of this important trait. The development and the utilization of molecular markers in marker-assisted selection (MAS) programs for improving grain quality have been reviewed and discussed.
| S-EPMC6853866 | biostudies-literature
Project description:Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
| S-EPMC7914919 | biostudies-literature
Project description:Grain yield (YLD) is affected by thousand kernel weight (TKW) which reflects the combination of grain length (GL), grain width (GW) and grain area (AREA). Grain weight is also influenced by heading time (HT) and plant height (PH). To detect candidate genes and quantitative trait loci (QTL) of yield components, a durum wheat recombinant inbred line (RIL) population was evaluated in three field trials. The RIL was genotyped with a 90K single nucleotide polymorphism (SNP) array and a high-density genetic linkage map with 5134 markers was obtained. A total of 30 QTL were detected including 23 QTL grouped in clusters on 1B, 2A, 3A, 4B and 6B chromosomes. A QTL cluster on 2A chromosome included a major QTL for HT co-located with QTL for YLD, TKW, GL, GW and AREA, respectively. The photoperiod sensitivity (Ppd-A1) gene was found in the physical position of this cluster. Serine carboxypeptidase, Big grain 1 and β-fructofuranosidase candidate genes were mapped in clusters containing QTL for seed size. This study showed that yield components and phenological traits had higher inheritances than grain yield, allowing an accurate QTL cluster detection. This was a requisite to physically map QTL on durum genome and to identify candidate genes affecting grain yield.
| S-EPMC7916090 | biostudies-literature