Dataset Information

In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum).

ABSTRACT: Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.

SUBMITTER: Dabab Nahas L

PROVIDER: S-EPMC6822720 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum).

Dabab Nahas Laila L Al-Husein Naim N Lababidi Ghinwa G Hamwieh Aladdin A

PloS one 20191031 10

Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were cl ...[more]

PMID: 31671113

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Project description:Drought is one of the most important yield-limiting factors in Morocco. Identification and deployment of drought-tolerant wheat varieties are important to cope with the challenge of terminal moisture stress and increase wheat productivity. A panel composed of 200 elite spring bread wheat genotypes was phenotyped for yield and agronomic traits for 2 years (2020 and 2021) in Morocco under rainfed and irrigated environments. The panel was genotyped using 20K SNPs and, after filtration, a total of 15,735 SNP markers were used for a genome-wide association study (GWAS) using a mixed linear model (MLM) to identify marker-trait associations (MTA) and putative genes associated with grain yield and yield-related traits under rainfed and irrigated conditions. Significant differences were observed among the elite genotypes for grain yield and yield-related traits. Grain yield performance ranged from 0.97 to 6.16 t/ha under rainfed conditions at Sidi Al-Aidi station and from 3.31 to 9.38 t/h under irrigated conditions at Sidi Al-Aidi station, while Grain yield at Merchouch station ranged from 2.32 to 6.16 t/h under rainfed condition. A total of 159 MTAs (p < 0.001) and 46 genes were discovered, with 67 MTAs recorded under rainfed conditions and 37 MTAs recorded under irrigated conditions at the Sidi Al-Aidi station, while 55 MTAs were recorded under rainfed conditions at Merchouch station. The marker 'BobWhite_c2988_493' on chromosome 2B was significantly correlated with grain yield under rainfed conditions. Under irrigated conditions, the marker 'AX-94653560' on chromosome 2D was significantly correlated with grain yield at Sidi Al-Aidi station. The maker 'RAC875_c17918_321' located on chromosome 4A, associated with grain yield was linked with the gene TraesCS4A02G322700, which encodes for F-box domain-containing protein. The markers and candidate genes discovered in this study should be further validated for their potential use in marker-assisted selection to generate high-yielding wheat genotypes with drought tolerance.

Project description:Background and aimsGluten proteins are the major storage protein fraction in the mature wheat grain. They are restricted to the starchy endosperm, which forms white flour on milling, and interact during grain development to form large polymers which form a continuous proteinaceous network when flour is mixed with water to give dough. This network confers viscosity and elasticity to the dough, enabling the production of leavened products. The starchy endosperm is not a homogeneous tissue and quantitative and qualitative gradients exist for the major components: protein, starch and cell wall polysaccharides. Gradients in protein content and composition are the most evident and are of particular interest because of the major role played by the gluten proteins in determining grain processing quality.MethodsProtein gradients in the starchy endosperm were investigated using antibodies for specific gluten protein types for immunolocalization in developing grains and for western blot analysis of protein extracts from flour fractions obtained by sequential abrasion (pearling) to prepare tissue layers.Key resultsDifferential patterns of distribution were found for the high-molecular-weight subunits of glutenin (HMW-GS) and γ-gliadins when compared with the low-molecular-weight subunits of glutenin (LMW-GS), ω- and α-gliadins. The first two types of gluten protein are more abundant in the inner endosperm layers and the latter more abundant in the subaleurone. Immunolocalization also showed that segregation of gluten proteins occurs both between and within protein bodies during protein deposition and may still be retained in the mature grain.ConclusionsQuantitative and qualitative gradients in gluten protein composition are established during grain development. These gradients may be due to the origin of subaleurone cells, which unlike other starchy endosperm cells derive from the re-differentiation of aleurone cells, but could also result from the action of specific regulatory signals produced by the maternal tissue on specific domains of the gluten protein gene promoters.

Dataset Information

In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum).

Publications

In-silico prediction of novel genes responsive to drought and salinity stress tolerance in bread wheat (Triticum aestivum).

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