scholarly journals Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

2020 ◽  
pp. 1-12
Author(s):  
Laila Dabab Nahas ◽  
Alsamman M. Alsamman ◽  
Aladdin Hamwieh ◽  
Naim Al-Husein ◽  
Ghinwa Lababidi
Keyword(s):  
Drought Tolerance ◽  
Bread Wheat ◽  
Ssr Markers ◽  
Web Sites ◽  
Wheat Breeding ◽  
Genic Ssr ◽  
Drought Tolerant ◽  
Ssr Loci ◽  
Weather Changes

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries

scholarly journals Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 27
Author(s):  
Mahmoud M. Gaballah ◽  
Azza M. Metwally ◽  
Milan Skalicky ◽  
Mohamed M. Hassan ◽  
Marian Brestic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Ssr Markers ◽  
Similarity Index ◽  
Stress Conditions ◽  
Yield Potential ◽  
Drought Tolerant ◽  
Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

scholarly journals Validation of SSR Molecular Markers Linked to Drought Tolerant in Some Wheat Cultivars

2018 ◽  
Vol 6 (3) ◽  
pp. 95-109
Author(s):  
Manal Eid
Keyword(s):  
Drought Tolerance ◽  
Ssr Markers ◽  
Dna Sequences ◽  
Molecular Descriptors ◽  
Genetic Relationships ◽  
Wheat Cultivars ◽  
Discrimination Power ◽  
Breeding Programs ◽  
Drought Tolerant ◽  
Germplasm Resource

The present study was carried out to conduct drought tolerance in three wheat cultivars including susceptible (Gemmiza7) and tolerant (Sakha93 and Sahel1). Molecular characterization was done by 26 SSR markers located on chromosome7 which was associated with drought tolerance in many previous studies. 26 SSR markers were polymorphic and thus showed 100% polymorphism. The number of alleles per locus varied from 2 to 3 alleles with an average (2.62). The polymorphism information content (PIC) value ranged from 0.34 to 0.59, with a mean of 0.51. The discrimination power (Dp) value ranged between 0.67 and 0.78 with an average of 0.71 per locus and Heterozygosity (He) value varied from 0.44 to 0.67 with an average of 0.59. The genetic relationships estimated by the polymorphism of SSR markers revealed a greater level of genetic variability in wheat cultivars of wide adaptability and applicability. Whereas an average of combined probability value for the SSR markers was 6.15 x 10-16, suggests the capability of the marker system to distinguish identity and purity of wheat cultivars. In addition to the SSR markers revealed various bands that were either absent or present within tolerant cultivars (Sakha93 and Sahel1) which were altogether absent in susceptible cultivar (Gemmiza7). Also, SSRs of diagnostic and curatorial importance were discerned as ‘stand-alone’ molecular descriptors for barcoding the application of DNA sequences of standardized genetic markers for the identification of wheat cultivars. However, the genetic information in this study could provide useful information to address breeding programs and germplasm resource management.

scholarly journals Root and canopy traits and adaptability genes explain drought tolerance responses in winter wheat

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0242472
Author(s):  
A. S. Nehe ◽  
M. J. Foulkes ◽  
I. Ozturk ◽  
A. Rasheed ◽  
L. York ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Vegetation Index ◽  
Root Traits ◽  
Wheat Breeding ◽  
Root Number ◽  
Breeding Lines ◽  
Drought Tolerant ◽  
Green Area ◽  
High Throughput Phenotyping ◽  
Semiarid Conditions

Bread wheat (Triticum aestivum L) is one of the three main staple crops worldwide contributing 20% calories in the human diet. Drought stress is the main factor limiting yields and threatening food security, with climate change resulting in more frequent and intense drought. Developing drought-tolerant wheat cultivars is a promising way forward. The use of holistic approaches that include high-throughput phenotyping and genetic markers in selection could help in accelerating genetic gains. Fifty advanced breeding lines were selected from the CIMMYT Turkey winter wheat breeding program and studied under irrigated and semiarid conditions in two years. High-throughput phenotyping was done for wheat crown root traits and canopy senescence dynamics using vegetation indices (green area using RGB images and Normalized Difference Vegetation Index using spectral reflectance). In addition, genotyping by KASP markers for adaptability genes was done. Overall, under semiarid conditions yield reduced by 3.09 t ha-1 (-46.8%) compared to irrigated conditions. Genotypes responded differently under drought stress and genotypes 39 (VORONA/HD24-12//GUN/7/VEE#8//…/8/ALTAY), 18 (BiII98) and 29 (NIKIFOR//KROSHKA) were the most drought tolerant. Root traits including shallow nodal root angle under irrigated conditions and root number per shoot under semiarid conditions were correlated with increased grain yield. RGB based vegetation index measuring canopy green area at anthesis was better correlated with GY than NDVI was with GY under drought. The markers for five established functional genes (PRR73.A1 –flowering time, TEF-7A –grain size and weight, TaCwi.4A - yield under drought, Dreb1- drought tolerance, and ISBW11.GY.QTL.CANDIDATE- grain yield) were associated with different drought-tolerance traits in this experiment. We conclude that–genotypes 39, 18 and 29 could be used for drought tolerance breeding. The trait combinations of canopy green area at anthesis, and root number per shoot along with key drought adaptability makers (TaCwi.4A and Dreb1) could be used in screening drought tolerance wheat breeding lines.

scholarly journals Screening of some rice Oryza sativa L. genotypes for drought tolerance using SSR-PCR technique

2014 ◽  
Vol 8 (2) ◽  
pp. 14-18
Author(s):  
Asmaa K. Aurabi ◽  
Kadhim M. Ibrahim ◽  
Shatha A. Yousif
Keyword(s):  
Oryza Sativa ◽  
Drought Tolerance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Oryza Sativa L ◽  
Sequence Repeat ◽  
Drought Tolerant ◽  
Simple Sequence

Simple Sequence Repeat (SSR) markers were used to investigate the variations between drought sensitive and drought tolerant genotypes. Patterns obtained using RM328 and RM302 detected polymorphism between T14, T15 and Amber33, Amber Baghdad genotypes and those obtained using RM316 and RM201 for the tested genotypes suggested that these primers may have the ability to produce drought tolerance markers. According to the patterns obtained using RM189, RM3825 and RM212 primers indicated that these primers cannot be relied on as markers for drought tolerance.

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