Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome.

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

Genetic parameters estimation for some wild wheat species and their F1 hybrids grown in different regions of Saudi Arabia.

Wheat (Triticum aestivum L.) is the most important crop for human nutrition that underpins the food safety of Saudi Arabia. The investigation here was to determine heterosis effects using different genetic methods: heterosis over better, mid parents, the genetic advance, and genotype, phenotypic coefficient of variation for estimation some traits among six wheat landraces and their F1 hybrids. In 2019, these landraces were sown using hand and after 100 days, the emasculation and crossing were made among these six landraces using hand emasculation of anthers. In 2020, seeds for these genotypes (six wheat landraces and their F1) were sown under normal irrigation accordingly done in 2019. The results showed that the most important parent was Mabia resulted with the highest value in number of tiller/ plant, 1,000-grain weight, and fresh shoot weight. The highest value of plant height among six parents was Naqra while highest value at the same trait among F1 hybrids was P3 XP6. The estimations of heterosis showed that out of 15 crosses, one cross (P1XP5) was significantly better yield than all crosses for these four traits. The genotype coefficient of variation (GCV) ranged from 12.5% to 8.7% while phenotypic coefficient of variation ranged from 17.7% to 11.3%. The correlation coefficients was found between fresh shoot weight and number of tiller and plant height and umber of tiller. Wild wheat still serve as a source of useful germplasm with proven adaption and productivity and thus assembles of the wild wheat assortments are the initial step of breeding program.

Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern.

Amino acids are essential measurements for the potential growth stage because of connecting to protein structures and functions. The objective of this paper was to analyze chromosomes feature at plastid region of rice represented by nucleotide, synonymous codon, and amino acid usage to predict gene expression through codon usage pattern. The results showed that the values of the codon adaption index ranged from 0.733 in chromosome 9 to 0.631 in chromosome 8 with full length of these two chromosomes were 3738 and 1635 respectively. The higher value of guanine and cytosine content was 60% in chromosomes 9 while the lower values was 37% in chromosomes 11. Eight chromosomes (ch1, ch2, ch3, ch5, ch7, ch8, ch10, and ch12) were greater value of modified relative codon bias than threshold (threshold: 0.66) especially in cysteine for ch1, ch2, ch5, ch10, and ch12. While other remaining chromosomes were less than the threshold. Relative synonymous codon usage found that the over-represented of amino acids were asparagine, aspartate, cysteine, glutamate, and phenylalanine across all 12 chromosomes. These results would establish a platform for more and further projects concerning rice breeding and genetics and codon optimization in the amino acids for developing varieties. These results also will help breeders to select desirable genes through the genome for improve target traits.

Prediction of gene expression under drought stress in spring wheat using codon usage pattern.

Spring wheat (Triticum aestivum) is a staple food providing sources of essential proteins for human. In fact, gene expressions of wheat play an important role in growth and productivity that are affected by drought stress. The objective of this work focused on analysis gene feature on spring wheat represented by nucleotide and gene expressions under drought stress. It was found that the higher codon adaptation index was in both wheat root and L-galactono-1, 4-lactone dehydrogenase. It was also found that guanine and cytosine content were high (55.56%) in wheat root. Whereas, guanine and cytosine content were low (41.28%) in L-galactono-1, 4-lactone dehydrogenase. Moreover, the higher relative synonymous codon usage value was observed in codon CAA (1.20), GAA (1.33), GAT (1.00), and ATG (1.00) in wheat root and thus about 62.95% of the total variation in relative synonymous codon was explained by principal component analysis. Additionally, high averages frequency number of codon were (above 15.76) in Met, Lys, Ala, Gly, Phe, Asp, Glu, His, and Tyr; whereas, low averages were in remaining amino acids and majority (90%) of modified relative codon bias values was between 0.40 and 0.90. Shortly, calculations and analysis of codon usage pattern under drought stress would help for genetic engineering, molecular evolution, and gene prediction in wheat studies for developing varieties that associate with drought tolerance.