The In Silico Predicton of the Chloroplast Maturase K Gene Polymorphism in Several Barley Varieties

Abstract

This study was conducted to describe the role of the chloroplast maturase K (matK) genetic polymorphism in the reciprocal crossing between five barley varieties using several in vitro / in silico tools. Besides, the final consequences of the matK gene polymorphism on its protein structure, function, and interactions were predicted computationally. Five parental varieties were crossed to each other by full reciprocal crossing design, DNA was extracted from seeds and two different primers’ pairs were designed to scan matK gene. Then, polymerase chain reaction - single-stranded conformation polymorphism (PCR-SSCP) were performed. Two distinct haplotypes in both parents and artificial F1 hybrids in the matK gene were observed in both amplified fragments. This finding indicated that the studied gene had no participation in the reciprocal crossing performed. Three SNPs were identified; two of them are non-synonymous (nsSNPs), namely G387V and L459M. The effect of these missense mutations on the matK protein was analyzed by several in silico tools. It was shown that the coding SNP, L459M was predicted to have much more effective consequences on matK protein structure and function. While the I-Mutant 2.0 prediction tool showed a decrease in stability for these two nsSNPs, which may destabilize the protein interactions to some extent. In conclusion, though the observed missense mutations in the matK gene have no suggestive role in the reciprocally crossed barley varieties, they caused dramatic alterations in several matK protein moieties, which may lead to potential subsequent changes in the matK protein-mediated RNA splicing mechanisms.

THE ABILITY OF matK AND trnL-trnL-trnF INTERGENIC SPACER TO DISCERN CERTAIN SPECIES ACCESSIONS OF THE FAMILIES SOLANACEAE AND FABACEAE

“…The average matK full length in angiosperms is approximately 1500 bp (Kar et al, 2015). The matK is a gene-coding maturase protein that functions to splice pre-mRNA (Mustafa et al, 2018) and has a higher mutation rate than the rbcL gene, therefore often used in plant DNA barcoding (Roslim, 2017). Some examples include DNA barcoding analysis in Metroxylon sagu and other palm species (Abbas et al, 2020), rice (Anggraini et al, 2020), dipterocarps from Sumatra (Moura et al, 2019), and Cucurbitaceae (Ho and Nguyen, 2020).…”

Sensitivity and applications of the PCR Single-Strand Conformation Polymorphism method

“…PCR-SSCP could be used for the authentication of snapper species by SSCP [ 48 ], the population genetic structure of zeugodacus tau species complex [ 49 ], for the genetic diversity of citrus trees [ 50 ], identification of phytophthora genes polymorphism of potato [ 51 ], identification of genetic diversity of lemon and mandarin varieties [ 52 ], detection of the genetic variation of alfalfa gene [ 53 ], prediction of the chloroplast gene polymorphism in barley varieties [ 54 ] and bacteria identification in wood tick [ 55 ].…”

Exploring the Potential and Limitations of PCR-RFLP and PCR-SSCP for SNP Detection: A Review

“…• Stained bands are easy to be read and interpret in almost all cases   However, both techniques have been employed to study several mechanisms in plants with a variety of genetic polymorphism purposes that ranged from splicing alterations to fingerprinting and diagnostic markers. [62][63][64] With respect to fish and amphibians, species identification and the detection of environmental samples and closely related organisms were recently conducted using PCR-RFLP. [56][57][58][59][60][61][62][63][64][65][66][67][68] The PCR-SSCP was used in the detection of parasite species.…”