Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes

Abstract

Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions - India (two), and Philippines (six), and Egypt (14) - were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).

Identification of Phenotypic Variation and Genetic Diversity in Rice (Oryza sativa L.) Mutants

“…The PIC values of the 56 polymorphism markers indicates moderate genetic diversity among rice mutants, and seven markers showed great PIC values (0.73 < PIC < 0.79). Salem et al [35] affirmed that markers with PIC values higher than 0.7 were very high PIC values, and they can be employed to enlarge the genetic foundation of the current genotypes. In addition, SSR markers with PIC value of 0.5 or higher considered as to be effective in discriminating the polymorphism rate [10,38], and they have a potential in evaluation of genetic divergence.…”

“…Therefore, it is necessary to do further study on these traits. In the previous reports, Kumbhar et al [27] and Salem et al [35] stated that it is difficult to discriminate close genotypes through phenotypic assessment. Furthermore, many agronomical characteristics such as quality and yield are highly affected by environmental conditions [36].…”

“…Genetic variation in a population is a worthy source for enlarging the range of genetic materials in plant breeding, and molecular markers, such as SSRs and SNPs, are effective tools to discover genetic diversity [9]. Compared to other genetic markers, SSR markers have remarkable potential to discriminate between rice genotypes [35,38]. Classification of genotypes based on polymorphism markers is a prevailing mean for assessment of genetic variance [27,38,39].…”

Utilize of genetic diversity and marker-trait association to improve drought tolerance in rice (Oryza sativa L.)

“…DNA extraction and simple sequence repeat marker analysis were extensively described in detail by Salem and Sallam (2016). The analysis of SSR markers on the 22 genotypes revealed 106 polymorphic alleles.…”

“…Population structure and genetic diversity were analyzed by Salem and Sallam (2016) and utilized in this study to genetically select the most promising drought-tolerant genotypes. the main average under normal conditions was lower than drought conditions in LR and SP traits.…”