Comparative Genetic Diversity Assessment and Marker–Trait Association Using Two DNA Marker Systems in Rice (Oryza sativa L.)

Abstract

In this paper, the genetic diversities of 12 rice genotypes (Oryza sativa L.), representing Indica, Japonica, and Indica–Japonica varieties, were assessed using twelve ISSR and five SSR markers. In addition, the rice genotypes were evaluated for 11 agro-morphological traits in a two-year trial. Association mapping was performed to detect any association between the DNA markers and the agro-morphological traits. An association analysis was conducted considering the relative kinship among the genotypes and accounting for the population structure using the unified mixed-model approach to avoid possible false-positive associations. Seventy-three alleles were collectively produced by ISSRs and SSRs, with an average of 6.3 and 2.8 alleles per locus, respectively. Both marker systems were informative, and the average polymorphism information content (PIC) was 0.222 and 0.352 for ISSRs and SSRs, respectively. The average expected heterozygosity (Hexp) was 0.264 for ISSRs compared to 0.457 for SSRs. After using the false discovery rate (FDR) method, the association analysis revealed a total of 12 significant marker–trait associations with six agro-morphological traits, including the no. of unfiled grains panicle−1, panicle length, panicle weight, the no. of panicles plant−1, the no. of tillers plant−1, and 1000-grain weight. ISSRs showed seven significant associations with five markers, while SSRs showed three significant associations with three markers. The phenotypic variance (R2) explained by each marker ranged between 29.2% for the ISSR marker HB11 (associated with 1000-grain weight) and 49.3% for the ISSR marker HB8 (associated with the no. of tillers plant−1). The identified marker–trait associations reported herein may improve the expected gain of future molecular-based rice-breeding programs, particularly those designed for improving grain-related or harvest-related traits.

Heat Tolerance and Genetic Diversity Analyses of Rice Accessions Using SSR Markers

“…These rice genotypes incurred divisions into two groups, with the first including three sensitive rice genotypes (Giza177, Sakha105, and Sakha101) and the second comprising four tolerant rice cultivars, i.e., Giza178, Giza179, IET144, and Sakha104. Similar results appeared with the principal component analysis in rice germplasm under hightemperature stress conditions (Mahendran et al, 2015;Soe et al, 2019;Ponsiva et al, 2019;Al-Daej et al, 2023). The PCA of quantitative traits implied that the first principal component accounted for 61.30% of the total variability, recording the traits for filled grains panicle -1 , flag leaf area, panicles plant -1 , unfilled grains panicle -1 , grain yield plant -1 , and tillers plant -1 with the values, i.e., 0.36, 0.36, 0.34, 0.34, 0.33, and 0.33, respectively (Figure 2).…”

Enhancing stress resilience in rice (Oryza sativa L.) through profiling early-stage morpho-physiological and molecular responses to multiple abiotic stress tolerance

“…Amplified bands were scored manually for the presence (indicated as “1”) or absence (indicated as “0”) of each SSR marker. The marker traits such as polymorphism information content (PIC), marker index (MI), resolving power (RP), and heterozygosity index (HI) were calculated following Al-Daej et al. (2023) .…”

Genetic variability and diversity analysis in Oryza sativa L. genotypes using quantitative traits and SSR markers

“…Nevertheless, the length of time needed to achieve the desired gain may make these methods less practical. By utilizing DNA markers in breeding programs, molecular breeding, on the other hand, may expedite the genotype screening procedure and reduce the time needed to get the anticipated gain ( Al-daej et al, 2023 ). Molecular markers are used to characterize the genotypes genetically, serving as a supplement to their morphological identification ( Rahman et al, 2009 , El-Beltagi and Mohamed, 2010 , Ghonaim et al, 2023 ).…”

“…Numerous DNA markers exist with varying purposes; however, selection of a DNA marker is largely influenced by criteria such as economic constraints and accuracy. Two of the most often used DNA markers in assessments of genetic diversity are simple sequence repeats (SSRs) and inter-simple sequence repeats (ISSRs) ( Al-daej et al, 2023 ).…”