Assessment of genetic diversity in Venezuelan rice cultivars using simple sequence repeats markers

Abstract

In Venezuela, pedigree analyses indicate that the rice varieties currently under cultivation are closely related. Effective breeding programs, based on knowledge of the genetic diversity of cultivars, are needed to broaden the genetic bases of rice germplasm in the country. In this study, we used a set of 48 simple-sequence-repeat (SSR) markers to assess the genetic diversity of 11 Venezuelan rice cultivars, released by the National Rice Breeding Program between 1978 and 2007. A total of 203 alleles were detected, the number of alleles ( NA ) per marker ranged from 2 to 9, with an average of 4.23. The average genic diversity ( H ) over all SSR loci for the 18 genotypes was 0.524, ranging from 0.105 to 0.815. Positive correlations were found between H at each locus, NA , the allele size range and the maximum number of repeats. Venezuelan cultivars showed lower H (mean = 0.37) and NA (total = 124, mean = 2.58) than the whole sample. UPGMA-cluster-analysis based on genetic distance coefficients clearly separated all the genotypes , and showed that the Venezuelan rice varieties are closely related. Molecular identification of 7 Venezuelan cultivars could be done with 9 primers pairs which produced 10 genotype-specific-alleles. Although the genetic diversity was low, SSRs proved to be an efficient tool in assessing the genetic diversity of rice genotypes. Implications of the low genetic diversity detected and relatedness of Venezuelan cultivars are discussed

Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

“…Nei's gene diversity, which varied from 0.16 for check accessions to 0.58 for Sabah varieties with an average value of 0.36, also indicated the high level of divergence in the population. This value aligned with that of [39], which reported mean Nei's gene diversity of 0.37 but lower than 0.50 [40]. …”

“…In another study, three distinct clusters were also found from 18 rice cultivars studied using 44 SSR markers [39]. The clustering patterns in the current study gave some consideration to the geographical origin of the populations.…”

Evaluation of SSR and important agronomical characters of promising mutant lines of soybean

“…The average gene diversity index was considerably high (0.90) (Table 4), indicating its relevance to previous reports that used similar universal SSR markers and displayed moderate to high variability in mutants (Tembo and Munyinda 2015;Yuliasti and Reflinur 2017). In addition, this study was in good agreement with previous report from Herrera et al (2008), that gene diversity of each SSR locus was correlated with the number of alleles and number of repeat motifs. Heterozygosity was also identified in a number of SSR loci in these mutants, suggesting the segregated soybean mutant lines observed in this study.…”

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

“…Screening and identification of highly tolerant donors for seedling stage cold tolerance from the germplasm pool is an important step for selection of donor parents in cold tolerance breeding program. Molecular markers, usually SSR or Simple Sequence Length Polymorphism (SSLP) are commonly being used for assessing rice genetic diversity (Panaud et al, 1996; Wu and Tanksley, 1996; Xiao et al, 1996; Olufowote et al, 1997; Thanh et al, 1999; Herrera et al, 2008; Pervaiz et al, 2010; Das et al, 2013; Babu et al, 2014; Anandan et al, 2016; Pradhan et al, 2016). Hence, genetic diversity available in parental lines should be assessed by using the trait linked SSRs and gene specific markers for seedling stage chilling stress tolerance before selection of parental lines.…”