Assessment of genetic diversity of rice (Oryza sativa) cultivars using ssr markers

Umadevi, M.; Veerabadhiran, P.; Manonmani, S.

doi:10.5897/ajb12.1406

Cited by 10 publications

(7 citation statements)

References 7 publications

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“…In soybean, Xavier et al (2018) estimated N e for the USDA soybean germplasm collection comprised of 19,652 accessions from Bandillo et al (2015) and reported it to be 106 individuals. Recent studies have shown that soybean possess several genetic bottlenecks (Guo et al 2010) and its genetic diversity has been reduced (Li et al 2013, Min et al 2010). The N e estimate of USDA set is relatively higher than soybean, implying greater diversity.…”

Section: Discussionmentioning

confidence: 99%

Effective Population Size in Field Pea

Johnson,

Piche,

Worral

et al. 2024

Preprint

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BackgroundEffective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smallerNecan lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance ofNehas become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the firstNeestimates based on linkage disequilibrium (LD) in the pea genome.ResultsWe calculated and comparedNeusing SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500Kb, with a genome-wide averager2of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimatedNefor the USDA was nearly three-fold higher (Ne=174) than NDSU (Ne=64), which can be confounded by a high degree of population structure due to the selfing nature of pea.ConclusionsOur results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitorNein successive cycles of breeding to sustain viability of the breeding efforts in the long term.

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Section: Discussionmentioning

confidence: 99%

Effective Population Size in Field Pea

Johnson,

Piche,

Worral

et al. 2024

Preprint

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“…Molecular markers such as Random amplified polymorphic DNA (RAPD), Simple-sequence repeats (SSR), expresses sequence tags (EST-SSR), Amplified fragment length polymorphism (AFLP), and Single nucleotide polymorphism (SNP) have been used to identify genetic diversity in soybean germplasm [20][21][22][23][24][25][26].SSR markers have been the most used for characterizing genes, analyzing genetic diversity, and mapping genetic linkages. SSR markers are very useful for genotype differentiation, pedigree analysis, assessing genetic distances among genotypes, and variety identification because they are short tandem repeats dispersed uniformly on the entire genome with high polymorphic information content (PIC) and reproducibility [27][28][29]. While use of functional molecular markers, such as those developed from expressed sequence tags (EST), directly access to the population diversity of important genes for agriculture, making it easier to link genotype to phenotype.…”

Section: Introductionmentioning

confidence: 99%

“…A comparative genetic diversity study on sugar beet cultivars using DArT, SNPs, and SSRs showed that SSR markers had the highest success rate due to their highly polymorphic characteristics [31,32]. Other studies have shown that SSR markers were extremely effective in estimating genetic diversity and association among soybean accessions [16,[28][29][30][31][32].…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers

et al. 2023

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Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0–0.184 (average 0.02), while the expected heterozygosity ranged from 0.20–0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity.

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“…Inter simple sequence repeat (ISSR) molecular markers easily recognise short DNA fragment repeats in whole genome that are of 2-6 bp length and highly polymorphic. Loci of ISSRs have an elevated polymorphism ratio, making it possible to observe many alleles (Moghaddam et al 2009). Thus, the potential for genetic variability of protected plant species can be evaluated by identifying polymorphism of various sections of genomic DNA using molecular genetic markers (Bronnikova 2009;Kwiecińska-Poppe et al 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Inter simple sequence repeat (ISSR) molecular markers easily recognise short DNA fragment repeats in whole genome that are of 2–6 bp length and highly polymorphic. Loci of ISSRs have an elevated polymorphism ratio, making it possible to observe many alleles (Moghaddam et al . 2009).…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity and DNA fingerprinting of rare species of the genus Crambe (Brassicaceae)

Chokheli

Shmaraeva

Корниенко

et al. 2022

Crop & Pasture Science

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Context Preservation of genetic diversity of species is a pressing issue; in particular, the preservation of the gene pool of many rare and endangered plants is a priority. Species of the genus Crambe (family Brassicaceae) have potential in agriculture and bioremediation. Aims This study aims to assess the genetic diversity and DNA fingerprint of five rare species of the genus Crambe, and to develop the concept of a genetic passport for rare plants. Methods DNA fingerprinting was conducted via the inter simple sequence repeat (ISSR) method, using six ISSR primers. Hierarchical cluster analysis of the species was performed. Key results In total, 145 polymorphic loci were detected. The studied species formed two different clusters on genetic dendrogram analysis. The first cluster comprised two species, Crambe steveniana and C. tataria from a single subsection (Tatariae), forming a common clade. They were the most genetically close species with genetic similarity of 0.8431. The remaining three species (C. cordifolia, C. maritima, C. pinnatifida), from another subsection of Crambe, formed nodes from the general clade. Conclusions The findings allow plants to be genetically certified using our methods and informative ISSR primers for rare plants. We were able to propose a genetic formula identifying a species and present an example of a genetic passport for rare plants. The genetic structure of C. pinnatifida was investigated for the first time. Implications The present findings contribute to the systematics and critical investigation of rare plant species with genetic resource potential. A genetic passport could be used in the protection of copyright of agricultural varieties.

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Assessment of genetic diversity of rice (Oryza sativa) cultivars using ssr markers

Abstract: Asses cultiva Centre fo A set of 36 somes have detected w from two to produced m 87.76% poly polymorphi value of 0.45 RM 266, RM similarity co

Cited by 10 publications

References 7 publications

Effective Population Size in Field Pea

Effective Population Size in Field Pea

Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers

Assessment of genetic diversity and DNA fingerprinting of rare species of the genus Crambe (Brassicaceae)

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