Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

Zhao, Weiguo; Chung, Jong‐Wook; Ma, Kyung‐Ho; Kim, Tae‐San; Kim, Seung Min; Shin, Dong-Il; Kim, Chang‐Ho; Koo, Han-Mo; Park, Yong‐Jin

doi:10.1007/bf03191201

Cited by 44 publications

(33 citation statements)

References 31 publications

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“…A similar trend was reported previously in strawberry (Yoon et al, 2012) and Italian millet (Zhao et al, 2012a). Among the 29 SSR markers, RM206, RM48, RM214, RM232, and RM249 showed a comparatively high number of alleles and exhibited strong GD in the 394 Korea rice landrace accessions, as reported by Lee et al (2006) and Zhao et al (2009). The observed difference in GD and PIC may be attributed to the variation in allele frequency between the datasets for the 2 loci.…”

Section: Discussionsupporting

confidence: 87%

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

Fp¹,

Ys²,

Kwon³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. This study analyzed 394 Korean rice landrace accessions, including 93 waxy varieties, for polymorphisms using 29 simple sequence repeat (SSR) markers. In total, 381 alleles served as raw data for estimating the genetic diversity (GD) and population structure. The number of alleles per locus ranged from 3 to 44 (average = 13.14). The expected heterozygosity and polymorphism information content (PIC) ranged from 0.0341 to 0.9358 (mean = 0.5623) and from 0.0783 to 0.9367 (mean = 0.5839), respectively. The mean GDs in waxy, low amylose content, intermediate amylose content, and high amylose content (HAC) varieties were 0.6014, 0.5922, 0.5858, and 0.7232, respectively, Genetic diversity and correlations among landrace rice whereas the mean PIC values for each SSR locus were 0.5701, 0.5594, 0.5550, and 0.6926, respectively. HAC varieties had the highest GD and PIC. Consistent with clustering by genetic distances, a model-based structural analysis revealed 3 subpopulations. Analysis of molecular variance revealed that the between-population component of genetic variance was 22.35%, and that of the within-population component was 77.65%. Significant correlations were observed between eating quality and protein content (r = -0.262), K + (r = -0.655), Mg 2+ (r = -0.680), 1000-GW (r = 0.159), and amylose content (r = -0.134). The overall F ST value was 0.2235, indicating moderate differentiation among the groups. Analysis of variance of the 3 genetic groups (mean of 9 phenotypic and 5 physicochemical traits) by the Duncan multiple range test showed significant differences in 10 traits. This preliminary study represents a first step toward more efficient conservation and greater utilization of rice landraces to broaden the genetic bases of commercially grown varieties.

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Section: Discussionsupporting

confidence: 87%

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

Fp¹,

Ys²,

Kwon³

et al. 2014

Genet. Mol. Res.

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“…Many molecular markers have been used to analyze diversity, such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs; Bao et al, 2006;Cheng et al, 2011;Feltus et al, 2004;Jin et al, 2010;Li et al, 2012;Liang et al, 1994;Nagaraju et al, 2002;Zhao et al, 2009). Different marker systems have been used to investigate genetic diversity (Tam et al, 2005), and random amplified polymorphic DNA (RAPD) markers and SSRs have been applied to study the genetic diversity and phylogenetic relationships among Amaranthus species (Khaing et al, 2013;Lee et al, 2008;Wassom and Tranel, 2005;Xu and Sun, 2001).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Genetic Structure of Amaranth Accessions from the United States

Park

2013

Weed & Turfgrass Science

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ABSTRACT. Amaranths (Amaranthus sp.), an endemic American crop, are now grown widely across the world. This study used 14 simple sequence repeat (SSR) markers to analyze the genetic diversity of 74 amaranth accessions from the United States, with eight accessions from Australia as controls. One hundred twenty-two alleles, averaging eight alleles per locus, were observed. The average major allele frequency, expected heterozygosity, and polymorphism information content (PIC) were 0.44, 0.69, and 0.65, respectively. The structure analysis based on genetic distance classified 77 accessions (94%) into three clusters, while five accessions (6%) were admixtures. Among the three clusters, Cluster 3 had the highest allele number and PIC values, while Cluster 2 had the lowest. The lowest F ST was between Clusters 1 and 3, indicating that these two clusters have higher gene flow between them compared to the others. This finding was reasonable because Cluster 2 included most of the Australian accessions. These results indicated satisfactory genetic diversity among U.S. amaranths. These findings can be used to design effective breeding programs involving different plant characteristics.

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“…Due to the agro-economic importance of amaranths, several studies of isozymes and various DNA markers have been performed to understand intra-and interspecific genetic diversity and/or evolutionary relationships (Lanoue et al, 1996;Chan and Sun, 1997;Sun et al, 1999). Several valuable methods for molecular marker systems, such as restriction-fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), sequencetagged sites (STS), amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSRs) or microsatellites, and single nucleotide polymorphisms (SNPs), have been developed and applied for estimation of genetic diversity (Suh et al, 1997;Nagaraju et al, 2002;Feltus et al, 2004;Bao et al, 2006;Zhao et al, 2009;Li et al 2012). Various marker systems have been used specifically to investigate genetic diversity (Tam et al, 2005).…”

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confidence: 99%

Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers

Oo¹,

Park

2013

Korean Journal of Crop Science

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Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.

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Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

Cited by 44 publications

References 31 publications

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

Analysis of genetic diversity and trait correlations among Korean landrace rice (Oryza sativa L.)

Evaluation of Genetic Structure of Amaranth Accessions from the United States

Analysis of the Genetic Diversity and Population Structure of Amaranth Accessions from South America Using 14 SSR Markers

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