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

Fp, Li; Ys, Lee; Kwon, Sung Won; G, Li; Yj, Park

doi:10.4238/2014.april.14.12

Cited by 26 publications

(18 citation statements)

References 29 publications

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“…This average value is higher in comparison with the average value published in earlier reports [ 7 , 27 , 46 , 47 ]. However, producing more alleles than the presence of its repeats by SSR markers is also well documented in literature [ 48 , 49 ] which corroborate our present findings.…”

Section: Discussionsupporting

confidence: 93%

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

et al. 2015

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BackgroundMajority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice.ResultsIn the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes.ConclusionThe present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0498-1) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 93%

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

et al. 2015

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“…The major allele frequency was also calculated for all 36 HvSSR markers which ranged from 0.37 (HvSSR03-37) to 0.97 (HvSSR06-16) with an average of 0.76 (Table 1). The average major allele frequency in the present study was higher as compared to the previous studies on Indian rice varieties [46] and Korean landraces [19]. …”

Section: Resultscontrasting

confidence: 85%

“…The relatively small value of alpha (α = 0.0829) in present study reveals that, only few individuals were admixed. Alpha value approaching zero indicates that most individuals in the study are from separate populations [19] whereas; an alpha value greater than 1 indicates that most of accessions of populations are admixed [28]. Distributions of rice varieties in different populations based on their traits were also studied.…”

Section: Resultsmentioning

confidence: 99%

Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

et al. 2016

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BackgroundThe knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diversity especially after green revolution. However, a detailed study of the trend of diversity in Indian rice varieties is lacking. SSR markers have proven to be a marker of choice for studying the genetic diversity. Therefore, the present study was undertaken with the aim to characterize and assess trends of genetic diversity in a large set of Indian rice varieties (released between 1940–2013), conserved in the National Gene Bank of India using SSR markers.ResultA set of 729 Indian rice varieties were genotyped using 36 HvSSR markers to assess the genetic diversity and genetic relationship. A total of 112 alleles was amplified with an average of 3.11 alleles per locus with mean Polymorphic Information Content (PIC) value of 0.29. Cluster analysis grouped these varieties into two clusters whereas the model based population structure divided them into three populations. AMOVA study based on hierarchical cluster and model based approach showed 3 % and 11 % variation between the populations, respectively. Decadal analysis for gene diversity and PIC showed increasing trend from 1940 to 2005, thereafter values for both the parameters showed decreasing trend between years 2006-2013. In contrast to this, allele number demonstrated increasing trend in these varieties released and notified between1940 to 1985, it remained nearly constant during 1986 to 2005 and again showed an increasing trend.ConclusionOur results demonstrated that the Indian rice varieties harbors huge amount of genetic diversity. However, the trait based improvement program in the last decades forced breeders to rely on few parents, which resulted in loss of gene diversity during 2006 to 2013. The present study indicates the need for broadening the genetic base of Indian rice varieties through the use of diverse parents in the current breeding program.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0437-7) contains supplementary material, which is available to authorized users.

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“…Most SSR markers differed in the number of alleles, ranging from 2 to 25. Of the 49 SSR markers, RM214, RM 249, RM48, and RM206 showed higher number of alleles in the 76 Korea rice landraces, which has been reported in previous studies (Lee et al 2006;Zhao et al 2009;Li et al 2014). In addition, 473 alleles were detected in the 76 Korea rice landraces using the 49 SSR markers, with an average of 9.65 alleles per locus.…”

Section: Discussionsupporting

confidence: 72%

“…Rice landraces are thought to be intermediate stages in the domestication process from the wild ancestor to cultivated rice. Thus, they represent unique and critical sources of genetically variable traits that can contribute to future rice improvement (Li et al 2014). In this study, we estimated the genetic diversity of 76 Korean rice landraces using rice characters and SSR markers.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Among Korean Rice Landraces (Oryza sativa L.) Based on Characters and SSR Markers

Lee¹,

Lee²,

Lee³

et al. 2015

Plant Breed. Biotech.

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In order to estimate genetic diversity of Korean rice landraces, rice characters and SSR markers of 76 rice germplasms were analyzed. Of 12 rice characters, amylose content (AC) showed as largest variance (4.9 to 28.9%), whereas grain length (GL) showed as the lowest variance (4.4 to 5.9 mm). In principal component analyses (PCA), the first principal component explained 60.3% of total variance, in which culm length (CL) and growth period (GP) showed as positive variance and AC showed as negative variance. The second principal component explained an additional 22.4% of the total variance, in which GP and AC showed highly positive variables and CL showed a negative variable. Forty nine SSR markers produced a total of 473 alleles with an average of 9.65 alleles. Polymorphism information content (PIC) was in the range of 0.11 to 0.93. Average observed heterozygosity ranged from 0.12 to 0.39, with an average value of 0.61. As a result of STRUCTURE analysis, 76 Korean rice landraces showed two subpopulations. In clustering analysis, rice characters and SSR markers were clustered into four groups and three groups, respectively. However, they were not significant different from each other. These results provided insight into the characteristics of Korean rice landraces, thus improving our knowledge on rice breeding.

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

Cited by 26 publications

References 29 publications

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)

Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

Genetic Diversity Among Korean Rice Landraces (Oryza sativa L.) Based on Characters and SSR Markers

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