Genetic Diversity Revealed by SSR Markers and Temporal Trends of Major Commercial Inbred Indica Rice Cultivars in South China in 1949–2005

2010 ◽  
Vol 36 (11) ◽  
pp. 1843-1852 ◽  
Author(s):  
Chuan-Guang LIU ◽  
Gui-Quan ZHANG
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
South China ◽  
Indica Rice ◽  
Temporal Trends ◽  
Rice Cultivars

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

scholarly journals Genetic Diversity and Population Genetic Structure of Cinnamomum camphora in South China Revealed by EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1019 ◽  
Author(s):  
Zhong ◽  
Yang ◽  
Li ◽  
Zhang ◽  
Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
South China ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Jiangxi Province ◽  
Group Method ◽  
Cinnamomum Camphora ◽  
Wild Populations ◽  
Arithmetic Means

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei’ gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

scholarly journals Asessment of genetic diversity of Vietnam rice by ssr markers to identify cross combinations for development of drought tolerant rice cultivars

2013 ◽  
Vol 35 (1) ◽  
Author(s):  
Vu Thi Bich Huyen ◽  
Le Thi Bich Thuy ◽  
Nguyen Anh Dung ◽  
Hoang Ba Tien ◽  
Nguyen Duc Thanh
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Rice Cultivars ◽  
Drought Tolerant

scholarly journals Assessment of Genetic Diversity of Philippine Rice Cultivars Carrying Good Quality Traits using SSR Markers

2007 ◽  
Vol 57 (4) ◽  
pp. 263-270 ◽  
Author(s):  
Victoria C. Lapitan ◽  
Darshan S. Brar ◽  
Toshinori Abe ◽  
Edilberto D. Redoña
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Quality Traits ◽  
Rice Cultivars

scholarly journals Genotypic and phenotypic dissection of Xanthomonas oryzae pv. oryzae on Indica rice cultivars for bacterial blight resistance

2021 ◽  
Vol 42 (6) ◽  
pp. 1578-1590
Author(s):  
J. Kumar ◽  
◽  
A. Hussain ◽  
P. Singh ◽  
S.K.Y. Baksh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bacterial Blight ◽  
Indica Rice ◽  
R Gene ◽  
Rice Cultivars ◽  
Eastern India ◽  
Gene Combination ◽  
North Eastern ◽  
North Eastern India ◽  
Blight Disease

Aim: To evaluate the level of virulence of different Xoo isolates/ pathotypes of Eastern and North-eastern India and to identify the suitable donors in rice cultivars having various R-gene combination against virulent Xoo races of Bacterial Blight disease of rice. Methodology: Thirty six Xoo isolates were collected from different places of Eastern and North-eastern India and genetic diversity/ similarity was examined by genotyping of pathotypes using JEL1/JEL2 markers. The 34 Indica rice cultivars carrying different R-gene combination were selected and grown in net house and inoculated artificially with Xoo inoculants from these races/ isolates bacterial of blight disease. Results: The selected 36 Xoo isolates of Eastern and North-eastern India were grouped into seven different isolates/ races based on their genetic diversity using JEL1/JEL2 markers. Among 34 Indica rice cultivars, three or more R-gene combination (xa5 + xa13 + Xa21 and/or Xa4 + xa5 + xa13 + Xa21) cultivars exhibited highly resistant as compared to cultivars with single and double gene combination cultivars against most of the Xoo isolates/ races. Interpretation: The cultivars may determine different level of resistance due to complementary effect of inheritance of suitable R-gene combination. Identified donors may be used for rice resistance breeding programme for Eastern and North-eastern India.

scholarly journals Evaluation of Genetic Diversity in Iranian Rice (Oryza Sativa L.) Cultivars for Resistance Blast Disease (Magnaporthe Oryzae) Using Microsatellite (SSR) Markers.

2019 ◽  
Author(s):  
Farzaneh Farahzadi ◽  
Asa Ebrahimi ◽  
Vahid Zarrinnia ◽  
Reza Azizinezhad
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Magnaporthe Oryzae ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Molecular Data ◽  
Blast Disease ◽  
Analysis Group ◽  
The People ◽  
The World

AbstractRice plays an important role in feeding the world’s population, specially the people who live in developing countries. Rice occupies one third of the world’s crops and provides 35 to 60 percent of calories consumed by 2.7 billion people in the world. More than 90 percent of world’s rice is produced and consumed in Asia. Blast disease caused by Magnaporthe Oryzae is one of the most important diseases of rice in the world. This study was evaluated the Power of ten blast specific SSR Markers in determination genetic diversity between thirty cultivars of Indica rice. The phenotypic evaluation was also performed using Magnaporthe Oryzae in stage of three or four leaves. The total of 23 effective alleles with an average of 2.21 alleles per locus affecting microsatellite markers were amplified in genotypes. The total of 28 alleles was also observed per locus with 2.8 average. Also, the average of PIC was estimated 42.0 for markers. The RM204 marker has the maximum of PIC (0.60) and RM413 marker has the minimum of PIC (0.081). The calculated similarities result between molecular data by Jacard similarity coefficient and UPGMA algorithm have divided thirty studied genotypes into three categories. This analysis between coordinates decides the cluster analysis group. In phenotypic testing, the calculated similarities between phenotypic has also occurred using coefficient similarity Dist and UPGMA algorithm. According to phenotypic evaluation the population was also divided into three groups. According to T-Student test for comparing the phenotypic and genotypic data, SSR markers "RM277" and “RM8225” were linked to semi-susceptible, and resistant phenotype.

scholarly journals Genetic Diversity and Population Structure of 93 Rice Cultivars (Lines) (Oryza Sativa Xian Group) in Qinba in China by 3 Types of Genetic Markers

2021 ◽  
Author(s):  
Yu Zhang ◽  
Yewen Wang ◽  
Peijiang Li ◽  
Yuexing Wang ◽  
Shimao Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Markers ◽  
Ssr Markers ◽  
Diversity Index ◽  
Indica Rice ◽  
Mantel Test ◽  
Phenotypic Traits ◽  
Phenotypic Analysis

Abstract Background: The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods: 15 phenotypic traits, a core set of 48 SSR markers as well as SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples.Results: The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions: The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

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