scholarly journals Genetic diversity of red-grained rice landraces in Hani’s terraced fields based on phenotypic characteristics

2018 ◽  
Author(s):  
Xiaomei Zhou ◽  
Yun Zheng ◽  
Tingting Zhang ◽  
Xiaoqian Zhang ◽  
Mengli Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Characteristics ◽  
Rice Landraces ◽  
Terraced Fields

scholarly journals Molecular Diversity Analysis in Boro Rice (Oryza sativa L.) Landraces using SSR Markers

2021 ◽  
pp. 36-48
Author(s):  
Farhana Afrin Vabna ◽  
Mohammad Zahidul Islam ◽  
Md. Ferdous Rezwan Khan Prince ◽  
Md. Ekramul Hoque
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Diversity ◽  
Genetic Relationships ◽  
Group Method ◽  
Diversity Analysis ◽  
Average Value ◽  
Rice Landraces ◽  
Boro Rice ◽  
Research Institute

Aims: The aim of the study was to determine the genetic diversity of twenty four Boro rice landraces using rice genome specific twelve well known SSR markers. Study Design: Genomic DNA extraction, PCR amplification, Polyacrylamide gel electrophoresis (PAGE) and data analysis-these steps were followed to perform the research work. Data was analysed with the help of following software; POWERMAKER version 3.25, AlphaEaseFC (Alpha Innotech Corporation) version 4.0. UPGMA dendrogram was constructed using MEGA 5.1 software. Place and Duration of Study: The study was conducted at the Genetic Resources and Seed Division (GRSD), Bangladesh Rice Research Institute (BRRI), Joydebpur, Gazipur, Bangladesh during the period of November 2017 to March 2018. Methodology: Simple Sequence Repeat (SSR) markers were used to assay 24 landraces of Boro rice collected from the Gene Bank of Bangladesh Rice Research Institute (BRRI). Results: A total fifty four (54) alleles were detected, out of which forty five (45) polymorphic alleles were identified. The Polymorphic Information Content (PIC) of SSR markers ranged from 0.08 (RM447) to 0.84 (RM206) with an average value of PIC = 0.49. Gene diversity ranges from 0.08 (RM447) to 0.86 (RM206) with an average value of 0.52. The RM206 marker can be considered as the best marker among the studied markers for 24 rice landraces. Dendrogram based on Nei’s genetic distance using Unweighted Pair Group Method of Arithmetic Mean (UPGMA) indicated the segregation of 24 genotypes into three main clusters. Conclusion: The result revealed that SSR markers are very effective tools in the study of genetic diversity and genetic relationships and this result can be conveniently used for further molecular diversity analysis of rice genotypes to identify diverse parent for the development of high yielding variety in rice.

scholarly journals Single Nucleotide Polymorphisms and Indel Markers from the Transcriptome of Garlic

2016 ◽  
Vol 141 (1) ◽  
pp. 62-65 ◽  
Author(s):  
Michael J. Havey ◽  
Yul-Kyun Ahn
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Characteristics ◽  
Single Nucleotide ◽  
Germplasm Collections ◽  
Indel Markers ◽  
Production Environments ◽  
Culinary Uses

Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

scholarly journals Analysis of Genetic Diversity and Population Structure of Some Bangladeshi Rice Landraces and HYV

2012 ◽  
Vol 4 (3) ◽  
pp. 757-767 ◽  
Author(s):  
M. M. Hassan ◽  
A. K. M. Shamsuddin ◽  
M. M. Islam ◽  
K. Khatun ◽  
J. Halder
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Allele Number ◽  
Rice Landraces ◽  
Efficient Management ◽  
Ssr Loci ◽  
Pattern Of Variation ◽  
Rice Improvement

Information on the patterns of genetic variation and population structure is essential for rational use and efficient management of germplasms. It helps in monitoring germplasm and can also be used to predict potential genetic gains. Therefore, in the present study genetic diversity of 59 rice genotypes were assessed using 8 simple sequence repeat (SSR) primers. By the DNA profiling, a total of 114 alleles were detected. Allele number per/locus ranged from 9 to 27, with an average of 14.25. Average polymorphism information content (PIC) value was 0.857 with lowest 0.767 to highest 0.857. Mean gene diversity over all SSR loci was 0.870 with a range from 0.792 to 0.948. Fst values for each locus varied from 0.071 to 0.262. Genetic distance between the variety pair ranged from 0.33 to 1.0. The lowest genetic distance was found between Rajashili and Kumragori (2). Cluster and principal coordinate analysis (PCoA) analysis revealed similar pattern of variation. Marker RM11300 was found most polymorphic and robust among the accessions and can be widely used for rice germplasm characterization. The exclusive variability and unique feature of germplasm found in this study can be a gateway for both domestic and global rice improvement.© 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved.doi: http://dx.doi.org/10.3329/jsr.v4i3.10416 J. Sci. Res. 4 (3), 757-767 (2012)

scholarly journals Evaluation of Genetic Diversity of Rice Landraces (Oryza sativa L.) in Yunnan, China

2007 ◽  
Vol 57 (2) ◽  
pp. 91-99 ◽  
Author(s):  
Yawen Zeng ◽  
Hongliang Zhang ◽  
Zichao Li ◽  
Shiquan Shen ◽  
Jianli Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Rice Landraces

Diachronic analysis of genetic diversity in rice landraces under on-farm conservation in Yunnan, China

2015 ◽  
Vol 129 (1) ◽  
pp. 155-168 ◽  
Author(s):  
Di Cui ◽  
Jinmei Li ◽  
Cuifeng Tang ◽  
Xinxiang A ◽  
Tengqiong Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
On Farm Conservation ◽  
Rice Landraces ◽  
Diachronic Analysis ◽  
On Farm

scholarly journals Assessment of the Genetic Diversity of Joha Rice Germplasms by using Simple Sequence Repeat Markers

2021 ◽  
Author(s):  
P. Saikia ◽  
B. Neog ◽  
N. Gogoi ◽  
D. Baruah
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Relationship ◽  
Simple Sequence Repeat ◽  
Similarity Index ◽  
Morphological Characters ◽  
Aromatic Rice ◽  
Sequence Repeat ◽  
Rice Landraces ◽  
Simple Sequence

Background: Joha Rice are aromatic rice landraces, having small to medium grain size, indigenous to Assam, India. Due to the introduction of high yielding hybrid varieties, many endemic rice landraces including Joha Rice, are in a verge of extinction, as these can only be conserved and maintained by repetitive cultivation. As there is a conflict of local names for these landraces, many landraces with similar morphological characters have been reported from various parts. Simple sequence repeat (SSR) markers with longer perfect repeats have earlier proved successful and essential in studying the genetic diversity among rice cultivars. The present study is aimed to evaluate the genetic relationship among fifteen (15) aromatic Joha rice landraces endemic to Upper Brahmaputra Valley, Assam.Methods: In the present investigation, different landraces of Joha rice were surveyed during 2016-2019. 15 landraces were selected, based on their morphological characters and local data. The collected germplasm of Joha rice was grown in the experimental plots and DNA from young, healthy leaves were isolated which were further used for determination of genetic diversity using SSR markers. Thirty-eight SSR markers were used to evaluate the genetic relationship among the fifteen aromatic rice landraces.Result: A total of 110 polymorphic alleles were detected by 34 markers across all the landraces, with an average of 3.25 per locus. The Polymorphic Information Content (PIC) ranged from 0.24 to 0.83, with an average of 0.5 for each marker. The marker RM154, RM454 and RM489 produced maximum six alleles showing PIC value of 0.82, 0.82 and 0.83, indicating a high polymorphism. UPGMA cluster analysis using Jaccard’s similarity index produced a dendrogram clustering the rice landraces in three major groups and five subgroups. Group II, which consisted of five sub-groups and 12 landraces, showed diverse genotypes. These landraces showed significant genetic similarities. 

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