SSR based molecular profiling of elite cultivars of basmati rice (Oryza sativa L.)

2021 ◽  
Vol 16 (12) ◽  
pp. 55-63
Author(s):  
Ashwani Yadav ◽  
Anubhuti Sharma ◽  
Ashwani Kumar ◽  
Renu Yadav ◽  
Rajendra Kumar
Keyword(s):  
Ssr Markers ◽  
Oryza Sativa L ◽  
Research Work ◽  
Similarity Coefficient ◽  
Basmati Rice ◽  
Bank Management ◽  
Genomic Study ◽  
Leaf Tissues ◽  
Maximum Similarity

The experiment was conducted to assess the available genetic variability amongst Indian Basmati rice and identify co-dominant and reproducible robust simple sequence repeat markers for drought resistance and their utilization in marker assisted selection for developing drought resistant / tolerant aromatic rice cultivars in various parts of India as well as in world. DNA was isolated from fresh and young leaf tissues of 35 cultivars of basmati rice using the CTAB procedure of Doyle and Doyle with slightly modifications. The DNA was further quantified by spectrophotometer at 260 nm and 280 nm. The quality and quantity of DNA were checked by agarose gel electrophoresis. Out of 60 SSR markers, 18 were found to be polymorphic and the rest 42 primers were monomorphic. One of the main purposes of SSR markers in genomic study is the characterization of genetic resources to help gene bank management. The informative (18) SSR markers were capable to discriminate the entire cultivars of basmati rice used in this research work. A total of 52 alleles at 18 loci could be scored. The allelic richness per locus diversified from 2 to 5 with an average of 2.89 alleles per locus. The amplitude of Polymorphism Information Content (PIC) value is 0.066 (RM 1068) to 0.730 (RM 1059) with an average of 0.505. The Jaccard’s similarity coefficient ranged from 0.79 to 0.95. Polymorphic finding content showed a positive correlation (r =0.69) with number of alleles at the SSR locus. However it is recommended that SSR markers can be efficiently utilized for this purpose. The maximum similarity coefficient was observed between Jeerakasab and Kalanamak with a coefficient value of 95% and the minimum similarity was found between Jeerakasab and Pusa basmati-1 with a coefficient value of 79%.

scholarly journals Assessment of diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties

2016 ◽  
Vol 8 (1) ◽  
pp. 69-76 ◽  
Author(s):  
A. Mishra ◽  
Pradeep Kumar ◽  
R. S. Sengar ◽  
P. Kumar ◽  
R. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Analysis ◽  
Oryza Sativa L ◽  
Quality Parameters ◽  
Basmati Rice ◽  
Molecular Approaches ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
Selection Of

The study investigates the genetic diversity among the Basmati rice genotypes. Selected nine Basmati rice genotypes were studied for twelve morphological traits, biochemical parameters and for molecular analysis with 11 SSR markers. Pusa Sugandha 5 and Basmati 370, showed strong aroma while other varieties showed medium aroma. Alkali spreading value were intermediate in Basmati 386, Vallabh Basmati 22 and Vallabh Basmati 24 while other varieties showed high values. Pusa Basmati 1 and Basmati 386 showed soft category of gel consistency while in rest varieties it was under medium category. Amylose percentage in grains were ranged from 18.02% (Taraori basmati) to 22.0% (Basmati370). Molecular analysis with 11 SSR markers showed 125 allels with an average number of allels 11.36 per locus. All the markers showed specific type of banding pattern along with 82 polymorphic allels in different genotypes. This study focuses on application of statistical methods and techniques in analysis of genetic diversity of the agronomic data, biochemical aspects related to quality parameters and at the molecular level using SSR markers for clustering procedure making dendrogram that helps the more accurate selection of the superior basmati genotypes for the further studies of the breeders and researchers.

scholarly journals Characterization of new plant type core set of rice (Oryza sativa L.) using QTL/gene-linked markers

2019 ◽  
Vol 56 (4) ◽  
pp. 352-360 ◽  
Author(s):  
Rachana B ◽  
Eswari KB ◽  
Jyothi B ◽  
Lakshmi Devi G ◽  
Jai Vidhya LRK ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Level ◽  
Oryza Sativa L ◽  
Similarity Coefficient ◽  
Functional Genes ◽  
Plant Type ◽  
Core Set ◽  
Rice Genotypes ◽  
Hybridization Programme

Genetic diversity in New Plant Type core set of rice was studied at molecular level employing 52 yield related and 12 randomly chosen markers. 42 markers were polymorphic among the genotypes with a total of 84 alleles. The number of alleles per locus ranged from 2 to 4 with an average of 3.0 per locus. The PIC value ranged from 0.07 to 0.51 with an average of 0.31. Gene specific markers (SCM2-indel2, Gn1a-indel3, TGW6-1d and GS5-03SNP), functional genes (Ghd7-sel and DEP1-promoter), linked markers RM8080 and RM340 were found to be the most appropriate marker to discriminate among the rice genotypes owing to the highest PIC value of more than 0.5. The cluster analysis distinguished these accessions in to eight clusters based on the principle of Unweighted Pair Wise Method using Arithemetic Average (UPGMA) constructed by Jaccard's similarity Coefficient. The dendrogram showed that the genotypes with common phylogeny and geographical orientation tend to cluster together. The highest similarity coefficient value was observed between the IRGC 25510 and IRGC 10658 (0.67) whereas lowest value was observed for Swarnadhan (0.18) and Azucena (0.21), showing highly diverse genotypes. Thus, these accessions were genetically diverse and could be directly utilized in hybridization programme for improvement of yield and related traits.

scholarly journals Molecular characterization of potato cultivars using SSR markers

2011 ◽  
Vol 29 (4) ◽  
pp. 542-547 ◽  
Author(s):  
Patrícia Favoretto ◽  
Elizabeth Ann Veasey ◽  
Paulo César Tavares de Melo
Keyword(s):  
Molecular Characterization ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Binary Data ◽  
Potato Crop ◽  
Similarity Coefficient ◽  
High Similarity ◽  
Commercial Cultivars ◽  
Simple Sequence

The potato crop has a very narrow genetic base, so the use of molecular markers is a very important tool in the characterization of germplasm banks and evaluation of genetic divergence. The objective of this study was to identify, using microsatellite or simple sequence repeat (SSR) markers, 38 accessions of potato from two collections of commercial cultivars. For the molecular characterization 10 loci were used, generating a total of 46 alleles, which were analyzed as binary data. A cluster analysis was performed with the Jaccard´s similarity coefficient and the UPGMA method, using the software NTSYSpc. On average, the number of alleles per locus was 4.6, ranging from two alleles for primers STM1049, STM 1053 and STM 1104 to 12 alleles per locus for primer STM0019a. Of the 46 alleles, only five were monomorphic, therefore presenting 89.1% polymorphism. The polymorphism information content (PIC) varied from 0.13 to 0.86, with an average of 0.54. The Jaccard´s coefficient varied from 0.41 to 0.93, showing high genetic variability among accessions. Two possible duplicates [Atlantic (Canada) and Atlantic (Chile), and Colorado and Ágata (EPAMIG) (duplicates with these SSRs, which did not separate them)] were identified. High similarity was also shown by cultivars Chipie and Melodie (EPAMIG), Voyager and Gourmandine (EPAMIG), Eole and Caesar (EPAMIG), and Cupido and Santé (Pirassu). The most genetically divergent accessions (Lady Rosetta and HPC-7B) were also identified.

scholarly journals Molecular Characterization of Saffron-Potential Candidates for Crop Improvement

2015 ◽  
Vol 7 (1) ◽  
pp. 81-89 ◽  
Author(s):  
Javid Iqbal MIR ◽  
Nazeer AHMED ◽  
Mudasir Hafiz KHAN ◽  
Taseem Ahmad MOKHDOMI ◽  
Sajad Hussian WANI ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Ssr Markers ◽  
Significant Variation ◽  
Rapd Markers ◽  
Crop Improvement ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Improvement Programs ◽  
Rapd And Issr

In this study, thirty one (31) morphologically distinct selections of saffron crop were used for molecular characterization. Molecular characterization was done through SSR, ISSR and RAPD markers. RAPD and ISSR markers showed significant variation; however, SSR markers did not reveal any variation between the selected clones. The Jaccard’s similarity coefficient ranged from 0.94 to 1.00 with an average of 0.98 among all 31 selections used. Minimum similarity value (0.94) was observed between CITH-S-107 and PAM-S-116 selections. The study provides sufficient knowledge to identify clones with better stigma characteristics for further crop improvement programs.

scholarly journals Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhao Zheng ◽  
Nannan Zhang ◽  
Zhenghui Huang ◽  
Qiaoying Zeng ◽  
Yonghong Huang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Genetic Improvement ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Genome Survey ◽  
Simple Sequence ◽  
Genome Survey Sequencing

AbstractPlatostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

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