scholarly journals Diversity and relationships between coefficient of parentage and genetic distance estimated by SSR markers in Japanese rice cultivars

2012 ◽  
Vol 14 (4) ◽  
pp. 106-113
Author(s):  
Osamu Ideta ◽  
Izumi Kono ◽  
Yoshinobu Takeuchi ◽  
Hideyuki Hirabayashi ◽  
Masakata Hirayama ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Rice Cultivars ◽  
Coefficient Of Parentage

scholarly journals Optimal use of SSR markers for varietal identification of upland cotton

2015 ◽  
Vol 50 (7) ◽  
pp. 571-581 ◽  
Author(s):  
Guilherme da Silva Pereira ◽  
Ana Luíza Ramos Cazé ◽  
Michelle Garcia da Silva ◽  
Vanessa Cavalcante Almeida ◽  
Fernanda Oliveira da Cunha Magalhães ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Discrimination Power ◽  
Arithmetic Average ◽  
Pair Group ◽  
Varietal Identification ◽  
The World ◽  
The Mean

Abstract: The objective of this work was to identify polymorphic simple sequence repeat (SSR) markers for varietal identification of cotton and evaluation of the genetic distance among the varieties. Initially, 92 SSR markers were genotyped in 20 Brazilian cotton cultivars. Of this total, 38 loci were polymorphic, two of which were amplified by one primer pair; the mean number of alleles per locus was 2.2. The values of polymorphic information content (PIC) and discrimination power (DP) were, on average, 0.374 and 0.433, respectively. The mean genetic distance was 0.397 (minimum of 0.092 and maximum of 0.641). A panel of 96 varieties originating from different regions of the world was assessed by 21 polymorphic loci derived from 17 selected primer pairs. Among these varieties, the mean genetic distance was 0.387 (minimum of 0 and maximum of 0.786). The dendrograms generated by the unweighted pair group method with arithmetic average (UPGMA) did not reflect the regions of Brazil (20 genotypes) or around the world (96 genotypes), where the varieties or lines were selected. Bootstrap resampling shows that genotype identification is viable with 19 loci. The polymorphic markers evaluated are useful to perform varietal identification in a large panel of cotton varieties and may be applied in studies of the species diversity.

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 ANALISIS KERAGAMAN GENETIK PLASMA NUTFAH KAKAO (Theobroma cacaoL.) BERDASARKANMARKA SSR / Analysis of Genetic Variability Germplasm of Cacao (Theobroma cacaoL.)Basedon SSR Marker

2020 ◽  
Vol 17 (4) ◽  
pp. 156
Author(s):  
Surti Kurniasih ◽  
Rubiyo Rubiyo ◽  
Asep Setiawan ◽  
Agus Purwantara ◽  
Sudarsono Sudarsono
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Theobroma Cacao ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Gene Diversity ◽  
Sequence Repeat ◽  
Theobroma Cacao L ◽  
Simple Sequence

<p>Microsatellite or simple sequence repeat (SSR) markers have proven to be an excellent tool for cultivar identification, pedigree analysis, and genetic distance evaluations among organisms. The objectives of this research were to characterize cacao collection of Indonesian Coffee and Cacao Research Institute (ICCRI) and to analyze their genetic diversity using SSR markers. In this research, 39 SSR primer pairs were used to amplify genomic DNA of 29 cacao clones. Amplified SSR fragments for each primer pair were scored as individual band and used to determine genetic distance among evaluated cacao clones. Results of the experiment indicated that all SSR primer pairs evaluated were able to produce SSR markers for 29 cacao clones. The results also indicated that 34 out of 39 microsatellite loci evaluated were polymorphic, while 5 others were monomorphic. The total number of observed alleles among 29 clones was 132. Number of alleles per locus ranged from 4-8, with an average of 5.5 alelles per locus. Results of data analysis indicated that the PIC value was 0.665, the observed heterozigosity (Ho) was 0.651, and the gene diversity (He) was 0.720. The PIC, Ho, and He values were considered high. Genetic distances were evaluated using NTSys version 2.1 and dendrogram was constructed. Results of analysis indicated that 12 cacao clones evaluated were clustered in the first group with diversity coefficient of &lt; 3.75. Nine cacao clones were in the second group but with the same value of diversity coefficient (&lt;7.50). The rest of the cacao clones were in the third group with diversity coefficient of&gt;7.50. Based on those finding, all SSR primer pairs evaluated could be used to analyze cacao genome and be useful for genetic diversity analysis of cacao germplasm. The SSR marker analysis in ICCRI cacao collections resulted in high PIC, high observed heterozygosity, and high genetic diversity.</p><p>Key words: Theobroma cacao L, microsatelite, molecular marker, genetic diversity, heterozygosity</p><p> </p><p><strong>Abstrak</strong></p><p>Marka mikrosatelit atau sekuens sederhana berulang (simple sequence repeat = SSR) terbukti merupakan alat yang bagus untuk identifikasi kultivar, analisis pedigree, dan evaluasi jarak genetik berbagai organisme. Penelitian ini bertujuan untuk:1) karakterisasi kakao koleksi Pusat penelitian Kopi dan Kakao Indonesia menggunakan marka SSR dan 2) analisis keragaman genetik klon-klon kakao koleksi dengan menggunakan marka SSR. Dalam penelitian ini, 39 pasangan primer SSR telah digunakan untuk amplifikasi DNA genomik dari 29 klon kakao. Skoring pita SSR hasil amplifikasi menggunakan masing-masing pasangan primer dilakukan secara terpisah dan digunakan untuk menentukan jarak genetik di antara klon kakao yang dievaluasi. Hasil percobaan menunjukkan bahwa semua pasangan primer SSR yang digunakan mampu menghasilkan pita DNA hasil amplifikasi (marka SSR) untuk 29 klon kakao yang diuji. Hasil penelitian juga menunjukkan bahwa 34 dari 39 lokus SSR yang dianalisis bersifat polimorfik sedangkan lima primer yang lain bersifat monomorfik. Dari 29 klon kakao yang dievaluasi, telah berhasil diamplifikasi sebanyak 132 alel, dengan kisaran antara 4-8 alel/lokus. Rataan jumlah alel per lokus sebanyak 5,50. Hasil analisis data yang dilakukan juga menunjukkan nilai PIC untuk marka SSR yang digunakan sebesar 0,665. Untuk populasi klon kakao yang dievaluasi, diperoleh nilai rataan heterosigositas pengamatan (Ho) sebesar 0,651 dan rataan diversitas gen (He) sebesar 0,720. Nilai PIC Ho dan He yang didapat tergolong tinggi. Berdasarkan analisis keragaman dengan menggunakan program NTSys, diperoleh hasil 12 klon kakao berada dalam grup pertama (koefisien keragaman&lt;3,75) dan9 klon berada dalam grup kedua, dengan koefisien keragaman &lt; 7,50. Sedangkan klon-klon lainnya mempunyai koefisien keragaman &gt; 7,50. Berdasarkan hasil penelitian dan analisis data disimpulkan bahwa marka SSR dapat digunakan untuk menganalisis keragaman genetik plasma nutfah kakao. Tingkat polimorfisme yang dihasilkan marka SSR relatif tinggi. Tingkat heterosigositas plasma nutfah kakao koleksi Puslit Kopi dan Kakao Indonesiarelatif tinggi, dan keragaman genetiknyacukup tinggi.</p><p>Kata kunci : Theobroma cacao L, mikrosatelit, marka molekuler, keragaman genetik, heterosigositas</p>

scholarly journals Genetic variability in trait-specific rice germplasm groups based on coefficient of parentage, SSR markers and fertility restoration

2014 ◽  
Vol 13 (1) ◽  
pp. 56-67
Author(s):  
Pawan Khera ◽  
Akhilesh Kumar Singh ◽  
Rahul Priyadarshi ◽  
Durga Khandekar ◽  
Rajani K Allu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Hybrid Rice ◽  
Fertility Restoration ◽  
Phenotypic Traits ◽  
Rice Breeding ◽  
Coefficient Of Parentage ◽  
Rice Germplasm ◽  
Cms Line ◽  
The Mean

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines.

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 GENETIC DIVERSITY OF UPLAND RICE LANDRACES FROM JAVA ISLAND AS REVEALED BY SSR MARKERS

2015 ◽  
Vol 16 (1) ◽  
pp. 1
Author(s):  
Sutoro Sutoro ◽  
Puji Lestari ◽  
Hakim Kurniawan
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Upland Rice ◽  
Diversity Index ◽  
Crop Improvement ◽  
Conservation Strategy ◽  
Genetic Diversity Index ◽  
Rice Landraces ◽  
Glutinous Rice

Java Island is one of origins of a large number of indigenous upland rice accessions, which may serve as valuable plant genetic resources for future crop improvement in Indonesia. However, these landraces especially non-glutinous and glutinous rice are rapidly being lost because of land-use, agricultural practices and other factors. A better understanding of genetic diversity of local upland rice is important for crop improvement program, crop management and conservation strategy. This study aimed to evaluate the genetic diversity of upland rice landraces originating from Java Island. A total of 82 upland rice accessions comprising of 55 non-glutinous rice and 27 glutinous type were genotyped using the 16 simple sequence repeat (SSR) markers. The result showed that a total of 74 alleles were found with major allele frequency found on RM431 (0.96). Most of the SSR markers (56.3%) showed high discriminating power as represented by polymorphic informa-tion content (PIC) value higher than 0.5. A moderate genetic diversity index was detected in all landraces, which was 0.55. Genetic diversity index of non-glutinous and glutinous rice were 0.54 and 0.53, respectively. Their genetic distance was about 0.057. The phylogenetic tree generated two main clusters that demonstrated discrimination among landraces according to the individual genetic properties rather than their geographical origins and grain types (non-glutinous and glutinous type). The levels of genetic diversity were varied across rice types and geographical origins. According to the regions, the closest genetic distance was found between upland rice landraces from Central Java and West Java (0.040). The information derived from this study is important, in combination with phenotypic data, to identify desired useful traits came from different origins of the gene pool to be used for breeding purposes.

scholarly journals Correlation of yield and heterosis of maize hybrids and their parental lines with genetic distance based on SSR markers

Genetika ◽  
2012 ◽  
Vol 44 (2) ◽  
pp. 399-408 ◽  
Author(s):  
Snezana Mladenovic-Drinic ◽  
Marija Kostadinovic ◽  
Danijela Ristic ◽  
Milan Stevanovic ◽  
Zoran Camdzija ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genetic Distance ◽  
Ssr Markers ◽  
F1 Hybrids ◽  
F1 Hybrid ◽  
Maize Hybrids ◽  
Average Value ◽  
Parental Inbred ◽  
The Mean ◽  
Parental Lines

The yield, grain yield heterosis and genetic distance based on SSR markers were analyzed in eight maize hybrids and their parental lines. The mean grain yield of all F1 hybrids was 11.37 tha-1. The F1 hybrid from the crosses between L4xL6 gave the highest grain yield of 12.12 tha-1. For the mid parent heterosis (MPH) grain yields of the F1 hybrids, the data showed the average value of 164.25%, and ranged from 136.72% (L4xL6) to 218.07% (L8xL2), and for better parent heterosis (BPH) from 100.70% (H4) to 212.60% (H2), averaged 137.36%. The average genetic distance among parental inbred lines of analyzed hybrids was 0.58 with a range from 0.55 to 0.61. The GD showed a positive correlation with the grain yield of the F1 hybrids (0.22), as well as with MPH and BPH, with the values of 0.12 and 0.45, respectively.

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