scholarly journals Genetic Diversity Analysis of Hybrid Rice Parental Lines and Genetic Purity Assessment of Hybrid Seeds of China

2020 ◽  
Vol 12 (5) ◽  
pp. 37
Author(s):  
Haiya Cai ◽  
Yuxia Lu ◽  
Gang Liu ◽  
Shuo Zhang ◽  
Haitao Jia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hybrid Rice ◽  
Southern China ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Japonica Rice ◽  
Similarity Coefficients ◽  
Genetic Purity ◽  
Genetic Diversity Analysis ◽  
Parental Lines

Thirty-five pairs of SSR primers were used for genetic diversity analysis and DNA fingerprinting of 31 hybrid rice core parental lines developed in central- and southern-China using one japonica rice line and three inbred rice lines as the check varieties. The average number of alleles (Na) per SSR locus was 4.02, with a range of two to eight, the effective number of alleles (Ne) was 83.16 with a mean of 2.38, ranging from 1.19 to 4.66. The polymorphic information content (PIC) ranged from 0.16 to 0.79, with an average number of 0.52. The results of the cluster analysis indicated that the check varieties viz., one japonica rice and three inbred rice, were clustered into two groups with similarity coefficients of 0.62 and 0.71 respectively indicating their relatedness. Thirty-one hybrid rice parental lines were clustered into 6 groups according to their different types, pedigrees and regions of development with similarity coefficients of approximately 0.76. The highest genetic similarity coefficient (0.94) was observed between Y58S and C815S, and the lowest (0.63) was observed between Quan9311A and Peiai64S. The purity of one hybrid rice cultivar was tested using characteristic marker and the field test, and it was demonstrated that the purities obtained using the two methods were similar. This research will be helpful for rice breeding, new cultivar registration and seed production.

scholarly journals Genetic Diversity Analysis of Soybean [Glycine max (L.) Merrill.] Germplasms in Bangladesh Using SSR Markers

2021 ◽  
Vol 13 (2) ◽  
pp. 1
Author(s):  
M. K. Khatun ◽  
M. A. Haque ◽  
M. A. Malek ◽  
M. H. Rashid ◽  
S. Islam ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Ammonium Bromide ◽  
Diversity Analysis ◽  
Dna Ladder ◽  
Genetic Diversity Analysis ◽  
Soybean Genotypes ◽  
The Mean

The purpose of the present study was to investigate the genetic diversity and molecular characterization of 50 soybean genotypes in Bangladesh with 20 SSR markers. Genomic DNA was isolated by modified standard cetyl tri-methyl ammonium bromide (CTAB) extraction protocol and alleles were amplified by polymerase chain reaction (PCR). Allele sizes were estimated in comparison with 50 bp DNA ladder. The software NTSYSpc version 2.2 and POPGENE version 1.31 were utilized for molecular data analysis and preparation of dendrogram. Polymorphic Information Content (PIC) values varied from 0.53 (Satt664) to 0.98 (Satt009, Satt330 and Satt522) with the mean value 0.897 and expected heterozygosity varied from 0.4059 (Satt685) to 0.1246 (Satt664) with the mean value 0.244. The dendrogram analysis depicted that the 50 genotypes were grouped in four (4) major clusters. The most diverse genotypes were SBG-1, PM-78-6-3-13, BS-3 and AGS-31, which suggest that the simple sequence repeat (SSR) markers are very efficient for genetic diversity analysis. The similarity matrix revealed the diversity among genotypes. The diverse genetic materials obtained from the present study on genetic diversity of soybean genotypes in Bangladesh may be utilized in the future breeding programme.

scholarly journals Pemilihan Tetua Persilangan pada Kubis (Brassica oleracea var. capitata) melalui Analisis Keragaman Genetik [Parental Line Selection in Cabbage (Brassica oleracea var. capitata) through Genetic Diversity Analysis]

2019 ◽  
Vol 28 (1) ◽  
pp. 33
Author(s):  
Nur Kholilatul Izzah ◽  
NFN Reflinur
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Brassica Oleracea ◽  
Diversity Analysis ◽  
Heterotic Groups ◽  
Genetic Diversity Analysis ◽  
National University ◽  
Parental Lines ◽  
Seoul National University ◽  
Simple Sequence

<p>Kubis (<em>Brassica oleracea</em> var. <em>capitata</em>) merupakan salah satu jenis sayuran yang mempunyai nilai ekonomis tinggi. Untuk meningkatkan hasil panen kubis tiap tahunnya perlu didukung oleh tersedianya varietas unggul yang tahan penyakit, terutama penyakit busuk hitam dan akar gada yang dapat menggagalkan panen. Metode yang dapat diaplikasikan untuk merakit varietas unggul adalah melalui persilangan. Penelitian ini bertujuan untuk memilih kombinasi tetua persilangan yang ideal pada tanaman kubis melalui analisis keragaman genetik menggunakan marka SSR (<em>Simple Sequence Repeats</em>). Penelitian dilakukan pada bulan Februari sampai Mei 2013 di laboratorium Functional Crop Genomics and Biotechnology, Seoul National University, Korea Selatan menggunakan 16 genotipe kubis yang diperoleh dari perusahaan benih Joeun, Korea Selatan. Keragaman genetik 16 genotipe kubis dianalisis menggunakan 35 marka SSR polimorfik, dan selanjutnya digunakan untuk menentukan keragaman genetik berdasarkan metode UPGMA. Nilai jarak genetik antar genotipe diperoleh berdasarkan rumus 1-nilai kesamaan genetik. Hasil analisis keragaman genetik membagi 16 genotipe kubis menjadi dua kelompok heterotik utama pada nilai kesamaan genetik 65,2%. Berdasarkan hasil analisis keragaman genetik dan nilai jarak genetik diperoleh empat kombinasi tetua persilangan ideal, yaitu genotipe IMO-03 vs IMO-08 (nilai jarak genetik 43%) dan IMO-03 vs IMO-10 (nilai jarak genetik 39%) untuk karakter ketahanan terhadap penyakit busuk hitam, serta genotipe IMO-18 vs IMO-10 dan IMO-17 vs IMO-10 dengan nilai jarak genetik masing-masing 45% dan 44% untuk karakter ketahanan terhadap penyakit akar gada. Keempat kombinasi tetua tersebut dipilih karena terletak pada kelompok heterotik berbeda serta mempunyai nilai jarak genetik yang jauh sehingga diharapkan dapat meningkatkan peluang heterosis pada progeni yang dihasilkan.</p><p><strong>Keywords</strong></p><p><em>Brassica oleracea</em> var. <em>capitata</em>; Genotipe; Keragaman genetik; Kubis; Pemilihan tetua</p><p><strong>Abstract</strong></p><p>Cabbage (<em>Brassica oleracea</em> var. <em>capitata</em>) is one of vegetable that has high economic value. The availability of high-yielding varieties that are resistant to some diseases, particularly black rot and clubroot disease is needed in order to increase cabbage yield per year. The method which can be applied to assemble new varieties is through crossbreeding program. The objective of this research was to select the ideal combination of parental lines in cabbage through analysis of genetic diversity by using SSR markers (Simple Sequence Repeats). The research was conducted from February to May 2013 in the laboratory of Crop Functional Genomics and Biotechnology, Seoul National University, South Korea using 16 cabbage genotypes obtained from Joeun seed company, South Korea. The genetic diversity of 16 cabbage genotypes were analyzed using 35 polymorphic SSR markers, and then used to determine the genetic diversity based on UPGMA method. Meanwhile, genetic distance value among cabbage genotypes obtained by the formula of 1-value genetic similarity. The results of genetic diversity analysis divided 16 cabbage genotypes into two main heterotic groups at genetic similarity value of 65.2%. Based on the results of genetic diversity analysis and genetic distance value, we selected four combinations of ideal parental lines, namely genotype IMO-03 vs IMO-08 (genetic distance value of 43%) and IMO-03 vs IMO-10 (genetic distance value of 39%) for black rot disease resistance character, as well as genotype IMO-18 vs IMO-10 and IMO-17 vs IMO-10 with genetic distance value of 45% and 44%, respectively for club root disease resistance character. These four parental lines combination were selected as ideal parental combinations due to they were located on a different heterotic groups and has high genetic distance value, which is expected to increase the chances of heterosis in their progeny.</p>

scholarly journals Genetic Diversity Analysis of Jatropha Curcas Provenances Using Randomly Amplified Polymorphic DNA Markers

2011 ◽  
Vol 7 (1) ◽  
pp. 47 ◽  
Author(s):  
Dani Satyawan ◽  
I Made Tasma
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Jatropha Curcas ◽  
Group Method ◽  
Diversity Analysis ◽  
Similarity Coefficients ◽  
Improvement Program ◽  
Genetic Diversity Analysis ◽  
Chain Reactions ◽  
Pair Group

<p>Genetic Diversity Analysis of Jatropha Curcas<br />Provenances Using Randomly Amplified Polymorphic<br />DNA Markers. Dani Satyawan and I Made Tasma.<br />Jatropha curcas nuts are rich in oil that is higly suitable for<br />Hak Cipta © 2011, BB-Biogen<br />the production of bio-diesel or to be used directly in<br />modified diesel engines. The objective of this study was to<br />assess the extent of genetic diversity among 50 J. curcas<br />provenances and one accession of J. integerrima using<br />RAPD markers. The fifty J. curcas provenances were<br />collected from ecologically diverse regions of Indonesia, and<br />planted in the Pakuwon Experimental Station (Sukabumi,<br />West Java). Fourteen RAPD primers with 60-80% G+C<br />content were used in this genetic diversity analysis and<br />produced 64 bands with 95.7% polymorphism level. The<br />Polymerase Chain Reactions used to generate the RAPD<br />bands sometimes produced inconsistent and nonreproducible<br />results, necessitating the duplication of each<br />reaction to prevent scoring errors. Sixty one validated bands<br />were subsequently used for genetic diversity analysis using<br />Unweighted Pair Group Method Arithmetic (UPGMA)<br />method and Dice coefficients. It was shown that the<br />similarity coefficients among the provenances ranged from<br />0.2 to 0.98 with an average similarity of 0.75. Dendrogram<br />analysis produced two major groups of provenances, with<br />one outlier from South Lampung. There was no tendency for<br />provenances originated from nearby regions to cluster<br />together in each group, and several provenances showed<br />more similarities with provenances originated from distant<br />regions. This pattern lent credence to reports that Jatropha<br />was introduced to Indonesia around four centuries ago and<br />was mainly spread by humans. Based on the mean<br />similarities among the accessions and their clustering<br />pattern, the genetic diversity of the Jatropha collection<br />appeared to be fairly low. Future additions of genetic<br />materials from more diverse genetic background will be<br />necessary to maintain the current progress of Jatropha<br />improvement program.</p>

scholarly journals Genetic Diversity Analysis in Chickpea (Cicer arietinum L) Genotypes Grown in Northwestern Algeria using Microsatellite Markers (SSR)

2019 ◽  
Author(s):  
Bouri Amina ◽  
Mediouni Mohammed Rida ◽  
Ameur Ameur Abdelkader ◽  
Udupa Sripada ◽  
Gaouar Souheil Bechir Semir
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Cicer Arietinum ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Diversity Analysis ◽  
Factorial Correspondence Analysis ◽  
Genetic Diversity Analysis ◽  
Cicer Arietinum L

The present study aimed to characterize a subset of 10 selected chickpea accessions (Cicer arietinum L.) using SSR. The result indicated a presence of a total of 59 alleles. The genetic diversity at the 15 microsatellites loci was varied from 0, 32 for TA22 to 0.78 for TA72 and TA117 with an average of 0.66. Polymorphic information content (PIC) values ranged from 0.27 to 0.74. This study also detected a high significant (P less than 0.01) positive correlation between alleles per locus, gene diversity (H) and polymorphism information content (PIC). In the dendrogram and on the PCoA bi-plots, chickpea genotypes were adjoined according to their geographic origin, type of chickpea (Kabuli/ Desi). Nevertheless, the distribution of the different grouping through the factorial correspondence analysis (AFC) is due to the genetic variability.

scholarly journals The genetic diversity and population structure of shallots (Allium cepa var. aggregatum) in Indonesia based on R gene-derived markers

2019 ◽  
Vol 20 (3) ◽  
pp. 696-703
Author(s):  
LINA HERLINA ◽  
REFLINUR REFLINUR ◽  
SOBIR SOBIR ◽  
AWANG MAHARIJAYA ◽  
SURYO WIYONO
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Information Content ◽  
Allium Cepa ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
R Gene ◽  
Gene Sequences ◽  
Genetic Diversity Analysis

Abstract. Herlina L, Reflinur, Sobir, Maharijaya A, Wiyono S. 2019. The genetic diversity and population structure of shallots (Allium cepa var. aggregatum) in Indonesia based on R gene-derived markers. Biodiversitas 20: 696-703. Molecular markers are very useful for determining plant genetic diversity, especially when they are associated with useful traits. In shallots, type of markers still very limited. Therefore, development of new molecular markers is challenging if the future demand for this crop is to be met. The present study reports the genetic diversity analysis of 36 accessions of shallots using molecular markers derived from partial R gene sequences. Six polymorphic R gene-derived markers (Acepa-1, Acepa-2, Acepa-3, Acepa-4, Acepa-5, and Acepa-6) were developed and applied to analyze the genetic diversity of shallots in Indonesia. These loci produced a total of 963 alleles with an average of 0.51 + 0.77 alleles per marker. The polymorphic information content value ranged from 0.2784 to 0.5236 with an average of 0.36015. The markers were able to differentiate the shallot genotypes into three major clusters, suggesting that shallots are characterized by poor levels of genetic diversity in Indonesia. After further validation, the markers will be very useful, serving as tools to support the breeding of disease-resistant shallot varieties.

scholarly journals Microsatellite based genetic variation among the buffalo breed populations in Pakistan

2017 ◽  
Vol 61 (4) ◽  
pp. 535-542 ◽  
Author(s):  
Tanveer Hussain ◽  
Masroor Ellahi Babar ◽  
Akhtar Ali ◽  
Asif Nadeem ◽  
Zia Ur Rehman ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Mean Value ◽  
Diversity Analysis ◽  
Phenotypic Differentiation ◽  
Genetic Diversity Analysis ◽  
Expected Heterozygosity ◽  
The Mean ◽  
Average Gene

AbstractIntroduction: Eight microsatellite loci were used to define genetic diversity among five native water buffalo breeds in Pakistan.Material and Methods: Blood samples (10 mL) from 25 buffaloes of each of the Nili, Ravi, Nili-Ravi, Kundhi, and Azi-Kheli breeds were collected aseptically from the jugular vein into 50 ml Falcon tubes containing 200 μl of 0.5 M EDTA. The phenol-chloroform method was used to extract DNA and the regions were amplified for microsatellite analysis. The eight microsatellite markers ETH10, INRA005, ILSTS029, ILSTS033, ILSTS049, ILSTS052, ETH225, and CSSM66 were analysed.Results: The effective number of alleles across all loci was as usual lower than the observed values with a mean value of 2.52 alleles per locus. The overall allele frequency varied from 0.0041 for alleles B, I, and J over respective loci ILSTS052, INRA005, and ILSTS029 to 0.80 for allele H over locus ILSTS029. The average observed and expected heterozygosity values across all polymorphic loci in all studied buffalo breeds were 0.43 and 0.53, respectively. The overall value for polymorphic information content of considered microsatellite markers was 0.53, suggesting their appropriateness for genetic diversity analysis in buffalo. The mean Fis value was 0.13 and all loci except ILSTS049 were found significantly deviated from HWE, most likely due to non-random breeding. The five buffalo populations were genetically less diverse as indicated by a small mean Fst value (0.07). The average gene flow (Nm) indicative for population migration was calculated as 3.31. Nei’s original measures of genetic distance (Ds) revealed ancient divergence of the Nili and Azi-Kheli breeds (Ds = 0.1747) and recent divergence of the Nili and Ravi breeds (Ds = 0.0374).Conclusion: These estimates of genetic diversity were seen to coincide with phenotypic differentiation among the studied buffalo breeds. The present study reports the first microsatellite marker-based genetic diversity analysis in Pakistani buffalo breeds, and might facilitate similar studies in other livestock breeds of Pakistan.

scholarly journals Genetic Diversity Analysis of Sorghum (Sorghum Bicolor L. Moench) Genotypes Using Rapd Markers

2018 ◽  
Vol 15 (4) ◽  
pp. 833-839
Author(s):  
Sumita Zinzala ◽  
Bharat K. Davda ◽  
K. G. Modha ◽  
Ritesh K. Patel ◽  
Vipul Baldaniya
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Rapd Markers ◽  
Similarity Coefficient ◽  
Diversity Analysis ◽  
Similarity Coefficients ◽  
Genetic Diversity Analysis ◽  
Considerable Potential ◽  
Average Linkage ◽  
Sorghum Bicolor L

Genetic diversity among 24 genotypes of sorghum was studied by using 20 random primers. The total number of amplified PCR bands was 591 of which 495 (83.75%) were polymorphic displaying PIC values ranging from 0.27 to 0.69 with an average of 0.52. Similarity coefficients among the genotypes were ranged from 0.33 to 0.89. The similarity coefficient was used to construct a UPGMA based dendrogram using average linkage between groups. The analysis illustrates considerable potential of RAPD markers for estimating genetic diversity among 24 genotypes of sorghum.

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