scholarly journals Elit Domuz Ayrığı (Dactylis glomerata L.) Genotiplerinde Genetik Çeşitliliğin SSR Markörleri ile Belirlenmesi

2019 ◽  
Vol 7 (1) ◽  
pp. 127
Author(s):  
Gonul Cömertpay ◽  
Hüseyin Özpınar
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Agricultural Research ◽  
Dactylis Glomerata ◽  
Distance Matrix ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Group A ◽  
Dactylis Glomerata L

Orchardgrass (Dactylis glomerata L.) is an economically important, and widely cultivated perennial forage grass. The aim of this study was to determine the genetic diversity and genetic relationship among the orchardgrass breeding lines developed in Aegean Agricultural Research Institute, using simple sequence repeat (SSR, microsatellite) molecular markers. The genetic diversity of 32 orchardgrass was assessed using a set of 24 SSR markers. SSR primer pair combinations yielded 126 alleles for all genotypes. The number of alleles per locus ranged from three to seven with an average of 5.25 alleles across 24 loci. The alleles size ranged from 101 to 354 and the polymorphism rate was 100%. Jaccard genetic distance coefficient varied from 0.21 to 0.84 among genotypes. The degree of genetic diversity among the genotypes was high. Total number of rare alleles was 28 alleles across 126 loci. Dendrogram constructed using neighbor-joining analysis based on Jaccard genetic distance matrix were clustered into three main groups A, B and C. Group A was the largest group contained 15 genotypes, while B had 13 genotypes originated mainly from same region. The group C was the smallest group contained genotypes originated from northern part of Turkey. The molecular analysis revealed that a significant genetic variation existed in this orhardgrass collection, and the genotypes studied have potential for ensure rich genetic resources in orchardgrass breeding program. In addition to this, it was concluded that SSR markers are suitable markers for the molecular identification of different orchardgrass genotypes.

Agromorphological and molecular analysis discloses wide genetic variability in sunflower breeding lines from USDA, USA

2019 ◽  
Vol 79 (02) ◽  
Author(s):  
K. T. Ramya ◽  
A. Vishnuvardhan Reddy ◽  
M. Sujatha
Keyword(s):  
Genetic Distance ◽  
Polymorphic Information Content ◽  
Distance Matrix ◽  
Coefficient Matrix ◽  
Male Sterile ◽  
Breeding Lines ◽  
Genetic Distance Matrix ◽  
Ssr Primers ◽  
Fertility Restorers ◽  
Simple Sequence

The present study investigates genetic divergence among 84 fertility restorers and 32 cytoplasmic male sterile (CMS) lines of sunflower augmented from USDA, USA along with the popular Indian parental lines using simple sequence repeats (SSR). Thirty-nine polymorphic SSR primers produced 139 alleles with an average of 3.56 alleles per locus. The polymorphic information content ranged from 0.23 to 0.69 with an average of 0.45. The average genetic distance was 0.45 and 0.42 for the R and CMS lines, respectively. Dendrogram based on the dissimilarity coefficient matrix grouped the CMS and R lines into separate clusters except for Cluster A which consisted of all CMS lines along with five R lines. Genetic distance matrix estimated from three sets of mitochondrial primers (BOX, ERIC and REP) grouped the 32 CMS lines into eight clusters. The results suggest the existence of considerable genetic diversity among the restorer and CMS lines of sunflower obtained from USDA, USA.

scholarly journals Genetic diversity of four cattle breeds using microsatellite markers

2003 ◽  
Vol 32 (1) ◽  
pp. 93-98 ◽  
Author(s):  
Marco Antonio Machado ◽  
Ivan Schuster ◽  
Mário Luiz Martinez ◽  
Ana Lúcia Campos
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Distance Matrix ◽  
Average Heterozygosity ◽  
Informative Locus ◽  
Holstein Breed ◽  
Cattle Breeds ◽  
Genetic Distance Matrix ◽  
Hardy Weinberg Equilibrium ◽  
Nei's Genetic Distance

Four cattle breeds (Gyr, Nellore, Guzerat and Holstein) were analyzed by amplification of genomic DNA using microsatellite loci to evaluate the genetic diversity within and among them. DNA samples of 18 animals from each breed were collected to access the genetic content of them. Allele frequencies were calculated and used to generate a Nei's genetic distance matrix what was used to build a dendrogram following UPGMA clustering. As expected, Holstein breed was the most distinct from the other breeds: 1.15 in relation to Gyr, 1.12 in relation to Nellore and 0.94 in relation to Guzerat. The closest genetic distance was 0.25 between Guzerat and Nellore. A total of 64 alleles in all four breeds were detected using nine microsatellite primers. Each breed showed 53% of the total number of alleles. The average number of alleles per locus was 7.11 ± 3.21. The most informative locus was BMS1237 with 53% of observed heterozygosity and the least informative locus was BMS3004 with 12% only. The average heterozygosity detected for the nine loci were 35% and the expected value for Hardy-Weinberg equilibrium was 53%. This low heterozygosity suggests a high endogamy level among the animals sampled within each breed.

Diversity comparison and phylogenetic relationships of cocksfoot (Dactylis glomerata L.) germplasm as revealed by SSR markers

2010 ◽  
Vol 90 (1) ◽  
pp. 13-21 ◽  
Author(s):  
W -G. Xie ◽  
X -Q. Zhang ◽  
X. Ma ◽  
H -W. Cai ◽  
L -K. Huang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Polymorphic Information Content ◽  
Morphological Variability ◽  
Dactylis Glomerata ◽  
Molecular Variation ◽  
Geographical Regions ◽  
Dactylis Glomerata L ◽  
High Degree

Phylogenetic relationships among and within 16 accessions collected from China, Russia, Kazakhstan, India and Japan were investigated using SSR markers. The 21 SSR primer pairs generated a total of 143 polymorphic alleles, with an average of 6.8 alleles per locus, and a range of 3-13 alleles. The average genetic diversity, as measured by the polymorphic information content (PIC), was 0.33. The average polymorphic rate (P) for this species was 90.7%, suggesting a high degree of genetic diversity. Analysis of molecular variation (AMOVA) revealed larger genetic variation within accessions (65.75%) and geographical regions (75.58%) rather than between them, while among ploidy level variance contributed only 2.62%. A high degree of genetic diversity within tetraploid group was detected based on the polymorphic rate (P = 94.23%) and shannon’ s information index of diversity (I = 0.4300) when compared with diploid group (P = 91.25%, I = 0.3922). The values of the genetic identity (GI) among accessions ranged from 0.7320 to 0.9691 and were used to produce a dendrogram using the UPGMA approach. The 16 accessions were grouped into two major clusters (GI = 0.876); specifically, all tetraploid (2n = 4x = 28) accessions originating from different regions were grouped into the same cluster, whereas the diploid (2n = 2x = 14) accessions were grouped into the two major clusters. The dendrogram was concordant with the morphological variability, agronomic traits and karyotype. Generally, the results of this study indicate that cocksfoot germplasm contains high molecular variation within accession and geographical region. The implications of these results for conversation of the species were discussed.Key words: Dactylis glomerata L.; simple sequence repeats; genetic diversity; phylogenetic relationship

Comparative analysis of genetic diversity in Canadian barley assessed by SSR, DarT, and pedigree data

Genome ◽  
2013 ◽  
Vol 56 (6) ◽  
pp. 351-358 ◽  
Author(s):  
Mebarek Lamara ◽  
Li Yi Zhang ◽  
Suzanne Marchand ◽  
Nicholas A. Tinker ◽  
François Belzile
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationships ◽  
Distance Matrix ◽  
Estimation Methods ◽  
Pedigree Data ◽  
Barley Cultivars ◽  
Genetic Distance Matrix ◽  
Ssr Loci ◽  
Good Agreement

The aim of this study was to measure genetic diversity and population structure among 92 Canadian barley cultivars using two types of molecular markers (SSRs and DArTs) and pedigree data. A total of 368 alleles were identified at 50 SSR loci. The number of alleles per locus ranged between 2 and 13 ([Formula: see text] = 7.36) and PIC values ranged from 0.34 to 0.86 ([Formula: see text] = 0.69). For the biallelic DArT markers, the genetic distance matrix was based on 971 markers whose PIC values ranged between 0.06 and 0.50 ([Formula: see text] = 0.39). A third distance matrix was computed based on the kinship coefficient. Clustering of genotypes was performed based on the genetic distance matrix and the three dendrograms obtained showed the genetic relationships among barley cultivars. The topological similarity of the three dendrograms was estimated using a congruence index and showed the three dendrograms to be in very good agreement. Statistical analysis also showed a highly significant correlation between the SSR and DArT matrices (r = 0.80, p < 0.002) compared with lower yet significant correlations of the pedigree data with both marker types (r = 0.46, p < 0.002; r = 0.52, p < 0.002). Finally, we assessed linkage disequilibrium in this germplasm and found it to be quite extensive, as the mean distance between marker pairs with significant (P < 0.001) r2 values >0.5 was 3.8 cM. Information obtained from comparing results of different genetic diversity estimation methods should be useful for the improvement and conservation of barley genetic resources.

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>

Genome Analysis of Mungbean [Vigna radiata (L.) Wilczek] using Simple Sequence Repeats (SSR) Mapping Data

2021 ◽  
Author(s):  
Babita Rani ◽  
Renu Singh ◽  
Minakshi Jattan ◽  
Shubham Kumar ◽  
Ram Kumar
Keyword(s):  
Genetic Diversity ◽  
Agricultural Research ◽  
Ammonium Bromide ◽  
Breeding Lines ◽  
Iron And Zinc ◽  
Zinc Concentrations ◽  
Increase Productivity ◽  
Cetyltrimethyl Ammonium ◽  
Simple Sequence

Background: Agricultural research chiefly focuses on the ways to increase productivity of staple food crops like wheat and rice, but still there are crops where research focus is meagre like nutritionally important mungbean crop grown by marginal farmers in crop rotation systems. Mungbean is leguminous crop which is high in protein content thus it offers health benefits at cheaper rates. The present work emphasizes on finding genetic diversity in mungbean germplasm on the basis of chemical and molecular analysis for micronutrients variation (iron and zinc). The identified molecular markers having linkage with high iron and zinc concentrations in the seeds can prove helpful in expansion of biofortification programme.Methods: Fifty-one green gram genotypes viz. varieties released from CCS Haryana Agricultural University (HAU), Hisar, Punjab Agricultural University (PAU), Ludhiana, Indian Institute of Pulse Research (IIPR), Kanpur and some advanced breeding lines were included in the study. Acid digested samples were used for determination of Fe and Zn by Atomic Absorption Spectrophotometer. Young seedlings leaves were used for isolation of genomic DNA using 2% CTAB (cetyltrimethyl ammonium bromide). Result: Total of fifty-one mungbean genotypes were tested using fifty simple sequence repeat (SSR) primers. Out of fifty primers screened, 16 primers generated 35 bands. Iron (Fe) and zinc (Zn) in mungbean lines was 36.90 to 107.1 mg/kg and 14.2 to 53.8 mg/kg respectively. The molecular studies based on SSR markers also indicates existence of ample genetic diversity at molecular level.

Evaluation of populations of Dactylis glomerata L. native to Mediterranean environments

2012 ◽  
Vol 63 (12) ◽  
pp. 1124 ◽  
Author(s):  
V. Copani ◽  
G. Testa ◽  
A. Lombardo ◽  
S. L. Cosentino
Keyword(s):  
Genetic Diversity ◽  
Biomass Yield ◽  
Agronomic Traits ◽  
Dactylis Glomerata ◽  
Leaf Length ◽  
Mediterranean Environment ◽  
Summer Dormancy ◽  
Low Levels ◽  
Dactylis Glomerata L ◽  
Different Levels

Several morphological and agronomic traits and the genetic diversity of nine Dactylis glomerata L. populations collected throughout Sicily (semi-arid Mediterranean environment) were evaluated for two successive years. Significant differences were recorded for morphological traits (plant height, leaf length, leaf width). In relation to the measurement of summer dormancy, the results suggest the expression of different levels of dormancy (completely dormant, semi-dormant, and non-dormant). For biomass yield, some Sicilian populations (SD63 and SD56) characterised by low levels of summer dormancy show production levels similar to the summer-active control varieties (Medly and Porto). However, SD46, with a much higher level of dormancy, gave biomass yield higher than the summer-dormant control variety (Kasbah). The genetic diversity evaluated by fAFLP analysis confirms the observed morphological and agronomic variability.

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