Assessment of genetic diversity in Australian canola (Brassica napus L.) cultivars using SSR markers

2009 ◽  
Vol 60 (12) ◽  
pp. 1193 ◽  
Author(s):  
J. Wang ◽  
S. Kaur ◽  
N. O. I. Cogan ◽  
M. P. Dobrowolski ◽  
P. A. Salisbury ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Genetic Variability ◽  
Ssr Marker ◽  
Principal Coordinate Analysis ◽  
Pedigree Structure ◽  
Brassica Napus L ◽  
Breeding Programs ◽  
Cultivar Variation ◽  
Simple Sequence

Australian canola (Brassica napus L.) has been relatively isolated from the global gene pool and limited knowledge is available for genetic variability based on DNA profiling. In the present study, genetic diversity of recent Australian canola cultivars was determined by simple sequence repeat (SSR) marker analysis. In total, 405 individuals from 48 varieties were genotyped with 18 primer pairs, resulting in 112 polymorphic features. The number of polymorphic features amplified by each SSR primer pair varied from 3 to 16. Analysis of molecular variance (AMOVA) detected 53.7% and 46.3% within- and between-cultivar variation, respectively. Intra-cultivar genetic variability differed according to cultivar. The number of polymorphic features per cultivar varied from 35 (Ag-Spectrum) to 72 (Ag-Insignia), while mean sum of squares (MSS) varied from 6.29 (Tornado TT) to 24.76 (Ag-Emblem). Genetic differentiation of cultivars generally reflected pedigree structure and origin by breeding organisation. Clustering and principal coordinate analysis (PCoA) indicated that the individuals were separated into 4 major groups. The genetic diversity information from this study will be useful for future Australian canola breeding programs.

QTL analysis of yield-related traits and their association with functional markers in Brassica napus L.

2007 ◽  
Vol 58 (8) ◽  
pp. 759 ◽  
Author(s):  
Yuanyuan Li ◽  
Jinxiong Shen ◽  
Tonghua Wang ◽  
Qingfang Chen ◽  
Xingguo Zhang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Agronomic Traits ◽  
High Yield ◽  
Functional Markers ◽  
Multiple Traits ◽  
Brassica Napus L ◽  
Breeding Programs ◽  
F2 Population ◽  
Expressed Sequence ◽  
Simple Sequence

Yield is one of the most important traits in Brassica napus breeding programs. Quantitative trait loci (QTLs) for yield-related traits based on genetic mapping would help breeders to develop high-yield cultivars. In this study, a genetic linkage map of B. napus, containing 142 sequence-related amplified polymorphism (SRAP) markers, 163 functional markers, 160 simple sequence repeat (SSR) markers, and 117 amplified fragment length polymorphism (AFLP) markers, was constructed in an F2 population of 184 individuals resulting from the cross SI-1300 × Eagle. This map covered 2054.51 cM with an average marker interval of 3.53 cM. Subsequently, QTLs were detected for 12 yield-related traits in Wuhan and Jingmen. In total, 133 QTLs were identified, including 14 consistent ones across the 2 locations. Fifteen of 20 linkage groups (LGs) were found to have QTLs for the 12 traits investigated, and most of the QTLs were clustered, especially on LGs N2 and N7, where similar QTL positions were identified for multiple traits. Eight of 10 QTLs for yield per plant (YP) were also associated with number of seeds per silique (SS), number of siliques per plant (SP), and/or 1000-seed weight (SW). In addition, 45 functional markers involved in 39 expressed sequence tags (ESTs) were linked to the QTLs of 12 traits. The present results may serve as a valuable basis for further molecular dissection of agronomic traits in B. napus, and the markers related to QTLs may offer promising possible makers for marker assisted selection.

Genetic diversity of Chinese and Swedish rapeseed (Brassica napus L.) analysed by inter-simple sequence repeats (ISSRs)

2003 ◽  
Vol 1 (2-3) ◽  
pp. 169-174 ◽  
Author(s):  
M. A. Chao-zhi ◽  
F. U. Ting-dong ◽  
Stine Tuevesson ◽  
Bo Gertsson
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Brassica Napus ◽  
Simple Sequence Repeats ◽  
Brassica Napus L ◽  
The Third ◽  
Principal Coordinates ◽  
Group I ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

AbstractWe have compared the genetic diversity of 24 Chinese weak-winter, Swedish winter and spring Brassica napus accessions by inter-simple sequence repeats (ISSRs). Using cluster analysis (UPGMA) based on 125 polymorphism bands amplified with 20 primers, the 24 accessions were divided into three groups. Six Swedish winter lines and eight Chinese weak-winter lines were in group I and group II consisted of two Chinese weak-winter lines, Xiangyou15 and Bao81. The third group contained eight Swedish spring lines. Principal coordinates (PCO) analysis showed similar groupings to cluster analysis. Results from cluster analysis and PCO analysis showed very clearly that Chinese weak-winter, Swedish spring and winter accessions were distinguished from each other and Chinese weak-winter accessions in this study were genetically closer to Swedish winter accessions than to Swedish spring accessions. The Chinese weak-winter accessions had larger diversity than the Swedish spring or winter accessions. This study indicated that ISSR is a suitable and effective tool to evaluate genetic diversity among rapeseed germplasm.

Analysis of Genetic Diversity in the Brassica napus L. Gene Pool Using SSR Markers

2005 ◽  
Vol 53 (4) ◽  
pp. 793-802 ◽  
Author(s):  
M. Hasan ◽  
F. Seyis ◽  
A. G. Badani ◽  
J. Pons-Kühnemann ◽  
W. Friedt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Ssr Markers ◽  
Gene Pool ◽  
Brassica Napus L

Vernalization response in spring oilseed rape (Brassica napus L.) cultivars

1994 ◽  
Vol 74 (2) ◽  
pp. 275-277 ◽  
Author(s):  
L. A. Murphy ◽  
R. Scarth
Keyword(s):  
Brassica Napus ◽  
Oilseed Rape ◽  
Vernalization Response ◽  
Brassica Napus L ◽  
Early Maturity ◽  
Breeding Programs ◽  
Cumulative Response ◽  
Cold Requirement ◽  
Key Words:Brassica

Early maturity is a major objective of oilseed rape (Brassica napus L.) breeding programs in western Canada. Maturity of crops is influenced by time of initiation and flowering. The presence of a vernalization requirement affects plant development by delaying floral initiation until the cold requirement of the plant has been satisfied. Five spring oilseed rape cultivars were screened for their response to vernalization. Vernalization treatments consisted of exposure of germinated seeds to 0–42 d at 4 °C. Plants were assessed under a 20-h photoperiod. In general, there was a cumulative response to vernalization, with a decrease in days to each developmental stage as exposure to 4 °C was increased. Vernalization treatment of 6 d at 4 °C was sufficient to decrease both the days to first flower and the final leaf number. The characterization of vernalization response is of interest because variation in flowering time in response to year-to-year variations in the environment could result. Key words:Brassica napus, canola, oilseed rape, vernalization

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>

Genetic structure of Plasmodiophora brassicae populations virulent on clubroot resistant canola (Brassica napus)

Plant Disease ◽  
2021 ◽  
Author(s):  
Homa Askarian ◽  
Alireza Akhavan ◽  
Leonardo Galindo González ◽  
Sheau-Fang Hwang ◽  
Stephen Ernest Strelkov
Keyword(s):  
Brassica Napus ◽  
Genetic Structure ◽  
Plasmodiophora Brassicae ◽  
Single Spore ◽  
Specific Primers ◽  
Brassica Napus L ◽  
Before And After ◽  
Differential Hosts ◽  
And Migration ◽  
Simple Sequence

Clubroot, caused by Plasmodiophora brassicae Woronin, is a significant threat to the canola (Brassica napus L.) industry in Canada. Clubroot resistance has been overcome in more than 200 fields since 2013, representing one of the biggest challenges to sustainable canola production. The genetic structure of 36 single-spore isolates derived from 12 field isolates of P. brassicae collected before and after the introduction of clubroot resistant (CR) canola cultivars (2005-2014) was evaluated by simple sequence repeat (SSR) marker analysis. Polymorphisms were detected in 32 loci with the identification of 93 distinct alleles. A low level of genetic diversity was found among the single-spore isolates. Haploid linkage disequilibrium and number of migrants suggested that recombination and migration were rare or almost absent in the tested P. brassicae population. A relatively clear relationship was found between the genetic structure and virulence phenotypes of the pathogen as defined on the differential hosts of Somé et al., Williams and the Canadian Clubroot Differential (CCD) set. Although genetic variability within each pathotype group, as classified on each differential system, was low, significant genetic differentiation was observed among the pathotypes. The highest correlation between genetic structure and virulence was found among matrices produced with genetic data and the hosts of the CCD set, with a threshold index of disease of 50% to distinguish susceptible from resistant reactions. Genetically homogeneous single-spore isolates provided a more complete and clearer picture of the population genetic structure of P. brassicae, and the results suggest some promise for the development of pathotype-specific primers.

scholarly journals Genetic diversity and population structure of feral rapeseed (Brassica napus L.) in Japan

PLoS ONE ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. e0227990
Author(s):  
Ruikun Chen ◽  
Ayako Shimono ◽  
Mitsuko Aono ◽  
Nobuyoshi Nakajima ◽  
Ryo Ohsawa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Brassica Napus ◽  
Brassica Napus L

scholarly journals Genetic Diversity in Commercial Rapeseed (Brassica napus L.) Varieties from Turkey as Revealed by RAPD

2013 ◽  
Vol 5 (1) ◽  
pp. 114-119 ◽  
Author(s):  
Özlem ÖZBEK ◽  
Betül Uçar GIDIK
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Dna Analysis ◽  
Diversity Index ◽  
Principal Component ◽  
Brassica Napus L ◽  
Binary Matrix ◽  
Crop Species ◽  
Commercial Crop ◽  
The Mean

In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD) technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides) produced 51 scorable loci, 31 loci of which were polymorphic (60.78%) and 20 loci (39.22%) were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs) and total (HT) were 0.15 and 0.19 respectively. The genetic differentiation (GST) and the gene flow (Nm) values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na), the mean number of effective alleles (nae), and the mean value of genetic diversity (He) were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

scholarly journals Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers

2014 ◽  
Vol 50 (No. 3) ◽  
pp. 216-225 ◽  
Author(s):  
L. Havlíčková ◽  
E. Jozová ◽  
A. Rychlá ◽  
M. Klíma ◽  
V. Kučera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Brassica Napus ◽  
Oilseed Rape ◽  
Issr Markers ◽  
Appropriate Technology ◽  
Winter Oilseed Rape ◽  
Brassica Napus L ◽  
High Genetic Diversity ◽  
Diversity Assessment ◽  
Breeding Programmes

The genetic diversity of 94 accessions of winter oilseed rape (Brassica napus L.), representing past and contemporary material utilized in the Czech breeding programmes, was determined using microsatellites (SSRs), ISSRs and AFLPs. All three kinds of markers differed in the range of observed polymorphism and differentiated clearly each accession. Altogether 89 SSR, 1003 AFLP and 53 ISSR markers were evaluated. Their average rates of polymorphic bands were 100%, 53.9% and 90.6%, respectively, indicating high genetic diversity among the accessions. The greatest genetic distance was found by ISSRs (62.3%) whereas significantly lower distances of 49.4% in SSRs and 35.5% in AFLPs were observed. The genetic similarity matrix clearly distinguished all accessions. A set of the most distinct varieties was established. The analysis of the genetic pattern of the accessions indicated two groups comprising most of the modern Czech breeding materials, revealing a distinct shift in breeding. Surprisingly, molecular analyses did not support&nbsp; breeders&rsquo; views about a narrow genetic base of the Czech breeding materials. The choice of appropriate technology for different aspects of germplasm evaluation is also discussed.

Sign in / Sign up

Export Citation Format

Share Document