Genetic variation of bread wheat accessions in response to the cereal cyst nematode, Heterodera filipjevi

Nematology ◽  
2018 ◽  
Vol 20 (9) ◽  
pp. 859-875 ◽  
Author(s):  
Marzieh Moatamedi ◽  
Eidi Bazgir ◽  
Mehdi Nasr Esfahani ◽  
Mostafa Darvishnia
Keyword(s):  
Genetic Diversity ◽  
Bread Wheat ◽  
Ssr Marker ◽  
Polymorphic Information Content ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Cyst Nematodes ◽  
Ssr Analysis ◽  
Heterodera Filipjevi ◽  
Simple Sequence

Summary Bread wheat, Triticum aestivum, produces large edible grains and is consumed by 75% of the world’s populations. Cereal cyst nematodes have a global distribution and cause significant economic yield losses in many countries. Therefore, there is an urgent need to identify new resistance sources. In this study, the genetic diversity of 43 wheat accessions in response to cereal cyst nematode, Heterodera filipjevi Isfahan pathotype, was assessed using a simple sequence repeat (SSR) marker. Seven primers were used, out of which five primers showed polymorphisms. Alleles per primer varied from one to three per locus (mean 2.85). The highest and lowest polymorphic information content of 0.81 and 0.44 (mean 0.66) were related to Xgwm 3012DL and Xgwm147, respectively. Genetic similarity was 29-88% between accessions. SSR analysis divided the accessions into five main groups. Resistant cultivars ‘Bam’ and ‘Behrang’ possessed both Cre1 and Cre8 resistant genes. The Cre3 and Cat genes were partially sequenced in five cultivars of different responses to H. filipjevi. The nucleotide sequences were compared to Cre3 and Cat homologues, indicating 93-100% and 86-92% homology, respectively. The MEGA program showed highest similarity of Cre3 and Cat genes amplified with the resistance gene analogues (RGA14) in the wheat and Cat3-A1 gene in ‘Carnamah’. This research showed that SRR markers could efficiently verify genetic diversity between wheat accessions, and the known resistance genes (Cre genes) against the cereal cyst nematodes could not control the H. filipjevi Isfahan pathotype populations, except the Cre1 gene.

Assessing drought tolerance and regional patterns of genetic diversity among spring and winter bread wheat using simple sequence repeats and phenotypic data

2010 ◽  
Vol 61 (10) ◽  
pp. 812 ◽  
Author(s):  
Dejan Dodig ◽  
Miroslav Zorić ◽  
Borislav Kobiljski ◽  
Gordana Šurlan-Momirović ◽  
Steve A. Quarrie
Keyword(s):  
Genetic Diversity ◽  
Drought Tolerance ◽  
Bread Wheat ◽  
Simple Sequence Repeats ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Phenotypic Traits ◽  
Vegetable Crops ◽  
Regional Patterns ◽  
Simple Sequence

This study was conducted to assess drought tolerance and regional-based patterns of diversity of bread wheat accessions and to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meeting the challenges posed by changing climate in Southern and Eastern Europe. For this, genetic diversity assessed by simple sequence repeats (SSR) markers was compared with diversity evaluated using 19 phenotypic traits averaged over irrigated and drought-stress field conditions. Thirty-six SSR were used to profile 96 wheat genotypes from the collection of genetic resources at the Institute of Field and Vegetable Crops, Novi Sad, Serbia. A total of 46 loci and 366 alleles were detected, with a range of 3–21 alleles per locus. The polymorphic information content was estimated to be 0.61. The genetic distance for all possible 4560 pairs of genotypes ranged from 0.06 to 0.91 with an average of 0.65. Genotypes were grouped according to their drought tolerance (high, medium, low) and region of origin. Analysis of molecular variance showed that over 96% of the total variation could be explained by the variance within the drought tolerance and geographical groups. As a whole, genetic diversity among the high drought tolerance genotypes was considerably higher than that among low drought tolerance genotypes. Comparative analysis of SSR diversity among six regional groups revealed that the genotypes from North America exhibited more genetic diversity than those from other regions. Two dendrograms were constructed based on phenotypic and molecular analyses using the Unweighted Pair Group Method with Arithmetic Mean method and were found to be topologically different. Genotypes characterised as highly drought tolerant were distributed among all SSR-based cluster groups. This implied that the genetic basis of drought tolerance in these genotypes was different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve drought tolerance in their breeding programs.

scholarly journals Genetic Diversity of Seashore Paspalum Revealed with Simple Sequence Repeat Markers

2020 ◽  
Vol 145 (4) ◽  
pp. 228-235
Author(s):  
Qing Shen ◽  
Hua Bian ◽  
Hai-yan Wei ◽  
Li Liao ◽  
Zhi-yong Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Principal Component ◽  
Sequence Repeat ◽  
Similarity Coefficients ◽  
Seashore Paspalum ◽  
Simple Sequence

Seashore paspalum (Paspalum vaginatum) is an important warm-season turfgrass distributed in tropical and coastal areas. It has excellent resistance to abiotic stresses, such as salinity, drought, and low temperature. However, the research on genetic diversity of local P. vaginatum collections from China is limited. In this study, the genetic diversity among 58 P. vaginatum accessions from four different provinces in China and four cultivars were assessed using simple sequence repeat (SSR) markers. The results indicated that a total of 45 alleles were detected by 19 polymorphic markers, with a range of 2 to 4 and an average of 2.4 alleles per marker. The genetic similarity coefficients between each pair of the 58 P. vaginatum accessions and four cultivars ranged from 0.51 to 1.00, with an average of 0.77. The range of variation of Shannon diversity index of each SSR marker was 0.047 to 1.075, with an average of 0.486. The polymorphic information content of each SSR marker varies from 0.016 to 0.577, with an average of 0.249. The results of cluster analysis and principal component analysis (PCA) showed that 58 P. vaginatum accessions and four cultivars were divided into four groups. These results provide the theoretical basis for the genetic diversity assessments and molecular marker–assisted breeding of P. vaginatum species.

A GWAS to identify the cereal cyst nematode (Heterodera filipjevi) resistance loci in diverse wheat prebreeding lines

2021 ◽  
Author(s):  
Abdelfattah Dababat ◽  
Mian Abdur Rehman Arif ◽  
Halil Toktay ◽  
Osameh Atiya ◽  
Sajid Shokat ◽  
...  
Keyword(s):  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Heterodera Filipjevi

scholarly journals First Report of the Cereal Cyst Nematode Heterodera filipjevi on Wheat in Serbia

Plant Disease ◽  
2012 ◽  
Vol 96 (10) ◽  
pp. 1583-1583 ◽  
Author(s):  
V. Oro ◽  
S. Živković ◽  
Ž. Ivanović ◽  
L. Waeyenberge
Keyword(s):  
New York ◽  
Tail Length ◽  
Its Region ◽  
Molecular Data ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Important Species ◽  
First Report ◽  
Wheat Field ◽  
Heterodera Filipjevi

The most globally recognized and economically important nematode on wheat is the cereal cyst nematode (CCN) complex (1). One of the most important species of this group is Heterodera filipjevi (Madžidov, 1981) Mulvey and Golden, 1983. During regular soil quarantine control in September 2010, Heterodera sp. cysts were found in soil samples originating from a wheat field in Gunaroš, Vojvodina Province, in northern Serbia. The wheat was a winter crop grown in a dryland production system and had an average cyst density of 2.50/100 cm3 of soil. Morphologically, the cysts were golden brown and lemon shaped with a posterior protuberance. The vulval cone was bifenestrate with horseshoe-shaped semifenestra, bullae, and underbridge. Cyst measurements (n = 30) ranged as follows: cyst length (without neck): 511.50 to 899.00 μm, cyst width: 201.50 to 682.00 μm, fenestral length: 44.80 to 65.60 μm, fenestral width: 24.00 to 40.00 μm, vulval bridge length: 12.80 to 20.80 μm, vulval bridge width: 6.40 to 14.40 μm, vulval slit: 6.00 to 12.80 μm, and underbridge length: 60.00 to 112.00 μm. The second-stage juveniles had an offset head, stylet with characteristic anchor-shaped basal knobs, four incisures, and a conical tail with a rounded tip. The J2 morphometrics (n = 30) were: length: 447.30 to 611.10 μm, width: 22.40 to 25.60 μm, stylet: 20.80 to 24.00 μm, tail length: 56.00 to 68.80 μm, tail width: 14.40 to 19.20 μm, and hyaline length: 35.20 to 44.80 μm. The ITS region was used for molecular analysis. Each DNA sample was extracted from a single cyst. Sequencing was done with primers TW81 and AB28 (2). In comparison with other H. filipjevi populations, the obtained sequence (GenBank Accession No. JX235959) revealed 99 to 100% similarity. Morphological and molecular data confirmed the existence of H. filipjevi. This is, to our knowledge, the first report of H. filipjevi from Serbia. Since wheat has important socioeconomic value for Serbia, after extensive surveys, additional phytosanitary measures may be necessary to prevent the spread of this parasite. References: (1) J. M. Nicol et al. Current Nematode Threats to World Agriculture. Genomics and Molecular Genetics of Plant-Nematode Interactions, Springer, New York, 2011. (2) A. M. Skantar et al. J. Nematol. 39:133, 2007.

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 variation and population dynamics of the cereal cyst nematode, Heterodera filipjevi in wheat areas of Bolu, Turkey

2017 ◽  
Vol 42 (5) ◽  
pp. 362-369 ◽  
Author(s):  
Mustafa Imren ◽  
Lieven Waeyenberge ◽  
A. Sami Koca ◽  
Nagihan Duman ◽  
Şenol Yildiz ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Genetic Variation ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Heterodera Filipjevi

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

HortScience ◽  
2015 ◽  
Vol 50 (8) ◽  
pp. 1143-1147 ◽  
Author(s):  
Benard Yada ◽  
Gina Brown-Guedira ◽  
Agnes Alajo ◽  
Gorrettie N. Ssemakula ◽  
Robert O.M. Mwanga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Analysis ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Population Improvement ◽  
High Level ◽  
Simple Sequence

Genetic diversity is critical in sweetpotato improvement as it is the source of genes for desired genetic gains. Knowledge of the level of genetic diversity in a segregating family contributes to our understanding of the genetic diversity present in crosses and helps breeders to make selections for population improvement and cultivar release. Simple sequence repeat (SSR) markers have become widely used markers for diversity and linkage analysis in plants. In this study, we screened 405 sweetpotato SSR markers for polymorphism on the parents and progeny of a biparental cross of New Kawogo × Beauregard cultivars. Thereafter, we used the informative markers to analyze the diversity in this population. A total of 250 markers were polymorphic on the parents and selected progeny; of these, 133 were informative and used for diversity analysis. The polymorphic information content (PIC) values of the 133 markers ranged from 0.1 to 0.9 with an average of 0.7, an indication of high level of informativeness. The pairwise genetic distances among the progeny and parents ranged from 0.2 to 0.9, and they were grouped into five main clusters. The 133 SSR primers were informative and are recommended for use in sweetpotato diversity and linkage analysis.

Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 841-851
Author(s):  
Xuekai Han ◽  
Ruyi Xu ◽  
Yuyu Zheng ◽  
Meirong Gao ◽  
Liying Sui
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Food Items ◽  
Geographical Populations ◽  
Geographic Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

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