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.

Assessing heat stress tolerance and genetic diversity among exotic and Indian wheat genotypes using simple sequence repeats and agro-physiological traits

2015 ◽  
Vol 15 (3) ◽  
pp. 208-220 ◽  
Author(s):  
K. T. Ramya ◽  
Neelu Jain ◽  
Nikita Gandhi ◽  
Ajay Arora ◽  
P. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heat Stress ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Phenotypic Traits ◽  
Heat Stress Tolerance ◽  
Simple Sequence

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers

2013 ◽  
Vol 93 (6) ◽  
pp. 1089-1096 ◽  
Author(s):  
Shiyong Chen ◽  
Xinquan Zhang ◽  
Xiao Ma ◽  
Linkai Huang
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Tibet Plateau ◽  
Group Method ◽  
Similarity Coefficients ◽  
Arithmetic Average ◽  
Pair Group ◽  
Elymus Nutans ◽  
Qinghai Tibet Plateau ◽  
Simple Sequence

Chen, S., Zhang, X., Ma, X. and Huang, L. 2013. Assessment of genetic diversity and differentiation of Elymus nutans indigenous to Qinghai–Tibet Plateau using simple sequence repeats markers. Can. J. Plant Sci. 93: 1089–1096. Elymus nutans Griseb., an important alpine forage grass, is widely distributed in the Qinghai–Tibet Plateau. A total of 50 E. nutans accessions from the eastern Qinghai–Tibet Plateau were analyzed using simple sequence repeats (SSR) markers from wheat and Elymus species. Our results show that a total of 144 reliable bands were generated, of which 132 (91.38%) were found to be polymorphic. Nei-Li's genetic similarity coefficients ranged from 0.515 to 0.870 with an average of 0.719, which shows a high level of genetic diversity and a broad genetic base among accessions. There was a low correlation between genetic distance and geographical distance (r=0.121, P=0.088) in the region, which is consistent with the unweighted pair group method with arithmetic average cluster analysis of accessions. The mountain ridges and river valleys in the eastern Qinghai–Tibet region could serve as genetic barriers for pollinator movement and seed dispersal. The rule of the most genetic diversity at medium altitude of E. nutans in the Qinghai–Tibet Plateau was also validated in the study. The implications of these results for the conservation of E. nutans are discussed.

scholarly journals Analysis of the genetic diversity and population structure of Salix psammophila based on phenotypic traits and simple sequence repeat markers

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6419 ◽  
Author(s):  
Lei Hao ◽  
Guosheng Zhang ◽  
Dongye Lu ◽  
Jianjun Hu ◽  
Huixia Jia
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Simple Sequence Repeat ◽  
Phylogenetic Analyses ◽  
Group Method ◽  
Phenotypic Traits ◽  
Germplasm Management ◽  
Sequence Repeat ◽  
Marginal Populations ◽  
Simple Sequence

Salix psammophila (desert willow) is a shrub endemic to the Kubuqi Desert and the Mu Us Desert, China, that plays an important role in maintaining local ecosystems and can be used as a biomass feedstock for biofuels and bioenergy. However, the lack of information on phenotypic traits and molecular markers for this species limits the study of genetic diversity and population structure. In this study, nine phenotypic traits were analyzed to assess the morphological diversity and variation. The mean coefficient of variation of 17 populations ranged from 18.35% (branch angle (BA)) to 38.52% (leaf area (LA)). Unweighted pair-group method with arithmetic mean analysis of nine phenotypic traits of S. psammophila showed the same results, with the 17 populations clustering into five groups. We selected 491 genets of the 17 populations to analyze genetic diversity and population structure based on simple sequence repeat (SSR) markers. Analysis of molecular variance (AMOVA) revealed that most of the genetic variance (95%) was within populations, whereas only a small portion (5%) was among populations. Moreover, using the animal model with SSR-based relatedness estimated of S. psammophila, we found relatively moderate heritability values for phenotypic traits, suggesting that most of trait variation were caused by environmental or developmental variation. Principal coordinate and phylogenetic analyses based on SSR data revealed that populations P1, P2, P9, P16, and P17 were separated from the others. The results showed that the marginal populations located in the northeastern and southwestern had lower genetic diversity, which may be related to the direction of wind. These results provide a theoretical basis for germplasm management and genetic improvement of desert willow.

scholarly journals Genome Wide Characterization, Comparative and Genetic Diversity Analysis of Simple Sequence Repeats in Cucurbita Species

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 143
Author(s):  
Lei Zhu ◽  
Huayu Zhu ◽  
Yanman Li ◽  
Yong Wang ◽  
Xiangbin Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Group Method ◽  
Motif Length ◽  
Pair Group ◽  
Ssr Loci ◽  
Ssr Frequency ◽  
Basic And Applied Research ◽  
Simple Sequence

Simple sequence repeats (SSRs) are widely used in mapping constructions and comparative and genetic diversity analyses. Here, 103,056 SSR loci were found in Cucurbita species by in silico PCR. In general, the frequency of these SSRs decreased with the increase in the motif length, and di-nucleotide motifs were the most common type. For the same repeat types, the SSR frequency decreased sharply with the increase in the repeat number. The majority of the SSR loci were suitable for marker development (84.75% in Cucurbita moschata, 94.53% in Cucurbita maxima, and 95.09% in Cucurbita pepo). Using these markers, the cross-species transferable SSR markers between C. pepo and other Cucurbitaceae species were developed, and the complicated mosaic relationships among them were analyzed. Especially, the main syntenic relationships between C. pepo and C. moschata or C. maxima indicated that the chromosomes in the Cucurbita genomes were highly conserved during evolution. Furthermore, 66 core SSR markers were selected to measure the genetic diversity in 61 C. pepo germplasms, and they were divided into two groups by structure and unweighted pair group method with arithmetic analysis. These results will promote the utilization of SSRs in basic and applied research of Cucurbita species.

scholarly journals Analisis Kesesuaian Marka SSR ( Simple Sequence Repeats ) untuk Identifikasi Keragaman Genetik pada Kacang Bambara Asal Jawa Barat

Agrikultura ◽  
2016 ◽  
Vol 27 (2) ◽  
Author(s):  
Safarinda Nurdianawati ◽  
Noladhi Wicaksana ◽  
Anas Anas
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeats ◽  
Polymorphic Information Content ◽  
Bambara Groundnut ◽  
Vigna Subterranea ◽  
Suitability Analysis ◽  
West Java ◽  
Crop Development ◽  
Alternative Sources ◽  
Simple Sequence

ABSTRACT Suitability Analysis of SSR Marker ( Simple Sequence Repeats ) for Genetic Diversity Identification in Bambara Groundnut West Java Origin Bambara groundnut ( Vigna subterranea ) is one of legume crops that has not been widely cultivated. It becomes food alternative sources in Indonesia as it has high of protein and carbohydrate content and low fat. Furthermore, bambara groundnut should be good production in marginal land. Molecular marker has been used for any crop development such as genetic diversity, matting system, clones identification, etc. This research used neutral genetic markers (SSR) to study genetic diversity in Bambara groundut population from West Java. Fifteen primers has used and the results showed that primer 1 and primer 19 were polymorphic and informative because the locus has high HE (heterozygosity) and PIC (Polymorphic Information Content) value compare to others. The higher HE and PIC value the more informative to distinguish each individual between genotype in one population. Keywords: Bambara groundnut ( Vigna subterranea ), Genetic diversity, Simple sequence repeats (SSR)  ABSTRAK Kacang bambara ( Vigna subterranea ) merupakan salah satu tanaman legume yang belum terlalu banyak dibudidayakan dan dapat menjadi sumber pangan alternative di Indonesia karena kandungan protein dan karbohidratnya  cukup tinggi dan rendah lemak. Selain itu, tanaman ini juga dilaporkan dapat berproduksi dengan baik pada lahan-lahan marginal. Penggunaan marka molekuler telah banyak digunakan pada tanaman untuk berbagai tujuan antara lain untuk mengevaluasi keragaman genetik suatu populasi, menduga system perkawinan, identifikasi klon dan lain-lain. Dalam penelitian ini digunakan marka netral (SSR) untuk mempelajari keragaman genetik populasi Kacang bambara ( Vigna subterranea ) asal Jawa Barat. Dari lima belas primer, primer 1 dan primer 19 merupakan primer yang bersifat polimorfik dan informative karena lokus tersebut memiliki nilai HE (heterozigositas) dan PIC ( P o l y m o r p h i c I n f o r m a t i o n Con tent ) yang tinggi dibandingkan dengan primer-primer lainnya. Semakin tinggi nilai HE dan PIC yang dihasilkan maka primer tersebut semakin informatif dalam membedakan individu antar genotip dalam populasi. Kata Kunci : Kacang bambara ( Vigna subterranea ), Keragaman genetik, Simple Sequence Repeats (SSR)

scholarly journals VALIDATION AND TRANSFERABILITY OF SIMPLE SEQUENCE REPEATS (SSR’S) FROM SOME SPECIES OF ACACIA GENUS TO ACACIA NILOTICA L.

2016 ◽  
Vol 8 (11) ◽  
pp. 95
Author(s):  
Amita Yadav ◽  
Manila Yadav ◽  
Sandeep Kumar ◽  
Dushyant Sharma ◽  
Jaya Parkash Yadav
Keyword(s):  
Genetic Diversity ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Climatic Conditions ◽  
Acacia Nilotica ◽  
Group Method ◽  
Acacia Species ◽  
Pair Group ◽  
High Level ◽  
Simple Sequence

Objective: In present study genetic transferability of SSR’s from related Acacia species to Acacia nilotica was evaluated along with its genetic diversity analysis from north Indian region. Methods: A total of 30 primers selected from 5 different Acacia species were screened for amplification and polymorphism. Dendrogram and 2 D Plot were constructed using NTSys PC version 2.02e. Different diversity parameters like Polymorphism information content (PIC), alleles per primer, number (no.) of amplicons were also calculated for each primer pair.Results: SSRs from Acacia tortilis, A. senegal and A. koa were highly transferable in A. nilotica. Out of 30, only twenty-two primers showed amplification with an average of 1.36 alleles per locus. Polymorphic information content (PIC) values ranged from 0.5 to 0.96 with an average of 0.81. Jaccard similarity coefficient (J) values ranged from 0.04 to 0.67 showing a high level of diversity. Un-weighted pair group method with arithmetic mean (UPGMA), based cluster analysis, divided all accessions into three main clusters.Conclusion: Geographical and climatic conditions showed a great impact on genetic diversity. The results indicated high transferability of genomic resources from related species and will facilitate more studies to characterize the relatively less studied Acacia niloticagenome. 

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.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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