scholarly journals Genetic variability for coloured caryopses in common wheat varieties determined by microsatellite markers

2013 ◽  
Vol 49 (No. 3) ◽  
pp. 116-122 ◽  
Author(s):  
M. Musilová ◽  
V. Trojan ◽  
T. Vyhnánek ◽  
L. Havel
Keyword(s):  
Microsatellite Markers ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Wheat Breeding ◽  
Wheat Varieties ◽  
Breeding Programmes ◽  
New Gene ◽  
Yellow Coloration ◽  
Selection Of

Products made from wheat are the most important components of the human diet, and could also become a source of functional foods and feed ingredients, e.g. minerals, vitamins and/or phytochemicals. The caryopses of certain wheat genotypes contain antioxidants, i.e. anthocyanins or carotenoids, which cause purple, blue or yellow coloration. The first step before the introduction of these traits into individual wheat cultivars is the characterization of relationships and the possibility of new gene combinations. In this study, relationships among 24 genotypes with different types of caryopsis colour were investigated by means of microsatellite markers. Using 44 SSR (Simple Sequence Repeat) markers it was possible to detect a total of 184 alleles; on average, approximately 4 alleles were detected at a microsatellite locus. Using a set of 5 SSR markers (Xgwm636, Xbarc077, Xwmc262, Xgwm397 and Xwmc219) with PIC (polymorphic information content) values higher than 0.70, it was possible to differentiate among all the genotypes analysed. A dendrogram was created on the basis of all SSR markers, and showed that the genotypes were divided into two groups. Three, and one genotype with purple and blue caryopsis, respectively, belonged to one cluster, while the remaining twenty formed the second, greater cluster, which was subdivided into 2 sub-clusters: one of them involved genotypes with blue caryopses, and the other those with yellow and red caryopses. The genotype of tall wheatgrass (Thinopyrum ponticum), as a possible donor of genes responsible for blue caryopses, was also classified. These results can be used in wheat breeding programmes aimed at the selection of functional foodstuffs.

scholarly journals Molecular and Elemental Characterization of Selected Turkish Durum Wheat Varieties

2014 ◽  
Vol 42 (2) ◽  
pp. 431-439
Author(s):  
Erdogan E. HAKKI ◽  
Nurdan DOGRAR ◽  
Anamika PANDEY ◽  
Mohd. Kamran KHAN ◽  
Mehmet HAMURCU ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Durum Wheat ◽  
Molecular Data ◽  
Wheat Varieties ◽  
Elemental Analyses ◽  
Principle Coordinate Analysis ◽  
Elemental Characterization ◽  
Selection Of

Combination of elemental and protein studies along with molecular data using microsatellite markers may lead to the better and realistic determination of relatedness between the varieties and their populations. In this study, the extent of diversity among five Turkish durum wheat cultivars and their populations has been assessed using seven microsatellite markers and the elemental analysis together with the differences in their protein content.In molecular analysis, total 23 alleles have been obtained among all the genotypes with middling of 4.6 per primer. On employing UPGMA Dendrogram, Principle Coordinate Analysis (PCoA) and Winboot analyses, both inter and intra varietal polymorphic studies had shown similar clustering with minor differences. As a result of AMOVA performed, the extent of diversity was found to be higher among the genotypes (76%) in comparison to the variability within the genotypes (24%). In elemental analyses, ‘Selcuklu-97’ was found to be the most efficient variety with high content of several elements. Also, strong and positive correlation has been observed between magnesium- phosphorus, magnesium-sulphur and sulphur-sodium, while noteworthy negative correlation has been observed between sodium and zinc. The protein content of the genotypes was found in the range of 15.17-16.90%.The diversity revealed in durum genotypes can be employed in genetic expansion of the crop. These involved varieties may aid to avoid genetic attrition coming up from the landraces. The information provided can be utilized by breeders for appropriate selection of both, genetically and nutritionally efficient durum wheat varieties.

scholarly journals Population structure of Chinese southwest wheat germplasms resistant to stripe rust and powdery mildew using the DArT-seq technique

2018 ◽  
Vol 48 (4) ◽  
Author(s):  
Tianqing Chen ◽  
Piyada Alisha Tantasawat ◽  
Wei Wang ◽  
Xu Gao ◽  
Liyi Zhang
Keyword(s):  
Population Structure ◽  
Disease Resistance ◽  
Polymorphic Information Content ◽  
Wheat Breeding ◽  
Wheat Varieties ◽  
Group I ◽  
Population Structure Analysis ◽  
Specific Allele ◽  
The Mean ◽  
Different Origins

ABSTRACT: Understanding genetic variability in existing wheat accessions is critical for collection, conservation and use of wheat germplasms. In this study, 138 Chinese southwest wheat accessions were investigated by genotyping using two resistance gene makers (Pm21 and Yr26) and DArT-seq technique. Finally, about 50% cultivars (lines) amplified the specific allele for the Yr26 gene (Gwm11) and 40.6% for the Pm21 gene (SCAR1265). By DArT-seq analysis, 30,485 markers (6486 SNPs and 23999 DArTs) were obtained with mean polymorphic information content (PIC) value 0.33 and 0.28 for DArT and SNP marker, respectively. The mean Dice genetic similarity coefficient (GS) was 0.72. Two consistent groups of wheat varieties were identified using principal coordinate analysis (PCoA) at the level of both the chromosome 6AS and the whole-genome, respectively. Group I was composed of non-6VS/6AL translocation lines of different origins, while Group II was composed of 6VS/6AL translocation (T6VS/6AL) lines, most of which carried the Yr26 and Pm21 genes and originated from Guizhou. Besides, a model-based population structure analysis revealed extensive admixture and further divided these wheat accessions into six subgroups (SG1, SG2, SG3, SG4, SG5 and SG6), based on their origin, pedigree or disease resistance. This information is useful for wheat breeding in southwestern China and association mapping for disease resistance using these wheat germplasms in future.

scholarly journals Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

2018 ◽  
Author(s):  
Bruce F Murray ◽  
Michael A Reid ◽  
Shu-Biao Wu
Keyword(s):  
Gene Flow ◽  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Extreme Variability ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing ◽  
Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

Use of SSR- markers for detection of stability of soy to cercosporosis

2021 ◽  
Author(s):  
O. N. Tarasova ◽  
Keyword(s):  
Microsatellite Markers ◽  
Ssr Markers ◽  
Selection Of

As part of the development of the methodology for identifying alleles of microsatellite markers Satt244 and Satt547 associated with resistance to cercosporosis in two selected soybean varieties of the selection of the FSBSI FRC ARSRIS, an allele of Satt244-154 characterizing resistance to C. sojina was identified.

scholarly journals Microsatellite markers for identification of a group of italian olive accessions

2009 ◽  
Vol 66 (5) ◽  
pp. 685-690 ◽  
Author(s):  
Innocenzo Muzzalupo ◽  
Francesca Stefanizzi ◽  
Amelia Salimonti ◽  
Rosanna Falabella ◽  
Enzo Perri
Keyword(s):  
Microsatellite Markers ◽  
Molecular Characterization ◽  
Ssr Markers ◽  
Olea Europaea ◽  
Fruit Trees ◽  
Ssr Primers ◽  
Olive Cultivars ◽  
Olea Europaéa

Cultivar characterization for fruit trees certification requires fast, efficient and reliable techniques. Microsatellite markers (SSR) were used in the molecular characterization of 23 genotypes of Olea europaea subsp europaea. The DNA from the olive cultivars was analyzed using nine pre-selected SSR primers (GAPU59, GAPU71A, GAPU71B, GAPU103A, UDO99-01, UDO99-12, UDO99-28 and UDO99-39) and revealed 29 alleles, which allowed each genotype to be identified. In the dendrogram, the nine primers allowed the 23 olive genotypes to be grouped into subgroups corresponding to the same cultivar denominations. SSR markers proved to be efficient and reliable for the molecular characterization of Italian olive cultivars.

Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Konrad Celiński ◽  
Ewa Pawlaczyk ◽  
Aleksandra Wojnicka-Półtorak ◽  
Ewa Chudzińska ◽  
Wiesław Prus-Głowacki
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Pinus Mugo ◽  
Genetic Studies ◽  
Transfer Rates ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
European Mountain ◽  
High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

scholarly journals Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

2020 ◽  
pp. 1-12
Author(s):  
Laila Dabab Nahas ◽  
Alsamman M. Alsamman ◽  
Aladdin Hamwieh ◽  
Naim Al-Husein ◽  
Ghinwa Lababidi
Keyword(s):  
Drought Tolerance ◽  
Bread Wheat ◽  
Ssr Markers ◽  
Web Sites ◽  
Wheat Breeding ◽  
Genic Ssr ◽  
Drought Tolerant ◽  
Ssr Loci ◽  
Weather Changes

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries

scholarly journals Development and characterization of novel cross-species tetranucleotide microsatellite markers for sterlet (Acipenser ruthenus) from Chinese sturgeon (Acipenser sinensis)

2019 ◽  
Author(s):  
Yacheng Hu ◽  
Jing Yang ◽  
Xueqing Liu ◽  
Kan Xiao ◽  
Binzhong Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Diversity Indices ◽  
Chinese Sturgeon ◽  
Acipenser Sinensis ◽  
Management Actions ◽  
Acipenser Ruthenus ◽  
The Mean ◽  
Sterlet Acipenser Ruthenus

Sterlet (Acipenser ruthenus) is an important economic fish because of its nourishing caviar, isinglass and flesh. In order to facilitate the recovery of this species, the full understanding of its population genetic structure is necessary for taking appropriate management actions. However, genetic data on the use of nuclear loci in sterlet is still quite poor because microsatellite markers in sterlet that had been developed appeared to be polyploidy which add difficulties in studying the genetic of the sterlet. In this study, 24 tetranucleotide microsatellite markers were developed in sterlet from 160 microsatellite markers of the endangered Chinese sturgeon (Acipenser sinensis). Ten (ZHX76, ZHX64, Z194, Z217, Z184, Z242, Z250, Z258, Z268 and Z269) of the 24 loci showed disomic patterns while the rest loci showed tetrasomic patterns. In this paper, 24 microsatellite markers were characterized in 16 sterlet individuals and all of them were polymorphic with 2 to 7 alleles per locus. The Hardy-Weinberg departure value (d), polymorphic information content (PIC), the observed heterozygosity (HO), the Shannon-Wiener Diversity Indices (H') and the mean expected heterozygosity (HE) of all 24 polymorphic loci ranged from -0.334 to 0.484, 0.367 to 0.725, 0.438 to 1, 0.659 to 1.695, from 0.466 to 0.777, respectively. The markers described here will help in addressing practical problems such as the study of population genetics, conservation genetics and evolution in the polyploidy derivative nature of sterlet.

scholarly journals Discovery of miRNAs and Development of Heat-Responsive miRNA-SSR Markers for Characterization of Wheat Germplasm for Terminal Heat Tolerance Breeding

2021 ◽  
Vol 12 ◽  
Author(s):  
Pooja Sihag ◽  
Vijeta Sagwal ◽  
Anuj Kumar ◽  
Priyanka Balyan ◽  
Reyazul Rouf Mir ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Heat Stress ◽  
Ssr Markers ◽  
Heat Tolerance ◽  
Wheat Varieties ◽  
Wheat Genotypes ◽  
Wheat Germplasm ◽  
Heat Tolerant

A large proportion of the Asian population fulfills their energy requirements from wheat (Triticum aestivum L.). Wheat quality and yield are critically affected by the terminal heat stress across the globe. It affects approximately 40% of the wheat-cultivating regions of the world. Therefore, there is a critical need to develop improved terminal heat-tolerant wheat varieties. Marker-assisted breeding with genic simple sequence repeats (SSR) markers have been used for developing terminal heat-tolerant wheat varieties; however, only few studies involved the use of microRNA (miRNA)-based SSR markers (miRNA-SSRs) in wheat, which were found as key players in various abiotic stresses. In the present study, we identified 104 heat-stress-responsive miRNAs reported in various crops. Out of these, 70 miRNA-SSR markers have been validated on a set of 20 terminal heat-tolerant and heat-susceptible wheat genotypes. Among these, only 19 miRNA-SSR markers were found to be polymorphic, which were further used to study the genetic diversity and population structure. The polymorphic miRNA-SSRs amplified 61 SSR loci with an average of 2.9 alleles per locus. The polymorphic information content (PIC) value of polymorphic miRNA-SSRs ranged from 0.10 to 0.87 with a mean value of 0.48. The dendrogram constructed using unweighted neighbor-joining method and population structure analysis clustered these 20 wheat genotypes into 3 clusters. The target genes of these miRNAs are involved either directly or indirectly in providing tolerance to heat stress. Furthermore, two polymorphic markers miR159c and miR165b were declared as very promising diagnostic markers, since these markers showed specific alleles and discriminated terminal heat-tolerant genotypes from the susceptible genotypes. Thus, these identified miRNA-SSR markers will prove useful in the characterization of wheat germplasm through the study of genetic diversity and population structural analysis and in wheat molecular breeding programs aimed at terminal heat tolerance of wheat varieties.

scholarly journals Molecular Mapping and Characterization of QBp.caas-3BL for Black Point Resistance in Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Cuihe Liu ◽  
Jie Song ◽  
Siyang Liu ◽  
Jingdong Liu ◽  
Dengan Xu ◽  
...  
Keyword(s):  
Reference Genome ◽  
Molecular Mapping ◽  
Triticum Aestivum L ◽  
Wheat Breeding ◽  
Marker Assisted Breeding ◽  
Nutrient Quality ◽  
Black Point ◽  
Kasp Marker ◽  
Selection Of

Abstract Wheat black point, which occurs in most wheat growing regions of the world, is detrimental to grain appearance, processing and nutrient quality. Mining and characterization of genetic loci for black point resistance is helpful for breeding resistant wheat cultivars. We previously identified a major QTL QBp.caas-3BL in a recombinant inbred line (RIL) population of Linmai 2/Zhong 892 across five environments. Here we confirmed the QTL in two additional environments. The genetic region of QBp.caas-3BL was enriched with newly developed markers. Using four sets of near isogenic lines QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five annotated genes according to IWGSC reference genome. TraesCS3B02G404300, TraesCS3B02G404600 and TraesCS3B02G404700 were predicted as candidate genes based on the analyses of sequence polymorphisms and differential expression. We also converted a SNP of TraesCS3B02G404700 into a breeding-applicable KASP marker and verified its efficacy for marker-assisted breeding in a panel of germplasm. The findings not only lay a foundation for map-based cloning of QBp.caas-3BL but also provide a useful marker for selection of resistant cultivars genotypes in wheat breeding.

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