scholarly journals Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia)

2018 ◽  
Author(s):  
Shuheng Shen ◽  
Xutian Chai ◽  
Dong Luo ◽  
Yanrong Wang ◽  
Zhipeng Liu
Keyword(s):  
Ssr Markers ◽  
Genetic Studies ◽  
Onobrychis Viciifolia ◽  
Ssr Loci ◽  
Wild Accessions ◽  
High Level ◽  
Genetic Structures ◽  
Paired End Sequencing ◽  
Band Number

Background: Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods: In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using denovo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results: Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion: Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

scholarly journals Development of polymorphic EST-SSR markers and characterization of the autotetraploid in sainfoin (Onobrychis viciifolia)

2018 ◽  
Author(s):  
Shuheng Shen ◽  
Xutian Chai ◽  
Dong Luo ◽  
Yanrong Wang ◽  
Zhipeng Liu
Keyword(s):  
Ssr Markers ◽  
Genetic Studies ◽  
Onobrychis Viciifolia ◽  
Ssr Loci ◽  
Wild Accessions ◽  
High Level ◽  
Genetic Structures ◽  
Paired End Sequencing ◽  
Band Number

Background: Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods: In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using denovo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results: Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion: Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

scholarly journals Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6542 ◽  
Author(s):  
Shuheng Shen ◽  
Xutian Chai ◽  
Qiang Zhou ◽  
Dong Luo ◽  
Yanrong Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Genetic Studies ◽  
Onobrychis Viciifolia ◽  
Ssr Loci ◽  
Wild Accessions ◽  
High Level ◽  
Genetic Structures ◽  
Paired End Sequencing

Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.

Mining, characterization and application of transcriptome-based SSR markers in Chinese jiaotou

2018 ◽  
Vol 16 (4) ◽  
pp. 306-314
Author(s):  
Chan Liu ◽  
Qing Tang ◽  
Chaohua Cheng ◽  
Ying Xu ◽  
Zemao Yang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Large Scale ◽  
Trinucleotide Repeat ◽  
De Novo ◽  
Local Varieties ◽  
Genetic Studies ◽  
Oxidation Reduction ◽  
Ssr Loci ◽  
Wild Accessions ◽  
Expressed Sequence

AbstractChinese jiaotou is an economically important crop that is widely cultivated in East Asia. The lack of simple sequence repeat (SSR) markers has been a major obstacle for genetic studies of this crop. In the present study, SSR markers were developed for Chinese jiaotou on a large scale, based on the crop's transcriptome assembledde novoby a previous study. A search for SSR loci in the transcriptome's expressed sequence tags (ESTs) revealed 2157 SSRs, of which primer pairs could be developed for 1494. Among these resulting SSRs, trinucleotide repeat motifs were the most abundant type, with GAA/TTC motifs occurring most frequently. Analysing the annotated function of SSR-containing ESTs revealed that they enriched into the GO categories involved in transcription regulation, oxidation–reduction, transport, etc. The quality and transferability of these markers were also assessed using 100 randomly selected EST–SSRs, and the result showed that these markers were of good quality and possessed high cross-species transferability. In addition, the developed SSR markers were used to analyse the genetic diversity of 19 cultivated and four wild accessions, resulting in three distinct groups, cluster I, II and III. Interestingly, all four wild accessions were assigned to cluster III, and two local varieties from northern Hunan, China, were closely related to the wild genotypes. These results provide new insights into the origin of Chinese jiaotou. The EST–SSRs developed herein represent the first large-scale development of SSR markers in Chinese jiaotou, and they can be widely used for genetic studies of the crop.

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 SSR Markers in the Gossypium Barbadense Genome

2021 ◽  
Author(s):  
Wenjuan ZHONG ◽  
Can YUAN ◽  
Zhengjie CHEN ◽  
Yonghang ZHOU ◽  
Siwei Chen ◽  
...  
Keyword(s):  
Ssr Markers ◽  
De Novo ◽  
Low Cost ◽  
Fiber Quality ◽  
Gossypium Barbadense ◽  
Pcr Analysis ◽  
Genetic Studies ◽  
Genome Wide ◽  
User Friendly

Abstract BackgroundThe fiber quality and resistance traits of Gossypium barbadense are considerably better than that of other Gossypium species. Simple sequence repeats (SSRs) are user friendly, low cost markers widely used in genetic studies. However, most SSRs have been developed from G. hirsutum, G. arboreum, and G. raimondii; no genome-wide SSRs have been developed from G. barbadense.The de novo sequences of G. barbadense cv. Xinhai21 were utilized to develop SSR markers and scanned to detect SSRs using the MIcroSAtellite (http://pgrc.ipk-gatersleben.de/misa/) identification tool. And then in silico PCR analysis was conducted to evaluate these primers polymorphism in five Gossypium species.ResultsIn total, 85,582 SSRs were identified with different motifs. 153,560 primer pairs were successfully designed for 73,419 SSRs. In silico analysis, we found that 8,466 primer pairs of 3,288 SSRs yielded one product (monomorphic) simultaneously in five Gossypium species. two Gossypium species (30 G. hirsutum and 27 G. barbadense accessions) were successfully separated by 300 primer pairs with the polymorphism information content (PIC) ranging from 0.00 to 0.93. ConclusionThese newly developed SSR markers will be helpful for the construction of genetic linkage maps, genetic diversity analyses, QTL mapping, and molecular breeding of Gossypium species.

scholarly journals Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Forests ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 61 ◽  
Author(s):  
Chengcai Zhang ◽  
Xiaohua Yao ◽  
Huadong Ren ◽  
Jun Chang ◽  
Jun Wu ◽  
...  
Keyword(s):  
Genetic Study ◽  
Polymorphic Information Content ◽  
Genetic Research ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Genetic Studies ◽  
New Development ◽  
Ssr Loci ◽  
Simple Sequence

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

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