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

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.

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

10.7287/peerj.preprints.27232 ◽

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.

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

Plant Genetic Resources ◽

10.1017/s1479262117000338 ◽

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.

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Development and Characterization of SSR Markers in the Gossypium Barbadense Genome

10.21203/rs.3.rs-870780/v1 ◽

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.

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De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens

Life ◽

10.3390/life11080803 ◽

2021 ◽

Vol 11 (8) ◽

pp. 803

Author(s):

Huapu Chen ◽

Xiaomeng Li ◽

Yaorong Wang ◽

Chunhua Zhu ◽

Hai Huang ◽

...

Keyword(s):

Ssr Markers ◽

De Novo ◽

Habitat Degradation ◽

Betta Splendens ◽

Orthologous Group ◽

Functional Genes ◽

Genetics Research ◽

Ssr Loci ◽

Paired End Sequencing ◽

Eukaryotic Orthologous Group

The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

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