Identification of microsatellites in cattle unigenes

Qu, Yan; Zhang, Yinghan; Li, Hongbin; Wei, Caihong; Niu, Lili; Guan, Shaokang; Li, Shangang; Du, Lixin

doi:10.1016/s1673-8527(08)60037-5

Cited by 17 publications

(14 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A total of 586 (5.25%) potential unigenes-contained microsatellite motifs were found, at a higher frequency than that previously reported in some plant ESTs (Cardle et al, 2000;Poncet et al, 2006). However, the overall frequency and the frequency of different repeat motifs might depend on not only the redundancy level of the sequence, but also the criteria and the datasets for searching for SSR (Yan et al, 2008). In general, about 5% of ESTs contained SSRs in many plant species when the minimum repeat length was set to be 20 bp (Varshney et al, 2005).…”

Section: Discussionmentioning

confidence: 77%

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Gong

Mao

et al. 2010

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

Abstract:The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

show abstract

Section: Discussionmentioning

confidence: 77%

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Gong

Mao

et al. 2010

J. Zhejiang Univ. Sci. B

View full text Add to dashboard Cite

show abstract

“…There were 235 (0.19%) unique ESTs that contained more than one SSR. This ratio was much lower than that in cattle (0.34%) (Yan et al 2008) and citrus (3.4%) (Jiang et al 2006). One important reason for this difference was that 454 sequencing-generated ESTs were shorter than ESTs generated by conventional methods.…”

Section: Identification Of Ssrs In Soybeanmentioning

confidence: 82%

“…Investigation of the distribution of SSR motifs can provide insight into the composition of the genome (Yan et al 2008). Our results showed that the motif types and abundance of soybean SSRs were not evenly distributed.…”

Section: Diversity Of Ssrs In Soybeanmentioning

confidence: 86%

Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

Li¹,

Zhao²,

Wang³

et al. 2010

Electron. J. Biotechnol.

View full text Add to dashboard Cite

Microsatellites, or simple sequence repeats (SSRs), in expressed sequence tags (ESTs) provide an opportunity for low cost SSR development. We looked for EST-SSRs in 403,511 ESTs (generated by 454 sequencing and representing 70,654 contigs and 52,082 singletons) from soybean globular stage embryos. Among 122,736 unique ESTs, 3,729 contained one or more SSRs. In total, 3,989 SSRs were identified including 304 mono, 1,374 di, 2,208 tri, 70 tetra, 13 penta and 20 hexanucleotide SSRs. Thirty three EST-SSRs were selected for primer design and polymorphism analysis using twenty soybean cultivars and one wild-type soybean. Successful amplification was obtained using 21 of these primer pairs, 11 of which detected polymorphisms in these soybean cultivars. These results demonstrated that 454 high throughput sequencing is a powerful tool for molecular marker development. From the 3,989 identified SSRs we expect to obtain a large number of makers with polymorphism among different soybean cultivars, which would be useful for analysis of genetic diversity and maker assisted selection in the soybean breeding programs.

show abstract

“…The high frequency and distribution of ESTSSRs in this study may be attributed to small genome size and due to criteria used for SSR search by using SSR Locator. Variation in the frequency in SSRs in the EST of a particular species have been attributed to the criteria adapted in SSR search in the database mining approaches and to the quantity of data used to identify SSRs (Varshney et al 2002 andYan et al 2008). …”

Section: Genetic Diversitymentioning

confidence: 99%

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta¹,

Sankar²,

Sreelakshmi³

et al. 2016

Physiol Mol Biol Plants

View full text Add to dashboard Cite

Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSRcontaining ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.

show abstract

Identification of microsatellites in cattle unigenes

Cited by 17 publications

References 22 publications

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Identification of SSR markers using soybean (Glycine max) ESTs from globular stage embryos

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Contact Info

Product

Resources

About