Development of EST-SSR markers for Taxus cuspidata from publicly available transcriptome sequences

2015 ◽  
Vol 63 ◽  
pp. 20-26 ◽  
Author(s):  
Saneyoshi Ueno ◽  
Yafeng Wen ◽  
Yoshihiko Tsumura
Keyword(s):  
Ssr Markers ◽  
Taxus Cuspidata ◽  
Transcriptome Sequences

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

2018 ◽  
Vol 17 (03) ◽  
pp. 280-284 ◽  
Author(s):  
Katina F. Olodo ◽  
Mame C. Gueye ◽  
Caroline Calatayud ◽  
Baye M. Diop ◽  
Ndjido A. Kane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
West Africa ◽  
Ssr Markers ◽  
Related Species ◽  
Evolutionary History ◽  
Genetic Difference ◽  
Transcriptome Sequences ◽  
Ssr Development ◽  
Digitaria Exilis

AbstractDigitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

scholarly journals Development and characterization of EST-SSR markers for Taxus mairei (Taxaceae) and their transferability across species

2016 ◽  
Vol 65 (1) ◽  
pp. 67-70 ◽  
Author(s):  
X. Wu ◽  
Y. Wen ◽  
S. Ueno ◽  
Y. Tsumura
Keyword(s):  
Molecular Markers ◽  
Genetic Analysis ◽  
Ssr Markers ◽  
Taxus Cuspidata ◽  
Genetic Analyses ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Taxus Mairei ◽  
Ssr Loci

AbstractTaxusis an important genus which is well-known for Taxol. Its genetic analyses were lagged behind those of other conifers due to lack of suitable molecular markers. In this paper, we explored polymorphic loci forTaxus maireiand tested their transferability across species based on 150 EST-SSR loci already developed forTaxus cuspidatapreviously. The results showed that 103 loci were polymorphic, the number of alleles per locus ranged from 2 to 11 over 16 individuals. The observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0 to 1 and 0.0625 to 0.891, respectively. ThePICvalues ranged from 0.11 to 0.754 with an average of 0.453. The average cross-species transferability was 96.07% among 5 species. Most of these loci can be used as universal markers inTaxusgenus. The PCA results showed these markers have strong power to identify different species. These markers will be useful for further studies on genetic analysis and conversation ofTaxus mairei.

Development of 28 EST‐SSR markers based on transcriptome sequences of Gobiobotia filifer and cross‐species amplification

2019 ◽  
Vol 35 (6) ◽  
pp. 1295-1299
Author(s):  
Weiwei Dong ◽  
Huiwu Tian ◽  
Dengqiang Wang ◽  
Lixiong Yu ◽  
Xinbin Duan ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Transcriptome Sequences

Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences

2014 ◽  
Vol 34 (4) ◽  
pp. 1853-1866 ◽  
Author(s):  
Jing Wu ◽  
Changfu Cai ◽  
Fangyun Cheng ◽  
Huliang Cui ◽  
Hua Zhou
Keyword(s):  
Ssr Markers ◽  
Tree Peony ◽  
Transcriptome Sequences

scholarly journals Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on transcriptome sequences

2013 ◽  
Vol 62 (1-6) ◽  
pp. 137-141 ◽  
Author(s):  
Y. Wen ◽  
S. Ueno ◽  
W. Han
Keyword(s):  
Ssr Markers ◽  
Southern China ◽  
Cunninghamia Lanceolata ◽  
Fixation Index ◽  
Expected Heterozygosity ◽  
Genomic Analyses ◽  
Plantation Species ◽  
Plus Tree ◽  
Transcriptome Sequences

Abstract The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C. lanceolata have lagged significantly behind those of other conifer species due to a lack of suitable markers. To address this issue, we examined 27,666,670 reads from C. lanceolata transcriptome sequences recorded in the SRA database. Assembly produced 35,633 contigs, 1,822 (5.11%) of which contained one or more SSRs. In total, 2,156 SSRs were identified, giving an average SSR density of 68.4 SSRs/Mb. The most common SSR types were tri-SSRs (41.7%), followed by hexa-(29.8%), penta- (12.7%), di-(11.1%) and tetra-(4.7%) SSRs. EST-SSR markers based on the 1,822 SSR-containing contigs were developed using the CMiB pipeline and primer pairs were designed to target 35 loci. Polymorphism was observed in 28 of these loci, for which the number of alleles per locus ranged from 3 to 12 over 16 plus-tree individuals. The observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (FIS) values for the targeted loci ranged from 0.125 to 0.938, 0.225 to 0.891 and -0.368 to 0.456, respectively. The corres - ponding PIC values ranged from 0.210 to 0.881, with an average of 0.573. Some of these markers have since been used in our ongoing genetic diversity analyses of C. lanceolata. To our knowledge, this is the first analysis of SSRs and EST-SSR markers in C. lanceolata, and the identified EST-SSR markers will be useful in future genetic analyses of C. lanceolata and related species.

scholarly journals Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.)

Genes ◽  
2017 ◽  
Vol 8 (7) ◽  
pp. 177 ◽  
Author(s):  
Qi Guo ◽  
Jin-Xing Wang ◽  
Li-Zhuo Su ◽  
Wei Lv ◽  
Yu-Han Sun ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Black Locust ◽  
Robinia Pseudoacacia ◽  
Transcriptome Sequences ◽  
Robinia Pseudoacacia L

scholarly journals Development and Application of EST-SSR Markers in Cephalotaxus oliveri From Transcriptome Sequences

2021 ◽  
Vol 12 ◽  
Author(s):  
Hanjing Liu ◽  
Yuli Zhang ◽  
Zhen Wang ◽  
Yingjuan Su ◽  
Ting Wang
Keyword(s):  
Ssr Markers ◽  
Genetic Information ◽  
Common Type ◽  
Trinucleotide Repeats ◽  
Biological Functions ◽  
Dinucleotide Repeats ◽  
Genetic Studies ◽  
Genetic Groups ◽  
Transcriptome Sequences ◽  
First Time

Cephalotaxus oliveri is an endemic conifer of China, which has medicinal and ornamental value. However, the limited molecular markers and genetic information are insufficient for further genetic studies of this species. In this study, we characterized and developed the EST-SSRs from transcriptome sequences for the first time. The results showed that a total of 5089 SSRs were identified from 36446 unigenes with a density of one SSR per 11.1 kb. The most common type was trinucleotide repeats, excluding mononucleotide repeats, followed by dinucleotide repeats. AAG/CTT and AT/AT exhibited the highest frequency in the trinucleotide and dinucleotide repeats, respectively. Of the identified SSRs, 671, 1125, and 1958 SSRs were located in CDS, 3′UTR, and 5′UTR, respectively. Functional annotation showed that the SSR-containing unigenes were involved in growth and development with various biological functions. Among successfully designed primer pairs, 238 primer pairs were randomly selected for amplification and validation of EST-SSR markers and 47 primer pairs were identified as polymorphic. Finally, 28 high-polymorphic primers were used for genetic analysis and revealed a moderate level of genetic diversity. Seven natural C. oliveri sampling sites were divided into two genetic groups. Furthermore, the 28 EST-SSRs had 96.43, 71.43, and 78.57% of transferability rate in Cephalotaxus fortune, Ametotaxus argotaenia, and Pseudotaxus chienii, respectively. These markers developed in this study lay the foundation for further genetic and adaptive evolution studies in C. oliveri and related species.

Application of SSR Technique for the Identification of Markers Linked to Salinity Tolerance in Rice

2013 ◽  
Vol 19 (2) ◽  
pp. 57-65
Author(s):  
MH Kabir ◽  
MM Islam ◽  
SN Begum ◽  
AC Manidas
Keyword(s):  
Salt Tolerance ◽  
Ssr Markers ◽  
Salinity Tolerance ◽  
Seedling Stage ◽  
Phenotypic Screening ◽  
Salt Tolerant ◽  
Marker Assisted Breeding ◽  
Hydroponic System ◽  
Rice Landrace ◽  
Salt Susceptible

A cross was made between high yielding salt susceptible BINA variety (Binadhan-5) with salt tolerant rice landrace (Harkuch) to identify salt tolerant rice lines. Thirty six F3 rice lines of Binadhan-5 x Harkuch were tested for salinity tolerance at the seedling stage in hydroponic system using nutrient solution. In F3 population, six lines were found as salt tolerant and 10 lines were moderately tolerant based on phenotypic screening at the seedling stage. Twelve SSR markers were used for parental survey and among them three polymorphic SSR markers viz., OSR34, RM443 and RM169 were selected to evaluate 26 F3 rice lines for salt tolerance. With respect to marker OSR34, 15 lines were identified as salt tolerant, 9 lines were susceptible and 2 lines were heterozygous. While RM443 identified 3 tolerant, 14 susceptible and 9 heterozygous rice lines. Eight tolerant, 11 susceptible and 7 heterozygous lines were identified with the marker RM169. Thus the tested markers could be efficiently used for tagging salt tolerant genes in marker-assisted breeding programme.DOI: http://dx.doi.org/10.3329/pa.v19i2.16929 Progress. Agric. 19(2): 57 - 65, 2008

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