Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

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Microsatellite markers in analysis of resistance to coffee leaf miner in Arabica coffee

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2011001200010 ◽

2011 ◽

Vol 46 (12) ◽

pp. 1650-1656 ◽

Cited By ~ 1

Author(s):

Gabriella Santos Pereira ◽

Lilian Padilha ◽

Edila Vilela Resende Von Pinho ◽

Rita de Kássia Siqueira Teixeira ◽

Carlos Henrique Siqueira de Carvalho ◽

...

Keyword(s):

Microsatellite Markers ◽

Ssr Markers ◽

Expressed Sequence Tag ◽

Leaf Miner ◽

Est Database ◽

Ssr Loci ◽

Leucoptera Coffeella ◽

Coffee Leaf Miner ◽

Expressed Sequence ◽

Simple Sequence

The objective of this work was to analyze coffee (Coffea arabica) genotypes resistant to the coffee leaf miner (Leucoptera coffeella) using microsatellite markers. Sixty-six loci were evaluated, of which 63 were obtained from the Brazilian Coffee Expressed Sequence Tag (EST) database. These loci were amplified in bulks of individuals from F5 progenies of 'Siriema' (C. arabica x C. racemosa) resistant and susceptible to the insect, in eight samples of C. racemosa, and in a F6 population of 'Siriema' with 91 individuals segregating for resistance to the leaf miner. Polymorphisms were verified for two simple sequence repeat (SSR) loci in bulks of the susceptible progenies. The two polymorphic alleles were present in around 70% of the susceptible genotypes in F5 and in approximately 90% of the susceptible individuals in F6. However, the polymorphic EST-SSR markers among populations contrasting for resistance to leaf miner were not correlated to the evaluated characteristics. SSR markers show inter- and intraspecific polymorphism in C. arabica and C. racemosa.

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Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽

10.1139/g03-001 ◽

2003 ◽

Vol 46 (2) ◽

pp. 277-290 ◽

Cited By ~ 33

Author(s):

Eline van Zijll de Jong ◽

Kathryn M Guthridge ◽

German C Spangenberg ◽

John W Forster

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Simple Sequence Repeat ◽

Fragment Length Polymorphism ◽

Sequence Repeat ◽

Pasture Grass ◽

Ssr Loci ◽

Expressed Sequence ◽

Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

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Development and Application of EST-SSR Markers for DNA Fingerprinting and Genetic Diversity Analysis of the Main Cultivars of Black Locust (Robinia pseudoacacia L.) in China

Forests ◽

10.3390/f10080644 ◽

2019 ◽

Vol 10 (8) ◽

pp. 644 ◽

Cited By ~ 2

Author(s):

Li Dong ◽

Yuhan Sun ◽

Keqi Zhao ◽

Jing Zhang ◽

Yuwei Zhang ◽

...

Keyword(s):

Ssr Markers ◽

Black Locust ◽

Robinia Pseudoacacia ◽

Diversity Analysis ◽

Simple Method ◽

Genetic Diversity Analysis ◽

Ssr Loci ◽

Robinia Pseudoacacia L ◽

Expressed Sequence ◽

Simple Sequence

Black locust (Robinia pseudoacacia L.) is an economically and ecologically important tree species which is used for pillar construction, honey production and soil improvement. More EST-SSR (Expressed sequence tag simple sequence repeat) markers of black locust can be used as a complement and improvement of Genomic-SSR markers for the identification of the function of gene and the construction of genetic map. Additionally, currently there is no simple method for identifying black locust cultivars. In this study, we obtained 2702 unigenes from 3095 expressed sequence tags (ESTs) from the National Center of Biotechnology Information (NCBI) database to identify simple sequence repeats (SSRs) in R. pseudoacacia samples. A total of 170 SSR loci were found to be distributed in 162 non-redundant sequences with a frequency of 6.29%. Dinucleotide repeats were the most predominant types among microsatellites (62.35%), followed by tri-nucleotide repeats (25.88%); the remaining SSRs accounted for less than 12%. The repeat motifs AG/TC (29.25%) and CT/GA (29.25%) were the most abundant among dinucleotides, and AAT/TTA (15.91%) was the most common among tri-nucleotides. A total of 62 primer pairs were designed to screen polymorphic and stable SSR loci. The resulting 25 EST-SSR markers capable of amplifying polymorphic, stable, and repeatable products. Eight newly developed EST-SSR markers and four published SSR markers were selected for DNA fingerprinting and genetic diversity analysis of the 123 main R. pseudoacacia cultivars in China. The 12 SSR loci amplified 102 alleles, with an average number of alleles per locus of 8.5 (range 4–15). The average polymorphism information content at the 12 SSR loci for the 123 cultivars was 0.670 (range 0.427–0.881). The 123 cultivars clustered into six main groups based on similarity coefficients, with most cultivars in one subgroup. Fingerprinting was performed using eight SSR markers; 110 black locust cultivars were distinguished. The results of this study increase the availability of EST-SSR markers in black locust and make it a simple method for checking the collection, the certification, and the correct attribution of clones and cultivars.

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Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽

10.1163/15685403-00003916 ◽

2019 ◽

Vol 92 (7) ◽

pp. 841-851

Author(s):

Xuekai Han ◽

Ruyi Xu ◽

Yuyu Zheng ◽

Meirong Gao ◽

Liying Sui

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Polymorphic Information Content ◽

Diversity Analysis ◽

Food Items ◽

Geographical Populations ◽

Geographic Populations ◽

Expressed Sequence ◽

Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

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Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

Theoretical and Applied Genetics ◽

10.1007/s00122-004-1685-x ◽

2004 ◽

Vol 109 (4) ◽

pp. 800-805 ◽

Cited By ~ 128

Author(s):

N. Nicot ◽

V. Chiquet ◽

B. Gandon ◽

L. Amilhat ◽

F. Legeai ◽

...

Keyword(s):

Ssr Markers ◽

Expressed Sequence Tags ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Expressed Sequence ◽

Simple Sequence

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Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

HortScience ◽

10.21273/hortsci.51.3.227 ◽

2016 ◽

Vol 51 (3) ◽

pp. 227-231 ◽

Cited By ~ 1

Author(s):

Wenting Wang ◽

Chao Feng ◽

Zehuang Zhang ◽

Liju Yan ◽

Maomao Ding ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Simple Sequence Repeat ◽

Mean Value ◽

Sequence Repeat ◽

Chinese Bayberry ◽

Cultivated Populations ◽

Expressed Sequence ◽

Simple Sequence

Chinese bayberry (Morella rubra) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (Na) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.

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Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugensStål)

Bulletin of Entomological Research ◽

10.1017/s0007485311000435 ◽

2011 ◽

Vol 102 (1) ◽

pp. 113-122 ◽

Cited By ~ 27

Author(s):

S. Jing ◽

B. Liu ◽

L. Peng ◽

X. Peng ◽

L. Zhu ◽

...

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Large Scale ◽

Brown Planthopper ◽

Nilaparvata Lugens ◽

Rice Varieties ◽

Genetics And Genomics ◽

Expressed Sequence ◽

Simple Sequence

AbstractTo assess genetic diversity in populations of the brown planthopper (Nilaparvata lugensStål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopperN. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

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Short note: Development of Six EST-SSR Markers in Larch

Silvae Genetica ◽

10.1515/sg-2011-0022 ◽

2011 ◽

Vol 60 (1-6) ◽

pp. 161-163 ◽

Cited By ~ 3

Author(s):

X. Yang ◽

X. Sun ◽

S. Zhang

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeats ◽

Expressed Sequence Tags ◽

Short Note ◽

Biological Applications ◽

Expressed Sequence ◽

Simple Sequence

Abstract Six simple sequence repeats (SSR) markers were developed from expressed sequence tags (ESTs) in the genus Larix. Based on evaluation with 49 L. kaempferi genotypes, the number of alleles per locus ranged from two to four, and the expected (He) and observed (Ho) heterozygosity values were 0.225−0.694 and 0.201−0.656, respectively. The inbreeding coffcient (FIS) for all loci were less than zero except that LAReSSR85 was 0.4383. All the six EST-SSR markers were transferable to L. gmelini, L. olgensis var Koreana, L. principisrupprechtii and L. olgensis. BlastX analysis showed that five of the EST-SSRs were homologous to known genes. The six EST-SSR markers developed here can be valuable for biological applications in Larix.

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