Use of expressed sequence tags-derived simple sequence repeat (SSR) markers for population studies of released and elite sweet potato

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 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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Identification and characterisation of functional expressed sequence tags-derived simple sequence repeat (eSSR) markers for genetic linkage mapping of Schistosoma mansoni juvenile resistance and susceptibility loci in Biomphalaria glabrata

International Journal for Parasitology ◽

10.1016/j.ijpara.2013.03.007 ◽

2013 ◽

Vol 43 (8) ◽

pp. 669-677 ◽

Cited By ~ 9

Author(s):

Wannaporn Ittiprasert ◽

André Miller ◽

Xin-zhuan Su ◽

Jianbing Mu ◽

Ganlayarat Bhusudsawang ◽

...

Keyword(s):

Schistosoma Mansoni ◽

Expressed Sequence Tags ◽

Linkage Mapping ◽

Simple Sequence Repeat ◽

Genetic Linkage ◽

Biomphalaria Glabrata ◽

Susceptibility Loci ◽

Sequence Repeat ◽

Expressed Sequence ◽

Simple Sequence

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Development of simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon)

Molecular Ecology Resources ◽

10.1111/j.1755-0998.2008.02290.x ◽

2008 ◽

Vol 8 (6) ◽

pp. 1494-1496 ◽

Cited By ~ 1

Author(s):

SUKHUMAN WHANKAEW ◽

SITHICHOKE TANGPHATSORNRUANG ◽

KANOKPORN TRIWITAYAKORN

Keyword(s):

Expressed Sequence Tags ◽

Simple Sequence Repeat ◽

Penaeus Monodon ◽

Sequence Repeat ◽

Simple Sequence Repeat Markers ◽

Black Tiger Shrimp ◽

Tiger Shrimp ◽

Expressed Sequence ◽

Simple Sequence

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Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.6.810 ◽

2008 ◽

Vol 133 (6) ◽

pp. 810-818 ◽

Cited By ~ 33

Author(s):

John McCallum ◽

Susan Thomson ◽

Meeghan Pither-Joyce ◽

Fernand Kenel ◽

Andrew Clarke ◽

...

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Snp Markers ◽

Sequence Repeat ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Bulb Onion ◽

Expressed Sequence ◽

Simple Sequence

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

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