Development and characterization of polymorphic genomic-SSR markers in Asian long-horned beetle (Anoplophora glabripennis)

AbstractThe Asian long-horned beetle (ALB), Anoplophora glabripennis (Motschulsky) (Coleoptera: Cerambycidae: Lamiinae), is a wood-borer and polyphagous xylophage that is native to Asia. It infests and seriously harms healthy trees, and therefore is a cause for considerable environmental concern. The analysis of population genetic structure of ALB and sibling species Anoplophora nobilis (Ganglbauer) will not only help to clarify the relationship between environmental variables and mechanisms of speciation, but also will enhance our understanding of evolutionary processes. However, the known genetic markers, particularly microsatellites, are limited for this species. SSRLocator software was used to analyze the distribution and frequencies of genomic simple sequence repeat (SSR), to infer the basic characteristics of repeat motifs, and to design primers. We developed SSR loci of 2–6 repeated units, including 10,650 perfect SSRs, and found 140 types of repeat motifs. A total of 2621 SSR markers were discovered in ALB whole-genome shotgun sequences. 48 pairs of SSR primers were randomly chosen from 2621 SSR markers, and half of these 48 pairs were polymorphic containing 4 di-, 7 tri-, 2 tetra-, and 11-hexamer SSRs. Four populations test the effectiveness of the primers. These results suggest that our method for whole-genome SSR screening is feasible and efficient, and the SSR markers developed in this study are suitable for further population genetics studies of ALB. Moreover, they may also be useful for the development of SSRs for other Coleoptera.

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Development and characterization of 53 polymorphic genomic-SSR markers in Siberian wildrye (Elymus sibiricus L.)

Conservation Genetics Resources ◽

10.1007/s12686-014-0225-5 ◽

2014 ◽

Vol 6 (4) ◽

pp. 861-864 ◽

Cited By ~ 9

Author(s):

Yunting Lei ◽

Yanyan Zhao ◽

Feng Yu ◽

Yuan Li ◽

Quanwen Dou

Keyword(s):

Ssr Markers ◽

Elymus Sibiricus ◽

Genomic Ssr

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Characterization of EST-SSR and genomic-SSR markers in the clam, Meretrix meretrix

Conservation Genetics Resources ◽

10.1007/s12686-011-9426-3 ◽

2011 ◽

Vol 3 (4) ◽

pp. 655-658 ◽

Cited By ~ 14

Author(s):

Xia Lu ◽

Hongxia Wang ◽

Ping Dai ◽

Baozhong Liu

Keyword(s):

Ssr Markers ◽

Meretrix Meretrix ◽

Genomic Ssr

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Development and Characterization of Polymorphic EST-SSR and Genomic SSR Markers for Tibetan Annual Wild Barley

PLoS ONE ◽

10.1371/journal.pone.0094881 ◽

2014 ◽

Vol 9 (4) ◽

pp. e94881 ◽

Cited By ~ 23

Author(s):

Mian Zhang ◽

Weihua Mao ◽

Guoping Zhang ◽

Feibo Wu

Keyword(s):

Ssr Markers ◽

Wild Barley ◽

Genomic Ssr

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Development and Characterization of Genomic SSR Markers for Anneslea fragrans (Pentaphylacaceae)

Applications in Plant Sciences ◽

10.3732/apps.1700086 ◽

2017 ◽

Vol 5 (10) ◽

pp. 1700086

Author(s):

Lijing Sun ◽

Kaikai Meng ◽

Boyong Liao ◽

Chunmei Li ◽

Yue Zhang ◽

...

Keyword(s):

Ssr Markers ◽

Genomic Ssr

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Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

10.36462/h.biosci.20203 ◽

2020 ◽

pp. 1-12

Author(s):

Laila Dabab Nahas ◽

Alsamman M. Alsamman ◽

Aladdin Hamwieh ◽

Naim Al-Husein ◽

Ghinwa Lababidi

Keyword(s):

Drought Tolerance ◽

Bread Wheat ◽

Ssr Markers ◽

Web Sites ◽

Wheat Breeding ◽

Genic Ssr ◽

Drought Tolerant ◽

Ssr Loci ◽

Weather Changes

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries

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Development and Characterization of SSR Markers from the Whole Genome Sequences of Saccharum officinarum (LA-purple)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2018.01400 ◽

2018 ◽

Vol 44 (9) ◽

pp. 1400

Author(s):

Heng-Bo WANG ◽

Nai-Yan XIAO ◽

Zhuan-Wei ZHU ◽

Cui-Cui LIU ◽

ALAM Intikhab ◽

...

Keyword(s):

Ssr Markers ◽

Saccharum Officinarum ◽

Whole Genome ◽

Genome Sequences

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Evaluation of Cross-Species Transferability of SSR Markers in Foeniculum vulgare

Plants ◽

10.3390/plants9020175 ◽

2020 ◽

Vol 9 (2) ◽

pp. 175 ◽

Cited By ~ 1

Author(s):

Domenico Aiello ◽

Nicoletta Ferradini ◽

Lorenzo Torelli ◽

Chiara Volpi ◽

Joep Lambalk ◽

...

Keyword(s):

Ssr Markers ◽

Genomic Information ◽

Foeniculum Vulgare ◽

Breeding Programs ◽

Breeding Lines ◽

Transcriptomic Data ◽

Genomic Ssr ◽

Ssr Loci ◽

Ssr Transferability ◽

Simple Sequence

Fennel (Foeniculum vulgare) is a species belonging to the Apiaceae family, well known for its nutritional and pharmacological properties. Despite the economic and agricultural relevance, its genomic and transcriptomic data remain poor. Microsatellites—also known as simple sequence repeats (SSRs)—are codominant markers widely used to perform cross-amplification tests starting from markers developed in related species. SSRs represent a powerful tool, especially for those species lacking genomic information. In this study, a set of primers previously designed in Daucus carota for polymorphic SSR loci was tested in commercial varieties and breeding lines of fennel in order to: (i) test their cross-genera transferability, (ii) look at their efficiency in assessing genetic diversity, and (iii) identify their usefulness for marker-assisted selection (MAS) in breeding programs. Thirty-nine SSR markers from carrot were selected and tested for their transferability score, and only 23% of them resulted suitable for fennel. The low rate of SSR transferability between the two species evidences the difficulties of the use of genomic SSR in cross-genera transferability.

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

Silvae Genetica ◽

10.1515/sg-2016-0009 ◽

2016 ◽

Vol 65 (1) ◽

pp. 67-70 ◽

Cited By ~ 1

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.

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