Dataset Information

Development of EST-SSR markers for Taxillus nigrans (Loranthaceae) in southwestern China using next-generation sequencing.

ABSTRACT: PREMISE OF THE STUDY:We developed transcriptome microsatellite markers (simple sequence repeats) for Taxillus nigrans (Loranthaceae) to survey the genetic diversity and population structure of this species. METHODS AND RESULTS:We used Illumina HiSeq data to reconstruct the transcriptome of T. nigrans by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them amplified successfully and demonstrated polymorphisms. Two loci that detected null alleles were eliminated, and the remaining 17, which were subjected to further analyses, yielded two to 21 alleles per locus. CONCLUSIONS:The markers will serve as a basis for studies to assess the extent and pattern of distribution of genetic variation in T. nigrans, and they may also be useful in conservation genetic, ecological, and evolutionary studies of the genus Taxillus, a group of plant species of importance in Chinese traditional medicine.

SUBMITTER: Miao N

PROVIDER: S-EPMC5584814 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Development of EST-SSR markers for <i>Taxillus nigrans</i> (Loranthaceae) in southwestern China using next-generation sequencing.

Miao Ning N Zhang Lei L Li Maoping M Fan Liqiang L Mao Kangshan K

Applications in plant sciences 20170824 8

<h4>Premise of the study</h4>We developed transcriptome microsatellite markers (simple sequence repeats) for <i>Taxillus nigrans</i> (Loranthaceae) to survey the genetic diversity and population structure of this species.<h4>Methods and results</h4>We used Illumina HiSeq data to reconstruct the transcriptome of <i>T</i>. <i>nigrans</i> by de novo assembly and used the transcriptome to develop a set of simple sequence repeat markers. Overall, 40 primer pairs were designed and tested; 19 of them a ...[more]

PMID: 28924510

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Project description:Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity.

Dataset Information

Development of EST-SSR markers for Taxillus nigrans (Loranthaceae) in southwestern China using next-generation sequencing.

Publications

Development of EST-SSR markers for <i>Taxillus nigrans</i> (Loranthaceae) in southwestern China using next-generation sequencing.

Similar Datasets

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