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Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies

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Title Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies
 
Creator Gimode, Davis
 
Contributor Odeny, Damaris
de Villiers, Etienne
Wanyonyi, Solomon
Dida, Mathews
Mneney, Emmarold E.
Muchugi, Alice
Machuka, Jesse
De Villiers, Santie M.
 
Subject sequencing technologies
ssr marker identification
genetic diversity
 
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.
 
Date 2017-03-16T00:00:03Z
2017-03-16T00:00:03Z
 
Type Journal Article
 
Identifier http://oar.icrisat.org/id/eprint/9612
https://mel.cgiar.org/reporting/download/hash/47yBd9zW
Davis Gimode, Damaris Odeny, Etienne de Villiers, Solomon Wanyonyi, Mathews Dida, Emmarold E. Mneney, Alice Muchugi, Jesse Machuka, Santie M. De Villiers. (25/7/2016). Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies. PLOS ONE, 11 (7), pp. 1-23.
https://hdl.handle.net/20.500.11766/6495
Open access
 
Language en
 
Rights CC-BY-NC-4.0
 
Format PDF
 
Publisher Public Library of Science
 
Source PLoS ONE;11,(2016) Pagination 1-23