Cassava Digital GeneBank genetic profiling using RAD sequencing
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1) CIAT is developing a persistent-identifier system using DNA barcoding to document over 6,000 cassava accessions from Latin America, Africa, Asia, and Southeast Asia. 2) They conducted RAD sequencing on 1,200 randomly selected accessions from Latin America to generate genetic profiles and uncover cassava's genetic variability. 3) The analysis identified 18,286 SNPs among 292 accessions, resolving 8 subpopulations that suggest two potential centers of cassava cultivation in Latin America.
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Cassava Digital GeneBank genetic profiling using RAD sequencing
- 1. 0 2 4 6 8 10 COL122 COL1486 COL1182 COL13 COL71 CUB16 COL674 VEN142 COL1552 COL704 COL543A COL173 COL1915 COL1313 COL2019 COL508 COL82 COL636 COL309 VEN45A COL2006 COL361 COL645 COL1112A COL2015 CUB65 VEN52 COL2261 MEX17 VEN143 COL282 COL976 VEN50 COL1818 COL2016 VEN312 COL335 COL9 COL670 COL991 COL2054 COL1912 MEX23 COL1761 VEN62 CUB74 COL340 COL1813 COL1823 ECU72 COL2061 VEN156 MAL3 COL414 CR2 COL882 PAN90 COL1802 CUB31 PAN114 COL2017 ECU82 COL1910 COL914 COL72 ECU169 COL1495 VEN25 COL1413 MEX1 PAN97 COL1643 VEN307 BRA20 COL948C COL2207 VEN77 COL1522 PAN51 COL113 PER245 PAN12B COL2215 COL688 MEX59 COL2060 PTR19 COL755 COL65 COL1292 COL1468 MEX11 MEX55 BRA5 VEN218 VEN270 COL1515 BRA12 COL1940 VEN305 VEN185 COL655A COL638 COL1684 COL1438 COL1505 PAN70 COL647 COL22 Cassava Digital GeneBank Becerra Lopez-Lavalle, L. A., Perea C. S., Duitama, J., Ruiz, M., Parsa, S., Ovalle, T. M. Alzate, A., Hershey, C., Dufour, D., Aranzales, E., Debouck, D. and J. Tohme INTRODUCTION To advance towards a collaborative global efforts for documenting cassava collections in Latin America and the Caribbean (center of origin), Africa, Asia and Southeast Asia, CIAT is developing a persistent-identifier system using life’s barcode (DNA). The utility of DNA for this purpose is self-evident not only because it provides the individuals fingerprint but it also generates is genetic profile essential to unravel its future potential for genetic improvement. The objective of this work is to generate high density genetic information using Restriction site Associated DNA (RAD) sequencing. RAD-seq is an effective next generation sequencing approach to screen for tens of thousands of single nucleotide polymorphisms (SNPs) that can then be used for hybridization and gene flow analysis, phylogeography, population genetics develop an accurate picture of the cassava genetic variability and its potential use for food security and nutritional goal for 2050. METODOLOGY Plant materials: Of the 6,240 cassava (Manihot esculenta) accessions hold at CIAT, nearly 20% (1200) have been selected for genetic profilling primarily at random using the georeference information (Figure 1B) and frequency of cassava landraces used in the generation of CIAT elite breeding lines or cultigenes. RESULTS SNP discovery and population structure analysis In all, 18,286 SNPs were obtained from 292 cassava LAC landraces. Eight subpopulations were resolved (Figure 3 A and B). Furthermore, these 8 populations also were phylogeographically distributed Sugesting two potential centers for cultivation of M esculenta (Figure 4) CONCLUSION Next generation sequencing approaches have given us a new level of understanding of how cassava may have been domesticated in Latin America. But more imporatnt highlights its relevance for breeding in Africa and SE-Asia RAD sequencing Genomic DNA is digested by restriction enzymes and tagged with barcode sequences in each sample. The resulting libraries are then pooled and sequenced (CIAT-BGI collaboration) (Figure 2) SNP calling NGSEP was used as SNP discovery bioinformatic pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. NGSEP was developed to work with restriction enzyme-based data, such as RAD-or the purpose of conducting population genomics and phylogeography. Figure 1 Figure 2 A B Figure 3 Figure 4