Carvajal-Yepes, Mónica

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The Digital Genebank and its contribution in mining alleles in cassava landraces for climate adaptationMonica Carvajal-Yepes PhDDigital Genebank, Future SeedsLeverage new technologies in genomics, in digital phenotyping and in information technologies to improve the conservation and use of crop diversity Cassava, Bean and Tropical Forages collectionsLandraces82% improved varieties10%Wild relatives8%97% of the collection was genotypedATT CGC CGT AA- - T CTC  CGT AAATT CGC CGT CAFuture seeds conserves the globally largest Cassava Collection Landraces Improved varietiesWild relatives5,965 accessionsExtracted DNA38,589 SNP markers DArTseqtechnology CurlyWhirly software 2022: co-analysis of Alliance and IITA International Cassava Genebank Collections0%20%40%60%80%100%CIAT GRC-IITA IITA-EAUnknownwildLandraceBreedersLineCenter / Status Total Lat/LonCIAT 6002 3826Breeding Lines 753 478* Landrace 4896 3120wild 353 228GRC-IITA 3222 1852Breeding/Research material 1409 681Landrace 1548 1129Unknown 240 17Wild relative 25 25IITA-EA 952 491Breeding 289 10Landrace 658 480Unkown 4wild-hybrid 1 1Total 10176 6169Global Diversity Analysis of Two International Cassava GenebankCollections4 conservation:Coordinated stratified curation • Identify redundancy within and across collections. To:• Optimize conservation costs• Resources for germplasm evaluation • Guiding cry-conservation efforts4 use:• Identify collection gaps• framework for genomics-assisted genebank management• Mining useful alleles for introgression of desired traits into cassava breeding programs.CIAT: 6002 samplesIITA :4174 samplesTotal: 10,176A remarkable degree of “genetic complementarity” between the two genebank collectionsComparison Number of comparisons mrd mean mrd sdCIAT_CIAT 18009001 0.3301 0.0508CIAT_IITA 19338444 0.3326 0.0421IITA-IITA 5189031 0.293 0.0408MDS analysisMining alleles for climate adaptation✓ Review the passport data  ✓ 3,112 landrace accessions✓ Geolocation of collection sites✓ Adapted to specific environmental conditions19 bioclimatic variables extractedadapted11 eVar8 eVarLat / Lon“Landraces are domesticated, locally adapted varieties that has developed overtime through adaptation to is natural and cultural environment”. (Camacho et al, 2007)Mining alleles for climate adaptationPassport data 3,112 accessionsGeolocation of collection sites19 bioclimatic variables extractedGenomic variants found in eachlandrace accessionATT CGC CGT AA- - T CTC  CGT AAATT CGC CGT CA Identify a total of 48 candidate markers distributed across the 18 cassava chromosomes and to one scaffold (9 eVar).Environmental association analysis4,505 samples (3093 CIAT and 1412 IITA)Mining 18,888 genomic variations to identify those variants associated with climate adaptationAcknowledgments:Peter WenzlJorge FrancoJessica OspinaMiguel CorreaMonica VelezEricson AranzalesNorma ManriqueXiaofei ZhangAna Maria LeivaLuis Augusto BecerraSarah Dyer, EMBL-EBI, Hinxton, United KingdomRajneesh PaliwalMichael AbbertonMorag E. Ferguson

The Digital Genebank and its contribution in mining alleles in cassava landraces for climate adaptation

https://cgspace.cgiar.org/bitstream/10568/131295/1/presentation.pdf

The Digital Genebank and its contribution in mining alleles in cassava landraces for climate adaptation

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