title: Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz).
abstract: BACKGROUND
  Accurate identification of crop cultivars is crucial in assessing the impact of crop improvement research outputs. Two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, have inherent uncertainty levels. Genotyping-by-sequencing (GBS) was used in a case study as an alternative method to track released varieties in farmers' fields, using cassava, a clonally propagated root crop widely grown in the tropics, and often disseminated through extension services and informal seed systems. A total of 917 accessions collected from 495 farming households across Ghana were genotyped at 56,489 SNP loci along with a "reference library" of 64 accessions of released varieties and popular landraces.
  
  
  RESULTS
  Accurate cultivar identification and ancestry estimation was accomplished through two complementary clustering methods: (i) distance-based hierarchical clustering; and (ii) model-based maximum likelihood admixture analysis. Subsequently, 30% of the identified accessions from farmers' fields were matched to specific released varieties represented in the reference library. ADMIXTURE analysis revealed that the optimum number of major varieties was 11 and matched the hierarchical clustering results. The majority of the accessions (69%) belonged purely to one of the 11 groups, while the remaining accessions showed two or more ancestries. Further analysis using subsets of SNP markers reproduced results obtained from the full-set of markers, suggesting that GBS can be done at higher DNA multiplexing, thereby reducing the costs of variety fingerprinting. A large proportion of discrepancy between genetically unique cultivars as identified by markers and variety names as elicited from farmers were observed. Clustering results from ADMIXTURE analysis was validated using the assumption-free Discriminant Analysis of Principal Components (DAPC) method.
  
  
  CONCLUSIONS
  We show that genome-wide SNP markers from increasingly affordable GBS methods coupled with complementary cluster analysis is a powerful tool for fine-scale population structure analysis and variety identification. Moreover, the ancestry estimation provides a framework for quantifying the contribution of exotic germplasm or older improved varieties to the genetic background of contemporary improved cultivars.
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. I.Rabbi@cgiar.org.
authors.forename: Ismail Y
authors.initials: IY
authors.lastname: Rabbi
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. P.Kulakow@cgiar.org.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Kulakow
authors.affiliation: Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), P.O. Box 3785, Kumasi, Ghana. jmaduening@yahoo.co.uk.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Manu-Aduening
authors.affiliation: Agriculture Innovation Consult, Kumasi, Ghana. dankyiaa@yahoo.com.
authors.forename: Ansong A
authors.initials: AA
authors.lastname: Dankyi
authors.affiliation: Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), P.O. Box 3785, Kumasi, Ghana. jyasibuo@gmail.com.
authors.forename: James Y
authors.initials: JY
authors.lastname: Asibuo
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. E.Parkes@cgiar.org.
authors.forename: Elizabeth Y
authors.initials: EY
authors.lastname: Parkes
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. T.Abdoulaye@cgiar.org.
authors.forename: Tahirou
authors.initials: T
authors.lastname: Abdoulaye
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. G.Tessema@cgiar.org.
authors.forename: Gezahegn
authors.initials: G
authors.lastname: Girma
authors.affiliation: International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria. M.Gedil@cgiar.org.
authors.forename: Melaku A
authors.initials: MA
authors.lastname: Gedil
authors.affiliation: Cornell University, Institute for Genomic Diversity, 175, Biotechnology Building, Ithaca, NY, 14853, USA. rp444@cornell.edu.
authors.forename: Punna
authors.initials: P
authors.lastname: Ramu
authors.affiliation: International Center for Tropical Agriculture (CIAT), Planes de Altamira, de Pizza Hut Villa Fontana, 1c Oeste, Edificio CAR III, Oficina 4-1, Managua, Nicaragua. b.reyes@cgiar.org.
authors.forename: Byron
authors.initials: B
authors.lastname: Reyes
authors.affiliation: Michigan State University, 446 W. Circle Drive, Room 89, East Lansing, MI, 48824, USA. maredia@msu.edu.
authors.forename: Mywish K
authors.initials: MK
authors.lastname: Maredia
mesh_terms: D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics*; D005869:Ghana; D006579:Heterozygote; D002365:Manihot / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D018744:DNA, Plant