Tracking crop varieties using genotyping-by-sequencing markers: a case study using cassava (Manihot esculenta Crantz)

Abstract

BackgroundAccurate 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.ResultsAccurate 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.ConclusionWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0273-1) contains supplementary material, which is available to authorized users.

Household Determinants of the Adoption of Improved Cassava Varieties using DNA Fingerprinting to Identify Varieties in Farmer Fields: A Case Study in Colombia

“…10 Results from these studies show a common misidentification of crop varieties in farmer fields and highlight a large number of varieties incorrectly identified by farmers as improved (Type I error) and varieties incorrectly identified by farmers as local cultivars (Type II error). The results of these studies underscore the importance of using DNA fingerprinting for correcting the misidentification of crop varieties Rabbi et al, 2015;Kosmowski et al, 2016;Maredia et al, 2016).…”

“…Likewise, accurate identification of crop varieties is critical to correctly assess the impact of crop improvement research. Yet, two commonly used identification approaches, elicitation of variety names from farmer interviews and morphological plant descriptors, involve much uncertainty (Rabbi et al, 2015). Awotide et al (2015) utilised data collected for cassava from the CGIAR's Diffusion and Impact of Improved Varieties in Africa (DIIVA) project, 9 which involved the validation of experts' estimates of adoption against household and community survey data.…”

“…In spite of these efforts, cassava varietal identification remains difficult since there are often differences between genetically unique cultivars and variety names as elicited from farmers (Rabbi et al, 2015). Furthermore, other confounding factors that may hinder proper varietal identification include: (1) some farmers' inability to identify varieties by names, (2) the inconsistency in the names of the varieties as identified by the farmers and those of official government/agriculture extension records (i.e.…”

Cassava Superelongation Disease in the Caribbean

“…Tracking of cassava varieties for cultivar identification through the use of genetic markers [22,23] is therefore currently a necessary exercise for the cassava industry in the Caribbean islands.…”

Batata-doce [<i>Ipomoea batatas</i> (L.) Lam.] nas roças e quintais do litoral paulista: diversidade genética morfoagronômica, com base em morfometria geométrica, descritores e produção de bioetanol

“…No entanto, Rabbi et al (2015), avaliando 917 acessos de um banco de germoplasma de mandioca, utilizando o sequenciamento por genotipagem, descrevem que o método não foi muito eficiente na discriminação dos grupos, provavelmente em virtude da estruturação contínua da população. Segundo Jombart, Devillard e Balloux (2010), o método ADCP tem um desempenho melhor em populações descontínuas, como no modelo de ilhas.…”