Varietal Identification in Household Surveys: Results From Three Household-Based Methods Against the Benchmark of Dna Fingerprinting in Southern Ethiopia

Abstract

SUMMARYAccurate crop varietal identification is the backbone of any high-quality assessment of outcomes and impacts. Sweetpotato (Ipomoea batatas) varieties have important nutritional differences, and there is a strong interest to identify nutritionally superior varieties for dissemination. In agricultural household surveys, such information is often collected based on the farmer's self-report. In this article, we present the results of a data capture experiment on sweet potato varietal identification in southern Ethiopia. Three householdbased methods of identifying varietal adoption are tested against the benchmark of DNA fingerprinting: (A) Elicitation from farmers with basic questions for the most widely planted variety; (B) Farmer elicitation on five sweet potato phenotypic attributes by showing a visual-aid protocol; and (C) Enumerator recording observations on five sweet potato phenotypic attributes using a visual-aid protocol and visiting the field. In total, 20% of farmers identified a variety as improved when in fact it was local and 19% identified a variety as local when it was in fact improved. The variety names given by farmers delivered inconsistent and inaccurate varietal identities. Visual-aid protocols employed in methods B and C were better than those in method A, but greatly underestimated the adoption estimates given by the DNA fingerprinting method. Our results suggest that estimating the adoption of improved varieties with methods based on farmer self-reports is questionable and point towards a wider use of DNA fingerprinting in adoption and impact assessments.

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

“…The DNA was treated for contaminating RNA using RNAse A, quantified and normalized using standard protocols. The DNA was then submitted for sequencing using the Diversity Array Technology's DArT-Seq method implemented by BecA's Integrated Genotyping Service and Support platform (IGSS) as described by [18], as separate genotyping projects. IGSS is a subsidized genotyping platform supported by the Bill and Melinda Gates Foundation to enhance use of genomics in breeding for SSA.…”

“…IGSS is a subsidized genotyping platform supported by the Bill and Melinda Gates Foundation to enhance use of genomics in breeding for SSA. Sequencing was done at 96-plex, high density and SNP calling done using DArT's proprietary software DArTSoft [18], with aligning to the diploid reference genome of Ipomoea trifida, a relative of sweetpotato [19]. Given that most commercial genotyping platforms have allele depth coverage~25x to 30x, previous studies [20] have shown that this depth of coverage is not adequate to call allele dosage with confidence in genotype quality for hexaploid sweetpotato.…”

Development of diagnostic SNP markers for quality assurance and control in sweetpotato [Ipomoea batatas (L.) Lam.] breeding programs

“…Issues with QA/QC of released varieties have been reported in sweetpotato and this is exacerbated because the extent of adoption of new varieties cannot be determined accurately especially with informal seed systems where genetic integrity is seldom considered ( Namanda et al 2011 ). In Ethiopia, Kosmowski et al (2018) used 17,220 DArTSeq developed markers to establish that about 20% of farmers confused local varieties for improved varieties and vice versa, and that farmers assigned different local names to the same variety or vice versa. Their study confirmed that data from survey studies ( Labeyrie et al 2014; Wossen et al 2017 ) were mostly unreliable.…”

“…The DNA was treated for contaminating RNA using RNAse A, quantified and normalized using standard protocols. The DNA was then submitted for sequencing using the Diversity Array Technology’s DArTSeq method implemented by BecA’s Integrated Genotyping Service and Support platform (IGSS) as described by Kosmowski et al (2018) . IGSS is a subsidized genotyping platform supported by the Bill and Melinda Gates Foundation to enhance use of genomics in breeding for SSA.…”

“…IGSS is a subsidized genotyping platform supported by the Bill and Melinda Gates Foundation to enhance use of genomics in breeding for SSA. Sequencing was done at 96-plex, high density and SNP calling done using DArT’s proprietary software DArTSoft ( Kosmowski et al 2018 ), with aligning to the diploid reference genome of Ipomoea trifida , a relative of sweetpotato ( Wu et al 2018 ). Given that most commercial genotyping platforms have allele depth coverage ∼25x to 30x, previous studies ( Gemenet et al under preparation ) have shown that this depth of coverage is not adequate to call allele dosage with confidence in genotype quality for hexaploid sweetpotato.…”