DOI: 10.25338/b8cs3z
title: Genetic Patterns of Common-Bean Seed Acquisition and Early-stage Adoption among Farmer Groups in Western Uganda

description: Widespread adoption of new varieties can be valuable, especially in
 developing countries, which tend to lack access to improved agricultural
 production technologies. However, as farmers adopt new varieties, in
 situ population structure and genetic diversity of their seed
 holdings can change drastically. Consequences of adoption are still poorly
 understood due to a lack of crop genetic diversity assessments and
 detailed surveys of farmers’ seed management practices.  Common
 bean (Phaseolus vulgaris) is an excellent model for these types of
 studies, as it has a long history of cultivation among smallholder
 farmers, exhibits eco-geographic patterns of diversity (e.g., Andean vs.
 Mesoamerican gene-pools), and has been subjected to post-Columbian
 dispersal and recent introduction of improved cultivars. The Hoima
 district of western Uganda additionally provides an excellent social
 setting for evaluating consequences of adoption because access to improved
 varieties has varied across farmer groups in this production region. This
 study establishes a baseline understanding of the common bean diversity
 found among household producers in Uganda and compares the crop population
 structure, diversity and consequences of adoption of household producers
 with different adoption practices. Molecular diversity analysis, based on
 4,955 single nucleotide polymorphism (SNP) markers, evaluated a total of
 1,156 seed samples that included 196 household samples collected from
 household producers in the Hoima district, nineteen breeder-selected
 varieties used in participatory breeding activities that had taken place
 prior to the study in the region, and a global bean germplasm collection.
 Households that had participated in regional participatory breeding
 efforts were more likely to adopt new varieties and, consequently,
 diversify their seed stocks than those that had not participated. Of the
 three farmer groups that participated in breeding efforts, households from
 the farmer group with the longest history of bean production were more
 likely to conserve “Seed Engufu”, a local “Calima”-type variety of the
 Andean bean gene pool, and, at the same time, introduce rare Mesoamerican
 gene pool varieties into household seed stocks.
description: <b>Plant
 Material</b> The collection included a set of 196 household samples
 collected from producers in Hoima district, nineteen breeder-selected
 varieties (<b>Table 1</b>) originating from either the CIAT-Kawanda,
 Uganda, or CIAT-Cali, Colombia, germplasm collections. For comparison,
 this study included a database of a world-wide reference germplasm
 collection that consisted of 502 accessions of the Andean Diversity Panel
 (Cichy et al., 2015), 363 accessions of the USDA core collection (McClean
 et al., 2012; S. Kuzay, P. Hamilton-Conaty
 and P. Gepts, unpubl. results),  and 57 reference and commercial
 cultivars. A subset of the breeder-selected samples included in the
 analysis had been evaluated and made available to breeding
 program-affiliated households through the CIAT-managed PVS trials from
 2012 to 2013. Within the breeder-selected varieties, NABE 11, 15, 17 and
 21 were bred locally by the national Ugandan bean program using CIAT-bred
 lines while the remaining NABE lines were bred under CIAT-led programs.
 The KAT lines had been bred locally by a Kenyan breeder at the Katumani
 Research Station in the 1990’s. The 196 household seed stock samples were
 collected from eight-two households between May and June of 2014, within
 2-3 weeks of the first harvest since PVS trials were completed.
 <b>SNP-Based
 Genotyping</b> The Illumina Infinium “BeadChip BARCBean6K-3” (Song et al.,
 2015) from the USDA National Institute of Food and Agriculture BeanCAP
 Project (Grant number 2009-01929) was used to genotype the entire seed
 collection. Single nucleotide polymorphism genotyping was conducted
 courtesy of Dr. Perry Cregan, USDA-ARS, Soybean Genomics Improvement
 Laboratory, BARC-West, Beltsville, MD, on the Illumina platform following
 the Infinium HD Assay Ultra Protocol (Illumina, San Diego, CA). Sequencing
 output of the BARCBean6K-3 BeanChip was evaluated using GenomeStudio
 software. Clusterw2 software was used to align sequences and generate SNP
 calls. In order to generate reliable SNP calls for household seed samples
 and breeder-selected samples, cluster files were calibrated from the
 default set of cluster files. 4,955 of the 5,398 single nucleotide
 polymorphism (SNP) markers were then called using the new cluster files
 with a Gencall score cutoff of 0.15, according to the GenomeStudio
 Genotyping Module v1.8.4 (Illumina, San Diego, CA). SNP data of samples
 from the global germplasm collection BARCBean6K-3 assay were filtered to
 include only those having less than 5% missing data and 5% heterozygosity.
 SNP data of the remaining samples were pruned to 1,870 markers to reduce
 linkage disequilibrium. Pruning was performed in a moving window of 50
 SNPs removing one of a pair of SNPs if the linkage disequilibrium was
 higher than 0.6. The steps of filtering and pruning were performed in
 PLINK (Purcell et al., 2007).