10.15140/SS8T-8294
Gepts, Paul
0000-0002-1056-4665
UC Davis
Wilkus, Erin
UC Davis (now at U. of Queensland)
Berny Mier y Teran, Jorge Carlos
UC Davis
Mukankusi, Clare
CIAT-Uganda
Kuzaay, Saarah
UC Davis
Hamilton-Conaty, Paige
0000-0001-6828-1708
UC Davis
Genetic Patterns of Common-Bean Seed Acquisition and Early-stage Adoption
among Farmer Groups in Western Uganda
UC Davis
2018
Kirkhouse Trust
John D. and Catherine T. MacArthur Fund
USDA National Institute of Food and Agriculture BeanCAP
2018-04-07T06:59:10Z
en
dataset
8885485 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Plant Material The collection included a set of 196 household samples
collected from producers in Hoima district, nineteen breeder-selected
varieties (Table 1) 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. SNP-Based Genotyping 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).