Genomic characterization of Ugandan smallholder farmer‐preferred cassava varieties

Abstract

Understanding the genetic relationships among farmer-preferred cassava (Manihot esculenta Crantz) varieties is indispensable to genetic improvement efforts. In this study, we present a genetic analysis of 547 samples of cassava grown by 192 smallholder farmers, which were sampled at random within four districts in Uganda. We genotyped these samples at 287,952 single nucleotide polymorphisms using genotyping-by-sequencing and co-analyzed them with 349 cassava samples from the national breeding program in Uganda. The samples collected from smallholders consisted of 86 genetically unique varieties, as assessed using a genetic distance-based approach. Of these varieties, most were cultivated in only one district (30 in Kibaale, 19 in Masindi, 14 in Arua, and three in Apac), and only three were cultivated across all districts. The genetic differentiation we observed among farming districts in Uganda (mean fixation index [F ST ] = .003) is similar to divergence observed within other countries. Despite the fact that none of the breeding lines were directly observed in farmer fields, genetic divergence between the populations was low (F ST = .020). Interestingly, we detected the presence of introgressions from the wild relative M. glaziovii Müll. Arg. on chromosomes 1 and 4, which implies ancestry with cassava breeding lines. Given the apparently similar pool of alleles in the breeding germplasm, it is likely that breeders have the raw genetic material they require to match the farmerpreferred trait combinations necessary for adoption. Our study highlights the importance of understanding the genetic makeup of cassava currently grown by smallholder farmers and relative to that of plant breeding germplasm.

Identification of cassava quality attributes preferred by Ugandan users along the food chain

“…Previously, a study by Iragaba et al . (2020) also found that smallholder farmers in different districts grow different varieties, a phenomenon that could tag varietal preferences to specific communities owing to relative ease of access of planting materials within a community as compared to ease of access between communities. With continued engagement of end users in the breeding process and increasing access to improved seed, such disparities could be reduced.…”

Flower Development in Cassava Is Feminized by Cytokinin, While Proliferation Is Stimulated by Anti-Ethylene and Pruning: Transcriptome Responses

“…Cassava improvement has recently received renewed attention with major projects to investigate the potential use of genomic selection in breeding (Wolfe et al, 2017), its sourcesink relationships (Sonnewald et al, 2020) and its photosynthetic efficiency (De Souza and Long, 2018). These improvement efforts are geared toward smallholder farmers with an interest in translating cassava end-product quality traits into breeding outcomes (Iragaba et al, 2020). Although cassava can be clonally propagated by stem cuttings, crop improvement via breeding requires genetic recombination using sexual crosses between parents from diverse genetic populations that flower in a timely and synchronous manner.…”

High density genotype storage for plant breeding in the Chado schema of Breedbase

“…The first dataset loaded is a VCF containing 314 Musa acuminata samples genotyped with 142,119 genotype-by-sequencing (GBS) markers; this data is available in the Breedbase instance https://musabase.org/breeders_toolbox/protocol/1 and contains triploid genotypes [ 26 , 27 ]. The second dataset loaded is a VCF containing 924 Manihot esculenta samples genotyped with 287,952 GBS markers and is available in the Breedbase instance https://cassavabase.org/breeders_toolbox/protocol/6 [ 28 ]. The third dataset loaded is a VCF containing 1,325 Zea mays samples genotyped with 955,690 GBS markers and is available in the Breedbase instance https://imagebreed.org/breeders_toolbox/protocol/5 [ 29 ].…”