Genetic diversity and population structure of trifoliate yam (Dioscorea dumetorum Kunth) in Cameroon revealed by genotyping-by-sequencing (GBS)

Abstract

Background: Yams (Dioscorea spp.) are economically important food for millions of people in the humid and sub-humid tropics. Dioscorea dumetorum (Kunth) is the most nutritious among the eight-yam species, commonly grown and consumed in West and Central Africa. Despite these qualities, the storage ability of D. dumetorum is restricted by severe postharvest hardening of the tubers that can be addressed through concerted breeding efforts. The first step of any breeding program is bound to the study of genetic diversity. In this study, we used the Genotyping-By-Sequencing of Single Nucleotide Polymorphism (GBS-SNP) to investigate the genetic diversity and population structure of 44 accessions of D. dumetorum in Cameroon. Ploidy was inferred using flow cytometry and gbs2ploidy.

Results: We obtained on average 6371 loci having at least information for 75% accessions. Based on 6457 unlinked SNPs, our results demonstrate that D. dumetorum is structured into four populations. We clearly identified, a western/north-western, a western, and south-western populations, suggesting that altitude and farmers-consumers preference are the decisive factors for differential adaptation and separation of these populations. Bayesian and neighbor-joining clustering detected the highest genetic variability in D. dumetorum accessions from the south-western region. This variation is likely due to larger breeding efforts in the region as shown by gene flow between D. dumetorum accessions from the south-western region inferred by maximum likelihood. Ploidy analysis revealed diploid and triploid levels in D. dumetorum accessions with mostly diploid accessions (77%). Male and female accessions were mostly triploid (75%) and diploid (69%), respectively. The 1C genome size values of D. dumetorum accessions were on average 0.333 ± 0.009 pg and 0.519 ± 0.004 pg for diploids and triploids, respectively.

Conclusions: Germplasm characterization, population structure and ploidy are an essential basic information in a breeding program as well as for conservation of intraspecific diversity. Thus, results obtained in this study provide valuable information for the improvement and conservation of D. dumetorum. Moreover, GBS appears as an efficient powerful tool to detect intraspecific variation.

Keywords: Cameroon; D. dumetorum; GBS; Genetic diversity; Ploidy; Population structure; Yam.

Fig. 1

Sampling map of D. dumetorum accessions in Cameroon. Boundaries of agro-ecological zones (AEZ) were defined according to [38]

Fig. 2

D. dumetorum tuber forms. 1a) Accession with few roots on the tuber and yellow flesh colour. 2a) accession with few roots on the tubers and white flesh colour b) accession with many roots on the tuber

Fig. 3

Phylogenetic relationships within D. dumetorum based on multilocus concatenated SNP sequences alignment from GBS data of 44 accessions

Fig. 4

STRUCTURE plot of 44 accessions of D. dumetorum with K = 4 clusters based on 6457 unlinked SNPs. Each accession is represented by a single row, which is partitioned into colored segments in proportion to the estimated membership in the three subpopulations

Fig. 5

Maximum likelihood tree of the inferred gene flow within D. dumetorum species on 157 SNPs. The colored lines represent the possible gene flow events