DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers' field and genebank collections

Abstract

A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers' field and genebank collections Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers' needs.

Keywords: Cassava varieties; Genetic variability; Germplasm; SNP markers.

Fig. 1

Dot map distribution of cassava plantations across different provinces and agro-ecological zones in Vietnam

Fig. 2

Pedigree of cassava varieties released in Thailand and Vietnam

Fig. 3

Numbers of varietal names recorded across 1570 genotypes collected in a survey of farms

Fig. 4

Frequency of heterozygosity observed across 96 SNPs markers selected (a) and from a set of 85 different cassava genetic groups identified across 1570 clones’ evaluated (b)

Fig. 5

Spatial distribution of cassava plantations modeled based on allele richness; red areas indicate high concentrations of alleles with single nucleotide polymorphisms (SNPs; 63.73% to 82.94%)

Fig. 6

Spatial frequency distribution of the ten main cassava varieties identified in farmer’s fields across 92 villages in mainland Vietnam

Fig. 7

Scatterplots of discriminant analysis of principal components (DAPC) of a set of 85 varieties representing maximum variability

Fig. 8

Cluster analysis of a portfolio of 85 varieties constructed with the neighbor joining (NJ) method using shared alleles to define genetic distances; differing internal colors represent DAPC groups