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

Key message A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers’ field and genebank collections Abstract 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.

Historic American Apple Cultivars: Identification and Availability

Apples (Malus Mill.) have been economically and socially important throughout the centuries in North America. Apple cultivar (Malus ×domestica Borkh.) collections that include historic cultivars are valued for their unique diversity, historical significance, and also as a resource to identify unknown trees; however, not all of the historically significant apple cultivars are currently included in these collections. We used historic books, publications, and nursery catalogs to develop an inventory of apple cultivars that were propagated and grown in the United States before 1908. We collected synonym, introduction date, and original source country information for 891 historic apple cultivars. Most of the historic American cultivars originated as seedlings first planted in the United States. Some cultivars were brought to the United States from the United Kingdom, France, Russia, Germany, and other European countries. We classified historic apple cultivars based on their availability over time and popularity in nursery catalogs. Ninety percent of the most popular historic apple cultivars in the United States were available in 2015 in the U.S. and U.K. national collections and within several commercial and private collections. This work identified high priority historic cultivars that are not currently protected within genebanks that could be added to genebank collections in the future.

Retrotransposon-Based Molecular Markers for Analysis of Genetic Diversity within the GenusLinum

SSAP method was used to study the genetic diversity of 22Linumspecies from sectionsLinum,Adenolinum, Dasylinum, Stellerolinum, and 46 flax cultivars. All the studied flax varieties were distinguished using SSAP for retrotransposonsFL9andFL11. Thus, the validity of SSAP method was demonstrated for flax marking, identification of accessions in genebank collections, and control during propagation of flax varieties. Polymorphism ofFl1a, Fl1b, andCassandrainsertions were very low in flax varieties, but these retrotransposons were successfully used for the investigation ofLinumspecies. Species clusterization based on SSAP markers was in concordance with their taxonomic division into sectionsDasylinum, Stellerolinum, Adenolinum, andLinum. All species of sect.Adenolinumclustered apart from species of sect.Linum. The data confirmed the accuracy of the separation in these sections. Members of sectionLinumare not as closely related as members of other sections, so taxonomic revision of this section is desirable.L. usitatissimumaccessions genetically distant from modern flax cultivars were revealed in our work. These accessions are of utmost interest for flax breeding and introduction of new useful traits into flax cultivars. The chromosome localization ofCassandraretrotransposon inLinumspecies was determined.

Population Structure and Molecular Characterization of Nigerian Field Genebank Collections of Cacao, Theobroma cacao L.

Inadequate knowledge of the population structure and diversity present often hamper the efficient use of germplasm collections. Using a high through-put system, twelve microsatellite loci were used to analyze genetic diversity and population structure in a national field genebank repository of 243 cacao accessions grouped into 11 populations based on their known sources. Based on multi-locus profiles, the Bayesian method was used for individual assignment to verify membership in each population, determine mislabeling and ancestry of some important accessions used in breeding program. A total of 218 alleles was revealed with a mean number of 18.2 alleles per locus. Gene diversity (He = 0.70) and allelic richness (4.34 alleles per locus) were highest in the F1 hybrid population. Differential mating system was suggested as responsible for the observed deficit and excess of heterozygotes observed among the populations. Analysis of molecular variance showed that within-population variance accounted for 63.0% of the total variance while the rest 37% was accounted for by the among-population variance. Cluster dendrogram based on UPGMA revealed two main subsets. The first group was made up of the Amelonado/Trinitario ancestry and the other of Nanay/Parinari ancestry. We found that Nanay and Parinari populations were the major source of Upper Amazon genes utilized while a large proportion of genetic diversity in the field genebank remained under-utilized in development of improved cultivars released to farmers in Nigeria. This study showed that the presence of alleles of the Upper Amazon Forasteros (Nanay, Parinari and Iquitos Mixed Calabacillo) genetic materials in the locally available accessions predated the formal large scale introduction of Upper Amazon materials in 1944. This is the first report of population structure of field genebank collections of cacao in Nigeria since more than seven decades of formal cacao breeding research.