Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato (I. batatas) Germplasm Collection

Abstract

The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.

Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato (Ipomoea batatas) collection

“…Not only were regional pairwise genetic differentiation and distance values for South America higher than average (F ST ≥ 0.71, genetic distance ≥ 0.48), Bayesian clustering exhibited minor admixture with other geographic regions. Upon population structure analysis of the CIP collection, Anglin et al suggested that accessions from Peru had been genetically isolated over time (Anglin et al, 2021). Of the 85 accessions from South America clustered in DAPC cluster 2 (Figure 3A and Table 3), 84 were from Peru, further confirming this idea.…”

“…Germplasm from 2 USDA collections (n=417) found that accessions were clustered into 4 genetic groups ( Wadl et al., 2018 ), whereas an analysis of accessions primarily from China (n=197) found that 3 genetic groups best describe the material in that collection ( Su et al., 2017 ). More recently, the International Center of Potato (CIP) genotyped 45% of the collection (n=5,979) using 20 simple sequence repeat markers and concluded 4 genetic clusters best describe the collection ( Anglin et al., 2021 ). While it is difficult to discern true population structure and clusters, we found that historical and experimental evidence from this study suggests that K=6 may better encapsulate sweetpotato population structure of the PGRCU collection.…”

Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives

“…Beginning in the 1990s, molecular markers based on allelic polymorphisms were developed, and they have been widely utilized to estimate genetic diversity in sweetpotato. Early studies of sweetpotato used a variety of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD) ( Jarret and Austin, 1994 ; Gichuki et al., 2003 ), amplified fragment length polymorphisms (AFLPs) ( Zhang et al., 2000 , 2004 ), inter-simple sequence repeats (ISSRs) ( Li et al., 2008 ; Moulin et al., 2012 ), ESTs ( Marian et al., 2018 ), and simple sequence repeats (SSRs) ( Veasey et al., 2008 ; Som et al., 2014 ; Yang et al., 2015 ; Zawedde et al., 2015 ; Feng et al., 2018 ; Lee et al., 2019 ; Palumbo et al., 2019 ; Anglin et al., 2021 ). These markers have been used to characterize and define the accessions in sweetpotato germplasm collections and to examine population structure and gene pools of sweetpotato originating from Latin America, South America, Central America, Oceania, Asia, and Africa ( Zhang et al., 2000 ; Gichuki et al., 2003 ; Li et al., 2008 ; Som et al., 2014 ).…”

The world’s largest potato cryobank at the International Potato Center (CIP) – Status quo, protocol improvement through large-scale experiments and long-term viability monitoring

“…Although the in vitro storage period can be extended to 2-3 years between subcultures or propagation cycles, the plant material needs to be renewed periodically and any handling of the genebank material exposes the collection to the risk of human error (mix up of accessions), fungi or bacteria contamination, or somaclonal variation sometimes produced from tissue culture. As the renewal process occurs repeatedly, the probability of changes, due to human error or biology of the conserved material, can add up over time ( Anglin et al., 2021 ). Many of the above-mentioned disadvantages can be lessened, mitigated, or eliminated using cryopreservation for clonal crop maintenance.…”