Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding

Abstract

The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions ― an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC’s genetic diversity. The analysis of molecular variance confirmed the CCC’s diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.

Promiscuous potato: elucidating genetic identity and the complex genetic relationships of a cultivated potato germplasm collection

“…The ADG species shown in green, split into two distinct groupings, one of which overlapped slightly with TBR. This was also observed in a separate study evaluating the Colombian Central Collection of potatoes ( Manrique-Carpintero et al., 2023 ). The other portion of ADG overlaps with most of the other cultivated potato species.…”

Conservation of medicinal germplasm: a proposal to establish priorities based on conservation biology and ethnobotanical criteria

“…Emerging programs are being developed with criteria of social or cultural relevance, considering emblematic species for human communities (e.g., Leontopodium alpinum Cass in Alpine regions, Dracaena draco L. in the Canary Islands, or Cedrus libani A. Rich in Lebanon, as well as landrace potato collections Solanum tuberosum L. in Colombia (Buchetta et al 2008, Manrique-Carpintero et al 2023. Furthermore, some of these programs are specifically focused on preserving species with medicinal value (ICAR 2023, Grace et al 2010.…”