Establishment of a core collection of chilli germplasm using microsatellite analysis

Abstract

Chilli (Capsicum spp.) is an economically important vegetable and spice. The Tropical Vegetable Research and Development Center, Kasetsart University, Kamphaeng Saen Campus has collected more than 2500 chilli germplasm accessions since 1989. Investment to maintain and evaluate such a large germplasm collection is high. For efficient germplasm management and to reduce the cost of germplasm maintenance, a core collection needs to be established. Therefore, this study aimed to investigate the genetic diversity of chilli germplasm using microsatellites. A total of 230 chilli germplasm accessions were evaluated using ten anchored Capsicum microsatellite loci. These loci generated 42 alleles with a size ranging from 87 to 323 bp. The average polymorphic information content was 0.57, ranging from 0.414 to 0.681, and the probability of identity (PI) ranged from 0.17 to 0.49. The combined PI of the ten microsatellite loci was 2.30 × 10− 6. The similarity index ranged from 0.29 to 1.00. The 230 chilli accessions were divided into two major groups. Group I comprised mainly C. annuum, and group II comprised all four Capsicum species with the majority being C. frutescens, C. chinense and C. baccatum. The matrix comparison showed that a cophenetic correlation of 0.798 indicated the best fit of the obtained dendrogram. The PowerCore program selected 28 representative chilli accessions to form a core collection, which maintained a similar level of diversity to that of the overall 230 chilli accessions. The representative alleles in those 28 core accessions equalled all the alleles present in the entire collection.

Construction of a core collection of native Perilla germplasm collected from South Korea based on SSR markers and morphological characteristics

“…These PGRs are utilized to provide new plant varieties with better resistance, adaptation, and nutritive qualities. Conservation and collection of PGRs is necessary to maintain higher genetic diversity for food security and use in the future 2 . Moreover, the conservation and collection of PGRs in most crops has been made possible by the establishment of genebanks in countries around the world.…”

A lima bean core collection based on molecular markers

“…However, the PowerCore method has been used successfully in the establishment of core collections of many economically important crops, such as Oryza sativa (Tiwari et al, 2015), Glycine max (Kaga et al, 2012;Gireesh et al, 2017), Cucumis melo (Hu et al, 2015), Vicia faba (Göl et al, 2017) and Capsicum spp. (Mongkolporn et al, 2015;Lee et al, 2016). Higher estimates of genetic diversity for the core collection in relation to the lima bean BGP-UFPI may be explained simply by the PowerCore method, which results in a better sampling of allelic diversity using a smaller number of individuals when compared to the entire collection.…”

Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan Capsicum annuum germplasm

“…Different types of descriptors like passport data, geographic origin, morphological, agronomical, biochemical and DNA markers can be used for phenotypic and genetic diversity evaluation and construction of core collections [12][13][14]. There are already some core collections of Capsicum using phenotypic data [15], genotypic data [16,17] as well as combined phenotypic and genotypic data [18][19][20]. Core collections for disease resistance against northern root-knot nematode and Potato virus y (PVy) have been constructed [21,22].…”

“…For K = 3 (Figure1(B)), the resulting clusters consisted of 35, 53, 51 and 35 genotypes for clusters 1, 2, 3 and admixed accessions, respectively. Cluster 1 included 4 Albanian,16 Bulgarian, 2 Greek, 3 Macedonian, 7 Romanian, 2 accessions from Serbia and one accession of unknown origin, CAPS-151A. More than a half (51.4%) of the genotypes in Cluster 1 had big pumpkin-shaped fruits, 34.4% had bell-or blocky-shaped fruits, three accessions had round fruit shape and two had a conical shape.…”