Molecular characterization of an international cacao collection using microsatellite markers

Abstract

Plant germplasm collections invariably contain varying levels of genetic redundancy, which hinders the efficient conservation and utilization of plant germplasm. Reduction of genetic redundancies is an essential step to improve the accuracy and efficiency of genebank management. The present study targeted the assessment of genetic redundancy and genetic structure in an international cacao (Theobroma cacao L.) collection maintained in Costa Rica. A total of 688 cacao accessions maintained in this collection were genotyped with 15 simple sequence repeat (SSR) loci, using a capillary electrophoresis genotyping system. The SSR markers provided a high resolution among the accessions. Thirty-six synonymously labeled sets, involving 135 accessions were identified based on the matching of multilocus SSR profiles. After the elimination of synonymous sets, the level of redundancy caused by closely related accessions in the collection was assessed using a simulated sampling scheme that compared allelic diversity in different sample sizes. The result of the simulation suggested that a random sample of 113 accessions could capture 90% of the total allelic diversity in this collection. Principal Coordinate Analysis revealed that the Trinitario hybrids from Costa Rica shared a high similarity among groups as well as among individual accessions. The analysis of the genetic structure illustrated that the within-country/within-region difference accounted for 84.6% of the total molecular variation whereas the among-country/among-region difference accounted for 15.4%. The Brazilian germplasm contributed most to this collection in terms of total alleles and private alleles. The intercountry/interregion relationship by cluster analysis largely agreed with the geographical origin of each germplasm group and supported the hypothesis that the Upper Amazon region is the center of diversity for cacao. The results of the present study indicated that the CATIE International Cacao Collection contains a high level of genetic redundancy. It should be possible to rationalize this collection by reducing redundancy and ensuring optimal representation of the genetic diversity from distinct germplasm groups. The results also demonstrated that SSR markers, together with the statistical tools for individual identification and redundancy assessment, are technically practical and sufficiently informative to assist the management of a tropical plant germplasm collection.

Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Upper Amazon using microsatellite DNA markers

“…The development of simple sequence repeat (SSR) markers in cacao (Lanaud et al 1999) has significantly increased the capacity of molecular characterization of cacao germplasm. SSRbased DNA fingerprinting has been increasingly applied in cacao germplasm characterization (Aikpokpodion et al 2005;Cryer et al 2006;Efombagan et al 2008;Johnson et al 2007;Lanaud et al 2001;Motamayor et al 2002Motamayor et al , 2008Schnell et al 2005;Sereno et al 2006;Zhang et al 2008Zhang et al , 2009. These studies generate important information relating to the genetic diversity and the origin of the crop.…”

Analisis Keragaman Genetik 28 Nomor Koleksi Kakao (Theobroma cacao L.) Berdasarkan Marka SSR

“…Analisis keragaman genetik kakao dengan menggunakan marka SSR sebelumnya telah dilakukan oleh Zhang, Mischke, Johnson, Phillips-Mora, & Meinhardt (2009), Kurniasih, Rubiyo, Setiawan, Purwantara, & Sudarsono (2011), dan Rubiyo, Izzah, Sulistiyorini, & Tresniawati (2015). Kurniasih et al (2011) …”

Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

“…In addition, one hundred international clones were used as references. Preparation of DNA samples for the reference international clones was described in Zhang et al (2009a;. DNA concentration was determined with a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE).…”

“…In the past few years, microsatellite markers have been widely used in cacao genotyping and individual identification, enabling systematic assessment of genetic identity in national and international cacao genebanks (Zhang , 2009a;Motilal et al, 2009Motilal et al, ,2010. In contrast to dominant markers, identical genotypes can have a 100% match in the multilocus SSR profiles without ambiguity, thus accuracy of identification is significantly improved.…”