Applying SNP marker technology in the cacao breeding programme in Ghana

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding programme. Investigation was based on the 5\u2019 nuclease SNPassay using Illustra Hot Start mix Ready-To-Go PCR strips and BioTek FLx800TBP Fluorescence Microplate Reader. In a group of six cacao plants labeled as PA150 clones and another five labeled as Pound7, one clone in each group was unambiguously determined as off-type or mislabeled. Similarly, in a cohort of 23 PA7 "clones", four genotypes were differentiated. Cross-checking the fidelity of five progeny from the parental stock under study, it was established that no errors were made in the crossing. The most significant outcome of this study, however, was that out of the four categories of 23 PA7 candidate parental trees only one category can be comparable to the reference clone in the International Cacao Germplasm collection, Trinidad (ICG,T); thus informing the need for further work to find the correct clone among these for the breeding programme. It was thus concluded that thissimple yet cutting-edge genotyping procedure can be used in applied cocoa breeding programmes in a cocoa producing country. This work represents a first step in the genotypic characterisation of the CRIG germplasm collection and Seed Gardens.Au cours de cette recherche, 45 plants de cacao parentaux et 5 descendants d\ue9rivant du stock parental ont \ue9t\ue9 g\ue9notyp\ue9 en utilisant 6 marqueurs SNP, afin de d\ue9terminer les clones mal \ue9tiquet\ue9s et d\u2019authentifier les croisements effectu\ue9s dans le programme d\u2019am\ue9lioration de l\u2019Institut de Recherche sur le Cacao au Ghana (CRIG). Cette \ue9tude a \ue9t\ue9 bas\ue9e sur les 5' nucl\ue9ases SNP en utilisant des bandes PCR "Hot Start mix Ready-To-Go PCR strips" et un Lecteur Microplat \ue0 Fluorescence "BioTek FLx800TBP". Au sein d\u2019un groupe de six plants de cacao \ue9tiquet\ue9 PA150 et d\u2019un autre groupe de cinq \ue9tiquet\ue9 Pound 7, il a \ue9t\ue9 d\ue9termin\ue9 sans ambigu\ueft\ue9 qu\u2019un clone par groupe \ue9tait mal \ue9tiquet\ue9. De fa\ue7on similaire, quatre g\ue9notypes diff\ue9rents ont \ue9t\ue9 identifi\ue9s dans une m\ueame cohorte de clones 23PA7. En v\ue9rifiant la fid\ue9lit\ue9 de cinq descendants issus du stock parental \ue9tudi\ue9, il a \ue9t\ue9 \ue9tabli qu\u2019aucune erreur n\u2019avait \ue9t\ue9 faite lors du croisement. Le r\ue9sultat le plus significatif de cette \ue9tude a \ue9t\ue9 que, sur quatre cat\ue9gories de 23 candidats PA7 de souches parentales, une seule pouvait \ueatre comparable au clone de r\ue9f\ue9rence dans la collection Internationale du Germoplasme de Cacao, Trinidad (ICG,T), d\ue9montrant ainsi la n\ue9cessit\ue9 de travaux suppl\ue9mentaires pour d\ue9terminer le clone exact parmi ceux \ue9voqu\ue9s pr\ue9c\ue9demment. Il a ainsi \ue9t\ue9 conclu que cette m\ue9thode avant-gardiste de g\ue9notypage, pourtantsimple, peut \ueatre utilis\ue9e dans les programmes appliqu\ue9s d\u2019am\ue9lioration du cacao dans un pays producteur. Ce travail repr\ue9sente une premi\ue8re \ue9tape dans la caract\ue9risation g\ue9n\ue9tique de la collection du germoplasme CRIG et jardins semenciers

The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao

Published online: 26 April 2015Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process.Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process.Evidence for the impact of mislabeling and/or pollen contamination on consistency of field performance has been lacking to reinforce the need for strict adherence to quality control protocols in cacao seed garden and germplasm plot management. The present study used SNP fingerprinting at 64 loci to examine the diversity, labeling errors and parentage in 2551 trees obtained from six seed gardens, breeders clone collection and single-cross progenies and a sample of farmers’ trees in Ghana. Clone mislabeling was pervasive, both within the seed garden clones and among clones of the breeders’ active collection. Among the seed garden clones, mislabeled trees were assigned to other parental clones used in the seed garden, pointing to labeling errors prior to planting as the principal cause of mislabeling. Among the breeders’ clone collection, both homonymous and synonymous mislabeling were identified in addition to trees with unique genotypes. This implicates pre-planting labeling errors and rootstocks overtaking budded scions. Parentage analysis supported the Amelonado ancestry of farmers’ varieties but with significant contribution of Upper Amazon introductions. Parentage of recently developed clones and of progenies of controlled crosses showed evidence of both pollen contamination and effects of mislabeled parents. The observed patterns of unexpected parentage had direct effects on the consistency of the variety performance between trials and increased within-plot variability for families with mixed ancestry. The results provide a strong basis for mainstreaming SNP fingerprinting in cacao breeding programs to improve the efficiency of the variety development process

Applying SNP marker technology in the cacao breeding programme in Ghana

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding programme. Investigation was based on the 5’ nuclease SNPassay using Illustra Hot Start mix Ready-To-Go PCR strips and BioTek FLx800TBP Fluorescence Microplate Reader. In a group of six cacao plants labeled as PA150 clones and another five labeled as Pound7, one clone in each group was unambiguously determined as off-type or mislabeled. Similarly, in a cohort of 23 PA7 "clones", four genotypes were differentiated. Cross-checking the fidelity of five progeny from the parental stock under study, it was established that no errors were made in the crossing. The most significant outcome of this study, however, was that out of the four categories of 23 PA7 candidate parental trees only one category can be comparable to the reference clone in the International Cacao Germplasm collection, Trinidad (ICG,T); thus informing the need for further work to find the correct clone among these for the breeding programme. It was thus concluded that thissimple yet cutting-edge genotyping procedure can be used in applied cocoa breeding programmes in a cocoa producing country. This work represents a first step in the genotypic characterisation of the CRIG germplasm collection and Seed Gardens.Au cours de cette recherche, 45 plants de cacao parentaux et 5 descendants dérivant du stock parental ont été génotypé en utilisant 6 marqueurs SNP, afin de déterminer les clones mal étiquetés et d’authentifier les croisements effectués dans le programme d’amélioration de l’Institut de Recherche sur le Cacao au Ghana (CRIG). Cette étude a été basée sur les 5' nucléases SNP en utilisant des bandes PCR "Hot Start mix Ready-To-Go PCR strips" et un Lecteur Microplat à Fluorescence "BioTek FLx800TBP". Au sein d’un groupe de six plants de cacao étiqueté PA150 et d’un autre groupe de cinq étiqueté Pound 7, il a été déterminé sans ambiguïté qu’un clone par groupe était mal étiqueté. De façon similaire, quatre génotypes différents ont été identifiés dans une même cohorte de clones 23PA7. En vérifiant la fidélité de cinq descendants issus du stock parental étudié, il a été établi qu’aucune erreur n’avait été faite lors du croisement. Le résultat le plus significatif de cette étude a été que, sur quatre catégories de 23 candidats PA7 de souches parentales, une seule pouvait être comparable au clone de référence dans la collection Internationale du Germoplasme de Cacao, Trinidad (ICG,T), démontrant ainsi la nécessité de travaux supplémentaires pour déterminer le clone exact parmi ceux évoqués précédemment. Il a ainsi été conclu que cette méthode avant-gardiste de génotypage, pourtantsimple, peut être utilisée dans les programmes appliqués d’amélioration du cacao dans un pays producteur. Ce travail représente une première étape dans la caractérisation génétique de la collection du germoplasme CRIG et jardins semenciers