Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping DOI Creative Commons
Angel Rafael Ramirez-Ramirez, Igor Bidot, Khaled Mirzaei

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(5), P. e0304753 - e0304753

Published: May 31, 2024

Proper cacao ( Theobroma L.) plant genotyping is mandatory for the conservation and use of species genetic resources. A set 15 international standard SSR markers was assumed as universal system. Recently, different SNPs SNP techniques have been exploited in cacao. However, a consensus on which to has not reached yet, driving search new approaches. To validate ddRADseq protocol genotyping, we compared performances population analysis dataset with 7,880 obtained from genotypic data aforementioned set, using 158 plants productive farms gene bank. Four groups were identified STRUCTURE ADMIXTURE softwares data, respectively. Similarities ancestries among these allowed identification analogous pairs individuals, referred as: G1 /G1 , G2 /G2 G3 /G3 G4 /G4 whether SSRs or used. Both marker systems Amelonado Criollo most abundant all samples. Genetic distance matrices both types significantly similar each other according Mantel test (p < 0.0001). PCoA UPGMA clustering mostly confirmed groups. AMOVA F ST pairwise comparison revealed moderate very large differentiation data. diversity parameters (H obs = 0.616, H exp 0.524 PIC 0.544) higher than that (0.288, 0.264, 0.230). In cases, carrying highest proportion (G1 ) had lowest The high congruence results validated employed genotyping. These could provide ways developing SNP-based system much needed studies.

Language: Английский

Morpho-Phenological, Chemical, and Genetic Characterization of Italian Maize Landraces from the Lazio Region DOI Creative Commons
R. Redaelli, Laura Bassolino, Carlotta Balconi

et al.

Plants, Journal Year: 2024, Volume and Issue: 13(22), P. 3249 - 3249

Published: Nov. 20, 2024

In the framework of a Collaboration Agreement between CREA and ARSIAL, morpho-phenological, chemical, genetic characterization maize populations native to Lazio region was carried out. During 2022 2023, set 50 accessions, belonging both ARSIAL collections, were multiplied in Bergamo. Morpho-phenological descriptors recorded field: plant height, ear male female flowering time. The grain chemical composition terms protein, lipid, starch, ash fiber evaluated by near-infrared spectroscopy (NIRS). A double-digest restriction-site-associated DNA sequencing (ddRADseq) strategy used genotype landraces. two collections not significantly different composition. On other hand, germplasm showed distribution three cluster-based population structure obtained ddRADseq, which largely corresponded map their collection sites. materials from maintained revealed be different. comparison groups landraces importance characterizing promote recovery valorization local biodiversity.

Language: Английский

Citations

1
Comparing the performances of SSR and SNP markers for population analysis in Theobroma cacao L., as alternative approach to validate a new ddRADseq protocol for cacao genotyping DOI Creative Commons
Angel Rafael Ramirez-Ramirez, Igor Bidot, Khaled Mirzaei

et al.

PLoS ONE, Journal Year: 2024, Volume and Issue: 19(5), P. e0304753 - e0304753

Published: May 31, 2024

Proper cacao ( Theobroma L.) plant genotyping is mandatory for the conservation and use of species genetic resources. A set 15 international standard SSR markers was assumed as universal system. Recently, different SNPs SNP techniques have been exploited in cacao. However, a consensus on which to has not reached yet, driving search new approaches. To validate ddRADseq protocol genotyping, we compared performances population analysis dataset with 7,880 obtained from genotypic data aforementioned set, using 158 plants productive farms gene bank. Four groups were identified STRUCTURE ADMIXTURE softwares data, respectively. Similarities ancestries among these allowed identification analogous pairs individuals, referred as: G1 /G1 , G2 /G2 G3 /G3 G4 /G4 whether SSRs or used. Both marker systems Amelonado Criollo most abundant all samples. Genetic distance matrices both types significantly similar each other according Mantel test (p < 0.0001). PCoA UPGMA clustering mostly confirmed groups. AMOVA F ST pairwise comparison revealed moderate very large differentiation data. diversity parameters (H obs = 0.616, H exp 0.524 PIC 0.544) higher than that (0.288, 0.264, 0.230). In cases, carrying highest proportion (G1 ) had lowest The high congruence results validated employed genotyping. These could provide ways developing SNP-based system much needed studies.

Language: Английский

Citations

1