Procruster analysis among molecular markers and quantitative traits in diallel crosses of selected tomato Recombinant Inbred Lines

PRATTA, GUILLERMO RAUL; RODRÍGUEZ, GUSTAVO RUBÉN; MAHUAD, SABINA L; ZORZOLI, ROXANA; PICARDI, LILIANA AMELIA

Córdoba

Congreso; 2º Congreso Argentino de Bioinformática y Biología Computacional; 2011

Eighteen tomato RILs selected for fruit weight and shelf life were obtained from an interspecific cross between the wild accession LA722 (P, Solanum pimpinellifolium) and the Argentinean cultivar Caimanta (C, S. lycopersicum). Sequence Related Amplified Polymorphisms (SRAP) are a new kina of molecular markers that preferably reveals coding DNA regions. Diallel crosses allow studying the inheritance of quantitative traits and presently they could be also applied to molecular markers. Procrustes analysis (PrCA) is a multivariate approach that measures the consensus among two sets of data in a given population. The objective of this work was to apply a PrCA to diallel crosses among five of the selected. Five selected RILs were crossed according to a complete diallel design without reciprocal to obtain the 10 possible hybrids. C, P, and F1 (CxP) were included as experimental testers. Eleven fruit quality traits (weight, diameter, height, shape index, soluble solid content, shelf life, firmness, chroma index, reflectance percentage, pH, and titrable acidity) were assessed in the 18 genotypes. Mean values of quantitative traits were compared by ANOVA, and Principal Component Analyses (PCA) was applied to measure the phenotypic variability. The standard protocol was used to generate the molecular profiles. SRAP fragments were classified as present / absent to calculate the percentage of polymorphism, and Principal Coordinate Analysis (PCoA) was applied to measure the genotypic variability. To estimate the consensus among phenotype and genotype data a PrCA was performed from PCA and PCoA results. Significant differences were observed among genotypes for all quantitative traits. Fruit weight, diameter, height, chroma index, and pH were the most variable traits according to PCA. The percentage of polymorphism was of 66% for SRAP, and PCoA determined that at least 8 fragments carried by P and 16 de novo fragments accounted for the greatest proportion of molecular variability. PrCA detected a general consensus of 75% between phenotype and genotype data, greatly due to the fragments contributed by the wild genotype. Hence these fragments would be associated to the most variable fruit traits. Consequently, PrCA results suggested that wild germplasm greatly contributes to modify traits determining tomato quality such as fruit weight, diameter, height, chroma index, and pH. PrCA among SRAP markers and quantitative traits evaluated in the diallel crosses of selected tomato RILs allowed verifying the consensus among both sets of data in this novel genetic backgroundSolanum pimpinellifolium) and the Argentinean cultivar Caimanta (C, S. lycopersicum). Sequence Related Amplified Polymorphisms (SRAP) are a new kina of molecular markers that preferably reveals coding DNA regions. Diallel crosses allow studying the inheritance of quantitative traits and presently they could be also applied to molecular markers. Procrustes analysis (PrCA) is a multivariate approach that measures the consensus among two sets of data in a given population. The objective of this work was to apply a PrCA to diallel crosses among five of the selected. Five selected RILs were crossed according to a complete diallel design without reciprocal to obtain the 10 possible hybrids. C, P, and F1 (CxP) were included as experimental testers. Eleven fruit quality traits (weight, diameter, height, shape index, soluble solid content, shelf life, firmness, chroma index, reflectance percentage, pH, and titrable acidity) were assessed in the 18 genotypes. Mean values of quantitative traits were compared by ANOVA, and Principal Component Analyses (PCA) was applied to measure the phenotypic variability. The standard protocol was used to generate the molecular profiles. SRAP fragments were classified as present / absent to calculate the percentage of polymorphism, and Principal Coordinate Analysis (PCoA) was applied to measure the genotypic variability. To estimate the consensus among phenotype and genotype data a PrCA was performed from PCA and PCoA results. Significant differences were observed among genotypes for all quantitative traits. Fruit weight, diameter, height, chroma index, and pH were the most variable traits according to PCA. The percentage of polymorphism was of 66% for SRAP, and PCoA determined that at least 8 fragments carried by P and 16 de novo fragments accounted for the greatest proportion of molecular variability. PrCA detected a general consensus of 75% between phenotype and genotype data, greatly due to the fragments contributed by the wild genotype. Hence these fragments would be associated to the most variable fruit traits. Consequently, PrCA results suggested that wild germplasm greatly contributes to modify traits determining tomato quality such as fruit weight, diameter, height, chroma index, and pH. PrCA among SRAP markers and quantitative traits evaluated in the diallel crosses of selected tomato RILs allowed verifying the consensus among both sets of data in this novel genetic background