The UGA NESPAL Molecular Cotton Breeding Laboratory - Publications - Pedigree vs/. DNA Marker Based Genetic Similarity Estimates in Cotton

Pedigree- vs. DNA Marker-Based Genetic Similarity Estimates in Cotton

Guillermo Van Becelaere, Edward L. Lubbers, Andrew H. Paterson and Peng W. Chee, 2005
Crop Science 45:2281-2287.

Knowledge of genetic diversity and relationships among breeding materials is essential to the improvement of crop species. Genetic similarity estimates among cultivars are helpful to select parental combinations for segregating populations so as to maintain genetic diversity in a breeding program. The objective of this study was to determine the correspondence between pedigree- and restriction frag- ment length polymorphism–based genetic similarity (RFLP-GS) estimates for a set of 36 Upland cotton (Gossypium hirsutum L.) cultivars. Coefficients of parentage (COPs) and genetic similarity estimates based on 261 codominant RFLP markers for all possible pairs of cultivars were compared. A significant though moderate association r 0.41, P 0.001) was detected between the COP and RFLP-GS matrices. Spearman’s rank correlation for the 142 pairs of related cultivars (COP 0.1) was somewhat higher (rS 0.53, P 0.001). There was a significant linear relationship between COP and RFLP-GS for the pairs of related cultivars; however, the coefficient of determination was low (R2 0.25), indicating that the COP only explained a small portion of the variation observed for RFLP-GS. COP and RFLP-GS estimate different types of genetic resemblance; however, the moderate association may have also resulted from violations to the assumptions made when computing COP. RFLP-GS is a more accurate estimate of true genetic resemblance among cotton cultivars. Nevertheless, the pedigree- and RFLP-based dendrograms were somewhat similar, suggesting that pedigree information will continue to be useful to inexpensively identify diverse parents in a breeding program.

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Knowledge of genetic diversity and relationships among breeding materials is essential to the improvement of crop species. Genetic similarity estimates among cultivars are helpful to select parental combinations for segregating populations so as to maintain genetic diversity in a breeding program. The objective of this study was to determine the correspondence between pedigree- and restriction frag- ment length polymorphism–based genetic similarity (RFLP-GS) estimates for a set of 36 Upland cotton (Gossypium hirsutum L.) cultivars. Coefficients of parentage (COPs) and genetic similarity estimates based on 261 codominant RFLP markers for all possible pairs of cultivars were compared. A significant though moderate association r 0.41, P 0.001) was detected between the COP and RFLP-GS matrices. Spearman’s rank correlation for the 142 pairs of related cultivars (COP 0.1) was somewhat higher (rS 0.53, P 0.001). There was a significant linear relationship between COP and RFLP-GS for the pairs of related cultivars; however, the coefficient of determination was low (R2 0.25), indicating that the COP only explained a small portion of the variation observed for RFLP-GS. COP and RFLP-GS estimate different types of genetic resemblance; however, the moderate association may have also resulted from violations to the assumptions made when computing COP. RFLP-GS is a more accurate estimate of true genetic resemblance among cotton cultivars. Nevertheless, the pedigree- and RFLP-based dendrograms were somewhat similar, suggesting that pedigree information will continue to be useful to inexpensively identify diverse parents in a breeding program.