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

by different approaches, which include the use of pedigrees and DNA fingerprinting. The COP measures the Knowledge of genetic diversity and relationships among breeding degree of genetic relatedness among genotypes based materials is essential to the improvement of crop species. Genetic similarity estimates among cultivars are helpful to select parental on pedigree information by estimating the probability combinations for segregating populations so as to maintain genetic that a random allele from one genotype is identical by diversity in a breeding program. The objective of this study was to descent to a random allele of another genotype at the determine the correspondence between pedigreeand restriction fragsame locus (Kempthorne, 1969). The accuracy of COP ment length polymorphism–based genetic similarity (RFLP-GS) estidepends on the availability of reliable and detailed pedimates for a set of 36 Upland cotton (Gossypium hirsutum L.) cultivars. gree records; at times these records may be either unCoefficients of parentage (COPs) and genetic similarity estimates available or unreliable. The calculations also do not based on 261 codominant RFLP markers for all possible pairs of account for the effects of selection, mutation, and gecultivars were compared. A significant though moderate association netic drift and require several simplifying assumptions (r 0.41, P 0.001) was detected between the COP and RFLP-GS that are generally not met. Nevertheless, pedigree informatrices. 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 mation offers plant breeders a simple and inexpensive a significant linear relationship between COP and RFLP-GS for the way to estimate genetic relatedness among breeding mapairs of related cultivars; however, the coefficient of determination terials. was low (R2 0.25), indicating that the COP only explained a small DNA markers, such as RFLPs, amplified fragment portion of the variation observed for RFLP-GS. COP and RFLP-GS length polymorphisms (AFLPs), random amplified polyestimate different types of genetic resemblance; however, the modermorphic DNAs (RAPDs), and simple sequence repeats ate association may have also resulted from violations to the assump(SSRs), can directly assess DNA sequence variation. tions made when computing COP. RFLP-GS is a more accurate estimate DNA-based genetic similarity measures the degree of of true genetic resemblance among cotton cultivars. Nevertheless, the genetic relatedness among genotypes by estimating the pedigreeand RFLP-based dendrograms were somewhat similar, sugproportion of alleles that are alike in state, thus differing gesting that pedigree information will continue to be useful to inexpensively identify diverse parents in a breeding program. from COP in the type of genetic resemblance estimated. As such, they provide a more precise estimate of genetic similarity among genotypes and do not require the assumptions inherent to pedigree analysis. All the DNA K of genetic diversity and relationships markers mentioned above can provide a large numamong breeding materials is essential to the plant ber of polymorphic loci and have been utilized to estibreeder in the efficient improvement of crop species. mate genetic similarity among genotypes in crop species Genetic similarity (or genetic distance) estimates among (Graner et al., 1994; Kim and Ward, 1997; Messmer et genotypes are helpful in selecting parental combinations al., 1993). for segregating populations so as to maintain genetic diverThe level of association between pedigreeand DNA sity in a breeding program. These estimates are, in turn, marker–based genetic similarity estimates may vary among estimates for availability of alternate alleles for desirable different crop species. In maize (Zea mays L.), for examtraits, which is the basis for long-term selection gains. ple, most studies found a close association between COP Crosses between genetically divergent parents are exand RFLP-based genetic similarity (RFLP-GS) (Messmer pected to have a larger genetic variance among progenies et al., 1993). However, in other species such as wheat than crosses between closely related parents (Messmer et (Triticum aestivum L.) (Kim and Ward, 1997), barley al., 1993), increasing the opportunity for selecting rare (Hordeum vulgare L.) (Graner et al., 1994), and oat progenies that may be superior. Despite this, the re(Avena sativa L.) (O’Donoughue et al., 1994) only modpeated crossing of closely related elite parents to deerate to low associations have been observed between velop new elite cultivars is common in many crop species both estimators. Therefore, it is important to determine and has likely narrowed their genetic base, increasing within each species whether pedigreeand DNA marker– their vulnerability to potentially widespread losses from based estimates of genetic similarity provide similar indiseases and pests. formation about the genetic relationships among germGenetic similarity among genotypes can be estimated plasm. The pedigrees of cotton cultivars have been assemG. Van Becelaere, E.L. Lubbers, and P.W. Chee, Dep. of Crop and bled and published (Calhoun et al., 1997) and have been Soil Sciences, Univ. of Georgia, Tifton, GA 31793; A.H. Paterson, Plant Genome Mapping Lab., Univ. of Georgia, Athens, GA 30602. used in selecting parents for crossing blocks; whereas Received 7 Dec. 2004. *Corresponding author ([email protected]). large-scale DNA marker data were not available until recently. Bowman et al. (1996) reported an average Published in Crop Sci. 45:2281–2287 (2005). COP of 0.07 for 260 Upland cotton cultivars released Plant Genetic Resources doi:10.2135/cropsci2004.0715 © Crop Science Society of America Abbreviations: COP, coefficient of parentage; RFLP-GS, restriction fragment length polymorphism–based genetic similarity. 677 S. Segoe Rd., Madison, WI 53711 USA 2281 Published online September 23, 2005