The breeding of new sweetpotato varieties is a highly inefficient process, confounded by incompatibility, poor fertility, open-pollination, and its hexaploid nature. Upwards of 12 to 20 lines are currently combined in open-pollinated nurseries based on good horticultural characteristics. Most progeny after several years of selection can be traced back to just three or four maternal lines. A method that would identify the paternal parent of superior progeny would enable breeders the ability to combine parents that exhibit superior combining ability in more-efficient, smaller nurseries. The objective of this work is to explore by means of computer simulation the application of genealogy reconstruction techniques on hexaploid individuals with PCR-based data. The progeny obtained on each female parent is fractionally assigned to each male with non zero exclusion probability proportional to its paternity likelihood. Computer simulations show that at least five different alleles per loci are needed to reach a reasonable discriminatory level. Also, the number of loci scored should not be less than 20. An increment in the number of alleles or loci increases the discriminatory power; but, the number of alleles produces a far more important effect than the number of loci.
Mario I. Buteler, Don LaBonte and Raul Macchiavelli
M.I. Buteler, D.R. LaBonte, R.L. Jarret and R.E. Macchiavelli
Using codominant molecular markers (microsatellites) for paternity identification was investigated in hexaploid sweetpotato [Ipomoea batatas (L.) Lam.]. Two experimental populations (CIP and LAES), each consisting of progeny of known parentage, were scored for the presence or absence of alleles segregating at IB-316 and IB-318 microsatellite loci. Paternity was assessed using paternity exclusion and the most-likely parent methods. In the former, paternity is assigned based on the identification of incompatible parent-progeny marker data. In contrast, the latter method incorporates paternity exclusion and a log-likelihood or LOD score that weighs progeny allelic patterns as to the likelihood that they could have come from a given paternal parent. The number of correctly allocated progeny differed for the methods. Paternity exclusion correctly allocated 7% and 25% of the progeny in the LAES and CIP populations, respectively. The most-likely parent method correctly allocated 23% and 88% of the progeny in the LAES and CIP populations, respectively. The greater misassignments in the LAES population were attributed to low allelic diversity at the LAES IB-318 locus and a larger parental population. This study demonstrates the feasibility of identifying paternity in sweetpotato using a minimal number of loci.
Aurora Díaz, Antonio Martín, Pilar Rallo and Raúl De la Rosa
(SSRs), or microsatellites, are increasingly becoming the markers of choice for paternity analysis in plants, because they now offer an easy and reliable way to test the paternity of seeds and seedlings by checking the presence of parental alleles in the
Hilde Nybom, Susan Gardiner and Charles J. Simon
Individual-specific DNA fragment patterns were obtained by hybridization of endonuclease-digested apple (Malus ×domestica Borkh.) DNA with a probe (pAR72) derived from the rDNA spacer region of the `White Angel' crab apple. Fragment detection was carried out with a nonradioactive method, using a horseradish peroxidase-catalyzed luminol oxidation. Paternity could be inferred by comparison of the fragment pattern generated by a seedling with those derived from putative parents.
Gerald S. Dangl, Keith Woeste, Mallikarjuna K. Aradhya, Anne Koehmstedt, Chuck Simon, Daniel Potter, Charles A. Leslie and Gale McGranahan
One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 14 loci were selected to analyze a diverse group of 47 persian walnut accessions and one J. hindsii (Jepson) Jepson ex R.E. Sm × J. regia hybrid (Paradox) rootstock. Among the 48 accessions, there were 44 unique multi-locus profiles; the accessions with identical profiles appeared to be synonyms. The pairwise genetic distance based on proportion of shared alleles was calculated for all accessions and a UPGMA (unweighted pair group method with arithmetic mean) dendrogram constructed. The results agree well with what is known about the pedigree and/or origins of the genotypes. The SSR markers distinguished pairs of closely related cultivars and should be able to uniquely characterize all walnut cultivars with the exception of budsports. They provide a more powerful and reliable system for the molecular characterization of walnut germplasm than those previously tested. These markers have numerous applications for the walnut industry, including cultivar identification, verification of pedigrees for cultivar and rootstock breeding programs, paternity analysis, and understanding the genetic diversity of germplasm collections.
Imen Rekik, Amelia Salimonti, Naziha Grati Kamoun, Innocenzo Muzzalupo, Oliver Lepais, Sophie Gerber, Enzo Perri and Ahmed Rebai
In the Mediterranean basin, a large number of olive varieties are present. This poses a series of problems concerning germplasm characterization and management. In addition, there is a problem arising from the existence of homonyms and synonyms. This makes cultivar identification very difficult and complex. Microsatellites or simple sequence repeat (SSR) are locus-specific codominant markers showing a high degree of polymorphism and multiple alleles per locus. Their high informativeness makes them the markers of choice in genetic diversity studies. This work presents the results of molecular characterization and identification of 20 Tunisian olive varieties using 10 SSR markers. All the SSR amplification products were sequenced to determine the number of repeats and the range of allele size. The number of alleles per SSR varied from three to six and the average heterozygosity rate ranged from 30% to 95%. Hierarchical classification of varieties base on similarity measures and clustering was globally consistent with the grouping of varieties by end use and phenotypic characteristics. The result is that varieties having the same name were found to have a clonal relationship. Paternity analysis showed also clone relationships between varieties not known to be related.
Jiang-Chong Wu, Jing Yang, Zhi-Jian Gu and Yan-Ping Zhang
, 2001 ) and paternity analysis ( Chaix et al., 2003 ). In this article, 20 polymorphic microsatellite markers isolated and characterized from M. oleifera are reported for which no SSRs have been developed to date. Materials and Methods Seeds were
Ying Wang, Ming Kang and Hongwen Huang
exclusionary power for the second parent [Pr ( Ex 2 )] were 0.9999, 0.9999, and 0.9998 for three chestnuts, indicating that these microsatellite loci are suitable for paternity analysis. High polymorphism and the codominant nature of microsatellite alleles in
Umesh R. Rosyara, Audrey M. Sebolt, Cameron Peace and Amy F. Iezzoni
statistical algorithms with different numbers of genomewide SNPs, thereby allowing a determination of optimal marker density for paternity analysis. The ability to identify the paternal parent of ‘Bing’ was facilitated by three factors. First, only a few sweet
Raúl De la Rosa, Angjelina Belaj, Antonio Muñoz-Mérida, Oswaldo Trelles, Inmaculada Ortíz-Martín, Juan José González-Plaza, Victoriano Valpuesta and Carmen R. Beuzón
expressed sequence tags of dicotyledonous species Genome 48 985 998 Mookerjee, S. Guerin, J. Collins, G. Ford, C. Sedgley, M. 2005 Paternity analysis using microsatellite markers to identify pollen donors in an olive grove Theor. Appl. Genet. 111 1174 1182