Identification of the Paternal Parent of ‘Bing’ Sweet Cherry and Confirmation of Descendants Using Single Nucleotide Polymorphism Markers

in Journal of the American Society for Horticultural Science

‘Bing’ is an iconic sweet cherry (Prunus avium L.) cultivar in the United States that even after more than 130 years of cultivation remains the most highly regarded dark sweet cherry and is the standard by which new sweet cherries are judged. ‘Bing’ has been repeatedly used as a parent in North American breeding programs and is found in the lineages of several important modern cultivars. The maternal parent of ‘Bing’ is reported to be ‘Black Republican’, an old cultivar commercially grown for fruit in the Willamette Valley, OR, after ≈1860 and now is usually only grown as a pollenizer cultivar; however, the paternal parent of ‘Bing’ is unknown. The objective of this study was to deduce the paternal parent of ‘Bing’ and validate the pedigree records for the relatives of ‘Bing’ using statistical algorithms that use genomewide single nucleotide polymorphism (SNP) data. With a high probability, it was determined that the sweet cherry cultivar Napoleon, also known as Royal Ann in the Pacific northwestern United States, a large, firm, blush-type, light-fleshed, and productive cherry, is the paternal parent of ‘Bing’. This parentage deduction results in an increase in the known relatedness among U.S. cultivated sweet cherry breeding germplasm because ‘Napoleon’ is an important founder previously known to be present in the ancestry of every self-compatible sweet cherry cultivar bred to date, directly and through ‘Bing’ and its descendants.

Abstract

‘Bing’ is an iconic sweet cherry (Prunus avium L.) cultivar in the United States that even after more than 130 years of cultivation remains the most highly regarded dark sweet cherry and is the standard by which new sweet cherries are judged. ‘Bing’ has been repeatedly used as a parent in North American breeding programs and is found in the lineages of several important modern cultivars. The maternal parent of ‘Bing’ is reported to be ‘Black Republican’, an old cultivar commercially grown for fruit in the Willamette Valley, OR, after ≈1860 and now is usually only grown as a pollenizer cultivar; however, the paternal parent of ‘Bing’ is unknown. The objective of this study was to deduce the paternal parent of ‘Bing’ and validate the pedigree records for the relatives of ‘Bing’ using statistical algorithms that use genomewide single nucleotide polymorphism (SNP) data. With a high probability, it was determined that the sweet cherry cultivar Napoleon, also known as Royal Ann in the Pacific northwestern United States, a large, firm, blush-type, light-fleshed, and productive cherry, is the paternal parent of ‘Bing’. This parentage deduction results in an increase in the known relatedness among U.S. cultivated sweet cherry breeding germplasm because ‘Napoleon’ is an important founder previously known to be present in the ancestry of every self-compatible sweet cherry cultivar bred to date, directly and through ‘Bing’ and its descendants.

‘Bing’ is the dominant fresh market sweet cherry cultivar grown in the western United States accounting for approximately half of the production acreage. The predominance of ‘Bing’ is the result of its heavy yields of large, firm, sweet, flavorful fruit with dark purplish flesh. Because of these desirable qualities, ‘Bing’ has been used in breeding and is well known as the mother of ‘Rainier’, the dominant U.S. cultivar in the yellow blush market class.

The original seedling that was later named ‘Bing’ was planted in 1875 in a nursery belonging to Seth Lewelling in Milwaukee, in the Willamette Valley of Oregon, and was later propagated and sold by the Lewelling Nursery (Hedrick, 1915). ‘Bing’ was derived from open pollination of ‘Black Republican’ and is believed to have been named after a Chinese workman (Hedrick, 1915). The seed parent, ‘Black Republican’, is an old and previously popular cultivar commercially grown for fruit in the Willamette Valley, OR, after ≈1860 and now is usually only planted as a pollenizer. The pollen part of ‘Bing’ was not recorded. Because all sweet cherry cultivars grown in the United States before 1968 were self-incompatible, ‘Bing’ could not have originated from self-pollination of ‘Black Republican’ (Lapins, 1970). Instead, it must have resulted from pollen that was compatible in styles of ‘Black Republican’. Other common cultivars growing in the region at that time included ‘Napoleon’, ‘Black Heart’, and ‘Black Tartarian’ (Hedrick, 1915).

As a result of the importance of ‘Bing’ as a commercial cultivar and its value as a breeding parent, knowledge of the paternal parent of ‘Bing’ and confirmation of its contribution to the pedigrees of modern cultivars would provide useful insight to inform genetic studies and breeding decisions. Complete and correct pedigree records are critical for breeding decision-making and also where pedigree-based statistical methods are used for genetic analyses of trait inheritance (Bink et al., 2008; Rosyara et al., 2009). For example, pedigree records help to increase power and precision while reducing false discovery rate in quantitative trait locus discovery studies (Bink et al., 2012; Lebrec et al., 2008). In addition, complete pedigree records increase the accuracy of estimates of relatedness among breeding material, informing crossing decisions to avoid or exploit inbreeding. Thus, performing paternity tests to validate or correct pedigree information is an important goal for sweet cherry breeding.

Paternity testing is a process in which candidates are examined for the most likely parents of a target offspring. The availability of DNA marker information has greatly facilitated the development of computational methods for parentage determination, pedigree reconstruction, estimation of relatedness, and inferences about genealogical relationships (Blouin, 2003). Several statistical strategies based on probability theory have been developed for such purposes. Most notably, DNA-based parentage confirmation is an accepted tool used in human paternity identification (Li et al., 2012). In clonally propagated perennial plants such as cherry (Prunus L.), where centuries-old potential ancestors are frequently available, DNA markers have been used to determine paternity. Paternity analyses have been conducted in apple (Malus ×domestica Borkh.) using random amplified polymorphic DNA markers (Harada et al., 1993) and chloroplast markers (Savolainen et al., 1995). Paternity analyses using simple sequence repeat (SSR) markers have been conducted in olive [Olea europaea L. (De la Rosa et al., 2004, 2013)], peach [Prunus persica L. (Yamamoto et al., 2003)], and wine grape [Vitis vinifera L. (Bowers et al., 1999)]. Schueler et al. (2003) used SSR markers for sweet cherry cultivar identification and studies of gene flow in wild sweet cherry where seed maternity and paternity were determined based on SSR genotypes of seed endocarp and embryos, respectively.

In the last two decades, SSR markers have been the DNA markers of choice for tests of paternity. However, SNP markers provide considerable advantages over SSRs including: 1) lower mutation rates; 2) suitability for standardized representation of genotyping results as a digital DNA signature (Fries and Durstewitz, 2001); and 3) suitability for high-throughput automation (Kruglyak, 1997). One disadvantage is that any individual SNP has a lower information content compared with a typical multiallelic SSR. However, this latter limitation can be compensated for by handling many more SNP markers.

Our objectives were to first determine the paternal parentage of ‘Bing’ sweet cherry and then to confirm the paternity of ‘Bing’ descendants. These analyses used 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 cherry cultivars existed in the United States in the 19th century and thus the number of potential paternal parents of ‘Bing’ is limited. These cultivars are still available. Second, sweet cherry is not native to the United States but rather to regions of Europe, the Middle East, and western Asia (Iezzoni et al., 1990). Finally, these analyses were possible as a result of the availability of new high-resolution genotypic data for sweet cherry. A genomewide 6K Infinium® II array (RosBREED 6K cherry SNP array v1) was developed and used to genotype a diverse array of 269 sweet cherry individuals (Peace et al., 2012). A total of 1825 SNPs were polymorphic in this germplasm (Peace et al., 2012), indicating that a large number of polymorphic markers suitable for paternity analysis were available.

Materials and Methods

Plant material and genotypic data.

The sweet cherry germplasm used (n = 48) consisted of founder cultivars, modern cultivars, breeding selections, and germplasm collection accessions (Table 1). All 48 individuals, which are part of the larger RosBREED sweet cherry Crop Reference Set representing North American sweet cherry breeding germplasm (C. Peace, J. Luby, E. van de Weg, M. Bink, and A. Iezzoni, unpublished data), were previously genotyped using the RosBREED cherry 6K SNP array v1 (Peace et al., 2012). A further subset of 15 cultivars and selections was tested for their probability of being the paternal parent of ‘Bing’. Of these, seven were included as negative controls because they were wild or landrace selections introduced to the United States after 1900 (Table 2). A subset of three descendant cultivars was tested to confirm ‘Bing’ as a parent, and eight descendant cultivars and selections were tested to confirm ‘Bing’ as a grandparent (Table 3).

Table 1.

Sweet cherry cultivars, selections, and wild accessions, their parents if known, coefficient of relatedness (ρ) to ‘Bing’ using single nucleotide polymorphism markers (n = 519), and S-locus genotype.z

Table 1.
Table 2.

Six historical sweet cherry cultivars tested for their probability of being the paternal parent of ‘Bing’ where ‘Black Republican’ is the reported maternal parent. Seven landrace and wild accessions introduced into the United States after 1900 were included as negative controls (italics).z

Table 2.
Table 3.

Sweet cherry cultivars and selections tested to confirm the reported parentage using the log of composite paternity index (LPCI) calculated with varying single nucleotide polymorphism marker numbers in sweet cherry.z

Table 3.

Different numbers of genomewide SNPs from the 6K array data set were used to evaluate whether marker number influenced the ability to determine parentage in sweet cherry. From all available SNPs, the first and largest set of 519 informative SNP markers was chosen that satisfied the following criteria: 1) minor allele frequency greater than 0.1; and 2) presence in the 48 accessions of all three genotypic classes, AA, AB, and BB. From this set, a second set of 180 SNPs was chosen that spanned all eight pseudo-chromosomes and with one SNP positioned approximately every 2 Mbp (≈8 cM) using the peach whole genome sequence, Peach v1.0 (Verde et al., 2013), as a proxy for the sweet cherry genome (Peace et al., 2012). A third set of 60 SNPs was chosen from the first set of SNPs using a wider spacing of approximately one marker at every 5 Mbp (≈20 cM). In this set of 60 markers, the minor allele frequency threshold was increased to greater than 0.2 to improve marker informativeness. Alleles at the self-incompatibility locus were from Haldar et al. (2010) and Iezzoni et al. (2005).

Statistical determination of parent–offspring relationships.

Candidates for the paternal parent of ‘Bing’ and the likelihood that ‘Bing’ was the true parent of other modern sweet cherry cultivars were tested using two statistical approaches: composite paternity index (CPI) and pairwise calculation of genetic relatedness. The CPI is based on the null hypothesis that there is no relationship vs. the alternative hypothesis that the pair under consideration is a parent and offspring relationship (Evett and Weir, 1998). The calculation of genetic relatedness, however, provides a quantitative measure of the degree of relatedness without knowledge of the type of relationship.

Composite paternity index.

Likelihood of parentage, expressed as the paternity index (PI) of Evett and Weir (1998), was used. In our case, we assumed that the maternal parent was known and the potential paternal parent was sought. As described in Evett and Weir (1998), Xi is the conditional probability that the alleged paternal parent is the true paternal parent, whereas Yi is the conditional probability that a random individual from the same population is the true paternal parent. Thus, PI for each marker (i) can be expressed as the ratio of the probability that the alleged parent could be the source of the allele acquired from the paternal parent (Xi) to the probability that a random individual of the same population could have contributed the allele (Yi). For the case of locus i with two codominant alleles A and B, as is the case with biallelic SNPs, with respective allele frequencies p and q (= 1 –p), the Xi and Yi for each of the possible parent–offspring combinations was derived following Elston (1986).

For combining information from multiple markers, the log-scaled CPI (LCPI) for n markers was determined according to Elston (1986) as: LCPI = –log10(PI1 × PI2 × ..× PIn), where the number of markers was 60, 180, or 519 depending on the SNP set used.

The LCPI was calculated using the program “paternity vs 1.0.0” written in R programming language and available from R-Forge mirror (Theußl and Zeileis, 2009). Positive evidence for paternity was set at a LCPI threshold of 1.3 or greater, which corresponds to a probability of paternity of 0.95 or greater. Therefore, if a candidate paternal parent had a LCPI of less than 1.3, it was excluded as a “likely” paternal parent. Of the potential paternal parents identified, the one with the highest LCPI value was considered most likely.

Pairwise calculations of genetic relatedness.

Pairwise calculations of the coefficient of relatedness between ‘Bing’ and other sweet cherry cultivars were done using the modified maximum likelihood method of Milligan (2003), Queller and Goodnight (1989), and Thompson (1975) implemented in the software KINGROUP (Konovalov et al., 2004). In this method, the coefficient of relatedness is calculated for two outbred diploid individuals X and Y that have been genotyped at L loci (in our analysis L = 519), where (a, b) and (c, d) denote their respective codominant alleles at a single locus. Using the marker information, the relatedness coefficient, ρ, can be defined as:

DE1
where is the Kronecker delta variable and a, b, c, d are alleles and their corresponding reference population allelic frequencies are pa, pb, pc, pd (Konovalov and Heg, 2008; Queller and Goodnight, 1989). In our study, allele frequencies were calculated at 519 SNP marker loci using 48 accessions. We used the extension of Konovalov and Heg (2008) that allows negative relatedness values, which are indications of no relationship. Using this formula, a coefficient of relatedness for a parent–offspring relationship would be ≈0.5, whereas 1.0 would be the value for paired samples of the same individual (i.e., clonal replicates).

Calculations of inbreeding coefficients.

The inbreeding coefficient of a diploid individual is defined as the probability that the two alleles carried by the gametes are identical by descent (Kempthorne, 1957). For an individual X, the inbreeding coefficient Fx is equal to the coancestry between its parents. Thus, if X has parents F and M, then the inbreeding coefficient of X is Fx = FFM.

Inbreeding coefficients for hypothetical matings between ‘Bing’ and ‘Stella’ and their offspring (Fig. 1) were calculated based on pedigree information only using the “inbreeding” function of the R package “pedigreemm” (Vazquez et al., 2010). Inbreeding coefficients were first calculated with the paternal parent of ‘Bing’ listed as unknown. Then the most likely paternal parent of ‘Bing’ was listed, and the coefficients were recalculated.

Fig. 1.
Fig. 1.

(A) Pedigrees for sweet cherry individuals in the ‘Bing’ lineage. The sweet cherry cultivar Napoleon is included as the newly identified paternal parent of ‘Bing’. The intensity of green illustrates the degree of relatedness (ρ) to ‘Bing’ according to pedigree records, whereas yellow indicates no known pedigree relationship to ‘Bing’. (B) Pedigrees of sweet cherry individuals in the ‘Stella’ lineage. The intensity of blue indicates the degree of relationship to ‘Stella’ according to pedigree records, whereas yellow indicates no known pedigree relationship to ‘Stella’. The online version is in color.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 139, 2; 10.21273/JASHS.139.2.148

Results

A total of 519 SNPs was available for paternity analysis because they met the first two SNP filtering criteria (Supplemental Table S1; Supplemental Fig. S1). The average marker density on the peach genome sequence for the 519 markers was 1 SNP per 0.41 Mbp with a maximum gap of 5.2 Mbp on scaffold 4 at the 21.6- to 26.8-Mbp interval. For the set of 180 markers, the average marker density was 1 SNP per 1.22 Mbp with a maximum gap of 5.62 Mbp also on scaffold 4 at 21.6 to 27.2 Mbp. Finally, for the set of 60 markers, the average marker density was 1 SNP per 3.85 Mbp with a maximum gap of 9.01 Mbp on scaffold 2 at 3.4 to 12.4 Mbp.

Among the six historical cultivars tested as the alleged paternal parent of ‘Bing’, ‘Napoleon’ received by far the greatest support for paternity, and better resolution was achieved using more markers (Table 2). Because these analyses were done using ‘Black Republican’ as the known maternal parent, this analysis also supports ‘Black Republican’ as the maternal parent of ‘Bing’. Although three other cultivars (Schneiders, Walpurgis, and Windsor) were supported as the possible parental parent of ‘Bing’ with the 60-SNP marker set, ‘Napoleon’ was the sole likely candidate when 180 and 519 SNPs were used, and support for ‘Napoleon’ was highest when 519 SNPs were used. ‘Emperor Francis’, ‘Schmidt’, and the seven landrace and wild selections used as negative controls were completely excluded as paternal parents of ‘Bing’ because they had LCPI values less than 1.3 for all marker sets indicating a probability of paternity of less than 0.95.

The estimated coefficients of relatedness (ρ) for ‘Bing’ paired with other individuals in the germplasm set ranged from 0 or less (unrelated) to 0.67 (Table 1). Individuals that had values consistent with a parent–offspring relationship (ρ≈0.5) included ‘Black Republican’ (ρ = 0.61), EE (ρ = 0.58), ‘Rainier’ (ρ = 0.50), ‘Chinook’ (ρ = 0.67), ‘Index’ (ρ = 0.55), ‘Napoleon’ (ρ = 0.66), and ‘Vic’ (ρ = 0.57). Of these individuals, ‘Black Republican’ is the reported maternal parent of ‘Bing’, whereas ‘Rainier’, ‘Chinook’, and ‘Vic’ are reported to be ‘Bing’ offspring and ‘EE’ is reported to be a second-generation ‘Bing’ offspring (Table 1). Therefore, these results also support ‘Black Republican’ as one of the parents of ‘Bing’ and ‘Napoleon’ as the likely other parent. The estimated coefficients of relatedness for ‘Bing’ and two individuals of unknown origin, PMR-1 and ‘Walpurgis’, were 0.35 and 0.32, respectively, suggesting a relationship.

The ‘Bing’ parentage of ‘Black Republican’ × ‘Napoleon’ was further confirmed with the SNP data because no inheritance errors were found. Using the 60-SNP set, the exclusive parental source, either ‘Black Republican’ or ‘Napoleon’, of 31 of the ‘Bing’ alleles could be determined. The parental source of the remaining 29 alleles could be either ‘Black Republican’ or ‘Napoleon’ (Fig. 2). With the 519-SNP set, the ‘Black Republican’ or ‘Napoleon’ source of alleles could be exclusively determined for 362 of the SNPs (Supplemental Fig. S2).

Fig. 2.
Fig. 2.

Graphical representation of probable parental source of alleles in sweet cherry cultivar Bing. Only 60 single nucleotide polymorphism (SNP) markers and the S locus are presented (for all markers, see Supplementary Fig. 2). Positions are physical positions (bp) of the peach whole genome sequence, Peach v1.0 (Verde et al., 2013). The online version is in color, where color indicates parent from which allele is inherited.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 139, 2; 10.21273/JASHS.139.2.148

The LCPI values for all SNP sets supported the pedigree records of ‘Bing’ as the parent of ‘Chinook’, ‘Rainier’, and ‘Vic’ (Table 3; Fig. 1A). The LCPI values also supported the reported paternal parents of these three ‘Bing’ offspring (i.e., ‘Gil Peck’, ‘Van’, and ‘Schmidt’, respectively). The correctness of the reported parents of the ‘Brooks’ (‘Bing’ grandchild through ‘Rainier’) and the seven other selections reported to have ‘Rainier’ as a parent was also supported with high probability. Similar to the ‘Bing’ analysis (Table 1), the reported parentages were probable with all marker numbers (i.e., 60, 180, and 519); however, the support was highest for 519 markers. The available S-locus genotypes (Table 3) also supported the reported parentages.

The finding that ‘Napoleon’ is the paternal parent of ‘Bing’ means that ‘Bing’ and ‘Stella’ share a common ancestor because ‘Napoleon’ is the grandparent of ‘Stella’ (Fig. 1A–B). With such a relationship, the inbreeding coefficient would be expected to be 0.125, which is consistent with the 0.18 coefficient of relatedness for ‘Bing’ and ‘Stella’ calculated using 519 SNP markers (Table 1). The expected inbreeding coefficients for hypothetical progeny between ‘Bing’ × ‘Stella’ and progeny from the ‘Bing’ and ‘Stella’ lineages with and without ‘Napoleon’ as the paternal parent of ‘Bing’ ranged from 0.008 to 0.328 (Table 4). In all cases, the pedigree-based inbreeding coefficients of the hypothetical offspring were much higher when ‘Napoleon’ was included as the paternal parent of ‘Bing’ compared with when they were calculated with the paternal parent of ‘Bing’ as unknown. The highest inbreeding coefficients were for hypothetical progeny from the use of ‘Selah’ as a parent because ‘Selah’ has parentage from both the ‘Stella’ and ‘Bing’ lineages (Fig. 1A–B). Inbreeding coefficients calculated for hypothetical progeny with and without the inclusion of ‘Napoleon’ as the parent of ‘Bing’ were also influenced by shared ancestry with other cultivars. ‘Early Burlat’ is a parent of ‘Brooks’, ‘Glacier’, and ‘Tieton’, whereas ‘Van’ is a parent of ‘Lapins’, ‘Rainier’, and ‘Sweetheart’ (Fig. 1). Therefore, pedigree-based inbreeding coefficients for hypothetical progeny from crosses within these groups of cultivars were increased beyond that expected with just shared ‘Bing’ ancestry (Table 4).

Table 4.

Inbreeding coefficients according to pedigree for progeny individuals generated from hypothetical crosses between sweet cherry cultivars Bing, Rainier, and Brooks and seven cultivars from the ‘Stella’ lineage.z

Table 4.

Discussion

‘Napoleon’ was identified as the paternal parent of ‘Bing’ and ‘Black Republican’ was confirmed as the maternal parent of ‘Bing’. This cross was possible because ‘Napoleon’ was among the first cultivars planted in Oregon in the late 1800s. The S-locus genotypes are also consistent with the proposed parentage, because it is possible for an S3-containing pollen grain from ‘Napoleon’ to have grown down a ‘Black Republican’ (S1S4) style and fertilized an S4 egg, resulting in the S3S4 pair of ‘Bing’. This parentage is also consistent with the inheritance of skin and flesh color in sweet cherry in which yellow fruit with a red blush is recessive to mahogany fruit (Schmidt, 1998). ‘Napoleon’ and ‘Rainier’ have yellow skin with a red blush, whereas ‘Bing’ fruit is mahogany. ‘Bing’ is heterozygous at the fruit color locus and passed the recessive allele for yellow fruit to ‘Rainier’.

Hedrick (1915) considered ‘Napoleon’ and ‘Black Tartarian’ to be the parents of ‘Black Republican’, thereby potentially increasing the contribution of ‘Napoleon’ to ‘Bing’ beyond the 50% of solely a parent–offspring relationship. The observed coefficients of relatedness based on 519 SNP makers (0.66 for ‘Bing’ and ‘Napoleon’, 0.61 for ‘Bing’ and ‘Black Republican’) are greater than would be expected for a solely parent–offspring relationship but lower than the 0.75 expected if ‘Napoleon’ were the parent of ‘Black Republican’. ‘Napoleon’ parentage of ‘Black Republican’ was used by Choi and Kappel (2004) in their analysis of inbreeding and coancestry in sweet cherry. Using our 519-SNP data set, ‘Napoleon’ as a parent of ‘Black Republican’ was supported (ρ = 0.48); however, ‘Black Tartarian’ could not be confirmed as a result of lack of a verified clone. An alternative hypothesis is that other unknown relationships exist among the founder cultivars, resulting in an increase in the SNP-based coefficients of relatedness compared with pedigree-based expectations.

‘Bing’ parentage of ‘Chinook’, ‘Rainier’, ‘Vic’, and eight other selections was also supported by the paternity analysis. Probabilities for detecting parentage (LCPI values) almost always increased when SNP numbers increased from 60 to 180 to 519, yet importantly, the conclusion that ‘Napoleon’ is the paternal parent of ‘Bing’ and that ‘Bing’ is the true parent or grandparent of 11 cultivars and selections were the same regardless of marker number. The cultivars for which ‘Bing’ parentage could not be ruled out with only 60 SNP markers may have ‘Napoleon’ or ‘Black Republican’ ancestry as a result of the limited diversity of sweet cherry available in the Pacific northwestern United States in the 1800s. Additionally, when considering the offspring and grandchildren of ‘Bing’, the high LCPI values using 60 and 180 SNPs indicate that, for sweet cherry, the lower number of markers provided sufficient discriminatory power. As expected, the larger number of SNPs increased the power of excluding false candidates and identifying parents.

The finding that ‘Bing’ and ‘Stella’ have a common ancestor increases the known degree of relatedness among cultivated and breeding germplasm of North American sweet cherry with implications for breeding decisions. ‘Stella’ is an extensively used parent in sweet cherry breeding worldwide because it is the donor of self-compatibility caused by the presence of a mutated S4 allele, i.e., S4′. This mutation originated from irradiated ‘Napoleon’ pollen that was used to pollinate ‘Emperor Francis’ (Lewis and Crowe, 1954). The cultivar Selah was unique in the germplasm set examined in having both ‘Bing’ and ‘Stella’ as ancestors and thus has ‘Napoleon’ ancestry from both sides. For other cultivars derived from ‘Stella’ and/or ‘Napoleon’, their close relatedness (ρ > 0.20) to ‘Bing’ could be the result of the common ‘Napoleon’ ancestor. For example, the maternal parent of ‘Lambert’ and ‘Gil Peck’ is ‘Napoleon’, and according to 520 markers, these cultivars had coefficients of relatedness with ‘Bing’ of 0.42 and 0.40, respectively.

In this study, the coefficient of relatedness also suggested a close relationship of ‘Bing’ with PMR-1 and ‘Walpurgis’, although no pedigrees are available. PMR-1 originated as a chance seedling in Washington State in the 1970s (Toyama et al., 1993). Therefore, it is possible that the relatedness of PMR-1 to ‘Bing’ could be the result of ancestry with ‘Bing’, ‘Napoleon’, and/or ‘Black Republican’. The S9 allele of PMR-1 could have been derived from ‘Early Burlat’ or ‘Beaulieu’. ‘Walpurgis’ on the other hand is a European cultivar; therefore, the relatedness to ‘Bing’ may be the result of ancestry with either ‘Napoleon’ or ‘Black Republican’ rather than directly with ‘Bing’.

Establishing complete and correct pedigree records, as illustrated for ‘Bing’, is an important requirement to maximize the ability to identify and validate quantitative trait loci using pedigree-based methods (Bink et al., 2008; Rosyara et al., 2009, 2013). The identification of previously unknown parents enables more precise estimates of coefficients of identity by descent. Identifying which ‘Napoleon’-derived chromosome segments, and which ‘Black Republican’-derived chromosome segments, are maintained in superior cultivars is now possible as a result of confirmation of parentage and the available genomewide set of polymorphic SNP markers.

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  • QuellerD.C.GoodnightK.F.1989Estimating relatedness using genetic-markersEvolution43258275

  • RosyaraU.R.BinkM.C.A.M.van de WegE.ZhangG.WangD.SeboltA.DirlewangerE.Quero-GarciaJ.SchusterM.IezzoniA.F.2013Fruit size QTL identification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherryMol. Breed.32875887

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    • Export Citation
  • RosyaraU.R.Gonzalez-HernandezJ.L.GloverK.D.GedyeK.R.SteinJ.M.2009Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustrationTheor. Appl. Genet.11816171631

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  • VerdeI.AbbottA.G.ScalabrinS.JungS.ShuS.MarroniF.ZhebentyayevaT.DettoriM.T.GrimwoodJ.CattonaroF.ZuccoloA.RossiniL.JenkinsJ.VendraminE.MeiselL.A.DecroocqV.SosinskiB.ProchnikS.MitrosT.PolicritiA.CiprianiG.DondiniL.FicklinS.MgoodsteinD.XuanP.Del FabbroC.AraminiV.CopettiD.GonzalezS.ShornerD.FalchiR.LucasS.MicaE.MaldonadoJ.LazzariB.BielenbergD.PironaR.MiculanM.BarakatA.TestolinR.StellaA.TartariniS.TonuttiP.ArúsP.OrellanaA.WellsC.MainD.VizzottoG.SilvaH.SalaminiF.SchmutzJ.MorganteM.RokhsarD.S.2013The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolutionNat. Genet.45487494

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    • Export Citation
  • YamamotoT.MochidaK.ImaiT.HajiT.YaegakiH.YamaguchiM.MatsutaN.OgiwaraI.HayashiT.2003Parentage analysis in Japanese peaches using SSR markersBreed. Sci.533540

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Supplemental Fig. S1.
Supplemental Fig. S1.

Physical map positions, according to the whole peach genome sequence, Peach v1.0 (Verde et al., 2013), of the 519 single nucleotide polymorphism (SNP) markers used in this sweet cherry paternity study. Three different sets were used for calculation of the log of composite paternity index (LCPI). Colors identify the set of 180 markers (blue and purple) and set of 60 markers (red and purple). The purple-colored markers are common in all marker sets (519, 180, and 60 markers).

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 139, 2; 10.21273/JASHS.139.2.148

Supplemental Fig. S2.
Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.Supplemental Fig. S2.

Graphic representation of probable parental source of alleles in sweet cherry cultivar Bing with all 519 single nucleotide polymorphism (SNP) markers. Positions are physical positions (bp) of the peach whole genome sequence, Peach v1.0 (Verde et al., 2013); NCBI National Center for Biotechnology Information (Bethesda, MD); ss submitted SNP; Chr chromosome.

Citation: Journal of the American Society for Horticultural Science J. Amer. Soc. Hort. Sci. 139, 2; 10.21273/JASHS.139.2.148

Supplemental Table S1.

List of 519 single nucleotide polymorphism markers, S-locus, and their peach physical map positions on the peach whole genome sequence, Peach v1.0 (Verde et al., 2013).z

Supplemental Table S1.Supplemental Table S1.Supplemental Table S1.Supplemental Table S1.Supplemental Table S1.

If the inline PDF is not rendering correctly, you can download the PDF file here.

Contributor Notes

This work was partially funded by USDA’s National Institute of Food and Agriculture–Specialty Crop Research Initiative project, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808).

Corresponding author. E-mail: iezzoni@msu.edu.

  • View in gallery

    (A) Pedigrees for sweet cherry individuals in the ‘Bing’ lineage. The sweet cherry cultivar Napoleon is included as the newly identified paternal parent of ‘Bing’. The intensity of green illustrates the degree of relatedness (ρ) to ‘Bing’ according to pedigree records, whereas yellow indicates no known pedigree relationship to ‘Bing’. (B) Pedigrees of sweet cherry individuals in the ‘Stella’ lineage. The intensity of blue indicates the degree of relationship to ‘Stella’ according to pedigree records, whereas yellow indicates no known pedigree relationship to ‘Stella’. The online version is in color.

  • View in gallery

    Graphical representation of probable parental source of alleles in sweet cherry cultivar Bing. Only 60 single nucleotide polymorphism (SNP) markers and the S locus are presented (for all markers, see Supplementary Fig. 2). Positions are physical positions (bp) of the peach whole genome sequence, Peach v1.0 (Verde et al., 2013). The online version is in color, where color indicates parent from which allele is inherited.

  • View in gallery

    Physical map positions, according to the whole peach genome sequence, Peach v1.0 (Verde et al., 2013), of the 519 single nucleotide polymorphism (SNP) markers used in this sweet cherry paternity study. Three different sets were used for calculation of the log of composite paternity index (LCPI). Colors identify the set of 180 markers (blue and purple) and set of 60 markers (red and purple). The purple-colored markers are common in all marker sets (519, 180, and 60 markers).

  • View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery View in gallery

    Graphic representation of probable parental source of alleles in sweet cherry cultivar Bing with all 519 single nucleotide polymorphism (SNP) markers. Positions are physical positions (bp) of the peach whole genome sequence, Peach v1.0 (Verde et al., 2013); NCBI National Center for Biotechnology Information (Bethesda, MD); ss submitted SNP; Chr chromosome.

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    • Search Google Scholar
    • Export Citation
  • RosyaraU.R.Gonzalez-HernandezJ.L.GloverK.D.GedyeK.R.SteinJ.M.2009Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustrationTheor. Appl. Genet.11816171631

    • Search Google Scholar
    • Export Citation
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    • Search Google Scholar
    • Export Citation
  • SchmidtH.1998On the genetics of fruit color in sweet cherriesActa Hort.4687781

  • SchuelerS.TuschA.SchusterM.ZiegenhagenB.2003Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) markers for individual identification and reproductive processesGenome4695102

    • Search Google Scholar
    • Export Citation
  • TheußlS.ZeileisA.2009Collaborative software development using R-ForgeR J1914

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    • Search Google Scholar
    • Export Citation
  • VerdeI.AbbottA.G.ScalabrinS.JungS.ShuS.MarroniF.ZhebentyayevaT.DettoriM.T.GrimwoodJ.CattonaroF.ZuccoloA.RossiniL.JenkinsJ.VendraminE.MeiselL.A.DecroocqV.SosinskiB.ProchnikS.MitrosT.PolicritiA.CiprianiG.DondiniL.FicklinS.MgoodsteinD.XuanP.Del FabbroC.AraminiV.CopettiD.GonzalezS.ShornerD.FalchiR.LucasS.MicaE.MaldonadoJ.LazzariB.BielenbergD.PironaR.MiculanM.BarakatA.TestolinR.StellaA.TartariniS.TonuttiP.ArúsP.OrellanaA.WellsC.MainD.VizzottoG.SilvaH.SalaminiF.SchmutzJ.MorganteM.RokhsarD.S.2013The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolutionNat. Genet.45487494

    • Search Google Scholar
    • Export Citation
  • YamamotoT.MochidaK.ImaiT.HajiT.YaegakiH.YamaguchiM.MatsutaN.OgiwaraI.HayashiT.2003Parentage analysis in Japanese peaches using SSR markersBreed. Sci.533540

    • Search Google Scholar
    • Export Citation
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