Sweetness and acidity are important fruit quality traits that drive consumer acceptability of swe... more Sweetness and acidity are important fruit quality traits that drive consumer acceptability of sweet cherry. Developing new sweet cherry cultivars with superior flavor attributes is a major objective in fruit breeding programs. This study was designed to facilitate development of new cultivars with exceptional taste characteristics through the identification of quantitative trait loci (QTL) associated with soluble solids content (SSC) and titratable acidity (TA) in sweet cherry. A total of 601 pedigree-linked individuals including founders, commercial cultivars, breeding parents and their F1 progeny seedlings were used. The five largest fruit from each individual were selected at commercial maturity for SSC measurement. Juice from a bulk sample of 25 fruit was used for TA measurement. Both SSC and TA data were collected in 2010, 2011 and 2012. One thousand and ninety one (1091) single nucleotide polymorphism (SNP) markers on the Infinium array of a total of 6000 SNPs along with four ...
Powdery mildew (PM), caused by Podosphaera clandestina, and bacterial canker (BC), caused by Pseu... more Powdery mildew (PM), caused by Podosphaera clandestina, and bacterial canker (BC), caused by Pseudomonas syringae pv. Syringae, are the major diseases of sweet cherry in the USA. Incorporation of natural resistance into elite cultivars would be an effective way to reduce reliance on fungicide and pesticide use and facilitate the transition to sustainable production systems. This study was designed to identify quantitative trait loci (QTL) underlying PM and BC infection to facilitate development of new resistant cultivars. Six hundred pedigree-linked germplasm were used in this study. PM was scored in the field on a 0-5 scale (0 = no visible symptoms and 5 = very severe infection on leaves) from 2011 to 2013. BC phenotyping was performed by inoculating five healthy and newly emerging leaves with 10 µl of 108 CFU/ml bacteria suspension mixed with 0.5% surfactant by mid-rib wound method in a detached leaf assay. Disease was scored in the lab on a 0-4 scale (0 = no necrosis and 4 = tota...
Horticultural crop improvement would benefit from a standardized, systematic, and statistically r... more Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were ...
S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the As... more S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the phylogenetic history of the S-RNase that determines pistil specificity. In Rosaceae, molecular characterizations of Prunus species, and species from the tribe Pyreae (i.e., Malus, Pyrus, Sorbus) revealed different numbers of genes determining S-pollen specificity. In Prunus only one pistil and pollen gene determine GSI, while in Pyreae there is one pistil but multiple pollen genes, implying different specificity recognition mechanisms. It is thus conceivable that within Rosaceae the genes involved in GSI in the two lineages are not orthologous but possibly paralogous. To address this hypothesis we characterised the S-RNase lineage and S-pollen lineage genes present in the genomes of five Rosaceae species from three genera: M. × domestica (apple, self-incompatible (SI); tribe Pyreae), P. persica (peach, self-compatible (SC); Amygdaleae), P. mume (mei, SI; Amygdaleae), Fragaria vesca (strawberry, SC; Potentilleae), and F. nipponica (mori-ichigo, SI; Potentilleae). Phylogenetic analyses revealed that the Malus and Prunus S-RNase and S-pollen genes belong to distinct gene lineages, and that only Prunus S-RNase and SFB-lineage genes are present in Fragaria. Thus, S-RNase based GSI system of Malus evolved independently from the ancestral system of Rosaceae. Using expression patterns based on RNA-seq data, the ancestral S-RNase lineage gene is inferred to be expressed in pistils only, while the ancestral S-pollen lineage gene is inferred to be expressed in tissues other than pollen.
A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for... more A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker-assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® and a 20K Apple Infinium® genotyping array. The cultivated strawberry is an allo-octoploid. This level and type of ploidy creates challenges which we addressed in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploited both site-specific, biological as well as designed reductions in ploidy. The array will target several polymorphism types, including indels and di- and multi-allelic SNPs. For apple, the new SNP markers are located in focal points of max 10 KB, an approa...
High-throughput genome scans are important tools for genetic studies and breeding applications. H... more High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® ass...
Theoretical and Applied Genetics - THEOR APPL GENET, 1998
Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunu... more Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunus cerasus L., 2n=4x=32) cultivars, Rheinische Schattenmorelle (RS) and Erdi Botermo (EB), were constructed from 86 progeny from the cross RS�EB. The RS linkage map consists of 126 single-dose restriction fragment (SDRF, Wu et al. 1992) markers assigned to 19 linkage groups covering 461.6 cM. The EB linkage map has 95 SDRF markers assigned to 16 linkage groups covering 279.2 cM. Fifty three markers mapped in both parents were used as bridges between both maps and 13 sets of homologous linkage groups were identified. Homoeologous relationships among the sour cherry linkage groups could not be determined because only 15 probes identified duplicate loci. Fifty nine of the markers on the linkage maps were detected with probes used in other Prunus genetic linkage maps. Four of the sour cherry linkage groups may be homologous with four of the eight genetic linkage groups identified in peach and...
Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by re... more Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by reducing production costs, reduced chemical use and higher density plantings. Despite the importance of rootstock-induced dwarfing, the cause of this phenomenon is not known. Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried out cDNA-AFLP analysis to investigate differential gene expression between the two graft combinations. Transcript-derived fragments (TDFs) identified as differentially expressed were cloned and printed on microarrays for further confirmation of the differential expression. A total of 99 TDFs were identified as differentially expressed between the 'Bing'/Gi5 and 'Bing'/Gi6 samples, including genes involved in transcription regulation, brassinosteroid signaling, flavonoid metabolism and cell wall biosynthesis or modification. Rootstock vigor has a significant effect on gene expression at the scion and the graft union. Timing of the differential gene expression in the dwarf trees coincides with the earlier cessation of terminal shoot growth, suggesting that these differentially expressed genes may be involved in the dwarfing phenomenon.
... intergenomic recom-bination. These results are consistent with previous allozyme inheritance ... more ... intergenomic recom-bination. These results are consistent with previous allozyme inheritance and cytogenetic data in sour cherry sugges-ting that 2 : 1 ratios are prevalent along with occasional intergenomic recombination. A 2 : 1 ...
... Kazuo Ikeda · Boris Igic · Koichiro Ushijima · Hisayo Yamane · Nathanael R. Hauck · Ryohei Na... more ... Kazuo Ikeda · Boris Igic · Koichiro Ushijima · Hisayo Yamane · Nathanael R. Hauck · Ryohei Nakano · Hidenori Sassa · Amy F. Iezzoni · Joshua R. Kohn ... First, we compared the null models that do not allow for positive selection (models M0 and M1) with successively more ...
Sweetness and acidity are important fruit quality traits that drive consumer acceptability of swe... more Sweetness and acidity are important fruit quality traits that drive consumer acceptability of sweet cherry. Developing new sweet cherry cultivars with superior flavor attributes is a major objective in fruit breeding programs. This study was designed to facilitate development of new cultivars with exceptional taste characteristics through the identification of quantitative trait loci (QTL) associated with soluble solids content (SSC) and titratable acidity (TA) in sweet cherry. A total of 601 pedigree-linked individuals including founders, commercial cultivars, breeding parents and their F1 progeny seedlings were used. The five largest fruit from each individual were selected at commercial maturity for SSC measurement. Juice from a bulk sample of 25 fruit was used for TA measurement. Both SSC and TA data were collected in 2010, 2011 and 2012. One thousand and ninety one (1091) single nucleotide polymorphism (SNP) markers on the Infinium array of a total of 6000 SNPs along with four ...
Powdery mildew (PM), caused by Podosphaera clandestina, and bacterial canker (BC), caused by Pseu... more Powdery mildew (PM), caused by Podosphaera clandestina, and bacterial canker (BC), caused by Pseudomonas syringae pv. Syringae, are the major diseases of sweet cherry in the USA. Incorporation of natural resistance into elite cultivars would be an effective way to reduce reliance on fungicide and pesticide use and facilitate the transition to sustainable production systems. This study was designed to identify quantitative trait loci (QTL) underlying PM and BC infection to facilitate development of new resistant cultivars. Six hundred pedigree-linked germplasm were used in this study. PM was scored in the field on a 0-5 scale (0 = no visible symptoms and 5 = very severe infection on leaves) from 2011 to 2013. BC phenotyping was performed by inoculating five healthy and newly emerging leaves with 10 µl of 108 CFU/ml bacteria suspension mixed with 0.5% surfactant by mid-rib wound method in a detached leaf assay. Disease was scored in the lab on a 0-4 scale (0 = no necrosis and 4 = tota...
Horticultural crop improvement would benefit from a standardized, systematic, and statistically r... more Horticultural crop improvement would benefit from a standardized, systematic, and statistically robust procedure for validating quantitative trait loci (QTLs) in germplasm relevant to breeding programs. Here, we describe and demonstrate a strategy for developing reference germplasm sets of perennial, clonally propagated crops, especially those with long juvenile periods. Germplasm is chosen to efficiently represent important members of larger pedigree-connected genepools. To facilitate validation of multiple QTLs, genome-wide representation of alleles is optimized for designated important breeding parents (IBPs) by estimating average allelic representation in relatives. The strategy and arising principles were demonstrated in a simulated germplasm set. Strong statistical power can be achieved with a carefully chosen germplasm set composed of IBPs, their numerous unselected progenies and close relatives, and all available founders and intermediate ancestors. Crop Reference Sets were ...
S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the As... more S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the phylogenetic history of the S-RNase that determines pistil specificity. In Rosaceae, molecular characterizations of Prunus species, and species from the tribe Pyreae (i.e., Malus, Pyrus, Sorbus) revealed different numbers of genes determining S-pollen specificity. In Prunus only one pistil and pollen gene determine GSI, while in Pyreae there is one pistil but multiple pollen genes, implying different specificity recognition mechanisms. It is thus conceivable that within Rosaceae the genes involved in GSI in the two lineages are not orthologous but possibly paralogous. To address this hypothesis we characterised the S-RNase lineage and S-pollen lineage genes present in the genomes of five Rosaceae species from three genera: M. × domestica (apple, self-incompatible (SI); tribe Pyreae), P. persica (peach, self-compatible (SC); Amygdaleae), P. mume (mei, SI; Amygdaleae), Fragaria vesca (strawberry, SC; Potentilleae), and F. nipponica (mori-ichigo, SI; Potentilleae). Phylogenetic analyses revealed that the Malus and Prunus S-RNase and S-pollen genes belong to distinct gene lineages, and that only Prunus S-RNase and SFB-lineage genes are present in Fragaria. Thus, S-RNase based GSI system of Malus evolved independently from the ancestral system of Rosaceae. Using expression patterns based on RNA-seq data, the ancestral S-RNase lineage gene is inferred to be expressed in pistils only, while the ancestral S-pollen lineage gene is inferred to be expressed in tissues other than pollen.
A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for... more A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker-assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® and a 20K Apple Infinium® genotyping array. The cultivated strawberry is an allo-octoploid. This level and type of ploidy creates challenges which we addressed in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploited both site-specific, biological as well as designed reductions in ploidy. The array will target several polymorphism types, including indels and di- and multi-allelic SNPs. For apple, the new SNP markers are located in focal points of max 10 KB, an approa...
High-throughput genome scans are important tools for genetic studies and breeding applications. H... more High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® ass...
Theoretical and Applied Genetics - THEOR APPL GENET, 1998
Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunu... more Restriction fragment length polymorphism (RFLP) linkage maps of two tetraploid sour cherry (Prunus cerasus L., 2n=4x=32) cultivars, Rheinische Schattenmorelle (RS) and Erdi Botermo (EB), were constructed from 86 progeny from the cross RS�EB. The RS linkage map consists of 126 single-dose restriction fragment (SDRF, Wu et al. 1992) markers assigned to 19 linkage groups covering 461.6 cM. The EB linkage map has 95 SDRF markers assigned to 16 linkage groups covering 279.2 cM. Fifty three markers mapped in both parents were used as bridges between both maps and 13 sets of homologous linkage groups were identified. Homoeologous relationships among the sour cherry linkage groups could not be determined because only 15 probes identified duplicate loci. Fifty nine of the markers on the linkage maps were detected with probes used in other Prunus genetic linkage maps. Four of the sour cherry linkage groups may be homologous with four of the eight genetic linkage groups identified in peach and...
Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by re... more Use of dwarfing rootstocks has dramatically increased the profitability of fruit production by reducing production costs, reduced chemical use and higher density plantings. Despite the importance of rootstock-induced dwarfing, the cause of this phenomenon is not known. Using two commercially available graft combinations consisting of a sweet cherry scion, 'Bing', on a dwarfing rootstock (Gi5) or a semi-vigorous rootstock (Gi6), we discovered that the difference in grafted tree height was due to a significantly earlier cessation of terminal meristem growth of the scion on Gi5 compared to Gi6 rootstock, rather than shorter metamer length. We then carried out cDNA-AFLP analysis to investigate differential gene expression between the two graft combinations. Transcript-derived fragments (TDFs) identified as differentially expressed were cloned and printed on microarrays for further confirmation of the differential expression. A total of 99 TDFs were identified as differentially expressed between the 'Bing'/Gi5 and 'Bing'/Gi6 samples, including genes involved in transcription regulation, brassinosteroid signaling, flavonoid metabolism and cell wall biosynthesis or modification. Rootstock vigor has a significant effect on gene expression at the scion and the graft union. Timing of the differential gene expression in the dwarf trees coincides with the earlier cessation of terminal shoot growth, suggesting that these differentially expressed genes may be involved in the dwarfing phenomenon.
... intergenomic recom-bination. These results are consistent with previous allozyme inheritance ... more ... intergenomic recom-bination. These results are consistent with previous allozyme inheritance and cytogenetic data in sour cherry sugges-ting that 2 : 1 ratios are prevalent along with occasional intergenomic recombination. A 2 : 1 ...
... Kazuo Ikeda · Boris Igic · Koichiro Ushijima · Hisayo Yamane · Nathanael R. Hauck · Ryohei Na... more ... Kazuo Ikeda · Boris Igic · Koichiro Ushijima · Hisayo Yamane · Nathanael R. Hauck · Ryohei Nakano · Hidenori Sassa · Amy F. Iezzoni · Joshua R. Kohn ... First, we compared the null models that do not allow for positive selection (models M0 and M1) with successively more ...
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