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Amy F Iezzoni - One of the best experts on this subject based on the ideXlab platform.
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The Cherry 6+9K SNP array: a cost-effective improvement to the Cherry 6K SNP array for genetic studies.
Scientific reports, 2020Co-Authors: Stijn Vanderzande, Amy F Iezzoni, Ping Zheng, Lichun Cai, Goran Barać, Ksenija Gasic, Dorrie Main, Cameron PeaceAbstract:Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in Cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb Cherry whole genome sequence. For sweet Cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet Cherry, the fruticosa subgenome of sour Cherry, and Cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet Cherry and the avium and the fruticosa subgenomes of sour Cherry, respectively. For sweet Cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original Cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in Cherry.
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A DNA test for fruit flesh color in tetraploid sour Cherry (Prunus cerasus L.)
Molecular Breeding, 2015Co-Authors: Travis Stegmeir, Audrey Sebolt, Lichun Cai, Fransiska R. A. Basundari, Amy F IezzoniAbstract:Fruit flesh color in tetraploid sour Cherry ( Prunus cerasus ) is an important market-driven trait in the USA where the fruit from the dominant cultivar has brilliant red skin but clear/yellow flesh. This brilliant red color in the processed products differentiates products from sour cherries grown in the USA compared to those in Europe where the cultivars predominantly have dark purple-red flesh. In sweet Cherry ( P. avium ), red skin and flesh colors were shown to be controlled by a major MYB10 -associated locus. Sour Cherry, which is derived from sweet Cherry and ground Cherry ( P. fruticosa ), also exhibits a range of flesh colors, but the genetic control of flesh color is not known. Our objectives were to test the hypothesis that the MYB10 locus controls flesh color in sour Cherry and develop a predictive DNA test for dark purple-red flesh color. Pedigree-linked sour Cherry plant materials were phenotyped for flesh color. Thirteen haplotypes for the sour Cherry MYB10 region were distinguished based on markers scored from the use of the Cherry 6K Infinium^® II SNP array. Six haplotypes were significantly associated with variation in flesh color, supporting a role for MYB10 in controlling flesh color variation in sour Cherry. A simple sequence repeat primer pair, designed from the peach genome sequence near MYB10 , amplified a fragment that uniquely identified the haplotype that was associated with the darkest purple-red flesh color. This marker can be used for marker-assisted breeding to identify individuals that are predicted to have dark purple-red flesh.
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self compatibility and incompatibility in tetraploid sour Cherry prunus cerasus l
Sexual Plant Reproduction, 2002Co-Authors: Nathanael R Hauck, Hisayo Yamane, Amy F IezzoniAbstract:Gametophytic self-incompatibility (GSI) typically "breaks down" due to polyploidy in many Solanaceous species, resulting in self-compatible (SC) tetraploid individuals. However, sour Cherry (Prunuscerasus L.), a tetraploid species resulting from hybridization of the diploid sweet Cherry (P. avium L.) and the tetraploid ground Cherry (P.fruticosa Pall.), is an exception, consisting of both self-incompatible (SI) and SC individuals. Since sweet Cherry exhibits GSI with 13 S-ribonucleases (S-RNases) identified as the stylar S-locus product, the objectives were to compare sweet and sour Cherry S-allele function, S-RNase sequences and linkage map location as initial steps towards understanding the genetic basis of SI and SC in sour Cherry. S-RNases from two sour Cherry cultivars that were the parents of a linkage mapping population were cloned and sequenced. The sequences of two S-RNases were identical to those of sweet Cherry S-RNases, whereas three other S-RNases had unique sequences. One of the S-RNases mapped to the Prunus linkage group 6, similar to its location in sweet Cherry and almond, whereas two other S-RNases were linked to each other but were unlinked to any other markers. Interspecific crosses between sweet and sour Cherry demonstrated that GSI exists in sour Cherry and that the recognition of common S-alleles has been maintained in spite of polyploidization. It is hypothesized that self-compatibility in sour Cherry is caused by the existence of non-functional S-RNases and pollen S-genes that may have arisen from natural mutations.
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polymorphic dna markers in black Cherry prunus serotina are identified using sequences from sweet Cherry peach and sour Cherry
Journal of the American Society for Horticultural Science, 2000Co-Authors: Suzanne L Downey, Amy F IezzoniAbstract:ADDITIONAL INDEX WORDS. microsatellites, simple sequence repeats, chloroplast sequence ABSTRACT. Black Cherry (Prunus serotina Ehrh.) is a common secondary forest species with a wide endemic distribution ranging from Nova Scotia south into Mexico, Ecuador, and Peru. Although planted in the United States for its valued lumber, black Cherry is essentially a wild species with small fruit ≈6 to 10 mm in diameter. In contrast, in Mexico and Ecuador, domesticates of this species called Capulin, have much larger (2 to 2.5 cm in diameter) edible fruit. To date, no studies of th e genetic diversity within North American black Cherry or the ancestral origin of the Capulin types have been conducted. Simple sequence repeats (SSRs, also termed microsatellites) would be the marker of choice for such genetic diversity studies due to their hypervariability; however, generation of these sequence-based markers is expensive. Therefore, our objective was to determine if markers already identified in other Prunus L. species would be informative in black Cherry. The black Cherry germplasm screened consisted of selections originating from Michigan, Mexico, and Ecuador. A chloroplast DNA marker, originally generated from sour Cherry (P. cerasus L.), amplified three different sized products in black Cherry. Four of the eight nuclear SSR markers tested from peach (P. persica L. Batsch (Peach Group)), sour Cherry, and sweet Cherry ( P. avium L.) also amplified and identified polymorphic markers. Together these four primer pairs resolved 54 putative alleles for the 66 black Cherry accessions assayed. Success of the sweet Cherry, peach, and sour Cherry primers in identification of polymorphic markers in black Cherry indicates it should be possible to use these markers for comprehensive molecular genetic studies in black Cherry.
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allozyme inheritance in tetraploid sour Cherry prunus cerasus l
Journal of the American Society for Horticultural Science, 1993Co-Authors: J A Beaver, Amy F IezzoniAbstract:Inheritance for seven enzyme loci was determined in seeds produced from crosses and self-pollinations involving four sour Cherry parents and one open-pollinated ground Cherry (P. fruticosa Pall.) parent. Segregation data were used to identify allozymes and determine whether sour Cherry is a naturally occurring allo- or autotetraploid. Three allozymes were identified at the 6-Pgd-1 locus, and two were identified at each of the following loci: Pgi-2, Lap-1, Adh-1, Idh-2, Pgm- 2, and 6-Pgd-2. Segregating allozyme patterns for the diagnostic loci Idh-2, Pgm-2, 6-Pgd-1, and 6-Pgd-2 tit disomic inheritance models and thus confirmed the allotetraploid hypothesis for sour Cherry. Chi-square tests of independence between loci indicated that Pgi-2, Adh-1, Idh-2, 6-Pgd-1, and 6-Pgd-2 were not linked. Sour Cherry (2n = 4x = 32) is a tetraploid, with P. avium L. (sweet Cherry, 2n = 2x = 16) and P. fruticosa Pall. (ground Cherry, 2n = 4x = 32) proposed as its progenitor species (Olden and Nybom, 1968). The distributions of these three species overlap in southeastern Europe and southwestern Asia (Hedrick, 1915). It remains unclear whether sour Cherry is an allotetraploid or an autotetraploid. In support of an allotetraploid origin, Olden and Nybom (1968) hybridized ground Cherry with several cultivars of sweet Cherry and produced interspecific hybrids that were mor- phologically and chemotaxonomically intermediate to the parents and strikingly similar to sour Cherry. Sour Cherry germplasm in the Michigan State Univ. collection exhibits a range in morphology from ground Cherry to sweet Cherry as demonstrated by principal component analysis (Hillig and Iezzoni, 1988). Other authors have suggested that sour Cherry is an autotetra- ploid (Raptopoulus, 1941) or a segmental allotetraploid (Galletta, 1959) based on cytogenetic criteria. If sour Cherry is an allotetra- ploid, meiosis I should result in the formation of 16 bivalents. Often, only 14 to 15 bivalents and two to four univalents are observed. Quadrivalents also occur at a low frequency (Galletta, 1959; Hruby, 1939). Although cytological evidence is useful for understanding polyploidy, meiotic chromosomal configurations cannot be used as the sole criterion to determine polyploid type because both allo- and autotetraploids may exhibit regular bivalent pairing and a lack of multivalent formation (Krebs and Hancock, 1989; Soltis and Rieseberg, 1986).
Lichun Cai - One of the best experts on this subject based on the ideXlab platform.
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The Cherry 6+9K SNP array: a cost-effective improvement to the Cherry 6K SNP array for genetic studies.
Scientific reports, 2020Co-Authors: Stijn Vanderzande, Amy F Iezzoni, Ping Zheng, Lichun Cai, Goran Barać, Ksenija Gasic, Dorrie Main, Cameron PeaceAbstract:Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in Cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb Cherry whole genome sequence. For sweet Cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet Cherry, the fruticosa subgenome of sour Cherry, and Cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet Cherry and the avium and the fruticosa subgenomes of sour Cherry, respectively. For sweet Cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original Cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in Cherry.
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A fruit firmness QTL identified on linkage group 4 in sweet Cherry (Prunus avium L.) is associated with domesticated and bred germplasm.
Scientific Reports, 2019Co-Authors: Lichun Cai, Teresa Barreneche, José Quero-garcia, Elisabeth Dirlewanger, Christopher Saski, Amy IezzoniAbstract:Fruit firmness is an important market driven trait in sweet Cherry (Prunus avium L.) where the desirable increase in fruit firmness is associated with landrace and bred cultivars. The aim of this work was to investigate the genetic basis of fruit firmness using plant materials that include wild Cherry (syn. mazzard), landrace and bred sweet Cherry germplasm. A major QTL for fruit firmness, named qP-FF4.1, that had not previously been reported, was identified in three sweet Cherry populations. Thirteen haplotypes (alleles) associated with either soft or firm fruit were identified for qP-FF4.1 in the sweet Cherry germplasm, and the "soft" alleles were dominant over the "firm" alleles. The finding that sweet Cherry individuals that are homozygous for the "soft" alleles for qP-FF4.1 are exclusively mazzards and that the vast majority of the bred cultivars are homozygous for "firm" alleles suggests that this locus is a signature of selection. Candidate genes related to plant cell wall modification and various plant hormone signaling pathways were identified, with an expansin gene being the most promising candidate. These results advance our understanding of the genetic basis of fruit firmness and will help to enable the use of DNA informed breeding for this trait in sweet Cherry breeding programs.
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Prediction of genetic value for sweet Cherry fruit maturity among environments using a 6K SNP array
Nature Publishing Group, 2019Co-Authors: Craig M. Hardner, Teresa Barreneche, Stijn Vanderzande, Lichun Cai, José Quero-garcia, Ben J. Hayes, Satish Kumar, Julia Piaskowski, José Antonio Campoy, Daniela GiovanniniAbstract:Genetics: Sweet news for Cherry breeders Or Genetics: Cherry-ripening is predictable in new environments The fruiting season of a Cherry is short and sweet, but at least it’s relatively consistent across different environments, a new genetic analysis suggests. The development of additional early- and late-maturing sweet Cherry cultivars is a major objective for Cherry-breeders, but the influence of the environment on the timing of fruit maturity—which could reduce the accuracy of selective breeding efforts - was unclear. So, Craig Hardner at the University of Queensland in St Lucia and colleagues used DNA markers to model relationships among individuals and examined the dates at which their fruit ripened at four different locations in Europe and the USA across two seasons. The timing of fruit maturity was relatively stable between related individuals across similar environments, suggesting that new Cherry cultivars could be developed without having to test them at multiple sites
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A DNA test for fruit flesh color in tetraploid sour Cherry (Prunus cerasus L.)
Molecular Breeding, 2015Co-Authors: Travis Stegmeir, Audrey Sebolt, Lichun Cai, Fransiska R. A. Basundari, Amy F IezzoniAbstract:Fruit flesh color in tetraploid sour Cherry ( Prunus cerasus ) is an important market-driven trait in the USA where the fruit from the dominant cultivar has brilliant red skin but clear/yellow flesh. This brilliant red color in the processed products differentiates products from sour cherries grown in the USA compared to those in Europe where the cultivars predominantly have dark purple-red flesh. In sweet Cherry ( P. avium ), red skin and flesh colors were shown to be controlled by a major MYB10 -associated locus. Sour Cherry, which is derived from sweet Cherry and ground Cherry ( P. fruticosa ), also exhibits a range of flesh colors, but the genetic control of flesh color is not known. Our objectives were to test the hypothesis that the MYB10 locus controls flesh color in sour Cherry and develop a predictive DNA test for dark purple-red flesh color. Pedigree-linked sour Cherry plant materials were phenotyped for flesh color. Thirteen haplotypes for the sour Cherry MYB10 region were distinguished based on markers scored from the use of the Cherry 6K Infinium^® II SNP array. Six haplotypes were significantly associated with variation in flesh color, supporting a role for MYB10 in controlling flesh color variation in sour Cherry. A simple sequence repeat primer pair, designed from the peach genome sequence near MYB10 , amplified a fragment that uniquely identified the haplotype that was associated with the darkest purple-red flesh color. This marker can be used for marker-assisted breeding to identify individuals that are predicted to have dark purple-red flesh.
Travis Stegmeir - One of the best experts on this subject based on the ideXlab platform.
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A DNA test for fruit flesh color in tetraploid sour Cherry (Prunus cerasus L.)
Molecular Breeding, 2015Co-Authors: Travis Stegmeir, Audrey Sebolt, Lichun Cai, Fransiska R. A. Basundari, Amy F IezzoniAbstract:Fruit flesh color in tetraploid sour Cherry ( Prunus cerasus ) is an important market-driven trait in the USA where the fruit from the dominant cultivar has brilliant red skin but clear/yellow flesh. This brilliant red color in the processed products differentiates products from sour cherries grown in the USA compared to those in Europe where the cultivars predominantly have dark purple-red flesh. In sweet Cherry ( P. avium ), red skin and flesh colors were shown to be controlled by a major MYB10 -associated locus. Sour Cherry, which is derived from sweet Cherry and ground Cherry ( P. fruticosa ), also exhibits a range of flesh colors, but the genetic control of flesh color is not known. Our objectives were to test the hypothesis that the MYB10 locus controls flesh color in sour Cherry and develop a predictive DNA test for dark purple-red flesh color. Pedigree-linked sour Cherry plant materials were phenotyped for flesh color. Thirteen haplotypes for the sour Cherry MYB10 region were distinguished based on markers scored from the use of the Cherry 6K Infinium^® II SNP array. Six haplotypes were significantly associated with variation in flesh color, supporting a role for MYB10 in controlling flesh color variation in sour Cherry. A simple sequence repeat primer pair, designed from the peach genome sequence near MYB10 , amplified a fragment that uniquely identified the haplotype that was associated with the darkest purple-red flesh color. This marker can be used for marker-assisted breeding to identify individuals that are predicted to have dark purple-red flesh.
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Cherry leaf spot resistance in Cherry (Prunus) is associated with a quantitative trait locus on linkage group 4 inherited from P. canescens
Molecular Breeding, 2014Co-Authors: Travis Stegmeir, Mirko Schuster, Audrey Sebolt, Umesh Rosyara, George W. Sundin, Amy IezzoniAbstract:Cherry leaf spot (CLS), caused by the fungal pathogen Blumeriella jaapii (Rehm) Arx (telomorph Phloeosporella padi [Lib.] Arx), is a major disease in all humid Cherry-growing regions worldwide causing leaf yellowing and defoliation. The diploid Prunus species, P. canescens , had previously been identified as a source of CLS resistance. Therefore, the objective of this study was to identify quantitative trait loci (QTL) for CLS resistance derived from P. canescens in both diploid sweet Cherry ( P. avium ) and tetraploid sour Cherry ( P. cerasus ). Because of the simpler genetics of diploid Cherry, the initial investigation was done with P. canescens -derived materials from crosses with sweet Cherry, followed by validation using P. canescens -derived plant materials from sour Cherry. A major QTL controlling P. canescens -derived CLS resistance, named CLSR_G4, was identified on linkage group 4 in sweet Cherry and validated in sour Cherry. All CLS-resistant individuals had one P. canescens -derived allele for CLSR_G4 . A second QTL may be necessary for CLS resistance as one-fifth–one-third of the progeny individuals with the P. canescens -derived allele for CLSR_G4 were susceptible.
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development and evaluation of a genome wide 6k snp array for diploid sweet Cherry and tetraploid sour Cherry
PLOS ONE, 2012Co-Authors: Cameron Peace, Travis Stegmeir, Audrey Sebolt, Umesh Rosyara, Dorrie Main, Nahla V Bassil, Stephen P Ficklin, Barbara Gilmore, Cindy Lawley, Todd C MocklerAbstract: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® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour Cherry genomes. SNPs were developed for each sour Cherry subgenome by using minor allele frequency in the sour Cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet Cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) Cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet Cherry, 13% of these originally developed for sour Cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour Cherry, one third of these being originally developed for sweet Cherry. This publicly available genomics resource represents a significant advance in Cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.
Cameron Peace - One of the best experts on this subject based on the ideXlab platform.
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The Cherry 6+9K SNP array: a cost-effective improvement to the Cherry 6K SNP array for genetic studies.
Scientific reports, 2020Co-Authors: Stijn Vanderzande, Amy F Iezzoni, Ping Zheng, Lichun Cai, Goran Barać, Ksenija Gasic, Dorrie Main, Cameron PeaceAbstract:Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in Cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb Cherry whole genome sequence. For sweet Cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet Cherry, the fruticosa subgenome of sour Cherry, and Cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet Cherry and the avium and the fruticosa subgenomes of sour Cherry, respectively. For sweet Cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original Cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in Cherry.
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development and evaluation of a genome wide 6k snp array for diploid sweet Cherry and tetraploid sour Cherry
PLOS ONE, 2012Co-Authors: Cameron Peace, Travis Stegmeir, Audrey Sebolt, Umesh Rosyara, Dorrie Main, Nahla V Bassil, Stephen P Ficklin, Barbara Gilmore, Cindy Lawley, Todd C MocklerAbstract: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® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour Cherry genomes. SNPs were developed for each sour Cherry subgenome by using minor allele frequency in the sour Cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet Cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) Cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet Cherry, 13% of these originally developed for sour Cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour Cherry, one third of these being originally developed for sweet Cherry. This publicly available genomics resource represents a significant advance in Cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.
Audrey Sebolt - One of the best experts on this subject based on the ideXlab platform.
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A DNA test for fruit flesh color in tetraploid sour Cherry (Prunus cerasus L.)
Molecular Breeding, 2015Co-Authors: Travis Stegmeir, Audrey Sebolt, Lichun Cai, Fransiska R. A. Basundari, Amy F IezzoniAbstract:Fruit flesh color in tetraploid sour Cherry ( Prunus cerasus ) is an important market-driven trait in the USA where the fruit from the dominant cultivar has brilliant red skin but clear/yellow flesh. This brilliant red color in the processed products differentiates products from sour cherries grown in the USA compared to those in Europe where the cultivars predominantly have dark purple-red flesh. In sweet Cherry ( P. avium ), red skin and flesh colors were shown to be controlled by a major MYB10 -associated locus. Sour Cherry, which is derived from sweet Cherry and ground Cherry ( P. fruticosa ), also exhibits a range of flesh colors, but the genetic control of flesh color is not known. Our objectives were to test the hypothesis that the MYB10 locus controls flesh color in sour Cherry and develop a predictive DNA test for dark purple-red flesh color. Pedigree-linked sour Cherry plant materials were phenotyped for flesh color. Thirteen haplotypes for the sour Cherry MYB10 region were distinguished based on markers scored from the use of the Cherry 6K Infinium^® II SNP array. Six haplotypes were significantly associated with variation in flesh color, supporting a role for MYB10 in controlling flesh color variation in sour Cherry. A simple sequence repeat primer pair, designed from the peach genome sequence near MYB10 , amplified a fragment that uniquely identified the haplotype that was associated with the darkest purple-red flesh color. This marker can be used for marker-assisted breeding to identify individuals that are predicted to have dark purple-red flesh.
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Cherry leaf spot resistance in Cherry (Prunus) is associated with a quantitative trait locus on linkage group 4 inherited from P. canescens
Molecular Breeding, 2014Co-Authors: Travis Stegmeir, Mirko Schuster, Audrey Sebolt, Umesh Rosyara, George W. Sundin, Amy IezzoniAbstract:Cherry leaf spot (CLS), caused by the fungal pathogen Blumeriella jaapii (Rehm) Arx (telomorph Phloeosporella padi [Lib.] Arx), is a major disease in all humid Cherry-growing regions worldwide causing leaf yellowing and defoliation. The diploid Prunus species, P. canescens , had previously been identified as a source of CLS resistance. Therefore, the objective of this study was to identify quantitative trait loci (QTL) for CLS resistance derived from P. canescens in both diploid sweet Cherry ( P. avium ) and tetraploid sour Cherry ( P. cerasus ). Because of the simpler genetics of diploid Cherry, the initial investigation was done with P. canescens -derived materials from crosses with sweet Cherry, followed by validation using P. canescens -derived plant materials from sour Cherry. A major QTL controlling P. canescens -derived CLS resistance, named CLSR_G4, was identified on linkage group 4 in sweet Cherry and validated in sour Cherry. All CLS-resistant individuals had one P. canescens -derived allele for CLSR_G4 . A second QTL may be necessary for CLS resistance as one-fifth–one-third of the progeny individuals with the P. canescens -derived allele for CLSR_G4 were susceptible.
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development and evaluation of a genome wide 6k snp array for diploid sweet Cherry and tetraploid sour Cherry
PLOS ONE, 2012Co-Authors: Cameron Peace, Travis Stegmeir, Audrey Sebolt, Umesh Rosyara, Dorrie Main, Nahla V Bassil, Stephen P Ficklin, Barbara Gilmore, Cindy Lawley, Todd C MocklerAbstract: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® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour Cherry genomes. SNPs were developed for each sour Cherry subgenome by using minor allele frequency in the sour Cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet Cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) Cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet Cherry, 13% of these originally developed for sour Cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour Cherry, one third of these being originally developed for sweet Cherry. This publicly available genomics resource represents a significant advance in Cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.