... Application of tissue culture and gene transfer methods have been successful. A clear differe... more ... Application of tissue culture and gene transfer methods have been successful. A clear difference in fluorescence between negative controls and the 63 regenerants obtained after cotyledon inoculation with A. tumefaciens carrying the GUS gene was detected in three plants. ...
Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is ... more Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four Prunus species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upr...
In the southeastern United States, Armillaria root rot (ARR) is caused by Desarmillaria tabescens... more In the southeastern United States, Armillaria root rot (ARR) is caused by Desarmillaria tabescens and has become the primary cause of premature mortality in peach orchards. Most rootstocks used in commercial orchards are susceptible and management options are limited. A postinfection practice known as root-collar excavation (RCE), which involves permanent removal of the soil from the base of the trunk, has been shown to improve yields and prolong the productive life of symptomatic trees. However, symptomatic trees already have an advanced infection at the base of the trunk. This study evaluated the efficacy of preventative RCE on the progression of tree mortality in two orchards that were planted in infested replant sites. To provide convincing data for growers, the study was carried out in a commercial orchard and an experimental orchard for 8 years. Furthermore, representative enterprise budgets and net present value (NPV) analysis were utilized to compare the profitability of the...
Bud break timing in peach [Prunus persica (L.) Batsch] is determined by the sequential fulfillmen... more Bud break timing in peach [Prunus persica (L.) Batsch] is determined by the sequential fulfillment of a chilling requirement (CR) and a heat requirement (HR) for development. Genotypic variation in CR has been well characterized in peach. Adapting peaches to low chilling environment through reduced CR can make them susceptible to crop destroying spring frosts, if bloom occurs too early. Potential variation in HR between accessions has received less attention due to the methodological difficulty in assessing HR independently of CR. HR could vary in the magnitude of growing degree hours (GDHs) and/or the base temperature at which GDH accumulation begins. Characterizing HR traits in peach accessions could allow improved bloom time modeling and selection of phenotypes with improved spring frost avoidance through delayed bloom. We estimated GDH and apparent base temperature for floral bud break by observing time to floral bud break at several constant forcing temperatures. We evaluated 5...
NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpr... more NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpretation Lon Phan, NIH/NLM/NCBI, Bethesda, MD The Variation Portal site (http://www.ncbi.nlm.nih.gov/variation/) at NCBI is a gateway for users to access databases and tools that can be used in the fields of genomics, genetics, and management of variation data for human and over 300 organisms. There are five NCBI databases that archive, analyze, display, and report information about germline and somatic variants and the relationship of these variants to phenotype and clinical significance. dbSNP houses short variations; dbVar houses large scale genomic variants; the database of Genotypes and Phenotypes (dbGaP) houses genotypes and phenotypes associations; ClinVar houses reported relationships between human variation and phenotypes; and the Genetic Testing Registry (GTR) provides a central location for accessing inherited and somatic genetic variations that are being tested for a specific ...
Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach d... more Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. Results We developed simple, accurate, and efficient Ppe.XapF DNA tests based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit and cull at the greenhouse stage. The objective of this research was to validate newly developed Ppe.XapF DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Conclusion Our study confirms that only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, are needed to distinguish between susc...
Background Environmental adaptation and expanding harvest seasons are primary goals of most peach... more Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and...
Bacterial spot [Xanthomonas arboricola pv. pruni (Xap)] is a serious disease of Prunus spp. that ... more Bacterial spot [Xanthomonas arboricola pv. pruni (Xap)] is a serious disease of Prunus spp. that causes premature defoliation, weak vigor of the plant, unmarketable fruit, and decline in production. Effective control methods are lacking; anti-bacterial sprays (copper-based compounds and oxytetracycline), are only partially effective in a low to medium disease pressure year and not effective at all in a high disease pressure year. Incorporating bacterial spot resistance in newly developed peach cultivars is a more promising control measure and has been a key trait of interest in peach breeding programs. Eight functional alleles, four at each QTL (Xap1 and Xap6, R1, R2, I and S respectively) associated with Xap resistance in peach fruit, have been identified in the RosBREED peach Crop Reference Set (CRS). The University of Arkansas breeding material comprises all detected Xap alleles and this program has never sprayed to control the disease in the 50-year effort. Thus selections again...
Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for... more Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for the adoption of marker-assisted breeding. Peach serves as a well resourced model fruit crop while cherry stands to directly benefit from research advances in its relative. Three “jewels in the genome” for peach and cherry are the current targets for application in breeding. Peach breeders select cultivar candidates that meet their criteria for fruit texture (melting vs. non-melting flesh) and pit adherence to the flesh (clingstone vs. freestone). These phenotypes are explained by genes at the Freestone-Melting flesh locus on peach chromosome 4 that contains the endoPG gene (a gene encoding a cell wall pectin-cleaving enzyme called endopolygalactouronase that plays a major role in fruit softening). Genetic tests are available for the functional alleles that can be used to predict whether peach fruit will be freestone melting flesh (FMF), clingstone melting flesh (CMF), clingstone non-mel...
Molecular techniques are becoming more commonly utilized in peach [Prunus persica (L.) Batsch] br... more Molecular techniques are becoming more commonly utilized in peach [Prunus persica (L.) Batsch] breeding programs for several purposes: to screen genotypes as juveniles before they produce fruit; to discard individuals that do not carry certain desired alleles; and to select parents for crossing based on specific alleles. Ultimately, this application will increase breeding efficiency and reduce operational costs, labor, and land. These new techniques are precise and when correctly applied can lead to accurate and useful results, but they only work if accurate and standardized phenotyping procedures are used over multiple years. Within the Arkansas peach breeding program a wide and unique range of flesh types are found, including melting-flesh (MF), non-melting flesh (NMF), non-softening flesh (NSF), and slow-melting flesh (SMF). These flesh types have different textures, firmness, and postharvest performance potential. As a part of the RosBREED project (www.rosbreed.org) the Universi...
Skin blush is an important trait for marketing peaches. The red skin pigmentation develops throug... more Skin blush is an important trait for marketing peaches. The red skin pigmentation develops through the flavonoid and anthocyanin pathways, and both genetic and environmental stimuli, and their interaction, control the regulation of these pathways. Blush is under polygenic control with one major QTL locus and several minor QTL loci throughout the genome. A study of one major QTL locus, Blush.Pp.ZC-3.1, associated with blush in peach discerned functional alleles/haplotypes with high/low probability of producing high/low blush phenotypes. The U.S. Prunus germplasm under the RosBREED collaborative effort was phenotyped in 2011 and 2012 for the percentage of blush covering the fruit skin using a scale from 0–5; 0 indicating no blush and 5 indicating full red surface color. High resolution genome scanning of RosBREED material provided necessary DNA information for determining distribution of high/low blush functional alleles/haplotypes in breeding germplasm. Four functional alleles define...
Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach d... more Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. Results We developed simple, accurate, and efficient Ppe.XapF DNA tests based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit and cull at the greenhouse stage. The objective of this research was to validate newly developed Ppe.XapF DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Conclusion Our study confirms that only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, are needed to distinguish between susc...
In-ovule embryo culture was used for obtaining seedlings from immature peach embryos 1-4 mm in le... more In-ovule embryo culture was used for obtaining seedlings from immature peach embryos 1-4 mm in length. Rapid micropropagation of Redhaven cultivar and B 52/2 vineyard peach selection was achieved by shoot tip proliferation. The two-stage rooting system, with a short auxin exposure followed by transfer to growth regulator-free half-strength basal media, proved to work much better than any other system published so far. Cotyledon regeneration was combined with Agrobacterium mediated genetic transformation. A clear difference in fluorescence between negative controls and the regenerants obtained after cotyledon inoculation with A. tumefaciens carrying the GUS gene was detected after 24 h indicating the production of chimeric peach plants.
... Application of tissue culture and gene transfer methods have been successful. A clear differe... more ... Application of tissue culture and gene transfer methods have been successful. A clear difference in fluorescence between negative controls and the 63 regenerants obtained after cotyledon inoculation with A. tumefaciens carrying the GUS gene was detected in three plants. ...
Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is ... more Bud dormancy is a genotype-dependent mechanism observed in Prunus species in which bud growth is inhibited, and the accumulation of a specific amount of chilling (endodormancy) and heat (ecodormancy) is necessary to resume growth and reach flowering. We analyzed publicly available transcriptome data from fifteen cultivars of four Prunus species (almond, apricot, peach, and sweet cherry) sampled at endo- and ecodormancy points to identify conserved genes and pathways associated with dormancy control in the genus. A total of 13,018 genes were differentially expressed during dormancy transitions, of which 139 and 223 were of interest because their expression profiles correlated with endo- and ecodormancy, respectively, in at least one cultivar of each species. The endodormancy-related genes comprised transcripts mainly overexpressed during chilling accumulation and were associated with abiotic stresses, cell wall modifications, and hormone regulation. The ecodormancy-related genes, upr...
In the southeastern United States, Armillaria root rot (ARR) is caused by Desarmillaria tabescens... more In the southeastern United States, Armillaria root rot (ARR) is caused by Desarmillaria tabescens and has become the primary cause of premature mortality in peach orchards. Most rootstocks used in commercial orchards are susceptible and management options are limited. A postinfection practice known as root-collar excavation (RCE), which involves permanent removal of the soil from the base of the trunk, has been shown to improve yields and prolong the productive life of symptomatic trees. However, symptomatic trees already have an advanced infection at the base of the trunk. This study evaluated the efficacy of preventative RCE on the progression of tree mortality in two orchards that were planted in infested replant sites. To provide convincing data for growers, the study was carried out in a commercial orchard and an experimental orchard for 8 years. Furthermore, representative enterprise budgets and net present value (NPV) analysis were utilized to compare the profitability of the...
Bud break timing in peach [Prunus persica (L.) Batsch] is determined by the sequential fulfillmen... more Bud break timing in peach [Prunus persica (L.) Batsch] is determined by the sequential fulfillment of a chilling requirement (CR) and a heat requirement (HR) for development. Genotypic variation in CR has been well characterized in peach. Adapting peaches to low chilling environment through reduced CR can make them susceptible to crop destroying spring frosts, if bloom occurs too early. Potential variation in HR between accessions has received less attention due to the methodological difficulty in assessing HR independently of CR. HR could vary in the magnitude of growing degree hours (GDHs) and/or the base temperature at which GDH accumulation begins. Characterizing HR traits in peach accessions could allow improved bloom time modeling and selection of phenotypes with improved spring frost avoidance through delayed bloom. We estimated GDH and apparent base temperature for floral bud break by observing time to floral bud break at several constant forcing temperatures. We evaluated 5...
NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpr... more NCBI Variation Portal: Databases and Tools for Genetic Variation Discovery, Analysis, and Interpretation Lon Phan, NIH/NLM/NCBI, Bethesda, MD The Variation Portal site (http://www.ncbi.nlm.nih.gov/variation/) at NCBI is a gateway for users to access databases and tools that can be used in the fields of genomics, genetics, and management of variation data for human and over 300 organisms. There are five NCBI databases that archive, analyze, display, and report information about germline and somatic variants and the relationship of these variants to phenotype and clinical significance. dbSNP houses short variations; dbVar houses large scale genomic variants; the database of Genotypes and Phenotypes (dbGaP) houses genotypes and phenotypes associations; ClinVar houses reported relationships between human variation and phenotypes; and the Genetic Testing Registry (GTR) provides a central location for accessing inherited and somatic genetic variations that are being tested for a specific ...
Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach d... more Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. Results We developed simple, accurate, and efficient Ppe.XapF DNA tests based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit and cull at the greenhouse stage. The objective of this research was to validate newly developed Ppe.XapF DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Conclusion Our study confirms that only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, are needed to distinguish between susc...
Background Environmental adaptation and expanding harvest seasons are primary goals of most peach... more Background Environmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs. Results Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and...
Bacterial spot [Xanthomonas arboricola pv. pruni (Xap)] is a serious disease of Prunus spp. that ... more Bacterial spot [Xanthomonas arboricola pv. pruni (Xap)] is a serious disease of Prunus spp. that causes premature defoliation, weak vigor of the plant, unmarketable fruit, and decline in production. Effective control methods are lacking; anti-bacterial sprays (copper-based compounds and oxytetracycline), are only partially effective in a low to medium disease pressure year and not effective at all in a high disease pressure year. Incorporating bacterial spot resistance in newly developed peach cultivars is a more promising control measure and has been a key trait of interest in peach breeding programs. Eight functional alleles, four at each QTL (Xap1 and Xap6, R1, R2, I and S respectively) associated with Xap resistance in peach fruit, have been identified in the RosBREED peach Crop Reference Set (CRS). The University of Arkansas breeding material comprises all detected Xap alleles and this program has never sprayed to control the disease in the 50-year effort. Thus selections again...
Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for... more Peach and cherry are the two Prunus stone fruit crops that are currently targeted in RosBREED for the adoption of marker-assisted breeding. Peach serves as a well resourced model fruit crop while cherry stands to directly benefit from research advances in its relative. Three “jewels in the genome” for peach and cherry are the current targets for application in breeding. Peach breeders select cultivar candidates that meet their criteria for fruit texture (melting vs. non-melting flesh) and pit adherence to the flesh (clingstone vs. freestone). These phenotypes are explained by genes at the Freestone-Melting flesh locus on peach chromosome 4 that contains the endoPG gene (a gene encoding a cell wall pectin-cleaving enzyme called endopolygalactouronase that plays a major role in fruit softening). Genetic tests are available for the functional alleles that can be used to predict whether peach fruit will be freestone melting flesh (FMF), clingstone melting flesh (CMF), clingstone non-mel...
Molecular techniques are becoming more commonly utilized in peach [Prunus persica (L.) Batsch] br... more Molecular techniques are becoming more commonly utilized in peach [Prunus persica (L.) Batsch] breeding programs for several purposes: to screen genotypes as juveniles before they produce fruit; to discard individuals that do not carry certain desired alleles; and to select parents for crossing based on specific alleles. Ultimately, this application will increase breeding efficiency and reduce operational costs, labor, and land. These new techniques are precise and when correctly applied can lead to accurate and useful results, but they only work if accurate and standardized phenotyping procedures are used over multiple years. Within the Arkansas peach breeding program a wide and unique range of flesh types are found, including melting-flesh (MF), non-melting flesh (NMF), non-softening flesh (NSF), and slow-melting flesh (SMF). These flesh types have different textures, firmness, and postharvest performance potential. As a part of the RosBREED project (www.rosbreed.org) the Universi...
Skin blush is an important trait for marketing peaches. The red skin pigmentation develops throug... more Skin blush is an important trait for marketing peaches. The red skin pigmentation develops through the flavonoid and anthocyanin pathways, and both genetic and environmental stimuli, and their interaction, control the regulation of these pathways. Blush is under polygenic control with one major QTL locus and several minor QTL loci throughout the genome. A study of one major QTL locus, Blush.Pp.ZC-3.1, associated with blush in peach discerned functional alleles/haplotypes with high/low probability of producing high/low blush phenotypes. The U.S. Prunus germplasm under the RosBREED collaborative effort was phenotyped in 2011 and 2012 for the percentage of blush covering the fruit skin using a scale from 0–5; 0 indicating no blush and 5 indicating full red surface color. High resolution genome scanning of RosBREED material provided necessary DNA information for determining distribution of high/low blush functional alleles/haplotypes in breeding germplasm. Four functional alleles define...
Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach d... more Background Bacterial spot, caused by Xanthomonas arboricola pv. pruni (Xap), is a serious peach disease with symptoms that traverse severe defoliation and black surface pitting, cracking or blemishes on peach fruit with global economic impacts. A management option for control and meeting consumer demand for chemical-free, environmentally friendly fruit production is the development of resistant or tolerant cultivars. Results We developed simple, accurate, and efficient Ppe.XapF DNA tests based on SNP genotyping with KASP technology to quickly test for bacterial spot resistance alleles in peach fruit and cull at the greenhouse stage. The objective of this research was to validate newly developed Ppe.XapF DNA tests that target the two major QTLs for fruit resistance in peach with diagnostic utility in predicting fruit response to bacterial spot infection. Conclusion Our study confirms that only two Ppe.XapF DNA tests, Ppe.XapF1-1 and Ppe.XapF6-2, are needed to distinguish between susc...
In-ovule embryo culture was used for obtaining seedlings from immature peach embryos 1-4 mm in le... more In-ovule embryo culture was used for obtaining seedlings from immature peach embryos 1-4 mm in length. Rapid micropropagation of Redhaven cultivar and B 52/2 vineyard peach selection was achieved by shoot tip proliferation. The two-stage rooting system, with a short auxin exposure followed by transfer to growth regulator-free half-strength basal media, proved to work much better than any other system published so far. Cotyledon regeneration was combined with Agrobacterium mediated genetic transformation. A clear difference in fluorescence between negative controls and the regenerants obtained after cotyledon inoculation with A. tumefaciens carrying the GUS gene was detected after 24 h indicating the production of chimeric peach plants.
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