Breeders, collection curators, and other germplasm users require genetic information, both genome... more Breeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus R f for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-bydescent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U. S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64-93% of the 181 individuals. Successful validation compared deduced R f and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.
One potential legacy of the widespread deforestation of the 1700-1800s and subsequent agricultura... more One potential legacy of the widespread deforestation of the 1700-1800s and subsequent agricultural abandonment and reforestation across the eastern United States (U.S.) during the 1900s is the establishment of introduced apple trees (Malus domestica) exclusive of naturally occurring native crab apple species. As these apple trees might provide ecological services and a genetic reserve of long-forgotten apple cultivars, a region-wide forest inventory was used to estimate the current extent, condition, and changes in the population of apple trees across eastern forests of the U.S. It was found that hundreds of millions of apple trees currently exist in the forests of the northern U.S. with indications of population senescence as the abundance of seedlings and saplings decline while the abundance of the largest-sized trees and standing dead trees increase. The distribution of forest apple trees is only aligned with native crab apple distributions in limited areas, suggesting distinct feral apple populations derived from agricultural abandonment decades ago. As these extant apple trees are likely relics of former orchards and/or their naturally dispersed progeny, these populations may serve as an in-situ gene bank representing hundreds, if not thousands, of apple cultivars forgotten long ago but adapted to local conditions and perhaps of importance to ensuring the future resilience of domestic apple production in the context of global change.
Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry crea... more Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions associated with the trait variation of a breedingrelevant magnitude, as well as to identify the parental sources of favorable alleles. The objectives of this research were to identify the quantitative trait loci (QTLs) associated with fruit cracking incidence and firmness, estimate the effects of single nucleotide polymorphism (SNP) haplotypes at the detected QTLs, and identify the ancestral source(s) of functional haplotypes. Fruit cracking incidence and firmness were evaluated for multiple years on 259 unselected seedlings representing 22 important breeding parents. Phenotypic data, in conjunction with genome-wide genotypic data from the RosBREED cherry 6K SNP array, were used in the QTL analysis performed via Pedigree-Based Analysis using the FlexQTL TM software, supplemented by a Genome-Wide Association Study using the BLINK software. Haplotype analysis was conducted on the QTLs to identify the functional SNP haplotypes and estimate their phenotypic effects, and the haplotypes were tracked through the pedigree. Four QTLs (two per trait) were consistent across the years and/or both analysis methods and validated the previously reported QTLs. qCrack-LG1.1m (the label given to a consistent QTL for cracking incidence on chromosome 1) explained 2-15.1% of the phenotypic variance, while qCrack-LG5.1m, qFirm-LG1.2m, and qFirm-LG3.2m explained 7.6-13.8, 8.8-21.8, and 1.7-10.1% of the phenotypic variance, respectively. At each QTL, at least two SNP haplotypes had significant effects and were considered putative functional SNP haplotypes. Putative low-cracking SNP haplotypes were tracked to an unnamed parent of 'Emperor Francis' and 'Schmidt' and unnamed parents of 'Napoleon' and 'Hedelfingen,' among others, and putative high-firmness haplotypes were tracked to an
The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains... more The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species’ centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were co...
Societal Impact StatementHistoric North American apple (Malus domestica) orchards that thrived in... more Societal Impact StatementHistoric North American apple (Malus domestica) orchards that thrived in the late 19th and early 20th centuries, with cultivar compositions unlike today's orchards, are vanishing. There are several reasons for this loss: tree aging, cost of tree maintenance, and urbanization. Many groups have collected local knowledge regarding the history and horticulture of apples using both phenotypic and genotypic identification methods. Some of these groups have joined with scientists to form the collaborative “Historic Fruit Tree Working Group of North America” to facilitate the conservation of heirloom apple cultivars in North America through documentation, identification, collaboration, and education.
Accurate prediction of genetic potential and response to selection in breeding requires knowledge... more Accurate prediction of genetic potential and response to selection in breeding requires knowledge of genetic parameters for important selection traits. Data from breeding trials can be used to obtain estimates of these parameters so that predictions are directly relevant to the improvement program. Here, a factor allocation diagram was developed to describe the sampling design used to assess the quality of fresh and post-storage (2 months) fruit from advanced selection trial in an apple breeding program from which models for analyses were developed. Genetic variation was the largest source of variation for the fruit size, red colour type, proportion of red skin colour and lenticels, and instrumentally assessed fruit diameter, mass, puncture force and titratable acidity. In contrast, residual variation was the largest for fruit shape, juiciness, sweetness, aromatic flavour, eating and overall quality, and instrumental crispness. Genetic effects for traits were generally stable over fixed effects, except for a significant interaction with storage duration for firmness. Genetic correlations among traits were generally weak except between fruit mass (and diameter) and sensory size (0.98), titratable acidity and sensory acidity (0.97), puncture force and sensory firmness (0.96-0.90), crispness and juiciness (0.87), sweetness and aromatic flavour (0.84) and instrumental and sensory crispness (0.75). Predictions of the performance for seven commercial cultivars are presented. This study suggests that the Washington State apple production area can be treated as a single target environment and sufficient diversity exists to generate new elite cultivars. In addition, options for evaluating the efficiency of apple breeding are discussed.
Peach and nectarine production worldwide is increasing; however consumption is flat or declining ... more Peach and nectarine production worldwide is increasing; however consumption is flat or declining because of the inconsistent eating quality experienced by consumers. The main factor for this inconsistent quality is mealiness or woolliness, a form of chilling injury that develops following shipping periods in the global fruit market today. Our research groups have devised various postharvest methods to prolong storage life, including controlled atmosphere and delayed storage; however, these treatments only delay mealiness. Mealiness texture results from disruption of the normal ripening process involving disassembly of cell wall material, and creates a soft fruit texture that is dry and grainy instead of juicy and smooth. Solving this problem is a prerequisite for increasing the demand for fresh peach and nectarine. Two approaches were used to reveal genes and their associated biochemical processes that can confer resistance to mealiness or wooliness. At the Volcani Center, Israel, a nectarine cultivar and the peach cultivar (isogenetic materials) from which the nectarine cultivar spontaneously arose, and at the Kearney Agricultural Center of UC Davis, USA, a peach population that segregates for quantitative resistance to mealiness was used for dissecting the genetic components of mealiness development. During our project we have conducted research integrating the information from phenotypic, biochemical and gene expression studies, proposed possible candidate genes and SNPs-QTLs mapping that are involved in reducing peach mealiness susceptibility. Numerous genes related to ethylene biosynthesis and its signal transduction, cell wall structure and metabolism, stress response, different transcription factor families were detected as being differentially accumulated in the cold-treated samples of these sensitive and less sensitive genotypes. The ability to produce ethylene and keep active genes involved in ethylene signaling, GTP-binding protein, EIN-3 binding protein and an ethylene receptor and activation of ethyleneresponsive fruit ripening genes during cold storage provided greater resistance to CI. Interestingly, in the functional category of genes differentially expressed at harvest, less chilling sensitive cultivar had more genes in categories related to antioxidant and heat sock proteins/chaperones that may help fruit to adapt to low temperature stress. The specific objectives of the proposed research were to: characterize the phenotypes and cell wall components of the two resistant systems in response to mealiness- inducing conditions; identify commonalities and specific differences in cell wall proteins and the transcriptome that are associated with low mealiness incidence; integrate the information from phenotypic, biochemical, and gene expression studies to identify candidate genes that are involved in reducing mealiness susceptibility; locate these genes in the Prunus genome; and associate the genes with genomic regions conferring quantitative genetic variation for mealiness resistance. By doing this we will locate genetic markers for mealiness development, essential tools for selection of mealiness resistant peach lines with improved fruit storability and quality. In our research, QTLs have been located in our peach SNPs map, and proposed candidate genes obtained from the integrated result of phenotypic, biochemical and gene expression analysis are being identified in our QTLs as an approach searching for consistent assistant markers for peach breeding programs.
Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (... more Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica L. Batsch) consumption. Pedigree-based analysis (PBA) using Visual FlexQTL software has been conducted on seven low to medium chill F 1 families along with the founders and parents. Phenotypic data were collected over two years at a high chill (Fowler, CA) and medium chill (College Station, TX) locations and genotyped using the 9K SNP Illumina array. The objectives of this study were to 1) identify QTL(s) associated with fruit quality traits; 2) estimate QTL genotypes for important breeding parents; 3) identify predictive single-nucleotide polymorphism (SNP) or haplotype alleles for desired QTL alleles; and 4) determine source of the alleles for three important fruit quality traits, namly blush (BL), soluble solids content (SSC), and titratable acidity (TA) through pedigree-based analysis (PBA) on Texas peach/nectarine germplasm. Our analysis detected one major QTL on the central part of LG4 for blush at interval 42-44 cM that explained about 20 % of the total phenotypic variance (PVE). A major QTL for TA co-localized with the major locus for low-acid fruit (D-locus) at the proximal end of LG5 at 0-0 cM. This QTL was consistent across all data sets, explaining about 60 % of the phenotypic variance. There was a QTL at the distal end of LG5 at 52-62 cM that was associated with both TA and SSC, which explained about 15 % of the phenotypic variance. In addition, haplotype analyses for these QTLs revealed unique SNP haplotypes that are associated with the predictive SNP marker(s) of desired QTL alleles along with their original sources. Our findings will help peach breeders develop new predictive DNA-based molecular marker tests that can be used routinely in marker-assisted breeding (MAB) for enhancing peach quality traits.
Frontiers in Plant Science 01 frontiersin.org Hardner et al. 10.3389/fpls.2022.960449 methods to ... more Frontiers in Plant Science 01 frontiersin.org Hardner et al. 10.3389/fpls.2022.960449 methods to improve understanding of G × E and also incorporate known QTL effects. In addition, the study generated baseline information to account for population structure in genomic prediction models in horticultural crop improvement.
Prediction of the genetic potential of a candidate cultivar is fundamental to achieving a respons... more Prediction of the genetic potential of a candidate cultivar is fundamental to achieving a response to selection in plant breeding. In the early phases of advanced selection plantings, a common strategy to increase selection intensity is field testing of many candidates at multiple locations with incomplete or limited replication among trials. Genetic analyses that incorporate genetic relationships among candidates can be used to improve the prediction accuracy, and indirectly predict performance at locations where a candidate is not planted. Here, we report on the prediction of breeding value for sensory crispness for unreplicated apple candidate progeny and parents established at three locations across the USA (Minnesota, New York State, Washington State) using relationships constructed from (i) pedigree records and (ii) 8K single nucleotide polymorphism (SNP) array data. The correlation between relationship coefficients estimated from either historical pedigree or SNP arrays was 0.76. Estimates of phenotypic variation and heritability were similar among three analyses (i.e., full data using pedigree relationship matrix, reduced data for only individuals with SNP genotypes available using a pedigree-based relationship matrix, or reduced data using a genomic relationship matrix estimated from the SNP arrays). Significant G×E was detected with all analyses, although there were some differences in the estimates of additive genetic correlation among locations from different analyses. This study demonstrates that dense SNP marker arrays may be used to predict breeding values for incompletely or unreplicated candidate cultivars established across multiple locations. This approach will be particularly valuable where the cost or logistics of replication at multiple locations is prohibitive and when pedigree records are incomplete and are not able to fully characterize the diversity of a candidate population.
Peach (Prunus persica L.), a member of the Rosaceae family is attaining a model status for fruit ... more Peach (Prunus persica L.), a member of the Rosaceae family is attaining a model status for fruit tree genetic studies. Fruit quality traits, including firmness, texture, stone adhesion, skin color, flesh color, sugars, acids, and flavor, determine usage and consumer acceptance. In many cultivars, such traits are negatively impacted by cold storage, a procedure used to extend fruit market life. The major symptoms of chilling injury are internal breakdown (flesh mealiness, browning, and bleeding) and loss of flavor. Understanding the genetic control of these traits, so that only cultivars free from chilling injury susceptibility are grown, promises to greatly benefit producers, shippers and consumers. A partial genetic linkage map was constructed for peach to locate genetic factors controlling fruit organoleptic traits and chilling injury symptoms. The map was developed from an F1 population derived from intraspecific crossing between the cultivars 'Dr. Davis' (clingstone, non-melting, bland-flavor, non-mealy, slight-browning, yellow-flesh fruit) and 'Georgia Belle' (freestone, melting, sharp-flavor, mealiness-prone, high-browning, white-flesh fruit). The linkage map, containing SSR, SRAP, RAF, candidate gene, and morphological markers and covering an estimated 90% of the genome, was used successfully to locate the Flesh color (Y) and Freestone-Melting flesh (F-M) loci. Major and minor QTLs controlling mealiness, browning, and bleeding were also localized, using phenotypic data collected for three harvest seasons. The endopolygalacturonase gene, at the F-M locus, is responsible for a major QTL controlling both mealiness and bleeding, while one of the minor QTLs for bleeding was located close to the Y locus. The goal is to develop molecular tools for efficient marker-assisted breeding of peach for improved postharvest fruit quality.
Breeders, collection curators, and other germplasm users require genetic information, both genome... more Breeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus R f for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-bydescent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U. S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64-93% of the 181 individuals. Successful validation compared deduced R f and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.
One potential legacy of the widespread deforestation of the 1700-1800s and subsequent agricultura... more One potential legacy of the widespread deforestation of the 1700-1800s and subsequent agricultural abandonment and reforestation across the eastern United States (U.S.) during the 1900s is the establishment of introduced apple trees (Malus domestica) exclusive of naturally occurring native crab apple species. As these apple trees might provide ecological services and a genetic reserve of long-forgotten apple cultivars, a region-wide forest inventory was used to estimate the current extent, condition, and changes in the population of apple trees across eastern forests of the U.S. It was found that hundreds of millions of apple trees currently exist in the forests of the northern U.S. with indications of population senescence as the abundance of seedlings and saplings decline while the abundance of the largest-sized trees and standing dead trees increase. The distribution of forest apple trees is only aligned with native crab apple distributions in limited areas, suggesting distinct feral apple populations derived from agricultural abandonment decades ago. As these extant apple trees are likely relics of former orchards and/or their naturally dispersed progeny, these populations may serve as an in-situ gene bank representing hundreds, if not thousands, of apple cultivars forgotten long ago but adapted to local conditions and perhaps of importance to ensuring the future resilience of domestic apple production in the context of global change.
Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry crea... more Breeding for decreased fruit cracking incidence and increased fruit firmness in sweet cherry creates an attractive alternative to variable results from cultural management practices. DNA-informed breeding increases its efficiency, yet upstream research is needed to identify the genomic regions associated with the trait variation of a breedingrelevant magnitude, as well as to identify the parental sources of favorable alleles. The objectives of this research were to identify the quantitative trait loci (QTLs) associated with fruit cracking incidence and firmness, estimate the effects of single nucleotide polymorphism (SNP) haplotypes at the detected QTLs, and identify the ancestral source(s) of functional haplotypes. Fruit cracking incidence and firmness were evaluated for multiple years on 259 unselected seedlings representing 22 important breeding parents. Phenotypic data, in conjunction with genome-wide genotypic data from the RosBREED cherry 6K SNP array, were used in the QTL analysis performed via Pedigree-Based Analysis using the FlexQTL TM software, supplemented by a Genome-Wide Association Study using the BLINK software. Haplotype analysis was conducted on the QTLs to identify the functional SNP haplotypes and estimate their phenotypic effects, and the haplotypes were tracked through the pedigree. Four QTLs (two per trait) were consistent across the years and/or both analysis methods and validated the previously reported QTLs. qCrack-LG1.1m (the label given to a consistent QTL for cracking incidence on chromosome 1) explained 2-15.1% of the phenotypic variance, while qCrack-LG5.1m, qFirm-LG1.2m, and qFirm-LG3.2m explained 7.6-13.8, 8.8-21.8, and 1.7-10.1% of the phenotypic variance, respectively. At each QTL, at least two SNP haplotypes had significant effects and were considered putative functional SNP haplotypes. Putative low-cracking SNP haplotypes were tracked to an unnamed parent of 'Emperor Francis' and 'Schmidt' and unnamed parents of 'Napoleon' and 'Hedelfingen,' among others, and putative high-firmness haplotypes were tracked to an
The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains... more The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species’ centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were co...
Societal Impact StatementHistoric North American apple (Malus domestica) orchards that thrived in... more Societal Impact StatementHistoric North American apple (Malus domestica) orchards that thrived in the late 19th and early 20th centuries, with cultivar compositions unlike today's orchards, are vanishing. There are several reasons for this loss: tree aging, cost of tree maintenance, and urbanization. Many groups have collected local knowledge regarding the history and horticulture of apples using both phenotypic and genotypic identification methods. Some of these groups have joined with scientists to form the collaborative “Historic Fruit Tree Working Group of North America” to facilitate the conservation of heirloom apple cultivars in North America through documentation, identification, collaboration, and education.
Accurate prediction of genetic potential and response to selection in breeding requires knowledge... more Accurate prediction of genetic potential and response to selection in breeding requires knowledge of genetic parameters for important selection traits. Data from breeding trials can be used to obtain estimates of these parameters so that predictions are directly relevant to the improvement program. Here, a factor allocation diagram was developed to describe the sampling design used to assess the quality of fresh and post-storage (2 months) fruit from advanced selection trial in an apple breeding program from which models for analyses were developed. Genetic variation was the largest source of variation for the fruit size, red colour type, proportion of red skin colour and lenticels, and instrumentally assessed fruit diameter, mass, puncture force and titratable acidity. In contrast, residual variation was the largest for fruit shape, juiciness, sweetness, aromatic flavour, eating and overall quality, and instrumental crispness. Genetic effects for traits were generally stable over fixed effects, except for a significant interaction with storage duration for firmness. Genetic correlations among traits were generally weak except between fruit mass (and diameter) and sensory size (0.98), titratable acidity and sensory acidity (0.97), puncture force and sensory firmness (0.96-0.90), crispness and juiciness (0.87), sweetness and aromatic flavour (0.84) and instrumental and sensory crispness (0.75). Predictions of the performance for seven commercial cultivars are presented. This study suggests that the Washington State apple production area can be treated as a single target environment and sufficient diversity exists to generate new elite cultivars. In addition, options for evaluating the efficiency of apple breeding are discussed.
Peach and nectarine production worldwide is increasing; however consumption is flat or declining ... more Peach and nectarine production worldwide is increasing; however consumption is flat or declining because of the inconsistent eating quality experienced by consumers. The main factor for this inconsistent quality is mealiness or woolliness, a form of chilling injury that develops following shipping periods in the global fruit market today. Our research groups have devised various postharvest methods to prolong storage life, including controlled atmosphere and delayed storage; however, these treatments only delay mealiness. Mealiness texture results from disruption of the normal ripening process involving disassembly of cell wall material, and creates a soft fruit texture that is dry and grainy instead of juicy and smooth. Solving this problem is a prerequisite for increasing the demand for fresh peach and nectarine. Two approaches were used to reveal genes and their associated biochemical processes that can confer resistance to mealiness or wooliness. At the Volcani Center, Israel, a nectarine cultivar and the peach cultivar (isogenetic materials) from which the nectarine cultivar spontaneously arose, and at the Kearney Agricultural Center of UC Davis, USA, a peach population that segregates for quantitative resistance to mealiness was used for dissecting the genetic components of mealiness development. During our project we have conducted research integrating the information from phenotypic, biochemical and gene expression studies, proposed possible candidate genes and SNPs-QTLs mapping that are involved in reducing peach mealiness susceptibility. Numerous genes related to ethylene biosynthesis and its signal transduction, cell wall structure and metabolism, stress response, different transcription factor families were detected as being differentially accumulated in the cold-treated samples of these sensitive and less sensitive genotypes. The ability to produce ethylene and keep active genes involved in ethylene signaling, GTP-binding protein, EIN-3 binding protein and an ethylene receptor and activation of ethyleneresponsive fruit ripening genes during cold storage provided greater resistance to CI. Interestingly, in the functional category of genes differentially expressed at harvest, less chilling sensitive cultivar had more genes in categories related to antioxidant and heat sock proteins/chaperones that may help fruit to adapt to low temperature stress. The specific objectives of the proposed research were to: characterize the phenotypes and cell wall components of the two resistant systems in response to mealiness- inducing conditions; identify commonalities and specific differences in cell wall proteins and the transcriptome that are associated with low mealiness incidence; integrate the information from phenotypic, biochemical, and gene expression studies to identify candidate genes that are involved in reducing mealiness susceptibility; locate these genes in the Prunus genome; and associate the genes with genomic regions conferring quantitative genetic variation for mealiness resistance. By doing this we will locate genetic markers for mealiness development, essential tools for selection of mealiness resistant peach lines with improved fruit storability and quality. In our research, QTLs have been located in our peach SNPs map, and proposed candidate genes obtained from the integrated result of phenotypic, biochemical and gene expression analysis are being identified in our QTLs as an approach searching for consistent assistant markers for peach breeding programs.
Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (... more Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica L. Batsch) consumption. Pedigree-based analysis (PBA) using Visual FlexQTL software has been conducted on seven low to medium chill F 1 families along with the founders and parents. Phenotypic data were collected over two years at a high chill (Fowler, CA) and medium chill (College Station, TX) locations and genotyped using the 9K SNP Illumina array. The objectives of this study were to 1) identify QTL(s) associated with fruit quality traits; 2) estimate QTL genotypes for important breeding parents; 3) identify predictive single-nucleotide polymorphism (SNP) or haplotype alleles for desired QTL alleles; and 4) determine source of the alleles for three important fruit quality traits, namly blush (BL), soluble solids content (SSC), and titratable acidity (TA) through pedigree-based analysis (PBA) on Texas peach/nectarine germplasm. Our analysis detected one major QTL on the central part of LG4 for blush at interval 42-44 cM that explained about 20 % of the total phenotypic variance (PVE). A major QTL for TA co-localized with the major locus for low-acid fruit (D-locus) at the proximal end of LG5 at 0-0 cM. This QTL was consistent across all data sets, explaining about 60 % of the phenotypic variance. There was a QTL at the distal end of LG5 at 52-62 cM that was associated with both TA and SSC, which explained about 15 % of the phenotypic variance. In addition, haplotype analyses for these QTLs revealed unique SNP haplotypes that are associated with the predictive SNP marker(s) of desired QTL alleles along with their original sources. Our findings will help peach breeders develop new predictive DNA-based molecular marker tests that can be used routinely in marker-assisted breeding (MAB) for enhancing peach quality traits.
Frontiers in Plant Science 01 frontiersin.org Hardner et al. 10.3389/fpls.2022.960449 methods to ... more Frontiers in Plant Science 01 frontiersin.org Hardner et al. 10.3389/fpls.2022.960449 methods to improve understanding of G × E and also incorporate known QTL effects. In addition, the study generated baseline information to account for population structure in genomic prediction models in horticultural crop improvement.
Prediction of the genetic potential of a candidate cultivar is fundamental to achieving a respons... more Prediction of the genetic potential of a candidate cultivar is fundamental to achieving a response to selection in plant breeding. In the early phases of advanced selection plantings, a common strategy to increase selection intensity is field testing of many candidates at multiple locations with incomplete or limited replication among trials. Genetic analyses that incorporate genetic relationships among candidates can be used to improve the prediction accuracy, and indirectly predict performance at locations where a candidate is not planted. Here, we report on the prediction of breeding value for sensory crispness for unreplicated apple candidate progeny and parents established at three locations across the USA (Minnesota, New York State, Washington State) using relationships constructed from (i) pedigree records and (ii) 8K single nucleotide polymorphism (SNP) array data. The correlation between relationship coefficients estimated from either historical pedigree or SNP arrays was 0.76. Estimates of phenotypic variation and heritability were similar among three analyses (i.e., full data using pedigree relationship matrix, reduced data for only individuals with SNP genotypes available using a pedigree-based relationship matrix, or reduced data using a genomic relationship matrix estimated from the SNP arrays). Significant G×E was detected with all analyses, although there were some differences in the estimates of additive genetic correlation among locations from different analyses. This study demonstrates that dense SNP marker arrays may be used to predict breeding values for incompletely or unreplicated candidate cultivars established across multiple locations. This approach will be particularly valuable where the cost or logistics of replication at multiple locations is prohibitive and when pedigree records are incomplete and are not able to fully characterize the diversity of a candidate population.
Peach (Prunus persica L.), a member of the Rosaceae family is attaining a model status for fruit ... more Peach (Prunus persica L.), a member of the Rosaceae family is attaining a model status for fruit tree genetic studies. Fruit quality traits, including firmness, texture, stone adhesion, skin color, flesh color, sugars, acids, and flavor, determine usage and consumer acceptance. In many cultivars, such traits are negatively impacted by cold storage, a procedure used to extend fruit market life. The major symptoms of chilling injury are internal breakdown (flesh mealiness, browning, and bleeding) and loss of flavor. Understanding the genetic control of these traits, so that only cultivars free from chilling injury susceptibility are grown, promises to greatly benefit producers, shippers and consumers. A partial genetic linkage map was constructed for peach to locate genetic factors controlling fruit organoleptic traits and chilling injury symptoms. The map was developed from an F1 population derived from intraspecific crossing between the cultivars 'Dr. Davis' (clingstone, non-melting, bland-flavor, non-mealy, slight-browning, yellow-flesh fruit) and 'Georgia Belle' (freestone, melting, sharp-flavor, mealiness-prone, high-browning, white-flesh fruit). The linkage map, containing SSR, SRAP, RAF, candidate gene, and morphological markers and covering an estimated 90% of the genome, was used successfully to locate the Flesh color (Y) and Freestone-Melting flesh (F-M) loci. Major and minor QTLs controlling mealiness, browning, and bleeding were also localized, using phenotypic data collected for three harvest seasons. The endopolygalacturonase gene, at the F-M locus, is responsible for a major QTL controlling both mealiness and bleeding, while one of the minor QTLs for bleeding was located close to the Y locus. The goal is to develop molecular tools for efficient marker-assisted breeding of peach for improved postharvest fruit quality.
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Papers by Cameron Peace