“RosBREED” is a large-scale initiative of the U.S. Rosaceae genomics, genetics, and breeding comm... more “RosBREED” is a large-scale initiative of the U.S. Rosaceae genomics, genetics, and breeding community with strong international involvement. This project is dedicated to genetic improvement of rosaceous crops by targeted application of genomics and socio-economics knowledge and tools to increase breeding efficiency, engage stakeholders, and train the next generation of plant breeders. Our goal is to sustainably integrate modern genomics tools with traditional breeding approaches. Ten teams carry out the RosBREED mission. The Socio-Economics Team has dissected current breeding priorities of U.S. Rosaceae breeders through a comprehensive survey. The Industry Team has initiated enhanced engagement of industry sectors in regional breeding efforts. The Breeding Team has cooperated across 12 breeding programs to establish reference germplasm sets representing their crops and programs and develop standardized phenotyping protocols with the first season of performance evaluation undertaken...
With the advent of genetic maps for apple that carry common transferable markers, it is possible ... more With the advent of genetic maps for apple that carry common transferable markers, it is possible to investigate genomic relationships between genes present in different accessions. Co-dominant markers, such as microsatellites, are particularly useful for this purpose. In recent years, genetic markers have been developed for a number of resistance genes for apple scab (Venturia inaequalis). In this paper, we present the discovery of a new scab resistance gene (Vh8) that maps to linkage group 2 (LG2). We then bring together the findings from different research groups on other scab resistance genes that also map to LG2 in an attempt to delineate their arrangement. These other genes comprise major genes (Vh2, Vr, Vbj and Vr2), as well as several race specific quantitative trait loci (QTLs) from `Discovery¿ and `TN10-8¿. Results indicate that Vh2 and Vr are probably identical, and that Vh2/Vr, Vh8, Vbj and at least one of the QTLs are closely linked to each other on the lower half of LG2...
ABSTRACT Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breedin... more ABSTRACT Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breeding programs as a source of scab resistance. The identity of SA has remained obscure, especially due to the existence of a series of ‘Antonovka’ cultivars with different origins. In this paper we show Schmidt's Antonovka to be identical to Анто́новка обыкновенный or ‘Common Antonovka’ (CA), an old Russian cultivar of unknown origin, by comparing simple sequence repeat (SSR) and SNP genotyping data from several first-generation descendants of SA from two European collections and a CA accession from the germplasm collection held at VNIISPK (The All-Russian Research Institute of Horticultural Breeding, Orel, Russia). The use of CA in Russian breeding programs is also briefly reviewed.
ABSTRACT Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar... more ABSTRACT Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar, as it is directly related to grower profitability. Therefore, determining the genetic control of fruit size in relevant breeding germplasm is a high priority. The objectives of this study were (1) to determine the number and positions of quantitative trait loci (QTL) for sweet cherry fruit size utilizing data simultaneously from multiple families and their pedigreed ancestors, and (2) to estimate fruit size QTL genotype probabilities and genomic breeding values for the plant materials. The sweet cherry material used was a five-generation pedigree consisting of 23 founders and parents and 424 progeny individuals from four full-sib families, which were phenotyped for fruit size and genotyped with 78 RosCOS single nucleotide polymorphism and 86 simple sequence repeat markers. These data were analyzed by a Bayesian approach implemented in FlexQTL™ software. Six QTL were identified: three on linkage group (G) 2 with one each on groups 1, 3, and 6. Of these QTL, the second G2 QTL and the G6 QTL were previously discovered while other QTL were novel. The predicted QTL genotypes show that some QTL were segregating in all families while other QTL were segregating in a subset of the families. The progeny varied for breeding value, with some progeny having higher breeding values than their parents. The results illustrate the use of multiple pedigree-linked families for integrated QTL mapping in an outbred crop to discover novel QTL and predict QTL genotypes and breeding values.
A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for... more A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker-assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® and a 20K Apple Infinium® genotyping array. The cultivated strawberry is an allo-octoploid. This level and type of ploidy creates challenges which we addressed in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploited both site-specific, biological as well as designed reductions in ploidy. The array will target several polymorphism types, including indels and di- and multi-allelic SNPs. For apple, the new SNP markers are located in focal points of max 10 KB, an approa...
“RosBREED” is a large-scale initiative of the U.S. Rosaceae genomics, genetics, and breeding comm... more “RosBREED” is a large-scale initiative of the U.S. Rosaceae genomics, genetics, and breeding community with strong international involvement. This project is dedicated to genetic improvement of rosaceous crops by targeted application of genomics and socio-economics knowledge and tools to increase breeding efficiency, engage stakeholders, and train the next generation of plant breeders. Our goal is to sustainably integrate modern genomics tools with traditional breeding approaches. Ten teams carry out the RosBREED mission. The Socio-Economics Team has dissected current breeding priorities of U.S. Rosaceae breeders through a comprehensive survey. The Industry Team has initiated enhanced engagement of industry sectors in regional breeding efforts. The Breeding Team has cooperated across 12 breeding programs to establish reference germplasm sets representing their crops and programs and develop standardized phenotyping protocols with the first season of performance evaluation undertaken...
With the advent of genetic maps for apple that carry common transferable markers, it is possible ... more With the advent of genetic maps for apple that carry common transferable markers, it is possible to investigate genomic relationships between genes present in different accessions. Co-dominant markers, such as microsatellites, are particularly useful for this purpose. In recent years, genetic markers have been developed for a number of resistance genes for apple scab (Venturia inaequalis). In this paper, we present the discovery of a new scab resistance gene (Vh8) that maps to linkage group 2 (LG2). We then bring together the findings from different research groups on other scab resistance genes that also map to LG2 in an attempt to delineate their arrangement. These other genes comprise major genes (Vh2, Vr, Vbj and Vr2), as well as several race specific quantitative trait loci (QTLs) from `Discovery¿ and `TN10-8¿. Results indicate that Vh2 and Vr are probably identical, and that Vh2/Vr, Vh8, Vbj and at least one of the QTLs are closely linked to each other on the lower half of LG2...
ABSTRACT Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breedin... more ABSTRACT Progenies of ‘Schmidt's Antonovka’ (SA) have been widely used in Western breeding programs as a source of scab resistance. The identity of SA has remained obscure, especially due to the existence of a series of ‘Antonovka’ cultivars with different origins. In this paper we show Schmidt's Antonovka to be identical to Анто́новка обыкновенный or ‘Common Antonovka’ (CA), an old Russian cultivar of unknown origin, by comparing simple sequence repeat (SSR) and SNP genotyping data from several first-generation descendants of SA from two European collections and a CA accession from the germplasm collection held at VNIISPK (The All-Russian Research Institute of Horticultural Breeding, Orel, Russia). The use of CA in Russian breeding programs is also briefly reviewed.
ABSTRACT Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar... more ABSTRACT Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar, as it is directly related to grower profitability. Therefore, determining the genetic control of fruit size in relevant breeding germplasm is a high priority. The objectives of this study were (1) to determine the number and positions of quantitative trait loci (QTL) for sweet cherry fruit size utilizing data simultaneously from multiple families and their pedigreed ancestors, and (2) to estimate fruit size QTL genotype probabilities and genomic breeding values for the plant materials. The sweet cherry material used was a five-generation pedigree consisting of 23 founders and parents and 424 progeny individuals from four full-sib families, which were phenotyped for fruit size and genotyped with 78 RosCOS single nucleotide polymorphism and 86 simple sequence repeat markers. These data were analyzed by a Bayesian approach implemented in FlexQTL™ software. Six QTL were identified: three on linkage group (G) 2 with one each on groups 1, 3, and 6. Of these QTL, the second G2 QTL and the G6 QTL were previously discovered while other QTL were novel. The predicted QTL genotypes show that some QTL were segregating in all families while other QTL were segregating in a subset of the families. The progeny varied for breeding value, with some progeny having higher breeding values than their parents. The results illustrate the use of multiple pedigree-linked families for integrated QTL mapping in an outbred crop to discover novel QTL and predict QTL genotypes and breeding values.
A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for... more A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker-assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® and a 20K Apple Infinium® genotyping array. The cultivated strawberry is an allo-octoploid. This level and type of ploidy creates challenges which we addressed in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploited both site-specific, biological as well as designed reductions in ploidy. The array will target several polymorphism types, including indels and di- and multi-allelic SNPs. For apple, the new SNP markers are located in focal points of max 10 KB, an approa...
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Papers by Eric Weg