Rosbreed: Enabling Marker-Assisted Breeding in Rosaceae

Iezzoni, Amy; Weebadde, Cholani; Luby, James J.; Yue, Chengyan; Weg, Eric van de; Fazio, Gennaro; Main, Dorrie; Peace, Cameron; Bassil, Nahla V.; McFerson, James R.

doi:10.17660/actahortic.2010.859.47

Cited by 81 publications

(56 citation statements)

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“…Rehder, Prunus davidiana (Carrière) Franch and Prunus mira Koehne. The germplasm investigated is part of the US reference set for peach germplasm ) of the RosBREED project (Iezzoni 2010;Iezzoni et al 2010) and represents the portion of RosBREED germplasm developed for improved processing quality (Gradziel et al 1993).…”

Section: Plant Materialsmentioning

confidence: 99%

“…PBA performs QTL discovery and subsequent characterization by utilizing the pedigrees of breeding programs (Iezzoni 2010;Peace et al 2010), as pursued in the RosBREED initiative (www.robreed.org). The identification and quantification of QTLs through PBA account for those chromosomal segments shared in identity by descent (IBD) through multiple (small or large) families with known pedigree and genotypic data and also connected to recent common ancestors.…”

Section: Introductionmentioning

confidence: 99%

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QTL mapping of pomological traits in peach and related species breeding germplasm

et al. 2015

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Peach is an economically important fruit tree crop that exhibits high phenotypic variability yet suffers from diversity-limited gene pool. Genetic introgression of novel alleles from related species is being pursued to expand genetic diversity. This process is, however, challenging and requires the incorporation of innovative genomic and statistical tools to facilitate efficient transfer of these exotic alleles across the multiple generations required for introgression. In this study, pedigree-based analysis (PBA) in a Bayesian QTL mapping framework was applied to a diverse peach pedigree introgressed with almond and other related Prunus species. The aim was to investigate the genetic control of eight commercially important fruit productivity and fruit quality traits over two subsequent years. Fifty-two QTLs with at least positive evidence explaining up to 98 % of the phenotypic variance across all trait/year combinations were mapped separately per trait and year. Several QTLs exhibited variable association with traits between years. By using the peach genome sequence as a reference, the intrachromosomal positions for several QTLs were shown to differ from those Electronic supplementary material The online version of this article (previously reported in peach. The inclusion of introgressed germplasm and the explicit declaration of the genetic structure of the pedigree as covariate in PBA enhanced the mapping and interpretation of QTLs. This study serves as a model study for PBA in a diverse peach breeding program, and the results highlight the ability of this strategy to identify genomic resources for direct utilization in markerassisted breeding.

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Section: Plant Materialsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

QTL mapping of pomological traits in peach and related species breeding germplasm

et al. 2015

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“…In addition, there are several large international programs that are focusing their efforts on developing better genetic tools to improve the quality of fruits. These include the RosBREED project in the USA (Iezzoni et al 2009 , http://www.rosbreed.org/ ) and the FruitBreedomics project in Europe ( http://fruitbreedomics.com/ ) among others.…”

Section: Consistent High Fruit Qualitymentioning

confidence: 99%

Trends in Fruit Breeding

Byrne

2011

Fruit Breeding

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Fruit breeding is a long-term process which takes a minimum of about a decade from the original cross to a fi nished cultivar. Thus, much thought needs to go into which objectives to be emphasized in the breeding. Although certain objectives, such as yield and basic quality, are always important, the overall lifestyle, environmental, marketing, and production trends affect the objectives that breeders emphasize in their programs as they strive to anticipate the future needs of the fruit industry. The importance of each trend varies with the crop and environment. The major trends are to develop cultivars which simplify orchard practices, have increased resistance to biotic and abiotic stress, extend the adaptation zones of the crop, create new fruit types, create fruit cultivars with enhanced health benefi ts, and provide consistently high quality. Keywords IntroductionFruit breeders need to anticipate cultivar needs at least 10 years into the future, as this is the minimum time that most fruit cultivars take to develop from pollination to release. This chapter explores the larger trends in our lives, such as environmental issues, health consciousness, consumer trends in lifestyle, and the expectations and needs of producers to examine how these affect the objectives of our fruit breeding programs. Trends in the Business of Plant BreedingImproved plant protection legislation in the USA, Europe, and throughout the world has stimulated substantial research and the development of new plants for commercial exploitation. This has also tended to shift the breeding into the private sector (Heisey et al. 2001 ;Frey 1996Frey , 1998Traxler 1999 ) . This shift was quicker for the annual large acreage crops, such as corn, where public-generated commercial cultivars in the USA disappeared in the 1940s and the use of publically generated inbred lines ceased in the 1970s. Currently, public corn breeders concentrate more on basic research into corn breeding and genetics (Traxler 1999 ) .In fruit crops, this shift has been slower and dependent on the crop, with those crops with shorter life cycles and larger markets shifting to the private sector more rapidly. Throughout the world, the proportion of peach releases from public programs has decreased from 45% in the 1980s to 34% in the early 1990s (Della Strada et al. 1996 ;Della Strada and Fideghelli 2003 ;Fideghelli et al. 1998 ) . During the last decade in the USA, only ~15% of the peach and nectarine cultivars were released by public institutions. Support for the development of apricots, cherries, and apples is still with public institutions, but this is eroding and the private sector is becoming more involved in the release and Another factor is decreased funding for public breeding programs. In the USA, the public funding dedicated to breeding activities has decreased dramatically since the 1970s as the government shifted from a philosophy of completely funding programs to assisting programs with partial funding (Moore 1993 ;Frey 1996 ;Heisey et al. 2001 ) . Thus, t...

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“…Currently, GDR also contains private breeding data from individual breeders and public breeding data from the RosBREED project (15). In fruit tree breeding programs, progeny of tree fruit breeding crosses are used for genotype and phenotype evaluations.…”

Section: Use Cases (Example Data Representations)mentioning

confidence: 99%

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

et al. 2011

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Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data sets is necessary. Chado, a generic, modular, community-based database schema is widely used in the biological community to store information associated with genome sequence data. To meet the need to also accommodate large-scale phenotyping and genotyping projects, a new Chado module called Natural Diversity has been developed. The module strictly adheres to the Chado remit of being generic and ontology driven. The flexibility of the new module is demonstrated in its capacity to store any type of experiment that either uses or generates specimens or stock organisms. Experiments may be grouped or structured hierarchically, whereas any kind of biological entity can be stored as the observed unit, from a specimen to be used in genotyping or phenotyping experiments, to a group of species collected in the field that will undergo further lab analysis. We describe details of the Natural Diversity module, including the design approach, the relational schema and use cases implemented in several databases.

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Rosbreed: Enabling Marker-Assisted Breeding in Rosaceae

Cited by 81 publications

References 4 publications

QTL mapping of pomological traits in peach and related species breeding germplasm

QTL mapping of pomological traits in peach and related species breeding germplasm

Trends in Fruit Breeding

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

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