A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds

Montanari, Sara; Perchepied, Laure; Renault, Déborah; Frijters, L.; Velasco, Riccardo; Horner, M.; Gardiner, Susan E.; Chagné, David; Bus, Vincent G. M.; Durel, Charles Eric; Malnoy, Mickaël

doi:10.1007/s11032-016-0473-z

Cited by 35 publications

(24 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Using three biparental breeding populations, a QTL was identified in a similar genomic location for each family 147 . This trait locus had been reported in previous studies 148 – 150 and its validation in RosBREED germplasm confirmed its utility as the most informative locus with the most effective resistance allele(s) available. Candidate resistance genes were identified using the recently available chromosome-scale pear genome assembled using a map generated from one of the RosBREED 2 mapping families 151 .…”

Section: Genomics and Socio-economics Knowledge Informs All Stages Ofsupporting

confidence: 75%

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

et al. 2020

View full text Add to dashboard Cite

The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a “chasm” existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project (“Ros” signifying a Rosaceae genomics, genetics, and breeding community initiative, and “BREED”, indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.

show abstract

Section: Genomics and Socio-economics Knowledge Informs All Stages Ofsupporting

confidence: 75%

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

et al. 2020

View full text Add to dashboard Cite

show abstract

“…In general, we identified SNPs that were able to discriminate between each pair of groups, except for Communis and Group 1 (Table 4). In addition, 10 robust PHR SNPs that were associated with important agronomic traits [7, 35] were given high priority, and four more were selected from other SNP categories, after visual evaluation of their cluster plots.…”

Section: Resultsmentioning

confidence: 99%

“…Recent advancements in sequencing and high-throughput genotyping technologies have greatly accelerated the discovery and profiling of millions of SNPs in many species [2]. Today, SNPs are the markers of choice for linkage and quantitative trait locus (QTL) mapping, and they have enabled the dissection of important traits in species with complex and highly heterozygous genomes [3–7]. These tools have also enabled genome-wide association studies (GWAS) in outcrossing species, which require several thousands of SNPs, because of the rapid linkage disequilibrium (LD) decay [8–10], and the implementation of genomic selection (GS) in a range of crops [11–13].…”

Section: Introductionmentioning

confidence: 99%

“…In the last few years, various technologies were applied in pear for SNP discovery and genotyping, including array development [27, 28] and different genotyping-by-sequencing (GBS) strategies [18, 29–32]. These technologies have enabled the construction of linkage maps in different families, including an integrated high-density consensus map [32], and the discovery of QTLs for control of a number of important traits [7, 33–37]. However, examples of successful application of marker-assisted selection (MAS) in pear are still lacking, and GWAS and GS are limited by the very low number of markers available.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

et al. 2019

Self Cite

View full text Add to dashboard Cite

Background Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear ( Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. Results By applying a two-step design process, which consisted of the construction of a first ‘draft’ array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic ( PolyHighResolution ). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. Conclusions The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus . Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.

show abstract

“…Microsatellites are widely distributed in the genome Pyrus and are used in cultivar identification (Bao et al, 2007), genetic relationship analysis (Bassil and Postman, 2010;Yue et al, 2018), and quantitative trait locus mapping (Montanari et al, 2016). Although the single nucleotide polymorphism markers based on genome sequencing were popular in the current study, the SSR markers were needed in a long period.…”

Section: Discussionmentioning

confidence: 94%

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

Jiang¹,

An²,

Wang³

et al. 2019

J. Amer. Soc. Hort. Sci.

View full text Add to dashboard Cite

Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In Pyrus, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from Pyrus species. A total of 49,147 SSR loci were identified in Pyrus, and their genotypes were evaluated by whole-genome resequencing data of 30 Pyrus accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all Pyrus accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of Pyrus species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in Pyrus.

show abstract

A QTL detected in an interspecific pear population confers stable fire blight resistance across different environments and genetic backgrounds

Cited by 35 publications

References 63 publications

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization

The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

Contact Info

Product

Resources

About