دورية أكاديمية
Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization
| العنوان: | Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization |
|---|---|
| المؤلفون: | Sara Montanari, Luca Bianco, Brian J. Allen, Pedro J. Martínez-García, Nahla V. Bassil, Joseph Postman, Mareike Knäbel, Biff Kitson, Cecilia H. Deng, David Chagné, Marc W. Crepeau, Charles H. Langley, Kate Evans, Amit Dhingra, Michela Troggio, David B. Neale |
| المصدر: | BMC Genomics, Vol 20, Iss 1, Pp 1-18 (2019) |
| بيانات النشر: | BMC, 2019. |
| سنة النشر: | 2019 |
| المجموعة: | LCC:Biotechnology LCC:Genetics |
| مصطلحات موضوعية: | Pyrus, Single nucleotide polymorphism, Genotyping, Germplasm, Genetic diversity, Breeding, Biotechnology, TP248.13-248.65, Genetics, QH426-470 |
| الوصف: | Abstract 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1471-2164 |
| العلاقة: | http://link.springer.com/article/10.1186/s12864-019-5712-3Test; https://doaj.org/toc/1471-2164Test |
| DOI: | 10.1186/s12864-019-5712-3 |
| الوصول الحر: | https://doaj.org/article/dfa866712e5f4ab7aa2b4b930108d1c8Test |
| رقم الانضمام: | edsdoj.fa866712e5f4ab7aa2b4b930108d1c8 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 14712164 |
|---|---|
| DOI: | 10.1186/s12864-019-5712-3 |