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

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 . Electronic supplementary material The online version of this article (10.1186/s12864-019-5712-3) contains supplementary material, which is available to authorized users.

Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function

“…As expected, the SNPs classified as modifier in our study were more abundant that the other categories, while the high impact SNPs were the smaller proportion. The same was observed in other crops, for example bean 70 , soybean 71 and pear 72 . In contrast, the SNPs with impact on protein efficiency and loss-of-function, that have a direct impact on gene function with adaptive interference during the course of selection, were reported in a smaller proportion.…”

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

“…Their utility, along with continued advances in genomics information and technologies, led to various groups designing and commercializing the next generation arrays with increased numbers of markers for all four crops: a 20K Infinium® and a 489K Axiom® array for apple 57 , 58 , a + 9K SNP “add on” to the 9K peach array 59 , a + 9K “add on” to the 6K cherry array 60 , and a 50K strawberry array based on the octoploid sequence assembly 61 . Axiom® arrays for pear (70K array 62 and 200K array 63 ) and rose (68K array 64 ) developed by other research groups enabled genetic discovery and validation of disease resistance loci.…”

Development and Validation of an Open Access SNP Array for Nile Tilapia (Oreochromis niloticus)

“…However, while all of these commercial strains are related to the GIFT strain (which underpins a large proportion of global tilapia aquaculture), their utility and performance in other farmed tilapia strains, especially those inhabiting Asia and Africa, is unknown. To develop platforms that are not exclusively informative in a focal strain, ideally additional SNP panels derived from genetically diverse populations should be evaluated during the SNP selection process (Montanari et al 2019). This strategy would allow to mitigate ascertainment bias, and thus broaden the applicability of a SNP array.…”