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

Table 1 Number of SNPs for different classes reported by SnpEff

	#SNPs annotated with SnpEff	#SNPs submitted	#SNPs tiled on the 700 K array	#SNPs classified as robust PHR	#SNPs tiled on the 70 K array
UCD-newly discovered SNPs	989,566	723,697	648,975	196,640	71,182
HIGH^a	1746	1746	1746	415	221
MODERATE^b	82,763	82,763	82,763	31,559	14,471
LOW^c	100,191	92,841	92,841	41,526	22,750
MODIFIER^d non-intergenic	583,645	447,790	447,790	120,839	33,647
MODIFIER^d intergenic	221,221	98,557	23,835	2301	93
Validated SNPs	–	3010	2966	318	181
Infinium® II 9 K SNP array	–	558	558	220	122
GBS P. communis	–	1440	1440	80	49
GBS P. × bretschneideri	–	1012	968	18	10
Totals	–	726,707	651,941	196,958	71,363

^a HIGH = The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense-mediated decay
^b MODERATE = A non-disruptive variant that might change protein effectiveness
^c LOW = Assumed to be mostly harmless or unlikely to change protein behavior
^d MODIFIER = Usually non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact
The newly discovered SNPs that passed the Affymetrix filter were annotated with the software SnpEff, which reported their predicted impact on the protein (HIGH, MODERATE, LOW or MODIFIER). The number of SNPs for each class is shown for all annotated SNPs, the final set of SNPs submitted to Affymetrix to build the first “draft” array, the SNPs tiled on the Axiom™ Pear 700 K Genotyping Array, the robust PolyHighResolution (PHR) SNPs of this array, the SNPs tiled on the Axiom Pear 70 K Genotyping Array. The numbers of validated SNPs are also shown

ISSN: 1471-2164