Targeted sequencing of VviAGL11 in a population of grapevine accessions

To analyze for any possible nucleotide sequence variation associated with grape stenospermocarpic seedlessness, the gene VviAGL11 (VIT_18s0041g01880, exons + introns) plus 2-kb upstream sequence (9,849-bp in total corresponding to positions chr18:26,888,672-26,898,521 in the PN40024 12X grapevine reference genome) were sequenced in a collection of grapevine cultivars. Genomic DNA was obtained form young leaves of 105 seeded and 5 seedless grapevine accessions. Agilent SureSelect (http://www.genomics.agilent.com) was used to target the VviAGL11 locus that was then sequenced by BGI company (http://www.genomics.cn/en) in 90 nt paired-end reads using Illumina HiSeq-2000. Sequencing reads were aligned to the PN40024 12X.0 grapevine reference genome using Bowtie 2.