SNP discovery for genetic diversity and population structure analysis coupled with restriction-associated DNA (RAD) sequencing in walnut cultivars of Sichuan Province, China

In this project, restriction-associated DNA sequencing was conducted to investigate the genetic variation and population structure among 41 walnut cultivars, and `Chandler? (J. regia) was used as the reference sequence. As a result, the average percentage of sequence reads that mapped to the reference genome was 88.51%, and 7 360 659 putative SNPs were obtained. The number of clean reads for each individual drastically varied between 7 018 308 and 22 424 696. After applying successive filters, 160 309 (2.18%) SNPs were deemed adequate. The 160 309 SNPs were aligned against the genome of J. regia `Chandler?. All of the SNPs were mapped across 4 743 of the 105 811 contigs in `Chandler?. The highest representation was obtained for LIHL01055144 (1116 SNPs), and 629 contigs were detected with only 1 SNP.