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Diversity of NBS-encoding genes in four groups

MS Manyi Sun
MZ Mingyue Zhang
JS Jugpreet Singh
BS Bobo Song
ZT Zikai Tang
YL Yueyuan Liu
RW Runze Wang
MQ Mengfan Qin
JL Jiaming Li
AK Awais Khan
JW Jun Wu
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To measure genetic diversity of the NBS-encoding gene family in pear, nucleotide diversity (π) and fixation index (FST) were used as population-differentiation statistics. The analysis was performed to compare the four pear groups (Asian wild, Asian cultivated, European wild, European cultivated). In brief, 338 NBS-encoding genes were combined to form a single sequence scaffold with the sorted order (Additional file 14), and SNPs were identified across them using the above defined methods. Then VCFtools (version 0.1.16) [67] was employed to further screen SNP data with the parameters: max-missing 0.50, maf 0.05. The resulting SNPs were used to calculate the π and FST with a 1000 bp sliding window and a step size of 500 bp across the linear sequence of all 338 NBS-encoding genes. The nucleotide diversity (π) was also calculated separately for the coding regions.

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