Genetic Polymorphisms in P. vulgaris Starch Genes Promoters

The reference genome used was Phaseolus vulgaris v2.1 (Phytozome genome ID: 442, NCBI taxonomy ID: 3885). Raw whole genome sequences of 126 common bean individual plants (NCBI, PRJNA471678) were processed using Trimmomatic and mapped to the v2.1 common bean reference genome with the BWA aligner. The alignments were then subjected to GATK MarkDuplicates to tag duplicated reads. Promoter regions of starch biosynthesis genes (2000 bp downstream to 200 bp upstream of the transcription start site) were extracted, and variants were called using BCFtools mpileup and call functions.List of Starch Biosynthesis Genes AnalyzedPhvul.004G029100Phvul.009G052100Phvul.003G078800Phvul.008G033800Phvul.011G044000Phvul.007G139400Phvul.003G069200Phvul.002G096000

本研究所用参考基因组为菜豆（Phaseolus vulgaris）v2.1版本（Phytozome基因组ID：442，NCBI分类学ID：3885）。针对126份普通菜豆单株的原始全基因组序列（NCBI，项目编号PRJNA471678），首先采用Trimmomatic工具完成质控处理，随后通过BWA比对工具将测序reads比对至v2.1版本菜豆参考基因组。所得比对结果经GATK MarkDuplicates工具标记重复测序reads。后续提取淀粉合成基因的启动子区域（转录起始位点上游200 bp至下游2000 bp），并利用BCFtools的mpileup与call函数进行变异位点识别。本研究分析的淀粉合成基因列表如下：
Phvul.004G029100、Phvul.009G052100、Phvul.003G078800、Phvul.008G033800、Phvul.011G044000、Phvul.007G139400、Phvul.003G069200、Phvul.002G096000