Genetic Polymorphisms in <i>P. vulgaris</i> Starch Genes Promoters

The reference genome used was <i>Phaseolus vulgaris</i> 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.<b>List of Starch Biosynthesis Genes Analyzed</b>Phvul.004G029100Phvul.009G052100Phvul.003G078800Phvul.008G033800Phvul.011G044000Phvul.007G139400Phvul.003G069200Phvul.002G096000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）。126份普通菜豆单株的全基因组原始测序数据（NCBI，PRJNA471678）经Trimmomatic处理后，使用BWA比对软件将测序reads比对至v2.1版本菜豆参考基因组。随后通过GATK MarkDuplicates工具标记重复测序reads。提取淀粉合成基因的启动子区域（转录起始位点下游2000 bp至上游200 bp区间），并利用BCFtools的mpileup与call功能进行变异检测。**本研究分析的淀粉合成基因列表** Phvul.004G029100 Phvul.009G052100 Phvul.003G078800 Phvul.008G033800 Phvul.011G044000 Phvul.007G139400 Phvul.003G069200 Phvul.002G096000