Additional file 11 of Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

Additional file 11: Table S5. List of annotated genes underlying genome-wide association loci of frost tolerance in pea. Genes that were located in an interval of ±1 Mb on both sides of markers significantly detected by GWAS and markers in linkage disequilibrium (LD; r2 > 0.8) with the former ones, are listed. For each identified gene, the nearest marker significantly detected by GWAS (underlined font) or marker in LD with associated marker(s) (non-underlined font) is shown. The annotation of genes was extracted from Pisum sativum v.1a genome JBrowse available at https://urgi.versailles.inra.fr/Species/Pisum [39]. Genes positions in the pea genome assembly v.1a are presented by their assigned chromosomes and physical positions indicated in bp. Genes which are not assigned to one of the seven chromosomes, are represented by their physical positions on unanchored scaffolds. a: Annotation refined with the homologous gene from Medicago truncatula available on the Pisum sativum v.1a genome JBrowse, and whose corresponding gene function was identified from the Medicago truncatula v4.0 genome JBrowse available on www.medicagogenome.org . b: Annotation refined with the homologous gene from Glycine max available on the Pisum sativum v.1a genome JBrowse and whose corresponding gene function was identified from the genome v9.0 assembly V1.1 available on http://soykb.org/gene_card.php . c: Annotation refined with the predicted protein function of transcript sequences corresponding to mapped SNPs, extracted from Table S10 in Tayeh et al. [36].

补充文件11：表S5。豌豆霜冻抗性全基因组关联分析位点相关注释基因列表。本列表收录了经全基因组关联分析（Genome-Wide Association Study, GWAS）显著检测到的标记两侧±1 Mb区间内，以及与上述标记存在连锁不平衡（Linkage Disequilibrium, LD；r²>0.8）的标记所关联的基因。对于每一个鉴定到的基因，将标注其最近的GWAS显著检测标记（下划线字体）或与关联标记存在连锁不平衡的标记（非下划线字体）。
基因注释信息提取自豌豆（Pisum sativum）v.1a版本基因组的JBrowse数据库，网址为https://urgi.versailles.inra.fr/Species/Pisum [39]。豌豆基因组v.1a版本组装体中基因的位置以其所在染色体及以碱基对（bp）为单位的物理位置进行标注。未分配至7条染色体的基因，以其在未锚定支架上的物理位置表示。
a：本次注释通过蒺藜苜蓿（Medicago truncatula）同源基因进行了优化，该同源基因可在豌豆v.1a基因组JBrowse数据库中获取，其对应基因功能从蒺藜苜蓿v4.0基因组JBrowse数据库（网址为www.medicagogenome.org）中鉴定得到。
b：本次注释通过大豆（Glycine max）同源基因进行了优化，该同源基因可在豌豆v.1a基因组JBrowse数据库中获取，其对应基因功能从网址为http://soykb.org/gene_card.php的大豆v9.0组装版本V1.1基因组中鉴定得到。
c：本次注释通过对应于已定位单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的转录本序列的预测蛋白功能进行了优化，该信息提取自Tayeh等人[36]研究中的表S10。