多倍体植物的SNP分析
-
https://www.cell.com/molecular-plant/pdf/S1674-2052(15)00130-6.pdf
Single Nucleotide Polymorphism Identification in Polyploids: A Review, Example, and Recommendations
提到多倍体植物SNP分析的难点：
SNP identification in polyploids,
however, is more challenging due to the need to distinguish
homeologous SNPs (polymorphic positions occurring across
subgenomes within and among individuals) from allelic SNPs
(polymorphic positions occurring within a single subgenome
among individuals). Increased genetic similarity among
subgenomes within a polyploid species exacerbates these
challenges, consequently slowing the rate of SNP marker
development and applications in the molecular breeding of
polyploid crops -
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4555216/
SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops
sweep对 homeologous SNPs 和 allelic SNPs 的区分We define "allelic" SNP in a polyploid crop as
originating from the same subgenome,
within the same locus,
and being polymorphic between genotypes.
等位SNP需要符合上面三个条件a homeologous SNP we define as a polymorphism that exists at homeologous loci and is polymorphic between subgenomes within genotypes.
-
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920642/
多倍体
同源多倍体：由两种相同物种的染色体叠加而成
autopolyploids result from genome doubling within one species (intraspecific)异源多倍体:由两种不同物种的染色体叠加而成
allopolyploids result from genome doubling following a hybridization between two different species (interspecific)subgenomes
"allelic" SNP in a polyploid crop as originating from the same subgenome, within the same locus, and being polymorphic between genotypes. In contrast, a homeologous SNP we define as a polymorphism that exists at homeologous loci and is polymorphic between subgenomes within genotypes.
https://zhuanlan.zhihu.com/p/91689320 -
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03704-1#availability-of-data-and-materials
Evaluation of variant calling tools for large plant genome re-sequencing
这个文章推荐的流程是bwa samtools/mpileup