在减数分裂过程中,非等位基因同源序列可能会错位并形成交叉,最终导致基因组结构重排。容易使非等位基因重组的基因组特征与SV的发生有关。 作物不同品种基因组结构变异分析实例: (一)香米不同品种基因组结构变异分析 图12 香米Basmati 334和Dom Sufid共有和特有PAVs变异数量分析( Choi et al., Genome Biology, 202...
缺失遗传力的解决受到几个因素的阻碍,包括因果基因组变异,特别是结构变异(SV)的不完全检测,这导致遗传标记和因果变异之间的不完全连锁不平衡(LD)引起的估计偏差,以及因果变异的遗传异质性,这降低了GWAS8,9,10的统计能力。为了克服这些瓶颈,需要一个详尽而精确的遗传变异目录。 通过将测序读数映射到单个线性参考基因...
we constructed a graph-based pan-genome by integrating the sequences and coordinates of identified SVs into the 9930 linear reference genome sequences (Fig.3h, i). The graph structure enabled proper mapping of short reads derived from SV flanking regions by embedding both reference and alternative...
a, Pie chart shows the proportion of the different SV types in wheat pan-genome. b, Percentage of PAVs overlapping with different genomic features. c, Distribution of PAVs based on their allele frequency in wheat accessions indicated most PAVs were present in one or only a few accessions. ...
近期,由于高质量基因组装的进步,更多基于高质量组装的植物研究已经解决了少数物种中的SV问题。然而,因为很少有种群规模的基于高质量组装的研究,所以植物中真实的遗传变异程度很难得知。尤其是基因拷贝数变异,它被认为是功能性序列基因变异的重要来源的变异。因此,建立一个基于高质量组装的泛基因组是值得的。泛基因组近期...
Graph-based genome enables SV-based GWAS in tomato Numerous studies have suggested that SVs are causative variants responsible for agronomically important traits12,13,36,37. However, population-scale SV genotyping is challenging in plants, impeding the exploitation of SVs in identifying genotype–phenoty...
respectively (Supplementary Fig.4a). Presence–absence variants (PAVs; large insertions and deletions) are key features of crop pan-genomes, and they were the most abundant SV type (Fig.3band Supplementary Table8) and tended to be enriched in intergenic repetitive regions (Fig.3cand Supplementary...
Based on the SV analyses, the pangenome size for poplar was estimated to be ∼497 Mbp, with 80.7% constituting the core genome, similar to other pangenome studies [40,72]. The study suggested that increasing the number of individuals will result in expansion of the dispensable genome for ...
(Fig.4f). Another possible explanation could be that SV events occur with a high mutation rate, as reflected by the appearance of a high proportion (47%) of multiple SV alleles (ranging from 2 to 135 nrSVs in a single site) in all the silkworms (Supplementary Fig.3d, e). Moreover,...
22). Among them, a BC4 locus containing multiple MYB genes on Chr2 associated with berry color42 based on the pangenome SV dataset (Supplementary Table 10). The FF6 locus explained 7.35% of the variation for flesh firmness, which differed between groups because the Table2 group had an ...