Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
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DOI：
10.1016/j.molp.2022.01.003
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发表时间：
2022-03-07
期刊：
影响因子：
27.5
通讯作者：
Finkers, Richard
中科院分区：
文献类型：
--
作者：
Hoopes, Genevieve;Meng, Xiaoxi;Finkers, Richard
栽培马铃薯是一种同源四倍体物种，具有高度异质性的基因组。包括两个染色体规模的相控基因组组件的六个品种的相控组件揭示了广泛的等位基因多样性，包括改变编码和转录序列，优先等位基因表达，和结构变异，共同导致一个高度复杂的转录组和预测的蛋白质组，分布在同源染色体。野生物种有助于广泛的等位基因多样性的四倍体品种，表现出祖先的基因渗入早于现代育种工作。四倍体马铃薯作为一种经过有限减数分裂的同源四倍体，其功能障碍和有害等位基因不会被清除。据预测，近四分之一的基因座突变对蛋白质功能有很大的负面影响，使育种者减少遗传负荷的努力复杂化。StCDF1基因座控制成熟，和六个四倍体基因组的分析显示，12个等位基因变异的StCDF1与成熟度在剂量依赖性的方式。四倍体马铃薯基因组的复杂性及其猖獗的结构变异和嵌入的有害和功能失调的等位基因的知识将不仅是实施四倍体栽培品种的精确育种的关键，而且是构建纯合的二倍体马铃薯种质的关键，所述种质含有有利的等位基因以利用F1杂种的杂种优势。
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.