PDF(Pubmed)
Abstract：
BACKGROUND: Tuber starch and steroidal glycoalkaloid (SGA)-related traits have been consistently prioritized in potato breeding, while allelic variation pattern of genes that underlie these traits is less explored.
RESULTS: Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism and 38 in the biosynthesis of steroidal glycoalkaloids, and discovered 96,166 allelic variants among 2,169 gene haplotypes in six autotetraploid potato genomes. Comparative analyses revealed an uneven distribution of allelic variants among gene haplotypes and that the vast majority of deleterious mutations in these genes are retained in heterozygous state in the autotetraploid potato genomes. Leveraging full-length cDNA sequencing data, we find that approximately 70% of haplotypes of the 119 genes are transcribable. Population genetic analyses identify starch and SGA biosynthetic genes that are potentially conserved or diverged between potato varieties with varying starch or SGA content.
CONCLUSIONS: These results deepen the understanding of haplotypic diversity within functionally important genes in autotetraploid genomes and may facilitate functional characterization of genes or haplotypes contributing to traits related to starch and SGA in potato.
RESULTS: Here, we focused on the genes involved in two important metabolic pathways in the potato: starch metabolism and SGA biosynthesis. We identified 119 genes consisting of 81 involved in starch metabolism and 38 in the biosynthesis of steroidal glycoalkaloids, and discovered 96,166 allelic variants among 2,169 gene haplotypes in six autotetraploid potato genomes. Comparative analyses revealed an uneven distribution of allelic variants among gene haplotypes and that the vast majority of deleterious mutations in these genes are retained in heterozygous state in the autotetraploid potato genomes. Leveraging full-length cDNA sequencing data, we find that approximately 70% of haplotypes of the 119 genes are transcribable. Population genetic analyses identify starch and SGA biosynthetic genes that are potentially conserved or diverged between potato varieties with varying starch or SGA content.
CONCLUSIONS: These results deepen the understanding of haplotypic diversity within functionally important genes in autotetraploid genomes and may facilitate functional characterization of genes or haplotypes contributing to traits related to starch and SGA in potato.
摘要：
背景：块茎淀粉和甾体糖生物碱（SGA）相关性状在马铃薯育种中一直被优先考虑，而作为这些特征基础的基因的等位基因变异模式研究较少。
结果：这里，我们重点研究了参与马铃薯中两个重要代谢途径的基因：淀粉代谢和SGA生物合成。我们确定了119个基因，其中81个参与淀粉代谢，38个参与甾体生物碱的生物合成，在六个同源四倍体马铃薯基因组中的2169个基因单倍型中发现了96,166个等位基因变异。比较分析显示，等位基因变体在基因单倍型中分布不均，并且这些基因中的绝大多数有害突变在同源四倍体马铃薯基因组中以杂合状态保留。利用全长cDNA测序数据，我们发现119个基因中大约70%的单倍型是可转录的.群体遗传分析确定了淀粉和SGA生物合成基因，这些基因在淀粉或SGA含量不同的马铃薯品种之间可能保守或分散。
结论：这些结果加深了对同源四倍体基因组中功能重要基因中单倍型多样性的理解，并可能有助于对马铃薯中与淀粉和SGA相关性状的基因或单倍型进行功能表征。
结果：这里，我们重点研究了参与马铃薯中两个重要代谢途径的基因：淀粉代谢和SGA生物合成。我们确定了119个基因，其中81个参与淀粉代谢，38个参与甾体生物碱的生物合成，在六个同源四倍体马铃薯基因组中的2169个基因单倍型中发现了96,166个等位基因变异。比较分析显示，等位基因变体在基因单倍型中分布不均，并且这些基因中的绝大多数有害突变在同源四倍体马铃薯基因组中以杂合状态保留。利用全长cDNA测序数据，我们发现119个基因中大约70%的单倍型是可转录的.群体遗传分析确定了淀粉和SGA生物合成基因，这些基因在淀粉或SGA含量不同的马铃薯品种之间可能保守或分散。
结论：这些结果加深了对同源四倍体基因组中功能重要基因中单倍型多样性的理解，并可能有助于对马铃薯中与淀粉和SGA相关性状的基因或单倍型进行功能表征。
