Genomic and phenotypic characterization of finger millet indicates a complex diversification history.
Genomic and phenotypic characterization of finger millet indicates a complex diversification history.
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手指小米的基因组和表型特征表明了复杂的多样化历史。
DOI：
10.1002/tpg2.20392
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Bancic J
中科院分区：
文献类型：
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作者：
Bancic J
测序技术的进步意味着，现在可以在主要主食以外的作物中探索对作物多样化的见解。我们使用异源四倍体孤儿作物指谷的基因组组合，在全基因组和亚基因组水平上分析DArTseq单核苷酸多态(SNPs)。利用一组8778个SNPs和13个农艺性状对来自非洲和亚洲的423个地方品种进行了分析。通过主成分分析和主成分判别分析，确定了4组不同的种质资源，它们与小米栽培的主要地理区域相吻合。值得注意的是，被认为是该作物原产地的东非表现出最低的遗传多样性。表型数据的主成分分析也揭示了地理差异，尽管地理区域之间的关系与基因组数据所显示的不同。利用相邻连接树对亚基因组A和B的进一步探索揭示了不同的特征，为指谷复杂的进化史提供了支持证据。尽管全基因组关联研究只发现了有限数量的显著标记-性状关联，但基于岭回归基因组模型获得的标记效应分布的聚类方法被用来研究性状复杂性。这一分析揭示了两个截然不同的星团。总体而言，这些发现表明，手指谷子经历了复杂的和特定背景的多样化，表明了漫长的驯化历史。这些分析为指谷未来的发展提供了洞察力。
Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub‐genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub‐genomes A and B using neighbor‐joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome‐wide association study found only a limited number of significant marker‐trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context‐specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.