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Nature Communications:甜玉米基因组与群体基因组揭示现代甜玉米的演化

已有 686 次阅读 2021-2-24 07:27 |个人分类:每日摘要|系统分类:论文交流

Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn

第一作者Ying Hu

第一单位佛罗里达大学

通讯作者Marcio F. R. Resende Jr.


 Abstract 


背景回顾Sweet corn is one of the most important vegetables in the United States and Canada. 


主要研究:Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2).


测序个体的背景:This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. 


结果1-组装:The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. 


结果2-比较基因组Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. 


结果3-系统发育Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. 


结果4-选择Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. 


结论:Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.


 摘 要 


甜玉米是美国和加拿大最重要的蔬菜之一。本文中,作者对shrunken2等位基因突变了的甜玉米自交系Ia453(Ia453-sh2)基因组进行了de novo组装。该突变积累了更多的糖分,存在于大多为加工和新市场开发的商业杂交种中。作者组装获得了10条拟染色体,覆盖了总组装的92%和预估基因组大小的99%,scaffold N50为222.2MB。该参考基因组完整组装出了导致sh2-R等位基因突变的巨大结构变异。此外,与6个田间玉米基因组的比较基因组学分析,揭示了单核苷酸多态性、结构变异和转座子组成的差异。通过对5381份不同种质的玉米和大刍草系统发育分析,揭示了甜玉米与其它类型玉米的亲缘关系。结果表明,美国种植的现代甜玉米共同起源于墨西哥北部。最后,群体基因组分析鉴定了基因组中被选择的区域以及与甜玉米性状相关的候选基因,如早花、胚乳组成、植株和雄穗结构以及籽粒行数。本文的研究为甜玉米的比较基因组学、功能研究和基因组辅助育种提供了高质量的参考基因组序列。


doi: https://doi.org/10.1038/s41467-021-21380-4


Journal: Nature Communications

Published date: Feb 23, 2021




http://blog.sciencenet.cn/blog-3158122-1273575.html

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