对13种菜加入的泛基因组分析揭示了与性染色体进化和菜的化特征相关的结构变异
Hongbing She1, Zhiyuan Liu1, Zhaosheng Xu1
1State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Plant biotechnology journal
|August 3, 2024
概括
这项研究构建了第一个全面的Spinacia泛基因组,识别了数百万个结构变异 (SV). 这些泛SV揭示了对菜进化,性别确定和化的见解,为作物改进提供了强大的工具.
科学领域:
- 基因组学就是基因组学.
- 植物科学 植物科学
- 进化生物学 进化生物学
背景情况:
- 结构变异 (SV) 对物种适应和化至关重要,但由于泛基因组资源有限,在菜中研究不足.
- 之前的研究缺乏对SVs在Spinacia物种的全面了解.
研究的目的:
- 构建一个全面的Spinacia泛基因组,并识别一大群泛SVs.
- 为了调查SVs在菜进化,性别决定和化中的作用.
- 评估泛SVs在菜中的基因组选择的实用性.
主要方法:
- 产生了种植和野生菜物种的八个染色体尺度组合.
- 整合了新的组合与现有数据,以创建一个Spinacia泛基因组.
- 在452个Spinacia加入中识别和基因型193,966个泛SV.
- 进行了全基因组关联研究 (GWAS) 并分析了 SV 频率.
主要成果:
- 建立了一个全面的Spinacia泛基因组,包含193,966个泛SVs.
- 全SV提供了关于性别决定的见解,86%的与性别相关的SV位于Y染色体上,导致基因表达减少.
- SV频率与养特征相关,如螺栓时间和种子休眠期.
- 在基因组选择中,Pan-SVs表现出比SNP更高的预测精度.
结论:
- 菜泛基因组和泛SV资源对菜基因组学非常有价值.
- 泛SV在菜的进化,性别决定和化中发挥着重要作用.
- 与SNP相比,Pan-SVs在作物改进和育种计划方面具有更高的潜力.
相关概念视频
Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
Genome-wide Association Studies-GWAS
13.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
13.3K
The Ratio of X Chromosome to Autosomes
8.5K
In most organisms, sex is determined by the ratio of X and Y chromosomes. However, in some organisms, such as Drosophila and C.elegans, sex is determined by the ratio of the number of X chromosomes to the number of sets of autosomes. The Y chromosome in Drosophila is active but does not determine sex. It contains genes responsible for the production of sperms in adult flies.
Normal male Drosophila has a ratio of one X chromosome to two sets of autosomes. In contrast, normal female...
Normal male Drosophila has a ratio of one X chromosome to two sets of autosomes. In contrast, normal female...
8.5K
Genomics
36.2K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.2K
Gene Evolution - Fast or Slow?
7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.1K
Single Nucleotide Polymorphisms-SNPs
14.9K
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
14.9K


