原网址：http://blog.sciencenet.cn/blog-491809-432700.html
genetic map-----bin map
已有 13226 次阅读 2011-4-13 14:50 |系统分类:科研笔记
Genetic map
A genetic map is a map based on the frequencies of recombination between markers during crossover of homologous chromosomes. The greater the frequency of recombination (segregation) between two genetic markers, the farther apart they are assumed to be. Conversely, the lower the frequency of recombination between the markers, the smaller the physical distance between them.
Recombination frequency
Recombination frequency is a measure of genetic linkage and is used in the creation of a genetic linkage map. Recombination frequency (θ) is the frequency that a single chromosomal crossover will take place between two genes during meiosis. A centimorgan (cM) is a unit that describes a recombination frequency of 1%. In this way we can measure the genetic distance between two loci, based upon their recombination frequency. This is a good estimate of the real distance. Double crossovers would turn into no recombination. In this case we cannot tell if crossovers took place. If the loci we're analysing are very close (less than 7 cM) a double crossover is very unlikely. When distances become higher, the likelihood of a double crossover increases. As the likelihood of a double crossover increases we systematically underestimate the genetic distance between two loci.
Bin map
With NGS development，bin map can be called as the prior period of genetic map. There are a lot of journal published.Such as:
Huang X, Feng Q, Qian Q, Zhao Q, Wang L, et al. (2009) High-throughput genotyping by whole-genome resequencing. Genome Research 19: 1068.
Huang等（2009）通过对水稻两个亲本Nipponbare与93-11及其150株RIL（重组近交系）群体重测序，共找到1,493,461个SNP位点，最终构建的bin-map全长1539.5cM。基于这张图谱，他们定位了一个株高相关的QTL，位置在100kb之内。
Xie W, Feng Q, Yu H, Huang X, Zhao Q, et al. (2010) Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci U S A 107: 10578–10583.
Xie等（2010）对238个RILs群体进行全基因组重测序，每个个体测序深度0.05X，共得到216，064个SNP，去掉假阳性还有209，240个，阴性率为3%。而每个RIL的SNP密度为100kb中有3个。得到高质量高密度的遗传图谱，结合表型数据，可以定位GW5基因。
Xu J, Zhao Q,Du P，et al.(2010) Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.).BMC Genomics 11:656.
Xu等（2010）通过对水稻一个亲本9311的高深度测序和128个CSSLs（染色体片段代换系）的低深度重测序，构建了一张高密度的bin map，检测到了7.68M的SNP位点，这128个CSSLs共携带了259个染色体代换片段。利用这张图谱，成功的将一个重要的QTL定位到了一号染色体的791,655bp范围之内，这段范围包括了著名的“绿色革命”sd1基因。
Yu H, Xie W, Wang J, Xing Y, Xu C, et al. (2011) Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers. PLoS ONE 6(3): e17595.
Yu等（2011）应用全基因组重测序对241株水稻RIL 进行~0.06X深度测序，以SNP为基础构建Bin map，与传统的SSR/RFLP构建的图谱进行相比，Bin map具有超高密度，能够检测到更多的QTL，同时检测的QTL更加精细。
转载本文请联系原作者获取授权，同时请注明本文来自简建波科学网博客。
链接地址：
网友评论