A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate
复制标题
DOI：
10.1101/gr.086538.108
复制
发表时间：
2009-03-01
期刊：
影响因子：
7
通讯作者：
Andersson, Leif
中科院分区：
文献类型：
--
作者：
Groenen, Martien A. M.;Wahlberg, Per;Andersson, Leif
本研究通过对鸡的三个现有作图群体（瓦赫宁根 (WU)、东兰辛 (EL) 和乌普萨拉 (UPP) 作图群体）的 12,945 个单核苷酸多态性 (SNP) 进行基因分型，显着提高了鸡共有连锁图谱的分辨率。可以包含多达8599个SNP，使当前共识连锁图谱中的标记总数达到9268个。性别平均图谱的总长度为3228 cM，比之前使用WU和EL群体的估计要小得多，反映了新图谱的更高质量。当前图谱由 34 个连锁群组成，涵盖 38 个常染色体中的至少 29 个。基于三个个体群体的图谱的性别特异性分析和比较显示，群体之间的重组率存在显着的异质性，但性别之间没有显着的异质性。与 WU 肉鸡群体相比，F(1) 红原鸡/白来航雄性和雌性的重组率显着较低，这与强人工选择下纯种家畜的较高重组率一致。染色体之间以及单个染色体上的重组率差异很大。对重组热点和冷点的序列组成的分析表明，富含 GC 的序列与高重组率之间存在很强的正相关性。富含 GC 的粘连蛋白结合位点尤其从其他富含 GC 的序列中脱颖而出，其重组热点的密度比冷点高 3.4 倍，这表明重组频率和粘连蛋白结合之间存在功能关系。
The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included, bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations, but no significant heterogeneity between sexes. The recombination rates in the F(1) Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.