A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
Wong GK-S., Liu B., Wang J., Zhang Y., Yang X., Zhang Z., Meng Q., Zhou J., Li D., Zhang J., Ni P., Li S., Ran L., Li H., Zhang J., Li R., Li S., Zheng H., Lin W., Li G., Wang X., Zhao W., Li J., Ye C., Dai M., Ruan J., Zhou Y., Li Y., He X., Zhang Y., Wang J., Huang X., Tong W., Chen J., Ye J., Chen C., Wei N., Li G., Dong L., Lan F., Sun Y., Zhang Z., Yang Z., Yu Y., Huang Y., He D., Xi Y., Wei D., Qi Q., Li W., Shi J., Wang M., Xie F., Wang J., Zhang X., Wang P., Zhao Y., Li N., Yang N., Dong W., Hu S., Zeng C., Zheng W., Hao B., Hillier LW., Yang S-P., Warren WC., Wilson RK., Brandström M., Ellegren H., Crooijmans RPMA., van der Poel JJ., Bovenhuis H., Groenen MAM., Ovcharenko I., Gordon L., Stubbs L., Lucas S., Glavina T., Aerts A., Kaiser P., Rothwell L., Young JR., Rogers S., Walker BA., van Hateren A., Kaufman J., Bumstead N., Lamont SJ., Zhou H., Hocking PM., Morrice D., de Koning D-J., Law A., Bartley N., Burt DW., Hunt H., Cheng HH., Gunnarsson U., Wahlberg P., Andersson L., Kindlund E., Tammi MT., Andersson B., Webber C., Ponting CP., Overton IM., Boardman PE., Tang H., Hubbard SJ., Wilson SA., Yu J., Wang J., Yang H., International Chicken Polymorphism Map Consortium None.
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.