Gheyas Almas, Vallejo-Trujillo Adriana, Kebede Adebabay, Dessie Tadelle, Hanotte Olivier, Smith Jacqueline
Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Midlothian, EH25 9RG, UK.
Cells, Organism and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK.
Sci Data. 2022 Feb 14;9(1):53. doi: 10.1038/s41597-022-01129-4.
Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes.
本土鸡在非洲家禽生产中占主导地位。尽管因其对恶劣热带环境的适应性而受到后院养殖的青睐，但与商业品系相比，这些鸡群的生产力相对较低。基因组分析可以揭示这些鸡在生产和抗逆性状方面的遗传改良潜力，从而造福非洲家禽养殖系统。在此，我们报告了来自埃塞俄比亚24个种群的234只本土鸡的全基因组序列，这些种群分布在不同的农业气候条件下。数据来自Illumina HiSeqX平台的超过8万亿字节的双端序列，平均覆盖度约为57倍。几乎99%的序列读数可以比对到鸡的参考基因组（GRCg6a），证实了数据的高质量。变异检测发现了约1500万个单核苷酸多态性（SNP），其中约86%是已知变异（即存在于公共数据库中），这进一步证明了数据质量。该数据集为研究遗传多样性和当地环境适应性提供了极好的资源，对品种改良和保护具有重要意义。
