Multiple Origins and Genomic Basis of Complex Traits in Sighthounds

• Published in: Molecular biology and evolution Vol. 40; no. 8
• Main Authors: Li, Wu-Lue, Liu, Yan-Hu, Li, Jin-Xiu, Ding, Meng-Ting, Adeola, Adeniyi C, Isakova, Jainagul, Aldashev, Almaz A, Peng, Min-Sheng, Huang, Xuezhen, Xie, Guoli, Chen, Xi, Yang, Wei-Kang, Zhou, Wei-Wei, Ghanatsaman, Zeinab Amiri, Olaogun, Sunday C, Sanke, Oscar J, Dawuda, Philip M, Hytönen, Marjo K, Lohi, Hannes, Esmailizadeh, Ali, Poyarkov, Andrey D, Savolainen, Peter, Wang, Guo-Dong, Zhang, Ya-Ping
• Format: Journal Article
• Language: English
• Published: US Oxford University Press 03-08-2023
• Subjects: Analysis; artificial selection; Discoveries; Dogs; Genes; Genomes; Genomics; origin; population genomics; sighthounds; Middle East; East Asia; Iran; China; Russia; sighthounds; population genomics; origin; artificial selection
• ISSN: 0737-4038; 1537-1719; 1537-1719
• DOI: 10.1093/molbev/msad158

Abstract
Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in “regulation of release of sequestered calcium ion into cytosol” (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.