Integrated environmental and genomic analysis reveals the drivers and genetic mechanisms of agro-climatic adaptation in geese

BACKGROUND: Adaptation is one of the key processes of animal domestication, environmental pressures will leave footprints in the genome. Geese are widely distributed across multiple geographical conditions with distinct adaptations. However, few reports have focused on the environmental adaptability of geese. Moreover, the key environmental drivers that trigger local adaptation and its genetic mechanisms are still unknown. To this end, 35 agro-climatic variables of 257 geese from 14 Chinese breeds were obtained, the key environmental drivers and its genetic mechanism were elucidated by combining the genome data. RESULTS: Five key environmental drivers, elevation, water scarcity (BIO14), two variables as proxies of food availability (Grass and Landuse), and one variable as proxy of disease resistance (Forest) were identified after dissecting 35 agro-climatic variables by using ecological niche modeling (ENM). Integrating five key environmental drivers with single-nucleotide polymorphism variations, we conduct genome-wide selection signature analyses and genome-environment analysis. This analysis identified 1984 key genes likely integral to the environmental adaptation and mainly enriched in MAPK signaling pathways and metabolic pathways. Allele frequency distribution and selective sweep analysis revealed that some genes play crucial roles in environmental adaptation, including SATB1, NTRK2 and CTIF involved in adapting to the high-altitude hypoxic environments; ARMH3 and BDH2 participated in adapting to water deficiency; COL5L1, ULK4 and PI4KA associated with disease resistance, and other genes involved in metabolic adaptations including IQSEC1, TBC1D14, GRK5, FGGY and LRP1B, etc. Notably, we noticed that feather colour differentiation in geese might be driven by human agricultural practices, with LRP1B involved in this process. CONCLUSIONS: Overall, our study elucidated the five key environmental drivers and their genetic mechanisms. The candidate genes related to environmental adaptability offer new insights into genetic resource development and breeding strategies of Chinese indigenous geese.