Comparative genome-wide association study on body weight in Chinese native ducks using four models

The Jinling White duck represents a newly developed breed characterized by a rapid growth rate and a superior meat quality, offering significant economic value and research potential; however, the genetic basis underlying their body weight traits remains less understood. Here, we performed whole-genome resequencing for 201 diverse Jinling White male ducks and conducted population genomic analyses, suggesting a rich genetic diversity within the Jinling White duck population. Equipped with our genomic resources, we applied genome-wide association analysis for body weight on birth (BWB), body weight on 1 wk (BW1), body weight on 3 wk (BW3), body weight on 5 wk (BW5) and body weight on 7 wk (BW7) using 4 statistical models. Comparative studies indicated that factored spectrally transformed linear mixed models (FaST-LMM) demonstrated the most superior efficiency, yielding more results with the minimal false positives. We discovered that PUS7, FBXO11, FOXN2, MSH6, and SLC4A4 were associated with BWB. RAG2, and TMEFF2 were candidate genes for BW1, and STARD13, Klotho, ZAR1L are likely candidates for BW3 and BW5. PLXNC1, ATP1A1, CD58, FRYL, OCIAD1, and OCIAD2 were linked to BW7. These findings provide a genetic reference for the selection and breeding of Jinling White ducks, while also deepened our understanding of Growth and development phenotypic in ducks.