An intercross population study reveals genes associated with body size and plumage color in ducks

Nature Communications
Zhengkui ZhouYu Jiang

Abstract

Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype-phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.

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Citations

Dec 13, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Qiuming ChenChuzhao Lei
Aug 14, 2019·Frontiers in Genetics·Feng ZhuZhuo-Cheng Hou
Aug 23, 2020·Animals : an Open Access Journal From MDPI·Hongwei XuYong Cai
Nov 11, 2019·Genetics, Selection, Evolution : GSE·Swati JivanjiMathew D Littlejohn
Feb 13, 2020·PloS One·Lihong GuShuisheng Hou
Oct 10, 2020·Frontiers in Genetics·Yuzhe WangNing Li
Jun 1, 2021·Animal Biotechnology·Suyun LiangShuisheng Hou
May 20, 2021·Genome Biology and Evolution·Quan-Kuan ShenYa-Ping Zhang
Jul 14, 2021·Animal Biotechnology·Hongfei LiuChuanying Pan

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Datasets Mentioned

BETA
KY114890.1
PRJNA471401
PRJNA450892

Methods Mentioned

BETA
PCR
protein extraction
electrophoresis
genotyping
PCA
Hi-C
RNA-seq

Software Mentioned

Genome Analysis Toolkit ( GATK )
house
ALLMAP
GATK
HiTC
HiC
count
TopHat
htseq
ADMIXTURE

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