RT Journal Article
SR Electronic
T1 Runs of Homozygosity in Modern Chicken Revealed by Sequence Data
JF G3: Genes|Genomes|Genetics
FD Genetics Society of America
SP g3.401860.2020
DO 10.1534/g3.120.401860
A1 Talebi, Reza
A1 Szmatoła, Tomasz
A1 Mészáros, Gábor
A1 Qanbari, Saber
YR 2020
UL http://www.g3journal.org/content/early/2020/10/19/g3.120.401860.abstract
AB Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear in a homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs. commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n=25), brown layer (BL, n=25), broiler line A (BRA, n=20), broiler line B (BRB, n=20) and Red Junglefowl (RJF, n=25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (±18.7) per bird, despite carrying it in short segments (0.3-1 Mb). Population-wise inbreeding measures based on Wright's (Fis) and genomic (FROH) metrics revealed highly inbred genome of layer lines relative to the broilers and Red Junglefowl. We further revealed the ROH islands, among commercial lines overlapped with QTLs related to limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response to Newcastle virus (ROBO2), and feather pecking. Comparison of ROH landscape in sequencing resolution demonstrated that a sizable portion of genome of commercial lines segregates in homozygote state, reflecting many generations of assortative mating and intensive selection in their recent history. In contrary, wild birds carry shorter ROH segments, likely suggestive of older evolutionary events.