Estimation of genetic variability and identification of regions under selection based on runs of homozygosity in Beijing-You Chickens

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

“…The diversity indices in the 2 local populations were quite similar to the range reported for Italian ( Strillacci et al, 2017 ; Cendron et al, 2020 ), European ( Malomane et al, 2019 ), and other native chicken populations ( Evelyne et al, 2022 ; Yuan et al, 2022 ; Wang et al, 2023 ). However, the values differed from the results of a previous study ( Cendron et al, 2020 ), in which the authors reported lower values of heterozygosity and higher values of inbreeding for Cornuta di Sicilia and Val Platani populations.…”

“…The ROH-based genomic inbreeding coefficients of the 2 Sicilian chickens were similar to the estimates in other local populations ( Zhang et al, 2018 ; Yuan et al, 2022 ; Wang et al, 2023 ). Considering the pattern of ROH, the mean number and the average length of the segments identified in Cornuta and Val Platani were comparable to those reported in broiler chickens ( Marchesi et al, 2018 ).…”

“…ROH islands might be indicative of genomic regions underwent natural and/or artificial selection ( Mastrangelo et al, 2017 ). In chicken, several studies showed ROH regions harboring candidate genes associated with production traits, immune responses and environmental adaptation ( Fleming et al, 2016 ; Strillacci et al, 2018 ; Yuan et al, 2022 ; Wang et al, 2023 ). Given the variable polymorphism content, the homozygosity threshold to call a ROH island was different between the 2 populations, as well as reported in other studies on chickens ( Talebi et al, 2020 ).…”

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

“…Furthermore, calculated runs of homozygosity (ROHs; long continuous homozygous stretches composed of two identical haplotypes in each individual) are more useful for elucidating inbreeding and detecting selection signatures in different populations [ 7 , 8 ]. This approach has been reported in cattle [ 9 ], pigs [ 10 ], goats [ 11 ], and chickens [ 12 ]. The inbreeding coefficient based on ROH (F ROH ) is more accurate and more closely represents real inbreeding at the population and individual levels, and a long ROH is more likely to be a result of recent inbreeding than a shorter ROH [ 13 ].…”

“…The inbreeding coefficient based on ROH (F ROH ) is more accurate and more closely represents real inbreeding at the population and individual levels, and a long ROH is more likely to be a result of recent inbreeding than a shorter ROH [ 13 ]. Wang et al compared the ROH distribution in one selected and one natural chicken line, and ROH length and number were significantly greater in the selected line than in the natural line [ 12 ]. Yuan et al calculated ROH numbers and lengths in five Tibetan chickens and identified a common candidate region harboring the AMY2A, NTNG1, and VAV3 genes [ 14 ].…”