Table 1 Literature review of ROH analysis settings on livestock species using medium density genotypes
Author | Species | LD pruning level (R2) | MAF pruning level | --homozyg-window | --homozyg | ||||
|---|---|---|---|---|---|---|---|---|---|
-snp | -threshold | -gap (kb) | -snp | -kb | -density (kb/SNP) | ||||
Bosse et al. (2012) [9] | Pig | – | – | 20 | 0.25 | – | 20 | 10 | 1000 |
Ai et al. (2013) [10] | Pig | – | 0.05 | 50 | – | – | – | 500 | – |
Bjelland et al. (2013) [11] | Cattle | > 0.5 | 0.05 | 30 | – | – | 30 | – | – |
Herrero-Medrano et al. (2013) [12] | Pig | – | – | – | – | 1000 | 20 | 10 | 1000 |
Biscarini et al. (2014) [13] | Cattle | – | – | – | – | 1000 | – | – | – |
Scraggs et al. (2014) [14] | Cattle | – | 0.05 | 50 | – | – | 50 | 1000 | – |
Zhang et al. (2010) [15] | Pig | > 0.5 | 0.01 | – | – | 1000 | 10 | 5000 | 500 |
Al-Mamun et al. (2015) [16] | Sheep | – | 0.01 | 1000 | – | 250 | – | 500 | – |
Mészáros et al. (2015) [17] | Cattle | – | 0.01 | – | – | – | 30 | 1000 | – |
Muchadeyi et al. (2015) [18] | Sheep | – | 0.05 | – | – | 500 | 20 | – | 50 |
Rodríguez-Ramilo et al. (2015) [19] | Cattle | – | – | – | – | 1000 | 30 | 4000 | 100 |
Zhang et al. (2015) [20] | Cattle | – | – | 20 | – | – | – | 10 | 1000 |
Zanella et al. (2016) [21] | Pig | – | 0.03 | 50 | – | – | 50 | 1000 | – |
François et al. (2017) [22] | Cattle | > 0.5 | 0.01 | 50 | – | 1000 | 45 | 500 | 120 |
Purfield et al. (2017) [23] | Sheep | – | 0.01 | 50 | – | 250 | – | 1000 | 100 |
Yang et al. (2017) [24] | Pig | – | 0.01 | 50 | – | – | – | 500 | – |
Bortoluzzi et al. (2018) [25] | Chicken | – | 0.00a | 30 | – | 1000 | – | 10 | 1000 |
Kumar et al. (2018) [26] | Goat | – | 0.01 | – | – | 1000 | – | – | 70 |
Mastrangelo et al. (2018) [27] | Sheep | – | 0.01 | – | – | 250 | 30 | 1000 | 100 |
Michailidou et al. (2018) [28] | Sheep | – | 0.01 | – | – | – | 20 | – | – |
Zhang et al. (2018) [29] | Pig | – | 0.05 | 50 | – | 250 | Lb | 1000 | 100 |
Gorssen et al. (2020) [30] | Pig | – | – | Lb | – | 1000 | Lb | 1000 | 150 |
Meyermans et al. (2020) [31] | Sheep | – | – | 50 | 0.05 | 200 | Lb | 1000 | 250 |