Table 4 Overlapping region among the ROH islands across commercials (layers, broilers) and Red Junglefowl
Chicken groupCHRStart position (bp)Stop position (bp)Number of SNPsSize (bp)Associated QTLAssociated GeneOverlapping region with Qanbari et al. 2019a
Layers22782671229293102631466.4
Broilers196797489972257881806428.5QTL:24387 “Antibody response to Newcastle virus”ROBO2
224570640251139522198217.3QTL:24925 “Eggshell color”GLCCI1, ICA1, UMAD1
225685016260728521515387.8QTL:24961 “Eggshell color”GLCCI1, ICA1, UMAD1
2133839172134258895994419.7
21434224821436911031602268.6RJFs/Coms, RJFs/LRs
384024798843607231401335.9
5300602673186349775081803.2QTL:153752 “Body weight 56 days”; QTL:14402 “Antibody titer to SRBC antigen”; QTL:15656 “Feather pecking”Meis2a.1, uc_338RJFs/Coms, RJFs/BRs, BRs/LRs
Red Junglefowl1562314955689000011264658.5
15732473359237097298511912.4QTL:57888 “Eggshell strength”; QTL:24832 “Visceral peritoneum pigmentation”ENSGALG00000034601, DNM1L, ENSGALG00000032288, ENSGALG00000032522, PTN, ENSGALG00000029704, CREB3L2, ENSGALG00000030026, DENND5B, ENSGALG00000037580, ENSGALG00000033096, IPO8, ENSGALG00000040988, CCDC77, WEE2, ENSGALG00000037563, C7orf73, SLC13A4, IQSEC3, ENSGALG00000039636, SSBP1, TMTC1, ENSGALG00000027056, FGD4, ENSGALG00000012947, gga-mir-1593, SLC6A12 KDM5A, gga-mir-490, ENSGALG00000019291, WASH1, ENSGALG00000035394, KIAA1147, FAM180A BICD1, gga-mir-6700, PKP2, ENSGALG00000012958, DGKI, AGK, ENSGALG00000035141, SYT10, AMN1 SLC6A13, MTPN, B4GALNT3, CHRM2, ENSGALG00000012969, NINJ2, ENSGALG00000034403, ENSGALG00000034718, ENSGALG00000012919, FAM60A
15926238660460076243111197.7QTL:57881,”Eggshell strength”; QTL:57882,”Eggshell strength”; QTL:57886,”Eggshell strength”; QTL:57887,”Eggshell strength”; QTL:57888,”Eggshell strength”; QTL:57892 “Eggshell thickness”; QTL:57893,”Eggshell thickness”; QTL:57894 “Eggshell thickness”; QTL:57895 “Eggshell thickness”; QTL:57896 “Eggshell thickness”
11163334531166750943428341.6
11911916721917406075886548.9QTL:64552 “Feed intake”
25231294952315876552.9
252841836528697702427.9
294716992949696462337252.7
2950700849512639267656.3
31170582211714324238.5
3122193701223231612012.9
386109072864068833322297.8
389916285907097577549793.5
41839737218778149923380.8QTL:24914 “Average daily gain”
541644677421397933630495.1
5422773474227915371.8
542432216427994414007367.2
72741556533623321379.2QTL:24982 “Age at sexual maturity”
  • a Overlapping ROH islands with the putative selective sweeps identified in Qanbari et al. 2019. RJFs/Coms: Red Junglefowls vs. Commercials; RJFs/LRs: Red Junglefowls vs. Layers; RJFs/BRs: Red Junglefowls vs. Broilers; BRs/LRs: Broilers vs. Layers.