B)Gga-Mir-6604 and 28 Overlapping QTL

Supplementary Figure S3.Genomic overlaps of five miRNA genes and 115 QTL in chicken. Overlapping QTL are presented in a condensed view, extended view and in a table.

a)gga-mir-6578 and 21 overlapping QTL

QTL / Trait / Location / Peak (cM) / QTL length (bp)
BW / Body weight (35 days) / 3:6645961-106970113 / 53.4 / 100324152
BW / Body weight / 3:37579996-108174898 / 158 / 70594902
BW / Body weight / 3:37579996-108174898 / 158 / 70594902
TIBPA / Tibia plateau angle / 3:84765752-106970113 / - / 22204361
TA / Tibia area / 3:96400522-108987649 / 292 / 12587127
TL / Tibia length / 3:96400522-108987649 / 292 / 12587127
ADG / Average daily gain / 3:98112208-110447801 / - / 12335593
CW / Carcass weight / 3:98112208-110170324 / - / 12058116
CHWID / Chest width / 3:98112208-108987649 / - / 10875441
GROW / Growth (post-challenge) / 3:98112208-106970113 / 276.8 / 8857905
PLASCO / Plasma coloration / 3:98112208-106970113 / 276.8 / 8857905
BW / Body weight (40 days) / 3:103804757-108174898 / - / 4370141
RFI / Residual feed intake / 3:103804757-108174898 / - / 4370141
BW / Body weight (70 days) / 3:103804764-108174898 / 277.7 / 4370134
BW / Body weight (84 days) / 3:103804764-108174898 / 277.7 / 4370134
BW / Body weight (42 days) / 3:103804764-108174898 / 278.8 / 4370134
BW / Body weight (77 days) / 3:103804764-108174898 / 278.8 / 4370134
BW / Body weight (49 days) / 3:103804764-108174898 / 279.8 / 4370134
CW / Carcass weight / 3:103804764-108174898 / 279.8 / 4370134
BW / Body weight (21 days) / 3:103804810-108174898 / - / 4370088
ADG / Average daily gain / 3:103804764-106970113 / - / 3165349

b)gga-mir-6604 and 28 overlapping QTL

QTL / Trait / Location / Peak (cM) / QTL length(bp)
SHKDIA / Shank diameter / 6:5574630-34951654 / 78 / 29377024
BTEMP / Body temperature / 6:4518765-33756171 / 59 / 29237406
LSS / Egg shell lightness / 6:3958223-29735045 / 31 / 25776822
RSS / Egg shell redness / 6:3958223-29735045 / 31 / 25776822
YSS / Egg shell yellowness / 6:3958223-29735045 / 31 / 25776822
VISAT / Visceral fat weight / 6:5555768-31244082 / 75.7 / 25688314
SCNF / Subcutaneous neck fat weight / 6:5686738-31192890 / 86.1 / 25506152
ABR-SRBC / Antibody response to SRBC antigen / 6:5574630-29735045 / 70 / 24160415
ABR-SRBC / Antibody response to SRBC antigen / 6:5574630-29735045 / 70 / 24160415
PLASCO / Plasma coloration / 6:14060241-34951654 / 77.6 / 20891413
HCT / Hematocrit value / 6:14060241-34951654 / 85.3 / 20891413
GL / Glucose level / 6:3958223-23888202 / 34 / 19929979
TWF / Total white fat weight / 6:8097069-27391590 / 63.3 / 19294521
BW / Body weight / 6:14060241-31613296 / 90 / 17553055
FEMWT / Femur weight / 6:13779970-26971183 / - / 13191213
TIBMD / Tibia marrow diameter / 6:13779970-26971183 / - / 13191213
BMWT / Breast muscle weight / 6:13779970-26971183 / - / 13191213
DRTHMW / Drumstick and thigh muscle weight / 6:13779970-26971183 / - / 13191213
DRTHMW / Drumstick and thigh muscle weight / 6:13779970-26971183 / - / 13191213
BW / Body weight (42 days) / 6:13779970-26971183 / - / 13191213
BW / Body weight (336 days) / 6:13779970-26971183 / - / 13191213
ADG / Average daily gain / 6:13779970-26971183 / - / 13191213
DSMWT / Drumstick muscle weight / 6:13779970-26971183 / 87 / 13191213
BW / Body weight / 6:13779970-26971183 / 91 / 13191213
BW / Body weight / 6:13779970-26971183 / 91 / 13191213
HBMC / Humerus bone mineral content / 6:18831832-29735045 / 72 / 10903213
HBMD / Humerus bone mineral density / 6:18831832-29735045 / 87 / 10903213
ABR-BA / Antibody response to BA (Brucella abortus) / 6:17197020-27588570 / 67.5 / 10391550

c)gga-mir-6565and 19 overlapping QTL

QTL / Trait / Location / Peak (cM) / QTL length(bp)
MD / Marek's disease-related traits / Z:20657675-70171166 / 49513491
AFE / Age at first egg / Z:36707738-69690210 / 109 / 32982472
ESS / Egg shell strength / Z:36707738-69690210 / 128 / 32982472
AF / Abdominal fat weight / Z:48390730-64537110 / 16146380
DRTHMW / Drumstick and thigh muscle weight / Z:48390730-64537110 / 16146380
DRTHMW / Drumstick and thigh muscle weight / Z:48390730-64537110 / 16146380
BW / Body weight (day of first egg) / Z:48390730-64537110 / 16146380
AF / Abdominal fat weight / Z:48390730-64537110 / 16146380
BDPTH / Body depth / Z:48390730-64537110 / 16146380
DSMWT / Drumstick muscle weight / Z:48390730-64537110 / 129 / 16146380
DSWT / Drumstick weight / Z:48390730-64537110 / 137 / 16146380
WINGWT / Wing weight / Z:48390730-64537110 / 141 / 16146380
INTES / Intestine length / Z:48390730-64537110 / 142 / 16146380
BW / Body weight (84 days) / Z:48390730-64537110 / 155 / 16146380
BW / Body weight (42 days) / Z:48390730-64537110 / 157 / 16146380
BW / Body weight (21 days) / Z:48390730-64537110 / 165 / 16146380
BW / Body weight (168 days) / Z:48390730-64537110 / 165 / 16146380
BW / Body weight / Z:48390730-64537110 / 165 / 16146380
BW / Body weight / Z:48390730-64537110 / 165 / 16146380

d)gga-mir-3538 and 33 overlapping QTL

QTL / Trait / Location / Peak (cM) / QTL length(bp)
AFE / Age at first egg / 1:37432130-186521273 / 285.2 / 149089143
SCFT / Subcutaneous fat thickness / 1:6448968-155027633 / 148578665
TWF / Total white fat weight / 1:25275933-171021359 / 78.2 / 145745426
EW / Egg weight / 1:25275933-165299647 / 143.8 / 140023714
EW / Egg weight / 1:25275933-161927460 / 144.8 / 136651527
SPLWT / Spleen weight / 1:37326855-171731178 / 401.9 / 134404323
VISAT / Visceral fat weight / 1:25275933-154045063 / 76.2 / 128769130
SHKLN / Shank length / 1:2329958-128331586 / 331.7 / 126001628
EW / Egg weight / 1:25275933-143852773 / 142 / 118576840
SHKLN / Shank length / 1:39249672-156472083 / 117222411
CW / Carcass weight / 1:25661943-139799837 / 203.4 / 114137894
BW / Body weight (140 days) / 1:33174045-134863919 / 193.5 / 101689874
SCNF / Subcutaneous neck fat weight / 1:25661943-114496420 / 83.6 / 88834477
CFWID / Cingular fat width / 1:6448968-94157976 / 87709008
ABR-SRBC / Antibody response to SRBC antigen / 1:6448968-84531095 / 259 / 78082127
BW / Body weight (63 days) / 1:2329958-64931354 / 81.5 / 62601396
DRTHW / Drumstick and thigh weight / 1:38695435-99079318 / 183.7 / 60383883
BW / Body weight / 1:28436329-63038738 / 141 / 34602409
BW / Body weight / 1:28436329-63038738 / 141 / 34602409
SHKLN / Shank length / 1:20864784-55261640 / 133 / 34396856
EN / Egg number / 1:42474406-63038738 / 145 / 20564332
EW / Egg weight / 1:47508279-64510252 / 149.2 / 17001973
Fear-walk / Fear-walk latency / 1:35456034-51915144 / 118.5 / 16459110
BCo / Breast color / 1:48175152-63038738 / 199.2 / 14863586
MD / Marek's disease-related traits / 1:40056783-51802185 / 128.4 / 11745402
BW / Body weight / 1:42474406-52428237 / 123 / 9953831
BSLEN / Body slope length / 1:42474406-51977644 / 9503238
HU / Haugh units / 1:48175152-53130073 / 143 / 4954921
BW / Body weight (40 days) / 1:47367912-51977644 / 4609732
CS / Conformation score / 1:47367912-51977644 / 4609732
BW / Body weight (200 days) / 1:47438096-51599318 / 131.6 / 4161222
AF / Abdominal fat weight / 1:48175152-51977644 / 3802492
DSWT / Drumstick weight / 1:48175152-51977644 / 145 / 3802492

e)gga-mir-6558 and 14 overlapping QTL

QTL / Trait / Location / Peak (cM) / QTL length(bp)
BW / Body weight (63 days) / 9:6503007-23441680 / 122.3 / 16938673
SHKDIA / Shank diameter / 9:6503007-23441680 / 126.5 / 16938673
EW / Egg weight / 9:5519312-21670350 / 59.7 / 16151038
EW / Egg weight / 9:4759086-20592955 / 62.8 / 15833869
ABR-SRBC / Antibody response to SRBC antigen / 9:1913910-15123057 / 70 / 13209147
BW / Body weight / 9:5124631-18131981 / 73 / 13007350
AF / Abdominal fat weight / 9:13658592-23441680 / 9783088
BW / Body weight (336 days) / 9:13658592-23441680 / 81 / 9783088
BW / Body weight (84 days) / 9:13658592-23441680 / 90 / 9783088
ADG / Average daily gain / 9:13658592-23441680 / 97 / 9783088
FI / Feed intake / 9:5701807-15123057 / 56 / 9421250
WINGWT / Wing weight / 9:12930630-19669473 / 6738843
BW / Body weight (200 days) / 9:13658592-19669473 / 6010881
GROW / Growth (46-112 days) / 9:13658592-19669473 / 6010881

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