Table 5. QTL detected for microbiota composition.
QTL number | Trait | GGA | Position (M) | Confidence interval (M) 1 | Markers flanking the confidence interval | NF 2 | Effect 4 | Chromosomewide P level | Genome wide P level | N genes in the region 6 |
---|---|---|---|---|---|---|---|---|---|---|
1 | Log(L. crispatus)/ Log(C. coccoides) | 1 | 2.560 | 2.541–2.567 | Gga_rs13911828, GGa_rs13913250 | 3F 3 | 0.814 | 0.048 | NS 5 | 14 |
2 | Log(C. leptum)/ Log(Lactobacillus) | 2 | 2.390 | 2.325–2.400 | Gga_rs15142674, GgaluGA164535 | 5 | 0.552 | 0.047 | NS | 42 |
3 | Log(L. salivarius)/ Log(Lactobacillus) | 3 | 2.320 | 2.301–2.336 | Gga_rs16324984, Gga_rs14399484 | 2 | 0.860 | 0.037 | NS | 18 |
4 | Log(L. crispatus)/ Log(C. leptum) | 6 | 0.630 | 0.581–0.839 | Gga_rs14579919, Gga_rs15807987 | 3 | 0.677 | 0.028 | NS | 220 |
5 | Log(C. leptum) | 6 | 0.920 | 0.912–0.950 | Gga_rs15813564, Gga_rs16565135 | 6 | 0.895 | <0.0001 | 0.090 | 36 |
6 | Log(C. leptum)/ Log(Lactobacillus) | 6 | 0.980 | 0.620–1.009 | GgaluGA300856, Gga_rs16006607 | 5 | 0.903 | 0.043 | NS | 306 |
7 | Log(C. leptum)/ Log(Lactobacillus) | 8 | 0.600 | 0.000–0.141 | Gga_rs15892308, GgaluGA323478 | 4F | 0.605 | 0.023 | NS | 129 |
8 | Log(Coli)/ Log(Lactobacillus) | 12 | 0.090 | 0.081–0.115 | Gga_rs15632811, Gga_rs14032854 | 4F | 0.520 | 0.029 | NS | 50 |
9 | Log(L. crispatus)/ Log(C. coccoides) | 14 | 0.240 | 0.235–0.246 | GgaluGA101400, GgaluGA101629 | 3 | 0.897 | 0.029 | NS | 8 |
10 | Log(L. crispatus) | 14 | 0.240 | 0.235–0.244 | GgaluGA101400, Gga_rs14074053 | 2F | 1.241 | 0.019 | NS | 6 |
11 | Log(L. salivarius)/ Log(Lactobacillus) | 14 | 0.480 | 0.440–0.561 | Gga_rs15738570, GgaluGA104485 | 3 | 0.591 | 0.014 | NS | 64 |
12 | Log(C. leptum)/ Log(C. coccoides) | 18 | 0.153 | 0.143–0.324 | GgaluGA119123, GgaluGA121355 | 4 | 0.476 | 0.048 | NS | 152 |
13 | Log(L. salivarius)/ Log(C. leptum) | 21 | 0.480 | 0.429–0.520 | Gga_rs14285137, Gga_rs14286198 | 3F | 0.605 | 0.045 | NS | 53 |
14 | Log(L. salivarius)/ Log(Lactobacillus) | 26 | 0.310 | 0.268–0.344 | GgaluGA196721, Gga_rs15235289 | 3 | 0.532 | 0.048 | NS | 74 |
1 1-LOD-drop off confidence interval (lower and upper boundaries, cM)
2 Number of F1 sires families heterozygous for the QTL (P<0.05, Student test)
3 F: the QTL is fixed in F1 sires families in which it is significant
4 QTL effect as a proportion of the phenotypic standard deviation of trait
5 NS: P>0.150 at the genome wide level
6 Number of genes in the QTL region, as found by http://annotqtl.genouest.org/ interrogation