## Table 6 |
|||||

Traits analyzed and their definitions and mode of calculation |
|||||

No^{a} |
G^{b} |
T^{c} |
ACR^{d} |
Definition |
Mode of calculation |

1 | NR^{k} |
NR^{k} |
WIC | Total weeks sampled | Total number of weeks sampled over the entire challenge period, according to batch number |

2 | P^{e} |
L | STR | Total observed parasitemia detections | Total number of observed weekly positive parasitemia detections over entire challenge period. |

3 | P^{e} |
L | STRTV | Total observed T. vivax detections |
Total number of observed positive T. vivax detections over entire challenge period. |

4 | P^{e} |
L | STRTC | Total observed T. congolense detections |
Total number of observed positive T congolense detections over entire challenge period. |

5 | P^{e} |
L | TPS | Sum of parasitemic scores | Sum of all parasitemic scores over the entire challenge period |

6 | P^{e} |
L | MPAR | Mean parasitemic score | TPS/STR |

7 | P^{e} |
L | %PARD | Percentage of weeks animal parasitemic | 100*STR/WIC |

8 | P^{e} |
L | NINF | Number of infection cycles | Total number of infection cycles, defined as number of new infections following initial exposure or treatment. |

9 | T^{f} |
L | NT | Number of treatments | Total number of treatments. If after first treatment PCV was still <18%, the animal was given a second treatment and this was counted as two treatments. |

10 | T^{f} |
L | NT1 | Number of treatments when PCV <18% | Total No. of treatments given when PCV <18% |

11 | T^{f} |
H | NIT | Proportion of non-treated parasitemia detections | (STR-NT)/STR |

12 | T^{f} |
L | MNT | Mean treatments per week | NT/WIC |

13 | T^{f} |
L | MNTI | Mean treatments per week when PCV<18% | NT1/WIC |

14 | IC^{1,g} |
H | DF1 | Days from exposure to first infection | No. of days from date animal is first exposed to tsetse challenge to date of first parasitemia detection |

15 | IC^{1,g} |
H | DT1 | Days from first infection to first treatment for that infection | No. of days from date of first parasitemia detection to date of first treatment for that infection (in some cases a second treatment was needed to control the infection). |

16 | IC^{1,g} |
H | DC1A | Length of first infection cycle, counting from exposure to treatment | DF1+DT1; This is length of first infection cycle counting from exposure to treatment. |

17 | IC^{1,g} |
H | DF2 | Days from first treatment to second infection | No. of days from date animal is first treated for first infection to date of second parasitemia detection (i.e., first parasitemia detection after final treatment for first infection). |

18 | IC^{1,g} |
H | DC1B | Length of first infection cycle counting from first infection | DT1+DF2; This is length of first infection cycle counting from first infection to second infection (after treatment for first infection). |

19 | IC^{1,g} |
H | DT2 | Days from second infection to treatment for that infection | No of days from second parasitemia detection to first treatment for that infection. |

20 | IC^{1,g} |
H | DC2A | Length of second infection cycle, counting from first treatment for first infection to first treatment for second infection. | DF2+DT2 |

21 | IC^{1,g} |
H | DC12 | Total length of first two infection cycles counting from exposure through first treatment for second infection. | DF1+DT1+DF2+DT2 = DC1A+DC2A |

22 | PC^{h} |
NR^{k} |
PCI | Initial PCV | Mean PCV of animal before challenge |

23 | PC^{h} |
H | MPC | Mean PCV | Mean PCV of animal during the entire challenge period |

24 | PC^{h} |
H | MXPC | Maximum PCV | Maximum PCV of animal during the entire challenge period |

25 | PC^{h} |
H | MNPC | Minimum PCV | Minimum PCV of animal during the entire challenge period |

26 | PC^{h} |
H | PCSR | PCV at first screening | PCV of animal when first screened |

27 | PC^{h} |
H | PCF1 | PCV at first infection | PCV of animal at first parasitemic detection |

28 | PC^{h} |
H | PCT1 | PCV at the first treatment | PCV of animal when first treated after first detection of parasitemia |

29 | PC^{h} |
H | PCF2 | PCV at the second infection | PCV of animal when infected for second time |

30 | PC^{h} |
H | PCT2 | PCV at second treatment | PCV of animal when treated after second infection |

31 | PC^{h} |
H^{2} |
PCIF1 | PCV change from before exposure to PCV at first infection | PCF1-PCI |

32 | PC^{h} |
H^{2} |
PCF1T1 | PCV change from first infection to PCV at first treatment | PCT1-PCF1 |

33 | PC^{h} |
H^{2} |
PCIT1 | PCV change from before exposure to PCV at first treatment | PCT1-PCI |

34 | PC^{h} |
L,H^{3} |
PCT1F2 | PCV change from first treatment to second infection | PCF2- PCT1 |

35 | WT^{i} |
NR^{k,4} |
WTI | Initial body weight | Mean of body weight of animal before challenge (within a month before exposure) |

36 | WT^{i} |
NR^{k,4} |
MWT | Mean body weight | Mean of body weight of animal during entire challenge period |

37 | WT^{i} |
NR^{k,4} |
MXWT | Maximum body weight | Maximum body weight during the entire challenge period |

38 | WT^{i} |
NR^{k,4} |
MNWT | Minimum body weight | Minimum body weight during the entire challenge period |

39 | WT^{i} |
NR^{k,4} |
WTF1 | Body weight at time of first infection | Body weight of animal at time of first parasitemia detection after initial exposure |

40 | WT^{i} |
NR^{k,4} |
WTT1 | Body weight at first treatment | Body weight of animal at first treatment |

41 | WT^{i} |
NR^{k,4} |
WTF2 | Body weight at second infection | Body weight of animal at second infection (i.e., at first parasitemia detection after first treatment) |

42 | WT^{i} |
NR^{k,4} |
WTE | Body weight at end of challenge period | Body weight of the animal in the last month of tsetse challenge period |

43 | WTC^{j} |
H^{2} |
WTIF1 | Body weight change from initial body weight to first infection | WTF1 - WTI |

44 | WTC^{j} |
H^{2} |
WTIT1 | Body weight change from initial body weight to weight at first treatment | WTT1 - WTI |

45 | WTC^{j} |
NR^{k,4} |
WTC | Mean Body weight change during challenge period | MWT - WTI |

46 | WTC^{j} |
NR^{k,4} |
WTC-W | Mean Body weight change per week during challenge | (WTC)/WIC |

47 | WTC^{j} |
H^{2} |
WTF1T1 | Body weight change from first infection to first treatment | WTT1 – WTF1 |

48 | WTC^{j} |
H^{2} |
WTT1F2 | Body weight change from first treatment to second infection | WTF2 - WTT1 |

49 | WTC^{j} |
H | WT1E | Body weight changefrom start to end of challenge period | WTE – WT1 |

^{a}trait number; ^{b}trait group; ^{c}direction of effect on trypanotolerance, i.e., whether high (H) or low (L) trait value
is associated with greater trypanotolerance; ^{d}trait acronym. Trait groups: ^{e} parasitemia; ^{f}treatments; ^{g}infection cycles; ^{h}PCV; ^{i}body weight; ^{j}body weight change; ^{k}not primarily related to trypanotolerance.

^{1} First infection cycle counted from first detection of parasitemia after initial exposure
to challenge to treatment of first infection; second infection cycle counted from
first detection of parasitemia after treatment of first infection to treatment for
second infection; third infection cycle counted from first detection of parasitemia
after treatment for second infection, to treatment for third infection, and so on.
If challenge period ended after infection but before treatment, this was counted as
a complete infection cycle.

^{2}Change generally negative. Therefore, a high algebraic value (i.e., small negative-value)
means greater trypanotolerance, a low algebraic value (large negative-value) means
lower trypanotolerance.

^{3} If the animal is susceptible there will be a large drop from infection to treatment,
and hence a large bounce back after treatment. If the animal is tolerant, there will
be a lower drop from infection to treatment (although still PCV <18%) and hence not
so large a bounce back after treatment. Thus, a low value means greater trypanotolerance.
However, it could also go the other way – following treatment a susceptible animal
may not recover to the same extent as a tolerant animal.

^{4}Traits 35 to 42, and 45, 46 are considered to be primarily affected by variation in
body weight due to segregation of body weight QTL derived from the Boran and N’Dama,
rather than by trypanotolerance QTL.

Orenge * et al.*

Orenge * et al.* *BMC Genetics* 2012 **13**:87 doi:10.1186/1471-2156-13-87