Table 6

Traits analyzed and their definitions and mode of calculation
Noa Gb Tc ACRd Definition Mode of calculation
1 NRk NRk WIC Total weeks sampled Total number of weeks sampled over the entire challenge period, according to batch number
2 Pe L STR Total observed parasitemia detections Total number of observed weekly positive parasitemia detections over entire challenge period.
3 Pe L STRTV Total observed T. vivax detections Total number of observed positive T. vivax detections over entire challenge period.
4 Pe L STRTC Total observed T. congolense detections Total number of observed positive T congolense detections over entire challenge period.
5 Pe L TPS Sum of parasitemic scores Sum of all parasitemic scores over the entire challenge period
6 Pe L MPAR Mean parasitemic score TPS/STR
7 Pe L %PARD Percentage of weeks animal parasitemic 100*STR/WIC
8 Pe L NINF Number of infection cycles Total number of infection cycles, defined as number of new infections following initial exposure or treatment.
9 Tf 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 Tf L NT1 Number of treatments when PCV <18% Total No. of treatments given when PCV <18%
11 Tf H NIT Proportion of non-treated parasitemia detections (STR-NT)/STR
12 Tf L MNT Mean treatments per week NT/WIC
13 Tf L MNTI Mean treatments per week when PCV<18% NT1/WIC
14 IC1,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 IC1,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 IC1,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 IC1,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 IC1,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 IC1,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 IC1,g H DC2A Length of second infection cycle, counting from first treatment for first infection to first treatment for second infection. DF2+DT2
21 IC1,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 PCh NRk PCI Initial PCV Mean PCV of animal before challenge
23 PCh H MPC Mean PCV Mean PCV of animal during the entire challenge period
24 PCh H MXPC Maximum PCV Maximum PCV of animal during the entire challenge period
25 PCh H MNPC Minimum PCV Minimum PCV of animal during the entire challenge period
26 PCh H PCSR PCV at first screening PCV of animal when first screened
27 PCh H PCF1 PCV at first infection PCV of animal at first parasitemic detection
28 PCh H PCT1 PCV at the first treatment PCV of animal when first treated after first detection of parasitemia
29 PCh H PCF2 PCV at the second infection PCV of animal when infected for second time
30 PCh H PCT2 PCV at second treatment PCV of animal when treated after second infection
31 PCh H2 PCIF1 PCV change from before exposure to PCV at first infection PCF1-PCI
32 PCh H2 PCF1T1 PCV change from first infection to PCV at first treatment PCT1-PCF1
33 PCh H2 PCIT1 PCV change from before exposure to PCV at first treatment PCT1-PCI
34 PCh L,H3 PCT1F2 PCV change from first treatment to second infection PCF2- PCT1
35 WTi NRk,4 WTI Initial body weight Mean of body weight of animal before challenge (within a month before exposure)
36 WTi NRk,4 MWT Mean body weight Mean of body weight of animal during entire challenge period
37 WTi NRk,4 MXWT Maximum body weight Maximum body weight during the entire challenge period
38 WTi NRk,4 MNWT Minimum body weight Minimum body weight during the entire challenge period
39 WTi NRk,4 WTF1 Body weight at time of first infection Body weight of animal at time of first parasitemia detection after initial exposure
40 WTi NRk,4 WTT1 Body weight at first treatment Body weight of animal at first treatment
41 WTi NRk,4 WTF2 Body weight at second infection Body weight of animal at second infection (i.e., at first parasitemia detection after first treatment)
42 WTi NRk,4 WTE Body weight at end of challenge period Body weight of the animal in the last month of tsetse challenge period
43 WTCj H2 WTIF1 Body weight change from initial body weight to first infection WTF1 - WTI
44 WTCj H2 WTIT1 Body weight change from initial body weight to weight at first treatment WTT1 - WTI
45 WTCj NRk,4 WTC Mean Body weight change during challenge period MWT - WTI
46 WTCj NRk,4 WTC-W Mean Body weight change per week during challenge (WTC)/WIC
47 WTCj H2 WTF1T1 Body weight change from first infection to first treatment WTT1 – WTF1
48 WTCj H2 WTT1F2 Body weight change from first treatment to second infection WTF2 - WTT1
49 WTCj H WT1E Body weight changefrom start to end of challenge period WTE – WT1

atrait number; btrait group; cdirection of effect on trypanotolerance, i.e., whether high (H) or low (L) trait value is associated with greater trypanotolerance; dtrait acronym. Trait groups: e parasitemia; ftreatments; ginfection cycles; hPCV; ibody weight; jbody weight change; knot 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.

2Change 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.

4Traits 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

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