CSIRO PUBLISHING
Animal Production Science http://dx.doi.org/10.1071/AN16450
Using temporal associations to determine maternal parentage in extensive beef herds D. Menzies A,B, K. P. Patison A, N. J. Corbet A and D. L. Swain A A
Central Queensland University, School of Medical and Applied Sciences, Precision Livestock Management Research Group, Rockhampton, Qld 4702, Australia. B Corresponding author. Email:
[email protected]
Abstract. The assignment of maternal parentage, although time-consuming and expensive using traditional methods, is essential for genetic improvement. Within the sheep industry the recording of time-based (temporal) associations without human intervention has been routinely used to derive maternal parentage, however it has not been researched in extensive beef production systems. To determine whether temporal associations could be used to assign maternal parentage, cows and calves had their identity recorded as they walked to water over a 27-day trial. Two methods of association were investigated, being the half-weight index and the time difference between a cow and calf having their identity recorded. The half-weight index, which is a measure of the number of times two individuals are recorded together, correctly assigned greater than 90% of maternal pairs. When investigating the duration of data recording it was shown that 85% of maternal parentage could be achieved within only 21 days. Further work is required to determine the effect of calf age, herd and paddock size; however, the results showed that the half-weight index method of determining maternal associations is a labour-saving and accurate alternative to traditional methods used to identify maternal parentage. Additional keywords: maternal parentage, mothering-up, Walk-over-Weighing technology.
Received 15 July 2016, accepted 28 October 2016, published online 30 January 2017
Introduction Genetic selection depends on the assignment of pedigree. Within extensive livestock production systems the recording of maternal parentage is an expensive and laborious process. Although the autonomous recording of animal associations has previously been used to deduce maternal parentage in the sheep industry, this technique has not been used in extensive beef production systems. Visual observations and telemetry data have shown that maternal association patterns are complex and variable. Swain and Bishop-Hurley (2007) used proximity loggers to measure close-proximity encounters between cows and their calves and showed that there were significant differences in both the frequency and total daily duration of encounters between a cow and its own calf and all other unrelated calves. Although both observational and telemetry data have provided valuable knowledge on livestock association patterns they are constrained by the inability to monitor large numbers of individuals in a more commercial setting. Genetic improvement requires information on pedigree, both maternal and paternal parents. Maternal parentage is typically assigned in seedstock operations by observing cows with newborns during daily calving checks; by observing cow/calf suckling pairs after a period of separation or by using DNA fingerprinting (Northern Territory Government 2009; Tropical Beef Technology Services 2014). Journal compilation CSIRO 2017
A major factor limiting the generation of parentage information in rangeland production systems is the time and expense involved in recording the data (Corrigan and Parnell 2006; Bell et al. 2013). Often the accuracy of the pedigree information, in particular maternal parentage and birth date, are compromised due to issues with cross-suckling and mismothering, which can be exacerbated by the interruption caused by physically recording parentage data (Dodds et al. 2005). There is also a potential safety issue with tagging neonatal calves when mothers can become very physical and defensive to protect their offspring (Drake et al. 2009). Although obtaining DNA samples and cross matching genetic material provides the most accurate data, it is expensive as well as labour intensive to collect and process hair samples from each individual animal for DNA analysis (Northern Territory Government 2009). Thus, developing an autonomous data collection method capable of accurately determining parentage information would enhance current management practices and meet industry needs. Radio frequency identification (RFID) of individual animals, through the mandatory introduction of the National Livestock Identification System in Australian cattle production systems, has enabled beef producers to more efficiently record performance data (McKellar 2012). Walk-over-Weighing (WoW) systems, which include RFID readers and liveweight scales to record an animal’s identity and weight in a paddock situation, are being www.publish.csiro.au/journals/an
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trialled at five locations in northern Australia (Cooperative Research Centre for Remote Economic Participation - NintiOne 2016). These systems are located at watering points and use a one-way race to force cattle to traverse a weigh platform thereby capturing an animal’s weight potentially on a daily basis. Within the sheep industry, the temporal sequence with which sheep walk to water and have their RFID number recorded has been used to derive maternal parentage (Richards and Atkins 2007; Richards et al. 2007). The commercialised system, known as Pedigree Matchmaker, relies on ewes coming to water in closer temporal proximity to their own lamb compared with unrelated lambs. There is, however, little published data on how the associations are derived and the accuracy of the mothering-up algorithm. The objective of this study was to assess whether maternal parentage could be derived based on the temporal frequency that cows and calves visit water using RFID technology to record their identity. The hypothesis was that temporal measures of association would be stronger in maternal than non-maternal pairs thereby enabling maternal parentage to be correctly assigned.
Materials and methods Animals All procedures used in the study were approved by the CQUniversity Animal Ethics Committee (approval number A14/09–315). The experiment was conducted at Belmont Research Station (150130 E, 2380 S), ~26 km north of Rockhampton, Qld, Australia. The small-scale study used 41 pluriparous Belmont Red (tropically adapted Bos taurus) cows and their progeny. The cattle had ad libitum access to pasture and water within a 22-ha paddock. The herd calved from 20 October 2014 until 20 January 2015. Maternal parentage was recorded, based upon visual observations, within 48 h of birth during daily inspections of the herd over the calving period. The data recorded at birth included cow identity and description, and calf identity, description, sex and weight. In addition to the assignment of maternal parentage by observation, hair samples were collected from 40 cows and 33 calves after the completion of the experimental data collection period for DNA extraction and parentage verification. The DNA analysis was considered the ‘gold standard’ in determining maternal parentage but not all cows and calves had DNA samples collected due to animals being removed from the herd following weaning. The DNA samples were analysed by the Animal Genetics Laboratory at the University of Queensland using 21 microsatellite markers, which is a recommendation of the International Society for Animal Genetics (ISAG 2012). There were therefore two maternal parentage lists, the visually observed maternal pairs containing 41 cows and 38 calves and the DNA assigned maternal pairs containing 40 cows and 33 calves, both of which were used to assess the accuracy of the temporal frequency data to assign maternal parentage. The DNA-verified data from this study clarified that one of the visually recorded cow/calf pairs was in fact incorrect with the correct maternal pair identified.
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Data collection A WoW compound was built around the water trough within the paddock the cattle grazed. Animals were trained to pass through a race to enter the compound and access water. As each animal walked over the WoW platform to access the watering point their RFID, weight, date and time was captured. An Aleis (Aleis, Capalaba, Qld, Australia) 8051 RFID reader captured the RFID number and a Tru-Test (Tru-Test Limited, Auckland, New Zealand) WoW platform captured the weight with a Tru-Test XR3000 indicator storing the weight and RFID. The system was powered by an 80-Watt solar panel with a solar regulator providing constant power to the indicator and RFID reader, and a 12-v 100-Ah AGM deep cycle battery stored excess power. To ensure one-directional flow through the WoW compound, spear gates (one-way gates) were installed at the end of the entry race after the WoW platform and at a separate exit point from the compound (Fig. 1). To confirm all animals were familiar with the system, they were trained for 21 days before data collection beginning. Animals were considered familiar when they voluntarily moved through the race and crossed the weigh platform without any human intervention. At the commencement of the experimental data collection on 1 April 2015, there were 41 cows and 38 calves with the calves aged between 2.5 and 5.5 months. Calves had RFID tags applied and the cow’s RFID tags were checked before data collection starting. Data processing and statistical analyses At the end of the 27 days of data collection, data were downloaded from the Tru-Test XR3000 indicator, using the Tru-Test Link3000 software, as a comma separated values file. The downloaded comma separated values file was processed and analysed using R Foundation for Statistical Computing (R Core Team 2014). The first four rows of header information; data before 1 April and rows of data that did not contain an RFID number was removed from the dataset. The date and time columns were combined into a single column. RFID numbers not associated with the trial animals were removed from the dataset; these numbers were from test tags that were used to manually check the system was functioning correctly. Preliminary statistics were calculated to determine the number of RFID reads for cows and calves and the different calf sexes to ascertain the frequency with which they had their identity recorded. Using time difference between RFID reads to identify maternal parentage The first temporal measure of association compared the average time that elapsed from when a cow and each calf passed the RFID reader throughout the data collection period. This was achieved by scanning all records for each cow RFID and calculating the average time between that cows RFID being read and each calf RFID being read. Starting with the first cow, the calf with the shortest mean time was determined and they were allocated as a cow/calf pair. These two animals were then removed from the dataset before the code re-iterated and searched for the shortest mean time between the second
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Fig. 1. Image of the Walk-over-Weighing (WoW) system showing the first cow pushing through the entry spear gates, the second cow stepping onto the weigh platform and a calf following.
cow and calf, and continued until all calves were assigned to a cow. These data were allocated as maternal and non-maternal pairs, and the percentage of correctly assigned pairs determined, based on both the visually recorded and the DNA assigned maternal pairs. The mean and s.e.m. of time interval between RFID reads for the maternal and non-maternal pairs was calculated. The data was checked for normality using the Shapiro–Wilk Normality Test and the Mann–Whitney statistical test used to determine whether the means for the maternal and non-maternal pairs were significantly different at P < 0.05 level. Using half-weight index to identify maternal parentage The second temporal measure of association compared the half-weight index (HWI) scores of all cow and calf combinations. The HWI calculated pairwise associations based on the number of times two individuals passed the RFID reader within a predefined time period, and compared it to the total number of times that each individual passed the RFID reader (Cairns and Schwager 1987). If two individuals always passed the RFID reader within the predefined time period they would have a HWI association of 1 and if they never passed the RFID reader within the predefined time period their HWI would be 0, such that: x HWI ¼ x þ 0:5ðYa þ Yb Þ where x is the total number of times animals A and B are identified passing the RFID reader within the predefined time interval, Ya the number of encounters where cow A passed the RFID reader but not calf B and Yb the number of encounters where calf B passed the RFID reader but not cow A. An algorithm was written to interrogate the dataset looking for each cow RFID and then calculating which calf RFID’s were seen within a predefined time frame. Once the HWIs were assigned, the dataset was sorted by the HWI score and the cow and calf with the strongest HWI were allocated as a cow/calf pair. Each subsequent iteration found the next strongest HWI cow/calf pair, but only if they had not already been allocated in
a previous iteration. The allocated cow/calf pairs were then compared with the maternal pairs, derived by either the visual assignment or DNA assignment methods, to ascertain the maternal parentage percentage. The use of the HWI measure of association is often based on a spatial association, such as cows within 20 m of each other (Finger et al. 2014). Our study used the time of RFID readings as a measure of proximity but rather than settle on a single time period in which RFID tags had to be recorded, a range of time periods were tested. To identify the optimal time period to assign cow/calf pairs, the HWI was calculated for time periods from 1 to 20 min. Thus, a HWI was calculated for all cows and calves that had their RFID read within the specified time interval. Once the maternal parentage percentages had been calculated for all 20 time intervals the results were graphed to determine the optimal time period for both the visual assignment and DNA assignment methods. Assessing the effect of duration of data capture on derived maternal parentage Following the calculation of the percentage of maternal pairs using the HWI, the effect of varying the duration of data capture was assessed on the derived maternal parentage. Using the optimal time interval for the visually assigned and DNA assigned datasets, the percentage of maternal pairs was calculated for 7, 14 and 21 days of data capture and compared with that derived for the full trial duration. Results In the data collection period there were 2556 data points recorded with the frequency with which RFID numbers were captured varying per animal. The mean number of times an animal was recorded passing the RFID reader was 32.35 9.33 s.d., with a minimum of 13 and maximum of 53 times. When comparing the cows and calves there was a tendency for cows to have their RFID tags read more frequently with a mean of 37.26 8.75 s.d. as opposed to the calves’ mean of
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26.42 5.66 s.d. There were many more male (23) to female calves (15); males tended to have a slightly higher frequency of RFID reads with a mean of 27.04 6.46 s.d. compared with females with a mean of 25.46 4.21 s.d.
a Mann–Whitney–Wilcoxon Test was run to compare the means, which resulted in a highly significant difference (P < 0.001) between the maternal and non-maternal pairs for both the visually mothered-up and DNA-derived datasets. Only 14 of the 38 cow/calf pairs (36.8%) were correctly identified using the time difference method from the visually mothered-up dataset. The result was similar for the DNA derived dataset with only 12 of the possible 33 maternal pairs (36.4%) correctly assigned.
Using time difference between RFID reads to identify maternal parentage The mean time intervals between RFID reads for the maternal and non-maternal pairs showed large differences for both the visually mothered-up and DNA derived data, with the maternal pairs having shorter intervals in both cases (Fig. 2). The differences (mean s.e.m.) were 124 min 42 min for the visually mothered-up dataset and 153 min 28 min for the DNA derived dataset. Due to the non-normal distribution of the data
Using half-weight index to identify maternal parentage When comparing the HWI-derived cow/calf pairs with the visually mothered-up dataset, the 5-min time interval resulted in 92% correctly assigned maternal parentage (Fig. 3). The DNA derived dataset, however, resulted in a slightly higher assignment of maternal parentage of 97% using a 13-min time interval (Fig. 4).
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As the length of data recording increased so did the percentage of correctly assigned HWI-derived maternal pairs. This was consistent when comparing both the visually mothered-up and the DNA-derived datasets, increasing from ~50% at 7 days to above 90% at the end of the trial (Fig. 5).
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Discussion The frequency that animals had their RFID number captured suggested that cows passed the RFID reader more frequently than calves. This could be explained by the fact that cows, especially those with young calves, routinely leave the calves in the paddock when they walk to water, with Bos taurus breeds tending to be ‘hiders’ rather than ‘followers’ and place their calves in a secure location while they go off and graze or water (Padilla de la Torre et al. 2016).
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Cow/calf relationships Fig. 2. Mean time interval between radio frequency identification reads for cows with their own calves (maternal) and cows with all other calves (non-maternal) compared with the visual mothering-up and DNA-verified parentage. Standard error of the means shown in error bars.
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Time interval used to group RFID reads (min) Fig. 3. Derived maternal parentage percentages using half-weight index and various time intervals for the visually recorded parentage. RFID, radio frequency identification.
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Time interval used to group RFID reads (min) Fig. 4. Derived maternal parentage percentages using half-weight index and various time intervals for the DNA-verified parentage. RFID, radio frequency identification. Method DNA
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Fig. 5. Half-weight index-derived maternal parentage percentages for various lengths of data collection compared with the visually assigned and DNA assigned maternal parentage.
Suckling calves obtain their daily hydration requirements from milk, negating the need to consume from the watering point. It is expected that as calves’ age they will be naturally weaned in which case they would spend less time with their mother and increase their water consumption. Reinhardt and Reinhardt (1981) showed that in Zebu cattle the average age of natural weaning was ~10 months but the cow/calf pair still maintained some proximity. It is not known whether the calves in our experiment were actually drinking at the water point or simply following their mothers to water. Further work is needed to assess the effect of calf age and cattle breed on watering frequency and the potential impact of the breaking of the cow/calf bond as calves are naturally weaned. In addition,
if poor nutrition impacts on the cow’s ability to maintain lactation calves may be naturally weaned, which could impact the optimal time of data recording. Sequence alone is not enough to correctly identify maternal parentage. It is the recurrent patterns over time that leads to increased accuracy in identifying maternal pairs. The HWI method provides a relative measure of association by comparing associations between a cow and its calf compared with all other unrelated calves. It could be surmised that due to the relative nature of the HWI method it was far more effective in identifying maternal pairs (~95%) compared with the time interval method that only achieved ~36%. The results from this study demonstrate that it is a much more accurate method when using temporal data to derive maternal parentage and worthy of further validation. The principle of using temporal sequencing to derive maternal parentage relies on a strong bond between mother and offspring and on them visiting water together (Hatcher et al. 2014). If the bond is broken, as was the case with one calf which became isolated from its mother before the start of data collection, the association could be weakened or lost. The weakening of the cow/calf association was highlighted by the fact that the calf had the lowest HWI (0.15) of the visually derived dataset of all cow/calf pairs (a hair sample was not collected from the calf and it therefore was not included in the DNA-verified dataset). Despite this relatively low association, the HWI algorithm was still able to correctly assign the calf to its mother. If mismothering occurs it may result in maternal parentage being incorrectly recorded. The effect of mismothering on incorrectly assigning maternal parentage may become more of a problem in larger groups of cattle where there are more mismothering events and potentially a greater number of cow/calf pairs that have smaller HWI measures. The time intervals of 5 min and 13 min to derive the HWI pairwise associations in the visually mothered-up and DNAverified datasets correctly assigned maternal parentage in 92% and 97% of cow/calf pairs, respectively. These results are
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consistent with similar studies that have used temporal RFID sequencing to derive maternal parentage in the sheep industry. Richards and Atkins (2007) showed the Pedigree MatchMaker system, which calculates the association by looking for a lamb’s RFID either one or two in front or behind the ewe RFID, was 85–96% accurate in predicting pedigree over a 3–4-week period when compared with mothering-up lambs shortly after birth. Similarly Court et al. (2010) found that Pedigree MatchMaker achieved an accuracy of between 83% and 88% maternal parentage in the two flocks they studied when compared with DNA profiling. One of the three cow/calf pairs that were incorrectly assigned at the 5-min level is the actual maternal pair, which was validated by the DNA analysis. Therefore, based on the visually recorded data the HWI-assigned association is incorrect but based on the DNA-verified parentage the algorithm had correctly assigned the maternal pair. It is well documented that manual methods of recording maternal parentage result in errors. Barnett et al. (1999) found that the average error rate was 8.1% for maternal parentage recorded at birth in merino studs. Similar issues with mismothering and transcription errors are known to cause inaccuracies when manually recording maternal parentage in beef studs (Tropical Beef Technology Services 2014). The fact that the HWI method was able to correctly assign maternal parentage for the cow/calf pair that had been incorrectly recorded when visually mothering-up increases the confidence in the use of this method. Further work will be required to determine whether the HWI method will provide better mothering-up compared with other methods that have used RFID sequencing. Likewise, a larger herd size in different environmental settings needs to be tested in order to determine the sensitivity of the automated mothering-up algorithm with different time intervals. Using a range of different time intervals and two different maternal parentage methods, this study indicated that accurate mothering-up (>90%) can be achieved with a time interval of ~5 min. Richards and Atkins (2007) showed in two separate studies that varying the length of data recording from 7, 14, 21, 28 and 35 days increased the percentage of correctly determined maternal pairs from 74% to 78%, 83% to 90%, 86% to 93%, 88% to 95% and 90% to 93%, respectively. The results from this study showed a similar trend with the maternal parentage percentage increasing over the length of data recording to the maximum at the completion of the trial period. This result is expected as the ability of the HWI to accurately identify a cow/ calf association increases with the more observations recorded. Although the HWI-derived mothering-up algorithm used in this study produced valuable results for this group of cattle, further research is required to refine and test the accuracy and suitability of the algorithm in different settings. Occurrences such as mismothering may affect the accuracy of using temporal associations to record maternal parentage, whereas identifying the optimal calf age when a calf consistently follows its mother to water could reduce the recording period. As the present study was reasonably small-scale, the effect of herd size will also require further work to determine whether the accuracy of automated maternal parentage will meet industry needs. In its current form, however, the results show that the combination of autonomous data collection and the HWI mothering-up
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algorithm are a labour-saving and accurate alternative to either visually mothering-up or using DNA profiling to identify maternal parentage. Acknowledgements Thanks go to Phil Orchard, the manager of Belmont Research Station, for his assistance in collecting visual mothering-up data and facilitating this research project. We acknowledge the generous support from Maynard Cattle Co. who supplied the cattle used in this experiment. We recognise the assistance of the Animal Genetics Laboratory, University of Queensland in performing the DNA parentage. This work is part of the first author’s PhD research, funded by Telstra and Meat & Livestock Australia.
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