Section 20: Proxies

From ICAR Wiki

Introduction

Large-scale measurements of enteric CH4 emissions from dairy cows are needed for effective monitoring of strategies to reduce the carbon footprint of milk production, as well as for incorporation of CH4 emissions into breeding programs. However, measurements on a sufficiently large scale are difficult and expensive. Proxies for CH4 emissions can provide an alternative, but each approach has limitations. Negussie et al. (2019)[1] recently showed the potential of proxies proxies that are easy to record in the farm. These proxies can be gathered in most farms and are a realistic threshold accuracy that can be obtained without more fancy proxies. Several techniques have been developed for the measurement of CH4 emissions from ruminants, with varying degrees of accuracy (see reviews by Cassandro et al., 2013[2] and Hammond et al., 2016A[3]), but routine individual measurements on a large scale (a requisite for genetic selection) have proven to be difficult and expensive (Pickering et al., 2015[4]; Negussie et al., 2016[5]). Therefore, identifying proxies (i.e. indicators or indirect traits) that are correlated to CH4 emission, but which are easy and relatively low-cost to record on a large scale, is a much needed alternative. Proxies might be less accurate, but could be measured repeatedly to reduce random noise. The (potential) proxies range from simple and low-cost measurements such as body weight, to high-throughput milk MIR, to more demanding measures like rumen morphology, rumen metabolites or microbiome profiling.

Combining proxies that are easy to measure and cheap to record could provide predictions of CH4 emissions that are sufficiently accurate for selection and management of cows with low CH4 emissions.

Available Proxies

A large array of CH4 proxies differing widely in accuracy and applicability under different conditions have been reported. The ideal proxy would be highly phenotypically and genetically correlated with CH4 emissions and could easily, and potentially repeatedly, be measured on a large scale. A systematic summary and assessment of existing knowledge is needed for the identification of robust and accurate CH4 proxies for future use. Table 5 summarizes proxies for CH4 production, and Table 6 summarizes results from combining proxies to improve predictability of proxies for CH4 prediction.

Proxy Description / conclusion Reference
(1) Feed intake and feeding behavior
Dry Matter Intake (DMI) DMI predict MeP with R2= 0.06-0.64, and ME intake predict MeP with R2= 0.53-0,55 Ellis et al. (2007);[6]

Mills et al. (2003)[7];

Negussie et al. (2019)[8]

Gross Energy intake (GE) Predict MeP with RMSPE= 3.01. Moraes et al. (2014)[9]
Feeding behavior Magnitude and direction of relation to MeP varies across studies Nkrumah et al. (2006);[10]

Jonker et al., 2014[11]

Rumination time High rumination relates to more milk, consume more concentrate and produce more CH4, lower RMP and MeI Watt et al. (2015)[12];

López- Paredes et al. (2020)[13]

Rumen microbiome The metagenome can predict DMI, and classify high vs low intakes Delgado et al. (2019)[14]
(2) Rumen function, metabolites and microbiome
Dietary antimethanogenic compounds Inhibitors of the enzyme methyl coenzyme-M reductase: bromochoromethane; chloroform; 3- nitrooxypropanol (not always) Denman et al., 2007;[15]

Knight et al., 2011;[16]

Haisan et al., 2014[17];

Romero-Perez et al., 2014[18]

Dietary antimicrobial compounds Induce reductions in both MeP and methanogens numbers: nitrates, anacardic acid (cashew nut shell liquid), monensin, isobutyrate Iwamoto et al., 2002;[19]

Kubo et al., 1993[20];

van Zijderveld et al., 2010[21];

Veneman et al., 2015[22];

Shinkai et al., 2012[23];

Wang et al., 2015[24]

Rumen microbiome profile High Fibrobacteres, Quinella ovalis and Veillonellaceae and low Ruminococcaceae, Lachnospiraceae and Clostridiales associate with low- CH4 phenotypes and high propionate

Protozoa concentration

Kittelmann et al., 2014[25];

Wallace et al., 2014[26];

Sun et al., 2015[27];

Guyader et al., 2014[28]

Rumen microbiome profile Predict MeP with R2 up to 0.55 Ross et al. 2013a[29];

Ross et al. (2013b)[30]

Microbial genes 20 (out of 3970 identified) related to CH4 emissions Roehe et al. (2016)[31]
Rumen volume (Xray Computed Tomography) and retention time Low-MeY sheep had smaller rumens. Faster passage= less time to ferment substrate - explained 28% of variation in MeP Pinares Patiño et al., 2003[32];

Goopy et al., 2014[33];

Okine et al. (1989)[34]

Blood triiodothyronine concentration Reduced MeY Barnett et al. (2012)[35]
Acetate to propionate ratio in ruminal fluid Positively associated with CH4 emissions, but not confirmed in all studies, sometimes opposite relation Mohammed et al., 2011;[36]

Fievez et al., 2012;

Chung et al., 2011;

Van Zijderveld et al., 2010

(3) Milk production and composition
Modelling approach Doubling milk production only adds 5 kg to the MeP and so greatly reduces MeY Kirchgessner et al. (1995);

Hristov et al. (2014)

Milk fat content key explanatory variable for predicting CH4: A moderate negative genetic correlation with infrared predicted

MeI: correlations MeP = 0,08 and MeI = - 0.13

Moreas et al. (2014);

Kandel et al., 2014A, B;

Vanlierde et al. (2015)

Milk fat content A positive relationship between VFA proportions and methanogenesis is expected as a consequence of the common biochemical pathways; Dietary unsaturated fatty acids are negatively associated with CH4 emissions Vlaeminck et al., 2006;

Van Lingen et al., 2014

Milk protein yield Correlation with Mel = - 0.47 or -0.09, MeP = 0.53 Kandel et al. (2014);

Vanlierde et al. (2015)

Lactose Variable correlations: MeP = 0,33; MeI = - 0.21; R = 0.19 for CH4 emission Miettinen and Huhtanen (1996);

Dehareng et al. (2012)

Somatic cell score Genetic correlation with infrared predicted MeI: R = 0.07 Kandel et al. (2014A, B)
Prediction equations Milk FA and CH4 emissions, including from MIR data R² ranged between 47 and 95%; relationships between the individual milk FA and MeP differed considerably and the correlations between CH4 and milk FA vary throughout the lactation Chilliard et al. (2009);

Delfosse et al. (2010);

Castro-Montoya et al. (2011);

Dijkstra et al. (2011);

Kandel et al. (2013);

Mohammed et al. (2011);

Van Lingen et al. (2014);

Williams et al. (2014);

Dijkstra et al. (2016);

Rico et al. (2016);

Van Gastelen and Dijkstra (2016); Vanrobays et al. (2016);

Bougoin et al., (2019)

(4) Hind-gut and feces
Whole tract digestibility (potential as supporting factors in the prediction of enteric CH4 emissions) Main effects relate to rumen (see above), but energy digestibility as a supporting factor to GE intake improved the accuracy of CH4 prediction, despite the fact that there was no direct linear relationship between energy digestibility and MeY and in % of GE intake Yan et al., 2009 C
Ratio of acetic and butyric acid divided by propionic acid Methane yield positive relation Moss et al., 2000
(5) Whole animal measurements
Body weight and conformation Prediction models; primary predictor for enteric MeP Moraes et al. (2014);

Holter and Young, 1992; Yan et al., 2009

Body weight Relationship with MeI: r = 0.44; relationship between body weight and rumen capacity Antunes-Fernandes et al. (2016);

Demment and Van Soest, 1985

Body weight Key explanatory variable for enteric MeP No reference available
Conformation traits: affects enteric MeP Indicators for rumen volume (via feed intake and rumen passage rates); BCS Agnew and Yan, 2000
Lactation stage Complementary proxy Vanlierde et al. (2015)

Table 5. Available methane proxies include: (1) feed intake and feeding behaviour, (2) rumen function, metabolites and microbiome, (3) milk production and composition, (4) hind-gut and faeces, and (5) measurements at the level of the whole animal. It is evident that no single proxy offers a good solution in terms of all of these attributes, though the low cost and high throughput make milk MIR a good candidate for further work on refining methods, improving calibrations and exploring combinations with other proxies.

  1. ↑ Negussie, E., González Recio, O., de Haas, Y., Gengler N., Soyeurt, H., Peiren, N., Pszczola, M., Garnsworthy, P., Battagin, M., Bayat, A., Lassen, J., Yan, T., Boland, T., Kuhla, B., Strabel, T., Schwarm, A., Vanlierde, A., and Biscarini, F. 2019. Machine learning ensemble algorithms in predictive analytics of dairy cattle methane emission using imputed versus non-imputed datasets. 7th GGAA – Greenhouse Gas and Animal Agriculture Conference held from August 4th to 8th, Iguassu Falls/Brazil. Oral communication, Book of Abstracts Page 40. http://www.ggaa2019.org/sites/default/files/proceedings-ggaa2019.pdf
  2. ↑ Cassandro, M., Mele, M., Stefanon, B.. 2013. Genetic aspects of enteric methane emission in livestock ruminants. Italian J. Anim. Sci. 12:e73: 450-458.
  3. ↑ Hammond, K.J., Crompton, L.A., Bannink, A., Dijkstra, J., Yáñez-Ruiz, D.R., O’Kiely, P., Kebreab, E., Eugenè, M.A., Yu, Z., Shingfield, K.J., Schwarm, A., Hristov, A.N., and Reynolds, C.K. 2016A. Review of current in vivo measurement techniques for quantifying enteric methane emission from ruminants. Anim. Feed Sci. Technol. 219:13–30. doi:10.1016/j.anifeedsci.2016.05.018.
  4. ↑ Pickering, N.K., Oddy, V.H., Basarab, J.A., Cammack, K., Hayes, B J., Hegarty, R.S., McEwan, J.C., Miller, S., Pinares, C., and de Haas, Y. 2015. Invited review: Genetic possibilities to reduce enteric methane emissions from ruminants. Animal 9:1431-1440.
  5. ↑ Negussie E., Lehtinen, J., Mäntysaari, P., Liinamo, A-E., Mäntysaari, E., and Lidauer, M.. 2016. Non-invasive individual methane measurements in dairy cows using photoacoustic infrared spectroscopy technique. 6th Greenhouse Gases Animal Agriculture Conference (GGAA2016) 14-18 February 2016. Melbourne, Australia. Abstract. p62.
  6. ↑ Ellis, J.L., Kebreab, E., Odongo, N.E., McBride, B.W., Okine, E.K., and France, J. 2007. Prediction of methane production from dairy and beef cattle. J. Dairy Sci. 90:3456–3466.
  7. ↑ Mills, J.A.N., Kebreab, E., Yates, C.M., Crompton, L.A., Cammell, S.B., Dhanoa, M.S., Agnew, R.E., and France, J. 2003. Alternative approaches to predicting methane emissions from dairy cows. J. Anim. Sci. 81:3141–3150.
  8. ↑ Negussie, E., González Recio, O., de Haas, Y., Gengler N., Soyeurt, H., Peiren, N., Pszczola, M., Garnsworthy, P., Battagin, M., Bayat, A., Lassen, J., Yan, T., Boland, T., Kuhla, B., Strabel, T., Schwarm, A., Vanlierde, A., and Biscarini, F. 2019. Machine learning ensemble algorithms in predictive analytics of dairy cattle methane emission using imputed versus non-imputed datasets. 7th GGAA – Greenhouse Gas and Animal Agriculture Conference held from August 4th to 8th, Iguassu Falls/Brazil. Oral communication, Book of Abstracts Page 40. http://www.ggaa2019.org/sites/default/files/proceedings-ggaa2019.pdf
  9. ↑ Moraes, L.E., Strathe, A.B., Fadel, J.G., Casper, D.P., and Kebreab, E. 2014. Prediction of enteric methane emissions from cattle. Glob. Change Biol. 20:2140–2148.
  10. ↑ Nkrumah, J.D.,  Okine, E.K., Mathison, G.W., Schmid, K., Li, C., Basarab, J.A., Price, M.A., Wang, Z., and Moore, S.S. 2006. Relationships of feedlot feed efficiency, performance, and feeding behavior with metabolic rate, methane production, and energy partitioning in beef cattle. J. Anim. Sci. 84:145-153.
  11. ↑ Jonker, A., Molano, G., Antwi, C., Waghorn, G.. 2014. Feeding lucerne silage to beef cattle at three allowances and four feeding frequencies affects circadian patterns of methane emissions, but not emissions per unit of intake. Anim. Prod. Sci.54:1350-1353.
  12. ↑ Watt, L.J., Clark, C.E.F., Krebs, G.L., Petzel, C.E., Nielsen, S., and Utsumi, S.A. 2015. Differential rumination, intake, and enteric methane production of dairy cows in a pasture-based automatic milking system. J. Dairy Sci. 98:7248–7263.
  13. ↑ Lopez-Paredes, J., Goiri, I., Atxaerandio, R., García-Rodríguez, A., Ugarte, E., Jiménez-Montero, J.A., Alenda, R and  González-Recio, O. 2020. Mitigation of greenhouse gases in dairy cattle via genetic selection (i): Genetic parameters of direct methane using non-invasive methods and its proxies. J. Dairy Sci. 103.
  14. ↑ Delgado, B., Bach A., Guasch I., González C, Elcoso G., Pryce J.E., Gonzalez-Recio O. (2019).Whole rumen metagenome sequencing allows classifying and predicting feed efficiency and intake levels in cattle. Scientific Reports 9: 11. doi:10.1038/s41598-018-36673-w
  15. ↑ Denman, S.E., Tomkins, N.W., and McSweeney, C.S. 2007. Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol. Ecol. 62:313-322.
  16. ↑ Knight, T., Ronimus, R.S., Dey, D., Tootill, C., Naylor, G., Evans, P., Molano, G., Smith, A., Tavendale, M., Pinares-Patiño, C.S., and Clark, H. 2011. Chloroform decreases rumen methanogenesis and methanogen populations without altering rumen function in cattle. Anim. Feed Sci. Technol. 166-167:101-112.
  17. ↑ Haisan, J., Sun, Y., Guan, L.L., Beauchemin, K.A., Iwaasa, A., Duval, S., Barreda, D.R., and Oba, M. 2014. The effects of feeding 3-nitrooxypropanol on methane emissions and productivity of Holstein cows in mid lactation. J. Dairy Sci. 97:3110-3119.
  18. ↑ Romero-Perez, A., Okine, E.K., McGinn, S.M., Guan, L.L., Oba, M., Duval, S.M., Kinderman,n M., and Beauchemin, K.A. 2014. The potential of 3-nitrooxypropanol to lower enteric methane emissions from beef cattle. J. Anim. Sci. 92:4682-4693.
  19. ↑ Iwamoto, M., Asanuma, N., and Hin,o T. 2002. Ability of Selenomonas ruminantium, Veillonella parvula, and Wolinella succinogenes to reduce nitrate and nitrite with special reference to the suppression of ruminal methanogenesis. Anaerobe. 8:209-215.
  20. ↑ Kubo, I., Muroi, H., Himejima, M., Yamagiwa, Y., Mera, H., Tokushima, K., Ohta, S., and Kamikawa, T. 1993. Structure-antibacterial activity relationships of anacardic acids. J. Agric. Food Chem. 41:1016-1019.
  21. ↑ Van Zijderveld, S.M., Gerrits, W.J.J., Apajalahti, J.A., Newbold, J.R., Dijkstra, J., Leng, R A., and Perdok, H.B. 2010. Nitrate and sulfate: effective alternative hydrogen sinks for mitigation of ruminal methane production in sheep. J. Dairy Sci. 93:5856-5866.
  22. ↑ Veneman, J.B., Muetzel, S., Hart, K.J., Faulkner, C.L., Moorby, J.M., Perdok, H.B., and Newbold, C.J. 2015. Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows? PLoS ONE 10(10): e0140282. doi: 10.1371/journal.pone.0140282
  23. ↑ Shinkai, T., Enishi, O., Mitsumori, M., Higuchi, K., Kobayashi, Y., Takenaka, A., Nagashima, K., and Mochizuki, M. 2012. Mitigation of methane production from cattle by feeding cashew nut shell liquid. J. Dairy Sci. 95:5308-5316.
  24. ↑ Wang, C., Liu, Q., Zhang, Y.L., Pei, C.X., Zhang, S.L., Wang, Y.X., Yang, W.Z., Bai, Y.S., Shi, Z.G., and Liu, X.N. 2015. Effects of isobutyrate supplementation on ruminal microflora, rumen enzyme activities and methane emissions in Simmental steers. J. Anim. Physiol. Anim. Nutr. (Berl). 99:123-131.
  25. ↑ Kittelmann, S., Pinares-Patiño, C.S., Seedorf, H., Kirk, M.R., Ganesh, S., McEwan, J.C., and Janssen, P.H. 2014. Two different bacterial community types are linked with the low-methane emission trait in sheep. PLoS One 9:e103171.
  26. ↑ Wallace, R. ., Rooke, J A., Duthie, C.-A., Hyslop, J.J., Ross, D.W., McKain, N., de Souza, S.M., Snelling, T.J., Waterhouse, A., and Roehe, R. 2014. Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle. Sci. Rep. 4:5892.
  27. ↑ Sun, X., Henderson, G., Cox, F., Molan,o G., Harrison, S.J., Luo, D., Janssen, P.H., and Pacheco, D. 2015. Lambs Fed Fresh Winter Forage Rape (Brassica napus L.) Emit Less Methane than Those Fed Perennial Ryegrass (Lolium perenne L.), and Possible Mechanisms behind the Difference. PLoS One 10(3):e0119697: DOI:    10.1371/journal.pone.0119697
  28. ↑ Guyader, J., Eugène, M., Nozière, P., Morgavi, D.P., Doreau, M., and Martin, C. 2014. Influence of rumen protozoa on methane emission in ruminants: a meta-analysis approach. Animal 8:1816-1825.
  29. ↑ Ross, E. M., P.J . Moate,  L.C. Marett, B.G. Cocks and B.J. Hayes. 2013a. Investigating the effect of two methane-mitigating diets on the rumen microbiome using massively parallel sequencing. J. Dairy Sci. 96:6030–6046.
  30. ↑ Ross, E. M., Moate, P. J., Marett, L.C., Cocks, B.G., and Hayes, B.J. 2013b. Metagenomic Predictions: From Microbiome to Complex Health and Environmental Phenotypes in Humans and Cattle. PLoS One DOI: 10.1371/journal.pone.0073056.
  31. ↑ Roehe R., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., McKain, N., Ross, D.W.,  Hyslop, J.J., Waterhouse, A., Freeman, T.C., Watson, M., and Wallace, R.J. 2016. Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance. PLoS Genet 12(2): e1005846. doi:10.1371/journal.pgen.1005846.
  32. ↑ Pinares-Patiño C.S., Hickey, S.M., Young, E.A., Dodds, K.G., MacLean, S., Molano, G., Sandoval, E., Kjestrup, H., Harland, R., Pickering, N.K., and McEwan, J.C. 2013. Heritability estimates of methane emissions from sheep. Animal 7: 316–321.
  33. ↑ Goopy, J.P., Donaldson, A., Hegarty, R., Vercoe, P.E., Haynes, F., Barnett, M., and Oddy, V.H. 2014. Low-methane yield sheep have smaller rumens and shorter rumen retention time. Br. J. Nutr. 111:578-585.
  34. ↑ Okine, E. ., Mathiso,n G.W., and Hardin, R.T. 1989. Effects of changes in frequency of reticular contractions on fluid and particulate passage rates in cattle. J. Anim. Sci. 67:3388–3396.
  35. ↑ Barnett, M.C., Goopy, J.P., McFarlane, J.R., Godwin, I.R., Nolan, J.V., and Hegarty, R.S. (2012). Triiodothyronine influences digesta kinetics and methane yield in sheep. Anim. Prod. Sci. 52:572-577.
  36. ↑ Mohammed, R., McGinn, S.M., and Beauchemin, K.A. 2011. Prediction of enteric methane output from milk fatty acid concentrations and rumen fermentation parameters in dairy cows fed sunflower, flax, or canola seeds. J. Dairy Sci. 94:6057–6068.
Retrieved from "http://wiki.icar.org/index.php?title=Section_20:_Proxies&oldid=1265"