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Commercial Genetic Test Validation

IGENITY Feed Efficiency for Bos indicus-influenced cattle:

Summary:

The IGENITY feed efficiency (Indicus) MBVs were found to be significantly and positively associated with daily feed intake (DFI) and residual feed efficiency (RFI) in a pooled population of ~1270 tropically adapted (TROP) Bos indicus-influenced cattle.  No significant associations of the feed efficiency (Indicus) MBVs with either trait were found in a purebred Brahman (BRAH) cattle population of ~750 cattle. This suggests the feed efficiency (Indicus) MBVs may be working in the tropically adapted breeds (i.e. Brahman ´ Bos taurus) by tracking loci with very different allele frequencies between the two subspecies.

TEST DATASET

Trait*

PANEL

b

P

N

TROP (CRC1&2)

RFI

INDICUS

0.107

0.005

~ 1270

 

DFI

INDICUS

0.140

0.02

~ 1270

BRAH (CRC1&2)

RFI

INDICUS

0.051

0.26

~ 760

 

DFI

INDICUS

0.159

0.09

~ 720

* note: daily feed intake (DFI) phenotypes were regressed on the DMI MBV

The column labeled ‘b’ is the regression of phenotypes in the test population on the MBVs reported for the DNA test. It is a measure of how well the MBV scales with the phenotype. There are many reasons that this value could differ from its nominally expected value of 1. Traits scale differently in different environments, management scenarios and methods of measurement. Therefore, we would not practically expect this value to be exactly 1. However, values substantially less than 1 suggest that differences in phenotypes observed in other cattle managed under conditions representative of U.S. beef production are likely to be less than those predicted by the MBV. This would not affect how animals would be ranked by the MBV, but would impact the weighting given to differences in MBVs relative to differences in EPDs based on phenotypic data.

This analysis provides an example in which ‘b’ is expected to differ from 1 because of a difference in method of measurement. The Igenity MBVs for RFI and DMI were developed from data in which feed intake was recorded on a dry matter basis. The data set used here for validation has feed intake recorded only on an “as fed” basis, with no opportunity to measure the dry matter content of the various rations used in the several studies. Because actual dry matter content is not known, the values in the table were not adjusted for it. However, if we assume that the dry matter content of the rations was likely not too different from 80%, the expected value of ‘b’ is (very roughly) 1/0.80 = 1.25. Another way of looking at it is that the values in the ‘b’ column multiplied by 80% would have an expected value of roughly 1. This adjustment applies to both DMI and RFI. Therefore, the differences in MBVs for these tests almost certainly overstate the expected differences in phenotypes very substantially.

Data analyses for this validation study were performed by Dr. David Johnston, Animal Genetics and Breeding Unit, University of New England, Armidale, Australia.

Test Claims:

The IGENITY® feed efficiency (Indicus) test includes multiple-marker analyses for traits related to feed efficiency - residual feed intake (RFI) and dry matter intake (DMI) - for Bos indicus-influenced cattle.

Test Details:

IGENITY reports a score (1-10) for residual feed intake (RFI) and dry matter intake (DMI) derived from the analysis of undisclosed SNP markers for these traits.

Sample Populations:

Cattle Populations Used for Validation

  1. CRC 1 Indicus-influenced (~ 650 Animals)
    · Santa Gertrudis and Belmont Red
  2. CRC 2 Indicus-influenced (747 animals)
    · Brahman, Senepol and Belmont Red infused composites
  3. CRC 1 Brahmans (~150 Animals)
    · Purebred Brahman
  4. CRC 2 Brahmans (700 animals)
    · Purebred Brahman

CRC1. This dataset consisted of a group of Bos indicus-influenced breeds (Santa Gertrudis and Belmont Red) and a group of purebred Brahman. These cattle were born between 1993 and 1998. The basic design of the project and phenotypic and genetic parameters have been fully described by Upton et al. (2001), Johnston et al. (2003) and Reverter et al. (2003). In brief, the progeny were generated in various producer/breeder herds which had only one breed, so herd of origin and breed are confounded. Progeny (steers and a proportion of heifers) were purchased by the CRC at weaning and then backgrounded as cohorts in mixed breed groups, finished (either feedlot or pasture) and slaughtered together at the 3 target market endpoint weights. Daily feed intake was recorded on a sub-set of the feedlot finished groups. Animals were recorded for feed intake for an average of 60 days and included animals fed for the 3 market endpoints.

CRC2. These data were from the northern breeding project (Burrow et al. 2003) and consisted of a Bos indicus-influenced composite group (Brahman, Senepol and Belmont Red infused composites from various pastoral companies) and a group of purebred Brahman These cattle were born between 1999 and 2003. This data has been described extensively by Barwick et al. 2008 and Wolcott et al. 2008. Only the steer portion of this experiment was considered (and thus genotyped) for this study. Steers were assembled at weaning into groups that were backgrounded at various locations, at approximately 400 kg live weight the whole cohort entered the feedlot, were fed for 120 days prior to being slaughtered as a single group with an average carcass weight of 300-320 kg. HPGs were used from weaning onwards through to finishing. Daily feed intake was recorded on a subset (about 2/3) of the steers for an average of 71 days.

Residual feed intake (RFI) and dry matter intake (DMI) molecular breeding value distribution*:

*Molecular breeding values (MBVs) were provided by Igenity based on the various SNP panels for each trait. These are the MBVs in the data analyzed and are not necessarily reflective of any purebred population..

Population

TRAIT

Panel

Mean

Max

Min

Indicus-influenced

(CRC1)

RFI

INDICUS

0.60

3.11

-2.60

DFI

INDICUS

-0.61

3.32

-1.26

Indicus-influenced

(CRC2)

RFI

INDICUS

0.28

2.78

-1.95

DFI

INDICUS

0.14

3.90

-1.17

Brahman

(CRC2)

RFI

INDICUS

0.14

2.46

-1.19

DFI

INDICUS

-0.32

2.86

-1.49

Significance of the Igenity Molecular Breeding Values (Indicus) for Residual Feed Intake (RFI) and Dry Matter Intake (DMI).:

CRC1 and CRC 2 Bos indicus-influenced cattle were combined into a “tropically-adapted” dataset (TROP), as were the CRC1 and CRC2 purebred Brahmans (BRAH). Both combined datasets were used to test the feed efficiency (Indicus) MBVs from the Igenity panel for residual feed intake (RFI) and dry matter intake (DMI). Molecular breeding values (MBVs) for each trait were provided by Igenity. All analyses were performed by Dr. David Johnston, Animal Genetics and Breeding Unit, University of New England, Armidale, Australia with sire included in the model as a random effect

Population

TRAIT Panel b p N

Indicus-influenced

Combined
(CRC1 + CRC2)

RFI

INDICUS

0.107

0.005

~1270

DFI

INDICUS

0.140

 0.02

~1270

Brahman

Combined

(CRC1 + CRC2)

RFI

INDICUS

0.051

0.26

~720

DFI

INDICUS

0.159

0.09

~750

Brahman

(CRC2)

RFI

INDICUS

0.093

0.24

605

DFI

INDICUS

-0.0001

0.50

605

* note: daily feed intake (DFI) phenotypes were regressed on the DMI MBV