Phenotypes Remain King in the Genomics Era

by IBBA Executive Vice President Tommy Perkins, PhD., PAS

 

Genomic selection has played an important role in cattle breeding programs for the last five or so years. Brangus breeders have DNA tested more than 11,000 animals in the past three years with low density (<50K) and high density (>50K) panels, which have resulted in monthly published genomic-enhanced expected progeny differences (GE-EPDs). The GE-EPDs have been a combination of the genotyped animals and phenotypic measures of performance as well as their pedigrees. Although genomics is the big buzz word and craze of the livestock industry, breeders in the International Brangus Breeders Association (IBBA) can’t forget the importance phenotype data plays in our genetic predictions.

 

The information to follow will summarize traits, which can be measured and reported to the association beyond the traditional birthweight (BW), weaning weight (WW) and yearling weight (YW) submissions. Note that you must remain steadfast in the collection and submission of large contemporary groups of animals with complete performance measures for BW, WW and YW.

 

We fully understand the collection of progeny data is time-consuming and generally expensive. However, the above-mentioned traits, as well as the following, are generally easy to collect and don’t need expensive tools or technologies to get a result to report. In fact, some of the data collected may be combined to produce expected progeny differences (EPDs)  or selection indexes for the more difficult individual traits to measure. For example, it can be difficult to collect reproductive performance traits or fertility traits with proper contemporary grouping. Breeding dates and palpation results can be collected for later use in producing selection tools for maternal abilities, such as stayability or heifer pregnancy. Likewise, leg conformation and hair shedding scores could facilitate longevity EPDs.

 

The collection of reproductive phenotype data is relatively scarce in the IBBA database so the development of a useful economic selection index appears to be challenging. The breed improvement committee has made this type of data collection high-priority to develop a selection index in the not-too-distant future. A good place to start may be the use of heifer pregnancy (a measure of early fertility) in combination with days to calving (more long-term fertility).

 

Calving Ease Scoring System

Calving ease (CE) scores should be recorded for use in determining BW, direct calving ease (CED) and maternal calving ease (CEM) EPDs. The association uses the scoring system below:

1 = No difficulty, no assistance

2 = Minor difficulty, some assistance

3 = Major difficulty, usually mechanical assistance

4 = Caesarian section or other surgery

5 = Abnormal presentation

Most of the IBBA data submitted to date has been no difficulty or no assistance (1). Therefore, it’s a must that breeders submit every birth that falls into the minor difficulty (2) to caesarian section (4) category so there is distinguishable variability in the trait for a more accurate and precise BW, CED and CEM EPD. Abnormal presentation scores (5) are excluded from the national cattle evaluations but there reporting is still recommended when they occur.

 

Calf Vigor Scoring System

It is important to note the overall vigor of the calf when it is born. Once born, make sure you note the approximate time from birth to standing and ultimate nursing. The sooner a calf begins to nurse, the sooner it will receive colostrum from the dam’s first milk. With each passing minute, the amount, and perhaps quality, of colostrum begins to decline, which is very important when considering the newborn’s ultimate immune function. Calf Vigor Score is shown below:

1 = Standing up and nursing within 30 minutes

2 = Standing up within 2 hours and nursing without assistance

3 = Nursing with assistance

4 = No suckle reflex and must be drenched

5 = Unwilling or can’t rise and dead soon after birth

 

Udder Suspension and Teat Scoring System

Udder suspension and teat size scores provide valuable data for use in stayability and other maternal selection tools. Udder and teat quality are economically important traits of beef cattle as they are generally accountable for the productive life of a female as well as the overall performance of their calf each year. Next to failure to breed, poor udder and teat conformation is the second most often used culling criteria for cows. The one-to-nine scoring system below describes numerical values that reflect differences in udder and teat quality used by IBBA.

 

Udder suspension scores are subjective recordings of udder support taken within 24 hours of the cow giving birth using the weakest quarter of the udder.

1 = Very pendulous (least desirable)

2 = A problem udder with weak rear or front attachment

3 = Pendulous

4 = Could become a problem udder

5 = Moderately tight

6 = Functional udder that lacks the balance of 7–9 scores

7 = Tight

8 = Level attachment in front and high rear attachment

9 = Very tight

 

Teat size scores are subjective recordings of teat length and circumference taken within 24 hours of the cow giving birth using the teat with the poorest quality.

1 = Very large (least desirable)

2 = Teats are large and balloon shaped

3 = Large

4 = Shape and size of teats may lead to problems

5 = Moderate (desirable)

6 = Problem free teat size

7 = Small (most desirable)

8 = Small, desirable teat size

9 = Very small (somewhat desirable)

 

Much of the IBBA data has been recorded as “5,5” indicating average udder suspension with moderate sized teats. It is important to properly inspect and report data using the worst quarter of the udder and least desired teat of the four. Proper reporting should indicate the true differences so that genetic variability can be evaluated in EPD calculations.

 

Feet and Leg Scoring System

Animals should have minimum structural requirements to ensure optimum levels of production and adaptability to the environment. Loss of structural integrity leads to financial losses. Commercial cattlemen continue to ask for selection tools to assess structural soundness differences in bull buying decisions. IBBA members should attempt to collect phenotypic data to develop a future selection index or EPD to serve this purpose. It is recommended that four different measures be taken prior to the animal reaching 600 days of age. They include front and rear foot angle, front and rear claw set, front and rear view leg set, and side profile leg set.

 

Front and Rear Foot Angle

1 = Too straight

2 = Slightly straight

3 = Correct angle

4 = Slightly too much set or angle

5 = Too much angle or set

 

Front and Rear Claw Set

1 = Widely spread

2 = Spread more than normal

3 = Narrow width, slight touching of claws

4 = Claw tips are long

5 = Claw tips cross over each other

 

Front and Rear View Leg Set

1 = Toed Out (Cow Hocked)

2 = Slightly Toed Out

3 = Correct angle or set

4 = Slightly Toed In

5 = Toed In (Bow Legged)

 

Side Profile Leg Set

1 = Too Straight (Post Legged)

2 = Slightly Straight

3 = Correct angle or set

4 = Slightly Too Much Angle or Set

5 = Too Much Angle or Set (Sickle hocked)

 

Hair Shedding Scoring System

Hair shedding scores are subjective, visual scores indicating the level of hair shedding by an animal. Members should report a value between one and five, with a score of five indicating no evidence of shedding their winter coat and a score of one indicating complete shedding of their winter coat which exhibits a slick, summer hair coat.

1 = complete shedding of winter hair coat (desirable)

2 = shedding about three-fourths (75%) of their winter hair coat

3 = shedding of half (50%) of their winter hair coat

4 = shedding about one-fourth (25%) of their winter hair coat

5 = no shedding of the winter hair coat (least desirable)

The increased shedding of winter hair coat leads to heavier weaning weights, which becomes even more pronounced the further south and east that you produce cattle. Hair shedding scores should be taken about four to six weeks after the last freeze, or last major cold front, of the year. This obviously varies from state to state or region to region.

 

Docility or Disposition Scoring “Pen Score” System

Animal response to human presence in a pen. Individual pen scoring should be applied to an animal placed in a pen with two to four other animals. The score ranges from one to five, with one being very calm and five being very aggressive.

1 = Extremely gentle, must kick to get out of the way

2 = Calm but moves away from you when you get close

3 = Calm but moves away from you sooner than a 2 (larger flight zone)

4 = Nervous and moves away rapidly when you enter their flight zone

5 = Extremely nervous and may attack the scorer in the pen

 

Breeding and Pregnancy Data Submission

Submission of heifer breeding data includes artificial insemination (AI) dates and/or natural service breeding dates. Collection of pregnancy status at the end of the breeding season can also be valuable data for use in developing heifer pregnancy EPDs. Heifer pregnancy EPDs generally estimate differences among individuals in the proportion of their daughters who will successfully conceive and calve at two years of age. Heifer exposure and pregnancy diagnosis reports can be submitted to IBBA.

 

Sheath and Navel Scoring System

Management of sheath and navel scores can have an impact on reproductive performance, but, also, can have an impact on your herd from an economic standpoint. Cattle with excessive underlines are not as marketable to the packers and feedlots and therefore may receive discounts. Reproductively, bulls with excessive or undesirable sheath designs are more susceptible to damage of their reproductive organs. Sheath and navel scores are valued from one to five in both bulls and females.

1 = Excessively clean, English type

2 = Optimum; Brahman influence indicated, but not excess leather in navel area. Sheath hangs at a 45° angle and is well

controlled.

3 = Acceptable; leather in navel slightly in excess of desirable amounts. Any excessively clean or optimum sheath which

opens at a 90° angle to the body wall should be scored as a three. Leather may run length of underline.

4 = Marginal; excessive loose leather in navel area, slightly pendulous sheath.

5 = Unacceptable; extremely pendulous sheath. Also includes all bulls with large prepucial openings.

 

Phenotypic (performance) data is as important today as it’s ever been. Current, correct and accurate collection of phenotype data is the best way to take advantage of an animal’s genotype data. The combination of pedigree, performance and genotype data submission and evaluation will lead to improvements in accuracy of prediction in current selection tools such as EPDs, selection indexes, etc. The collection and submission of phenotypic information by breeders will only make our traditional selection tools better or may even lead to new discoveries for faster genetic gain through selection. In other words, genomics merely adds to the strength of our sire summary when it is backed by sound performance data.