Official Breeding Values Research Articles

Correlations of feed intake predicted with milk infrared spectra and breeding values in the Dutch Holstein population

Feed is a major cost in dairy production, and substantial genetic variation in feed efficiency exists between cows. Therefore, breeders aim to improve feed efficiency of dairy cattle. However, phenotypic data on individual feed intake on commercial farms is scarce, and accurate measurements are very costly. Several studies have shown that information from Fourier-transformed infrared spectra of milk samples (milk infrared, milk IR) can be used to predict phenotypes such as energy balance and energy intake, but this is usually based on small data sets obtained under experimental circumstances. The added value of information from milk IR spectra for estimation of breeding values is unknown. The objectives of this study were (1) to develop prediction equations for dry matter intake (DMI) and residual DMI (rDMI) from milk IR spectra; (2) to apply these for a data set of milk IR spectra from commercial Dutch dairy farms; (3) to estimate genetic parameters for these traits; and (4) to estimate correlations between these predictions and other traits in the breeding goal. We used data from feeding trials where individual feed intake was recorded daily and for which milk IR spectra were determined weekly to develop prediction equations for DMI and rDMI with partial least squares regression. This data set contained over 7,600 weekly averaged DMI records linked with milk IR spectra from 271 cows. The equations were applied for a data set with test day information from 676 Dutch dairy herds with 621,567 records of 78,488 cows. Both milk IR-predicted DMI and rDMI were analyzed with an animal model to obtain genetic parameters and sire effect estimates that could be correlated with breeding values. A partial least squares regression model with 10 components from the milk IR spectra explained around 25% of DMI variation and less than 10% of rDMI variation in the validation set. Nearly all variation in the milk IR spectra was captured by 7 components; additional components contributed marginally to the spectral variation but decreased prediction errors for both traits. Accuracies of predictions of DMI and rDMI from milk IR spectra for a large feeding experiment were 0.47 and 0.26 on average, respectively, with small differences between ration treatments (ranging from 0.43 to 0.55 and from 0.21 to 0.34, respectively) and among lactation stages (ranging from 0.24 to 0.59 and from 0.13 to 0.36, respectively), with the highest prediction accuracies in early lactation. The estimated heritabilities for predicted DMI and rDMI were 0.3 and 0.4, respectively, which suggests genetic potential for both predicted traits. The correlations of sire estimates for milk IR-predicted DMI with official Dutch breeding values were strongest with milk production (0.33), longevity (0.26), and fertility (-0.27), indicating that cows that eat more produce more, live longer, and have poorer fertility. The correlations of sire estimates for predicted DMI and rDMI with the official breeding values for DMI were low (0.14 and 0.03, respectively). This implies that the added value of including milk IR-predicted DMI information in the estimation procedure of breeding values for DMI would be considered insufficient for practical application.

Substantial Genetic Progress in the International Apis mellifera carnica Population Since the Implementation of Genetic Evaluation.

Simple SummaryThe Apis mellifera carnica subspecies of the honeybee is known for its gentleness and good honey yield. In the early 20th century, systematic breeding efforts began. Breeding progress was slow before the introduction of modern techniques of genetic evaluation in the mid 1990s. Here, the results of the official breeding value estimation in BeeBreed.eu are analyzed. From about 2000 onward, breeding progress accelerated. The result is a considerable gain in honey yield and desirable properties without increased inbreeding coefficients. The success of A. m. carnica breeding shows the potential of genetic evaluation.The Apis mellifera carnica subspecies of the honeybee has long been praised for its gentleness and good honey yield before systematic breeding efforts began in the early 20th century. However, before the introduction of modern techniques of genetic evaluation (best linear unbiased prediction, BLUP) and a computerized data management in the mid 1990s, genetic progress was slow. Here, the results of the official breeding value estimation in BeeBreed.eu are analyzed to characterize breeding progress and inbreeding. From about the year 2000 onward, the genetic progression accelerated and resulted in a considerable gain in honey yield and desirable properties without increased inbreeding coefficients. The prognostic quality of breeding values is demonstrated by a retrospective analysis. The success of A. m. carnica breeding shows the potential of BLUP-based breeding values and serves as an example for a large-scale breeding program.

РАСПРЕДЕЛЕНИЕ БЫКОВ АЙРШИРСКОЙ ПОРОДЫ ПЛЕМЕННЫХ ПРЕДПРИЯТИЙ РОССИИ ПО КРОВНОСТИ РОДСТВЕННЫХ ПОРОД

He significance of blood count of related breeds of the Ayrshire group of dairy cattle investigated. Information processed on the pedigrees of 181 bulls whose sperm found in 10 breeding enterprises of the RF. The average blood pressure of bulls in the Finnish Ayrshire breed was 54.2%, Swedish red - 9.9%, Norwegian red - 8.8%, Canadian - 25.7% and others - 1.4%. Bulls distributed according to the presence in their pedigrees of blood residues of related breeds of the Ayrshire group in the age aspect depending on the place of their birth and breeding enterprises, and the level of breeding value by milk of their daughters and pedigree. Most of the bulls were born in Russia and Finland (45.9 and 46.4% respectively) in their pedigrees the Finnish Ayrshire breed predominates. The ranking of bulls by official breeding value (BV) and by pedigree (BV PED ) revealed that in the best bulls according to these indicators (+100 kg and more) bloodline prevails in pedigrees by Finnish Ayrshire breed compared to the worst group (less than -100 kg). This regularity noted in pedigrees in 57.2 and 77.6% of bulls, depending on the assessment options. The BV of bulls and predicted positively and reliably correlates with the presence of Finnish blood in the pedigree (+ 0.233 * and + 0.308 **) and significantly negatively with Canadian (-0.252 * and -0.467 **). The findings are consistent with previous 2013 studies on the best rated Viking Genetics bulls.

Identification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data.

BackgroundFemale fertility is an important trait in cattle breeding programs. In the Nordic countries selection is based on a fertility index (FTI). The fertility index is a weighted combination of four female fertility traits estimated breeding values for number of inseminations per conception (AIS), 56-day non-return rate (NRR), number of days from first to last insemination (IFL), and number of days between calving and first insemination (ICF). The objective of this study was to identify associations between sequence variants and fertility traits in Jersey cattle based on 1,225 Jersey sires from Denmark with official breeding values for female fertility traits. The association analyses were carried out in two steps: first the cattle genome was scanned for quantitative trait loci using a sire model for FTI using imputed whole genome sequence variants; second the significant quantitative trait locus regions were re-analyzed using a linear mixed model (animal model) for both FTI and its component traits AIS, NRR, IFL and ICF. The underlying traits were analyzed separately for heifers (first parity cows) and cows (later parity cows) for AIS, NRR, and IFL.ResultsIn the first step 6 QTL were detected for FTI: one QTL on each of BTA7, BTA20, BTA23, BTA25, and two QTL on BTA9 (QTL9–1 and QTL9–2). In the second step, ICF showed association with the QTL regions on BTA7, QTL9–2 QTL2 on BTA9, and BTA25, AIS for cows on BTA20 and BTA23, AIS for heifers on QTL9–2 on BTA9, IFL for cows on BTA20, BTA23 and BTA25, IFL for heifers on BTA7 and QTL9-2 on BTA9, NRR for heifers on BTA7 and BTA23, and NRR for cows on BTA23.ConclusionThe genome wide association study presented here revealed 6 genomic regions associated with FTI. Screening these 6 QTL regions for the underlying female fertility traits revealed that different female fertility traits showed associations with different subsets of the individual FTI QTL peaks. The result of this study contributed to a better insight into the genetic control of FTI in the Danish Jersey.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0210-3) contains supplementary material, which is available to authorized users.

Genome-wide association study for jumping performances in French sport horses.

A genome-wide association study was performed to identify single nucleotide polymorphisms (SNPs) associated with jumping performances of warmbloods in France. The 999 horses included in the study for jumping performances were sport horses [mostly Selle Français (68%), Anglo-Arabians (13%) and horses from the other European studbooks]. Horses were genotyped using the Illumina EquineSNP50 BeadChip. Of the 54,602 SNPs available on this chip, 44,424 were retained after quality testing. Phenotypes were obtained by deregressing official breeding values for jumping competitions to use all available information, that is, the performances of each horse as well as those of its relatives. Two models were used to test the effects of the genotypes on deregressed phenotypes: a single-marker mixed model and a haplotype-based mixed model (significant: P < 1E-05; suggestive: P < 1E-04). Both models included a polygenic effect to take into account familial structures. For jumping performances, one suggestive quantitative trait locus (QTL) located on chromosome 1 (BIEC2_31196 and BIEC2_31198) was detected with both models. This QTL explains 0.7% of the phenotypic variance. RYR2, a gene encoding a major calcium channel in cardiac muscle in humans and mice, is located 0.55 Mb from this potential QTL.

Genetic Parameters of Claw and Foot Disorders Estimated with Logistic Models

The primary aim of this study was to estimate heritabilities for different types of claw and foot disorders and the genetic relationship of disorders with milk yield and selected conformation traits by applying logistic models in Holstein dairy cattle. The study included data from 5634 Holstein cows kept on large-scale dairy farms in Eastern Germany. Dichotomous response variables were the presence or absence of the disorder in 2003. Cows that were present in herds for <6 wk in 2003 were excluded from the analysis. Incidences, disregarding repeated measurements, for digital dermatitis (DD), sole ulceration (SU), wall disorder (WD), and interdigital hyperplasia (IH) in rear legs were 13.2, 16.1, 9.6, and 6.3%, respectively. The herd effect was highly significant for all disorders. Incidences increased with increasing parities for SU and WD, but were highest among heifers for DD. High milk yield at the first 2 test d after calving was associated with a greater risk for claw and foot disorders in the same lactation. Estimates of heritability were 0.073 for DD, 0.086 for SU, 0.104 for WD, and 0.115 for IH. Genetically, health problems appear to occur in clusters (i.e., a cow showing one disease has an increased genetic risk of showing another claw disease). This phenomenon was also observed between claw and foot disorders and the somatic cell score. Genetic correlations between milk yield in early lactation and disorders were 0.240 for DD, 0.057 for SU, 0.270 for WD, and 0.336 for IH, indicating a physiological antagonism. Correlations between breeding values for claw and foot disorders of bulls and official breeding values for functional type traits were mostly favorable. Routine recording of claw data will offer a new chance to improve claw health within the population as was elaborated by different scenarios applying selection index procedures.

Genetische Analyse von Klauenmaßen aus der Eigenleistungsprüfung von Jungbullen

Abstract. Title of the paper: Genetic analysis of claw measurements from the performance test of young bulls The present study deals with the analysis of the claw measurements length of dorsal wall, length of heel, high of heel, diagonal, angle of dorsal wall and hardness of claw horn from the performance test of young bulls. Data collection take place at one fore leg and one hind leg from 798 young German Holstein bulls (black and white, red and white) and 89 young Angler bulls. The analysis of the systematic fixed effects was followed by the estimation of genetic parameters. A breeding value estimation was done with some of the claw traits and rank correlation for the breeding values of the claw traits and some official exterieur breeding values and the length of productive life were calculated. Heritabilities ranked from 0.00 (hardness of claw horn, upper point of measurement of hind leg) to 0.45 (diagonal of the foreleg). Genetic correlation between fore leg and hind leg vary between 0.14 and 0.99. Rank correlation of the claw trait breeding values ranked from –0.65 to 0.64. Rank correlation between official breeding values and claw trait breeding values vary from –0.27 to 0.37.