A predictive assessment of genetic correlations between traits in chickens using markers

International audienceAbstractBackgroundGenomic selection has been successfully implemented in plant and animal breeding programs to shorten generation intervals and accelerate genetic progress per unit of time. In practice, genomic selection can be used to improve several correlated traits simultaneously via multiple-trait prediction, which exploits correlations between traits. However, few studies have explored multiple-trait genomic selection. Our aim was to infer genetic correlations between three traits measured in broiler chickens by exploring kinship matrices based on a linear combination of measures of pedigree and marker-based relatedness. A predictive assessment was used to gauge genetic correlations.MethodsA multivariate genomic best linear unbiased prediction model was designed to combine information from pedigree and genome-wide markers in order to assess genetic correlations between three complex traits in chickens, i.e. body weight at 35 days of age (BW), ultrasound area of breast meat (BM) and hen-house egg production (HHP). A dataset with 1351 birds that were genotyped with the 600 K Affymetrix platform was used. A kinship kernel (K) was constructed as K = λG + (1 − λ)A, where A is the numerator relationship matrix, measuring pedigree-based relatedness, and G is a genomic relationship matrix. The weight (λ) assigned to each source of information varied over the grid λ = (0, 0.2, 0.4, 0.6, 0.8, 1). Maximum likelihood estimates of heritability and genetic correlations were obtained at each λ, and the “optimum” λ was determined using cross-validation.ResultsEstimates of genetic correlations were affected by the weight placed on the source of information used to build K. For example, the genetic correlation between BW–HHP and BM–HHP changed markedly when λ varied from 0 (only A used for measuring relatedness) to 1 (only genomic information used). As λ increased, predictive correlations (correlation between observed phenotypes and predicted breeding values) increased and mean-squared predictive error decreased. However, the improvement in predictive ability was not monotonic, with an optimum found at some 0 < λ < 1, i.e., when both sources of information were used together.ConclusionsOur findings indicate that multiple-trait prediction may benefit from combining pedigree and marker information. Also, it appeared that expected correlated responses to selection computed from standard theory may differ from realized responses. The predictive assessment provided a metric for performance evaluation as well as a means for expressing uncertainty of outcomes of multiple-trait selection

Environmental Factors Affecting Fleece Traits in Raeini Cashmere Goat

The objective of this study was to evaluate some environmental factors (sex, age and management system) on fibrecharacteristics of Raeini Cashmere goats in Baft stations (BS) and of Raeini Cashmere goats raised in nomadic conditions (NC) as commercial flocks. Fiber samples including cashmere and hair were taken from 150 and 120 Raeini Cashmere goats (aged 1-8 years old) from BS and NC, respectively. The Fleece traits measured included staple length (SL), percentage of cashmere in fleece (C), percentage of guard hair in fleece (H), cashmere's mean fiber diameter (CMFD) and the coefficient of variation of cashmere's fiber diameter (CVFD). Mean SL, C, H, CMFD and CVFD in BS were 6.35 ±0.1 cm, 66.51± 0.72 %, 33.5 ± 0.72 %, 20.19 ±0.11 micron and 19.57± 0.21% and thosein NC were 5.62 ± 0.1 cm, 69.06 ± 0.74 %, 30.94 ±0.74 %, 19.53±0.15 micron and 17.88 ± 0.19 %, respectively. There were significant differences (P<0.05) between the two production management systems for all traits investigated. The value for C was significantly higher in males than females (P<0.05). The results showed that the fleece traits were affected by age. However, the effect of age on these traits was not the same. Significant phenotypic correlations were found between SL and CMFD (0.16) and between SL and CVFD (0.13). The results of this study indicated that the fixed effects of age, sex and management systems as well as the relationship between fleece traits should  be considered in the Raeini Cashmere goat breeding programs

Influence of milking frequency on genetic parameters associated with the milk production in the first and second lactations of Iranian Holstein dairy cows using random regression test day models

Abstract Background The milk yield can be affected by the frequency of milking per day, in dairy cows. Previous studies have shown that the milk yield is increased by 6–25 % per lactation when the milking frequency is increased from 2 to 3 times per day while the somatic cell count is decreased. To investigate the effect of milking frequency (3X vs. 4X) on milk yield and it’s genetic parameters in the first and second lactations of the Iranian Holstein dairy cows, a total of 142,604 test day (TD) records of milk yield were measured on 20,762 cows. Results Heritability estimates of milk yield were 0.25 and 0.19 for 3X milking frequency and 0.34 and 0.26 for 4X milking frequency throughout the first and second lactations, respectively. Repeatability estimates of milk yield were 0.70 and 0.71 for 3X milking frequency and 0.76 and 0.77 for 4X milking frequency, respectively. In comparison with 3X milking frequency, the milk yield of the first and second lactations was increased by 11.6 and 12.2 %, respectively when 4X was used (p < 0.01). Conclusions Results of this research demonstrated that increasing milking frequency led to an increase in heritability and repeatability of milk yield. The current investigation provided clear evidences for the benefits of using 4X milking frequency instead of 3X in Iranian Holstein dairy cows

Modelling genetic covariance structure across ages of mean fibre diameter in sheep using multivariate and random regression analysis

Mean fibre diameter measurements from yearling to 5-year-old Australian fine- and medium-wool Merino sheep were analysed using several multivariate models that varied in covariance structure. A pre-structured multivariate model was found to be the most parsimonious model in comparison with the other models fitted such as banded, autoregressive and random regression. In the preferred model, the ages of mean fibre diameter for fine-wool data were genetically partitioned into yearling, 2 years, 3 years and later ages and for medium-wool data into hogget, 2 years and later ages. The estimates of genetic correlations between mean fibre diameter measured at different ages for medium-wool sheep were higher (0.89-1.00) than those for fine-wool Merino (0.75-1.00)

Heritabilties for skin follicle traits and their correlations with production traits in Australian fine wool Merino sheep

Genetic parameters for skin follicle traits, wool traits, body weight and number of lambs weaned per ewe joined were estimated for fine wool Merinos. Total, secondary and primary follicle number index, which are based on skin surface area and skin follicle density, were considered. Heritability estimates for total, secondary and primary follicle number index were 0.45, 0.46 and 0.38 respectively. The genetic correlations between total follicle number index and clean fleece weight, mean fibre diameter, staple strength, coefficient of variation of fibre diameter, body weight and number of lambs weaned were 0.16, -0.67, 0.00, 0.22 and 0.22, respectively

A genome-wide scan to detect signatures of recent selection in Australian Merino sheep

Domestication and selection are processes that conserve the pattern of genetic diversities between and within populations. Identification of genomic regions that are targets of selection for phenotypic traits is one of the main aims of research in animal genetics. An approach for identifying divergently selected regions of the genome is to compare FST values among loci to estimate the genetic variability between and within populations. In this study, a whole genome scan using the 50K Illumina Ovine SNP chip was performed in seventeen flocks of Australian Merino sheep (8 CRC flocks and 9 SG flocks). Population differentiation using FST in these flocks revealed seven genomic regions. These areas were located on chromosomes 2 (two region), 3, 6, 7, 16 and 26 (Wintheta&gt; 0.15). In this study, a number of candidate genes associated with reproductive and growth traits were identified. Study of the reported QTLs in these regions of the ovine and bovine genomes also showed that they associated with important traits such as reproduction, carcass yield, growth and wool traits. Further validation studies of these regions can be used to identify the candidate genes for economically important traits in sheep breeds. The results also provided intuitions for further understanding of the genetic diversities among the Merino flocks

Mitochondrial DNA sequence variation in Iranian native dogs

<p>The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (<i>n</i> = 305) in comparison with published European (<i>n</i> = 443) and Southwest Asian (<i>n</i> = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. In Iran, haplotype and nucleotide diversities were highest in east, southeast and northwest populations while western population had the least. Sarabi and Saluki dog populations can be assigned into haplogroups A, B, C and D; Qahderijani and Kurdi to haplogroups A, B and C, Torkaman to haplogroups A, B and D while Sangsari and Fendo into haplogroups A and B, respectively. Evaluation of population differentiation using pairwise <i>F</i>_ST generally revealed no clear population structure in most Iranian dog populations. The genetic signal of a recent demographic expansion was detected in East and Southeast populations. Further, in accordance with previous studies on dog-wolf hybridization for haplogroup d2 origin, the highest number of d2 haplotypes in Iranian dog as compared to other areas of Mediterranean basin suggests Iran as the probable center of its origin. Historical evidence showed that Silk Road linked Iran to countries in South East Asia and other parts of the world, which might have probably influenced effective gene flow within Iran and these regions. The medium nucleotide diversity observed in Iranian dog calls for utilization of appropriate management techniques in increasing effective population size.</p