A genome-wide association analysis for body weight at 35 days measured on 137,343 broiler chickens

Background Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a “large” number of genes with “small” effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size. Methods The GWAS included 137,343 broilers spanning 15 pedigree generations and 392,295 imputed single nucleotide polymorphisms (SNPs). A false discovery rate of 1% was adopted to account for multiple testing when declaring significant SNPs. A Bayesian ridge regression model was implemented, using AlphaBayes, to estimate the contribution to the total genetic variance of each region harbouring significant SNPs (1 Mb up/downstream) and the combined regions harbouring non-significant SNPs. Results GWAS revealed 25 genomic regions harbouring 96 significant SNPs on 13 Gallus gallus autosomes (GGA1 to 4, 8, 10 to 15, 19 and 27), with the strongest associations on GGA4 at 65.67–66.31 Mb (Galgal4 assembly). The association of these regions points to several strong candidate genes including: (i) growth factors (GGA1, 4, 8, 13 and 14); (ii) leptin receptor overlapping transcript (LEPROT)/leptin receptor (LEPR) locus (GGA8), and the STAT3/STAT5B locus (GGA27), in connection with the JAK/STAT signalling pathway; (iii) T-box gene (TBX3/TBX5) on GGA15 and CHST11 (GGA1), which are both related to heart/skeleton development); and (iv) PLAG1 (GGA2). Combined together, these 25 genomic regions explained ~ 30% of the total genetic variance. The region harbouring significant SNPs that explained the largest portion of the total genetic variance (4.37%) was on GGA4 (~ 65.67–66.31 Mb). Conclusions To the best of our knowledge, this is the largest GWAS that has been conducted for BW in chicken to date. In spite of the identified regions, which showed a strong association with BW, the high proportion of genetic variance attributed to regions harbouring non-significant SNPs supports the hypothesis that the genetic architecture of BW35 is polygenic and complex. Our results also suggest that a large sample size will be required for future GWAS of BW35.

Additive and Non-Additive Genetic Variances for Tree Growth in Several Hybrid Poplar Populations and Implications Regarding Breeding Strategy

Populus species (P. deltoides, P. maximowiczii, P. nigra) and their inter-specific hybrids were tested for growth rate over a five year period at four test locations in Minnesota, USA, to estimate genetic variance components. The breeding scheme incorporated recurrent selection of full-sib families of pure species parents, production of F1 inter-specific hybrids from selected families, and selection of clones within the F1s. Improvement of yield through time using this scheme is predicated on the assumption that additive effects comprise a significant portion of the total genetic variance. The estimates of additive and non-additive variances reported are not traditional point estimates, because a fully balanced mating design was impossible due to parental incompatibilities which result in incomplete breeding matrices. Instead, bounded estimates, not previously used in tree genetics research, are derived from linear combinations of formulae of genetic expectations observed among-family, among-clone, and environmental variances. Our results suggest that combined family and mass selection would lead to increases in growth rate of 27 % and 47 % per generation in P. deltoides and P. nigra, respectively. Broad sense-based clonal selection within the F1 could yield selection responses in excess of 90 % of the mean of such populations. Among-family variance comprised about 1/3 of total genetic variance while within-family variance was always about 2/3 of total genetic variance, regardless of pedigree. The results indicate that recurrent intraspecific selective breeding followed by interspecific hybridization and non-recurrent selection based on broad sense genetic variation would constitute an effective yield improvement strategy.

QTL explaining variation in production traits and udder health in the Danish Holstein population

The main objective was to locate QTL and estimate the proportion of total genetic variance attributable to quantitative trait loci (QTL) for production index traits and the udder health index identified on six Bos taurus autosomes in the Danish Holstein dairy cattle population. Data were obtained from a granddaughter design of 20 sire families with a total of 1 869 progeny tested sons. The number of sons per grandsire ranged from 20 to 284, with an average family size of 93.5. Indexes of the estimated breeding values were obtained for the milk production traits and for the udder health index from the Danish Agricultural Advisory Service database. A random-QTL model was applied to incorporate marker information into parameter estimation for each single QTL. The procedure allowed us to detect new QTL on BTA3, BTA16 and BTA28 and to estimate the proportion of total genetic variance attributed to different QTL on a total of six Bos taurus autosomes for the udder health index and yield index traits in the Danish Holstein population. Variance estimates vary between 2 to 58 % of the total variance for different QTL and seem to explain a substantial part of the variance at certain positions of the cattle genome. The results are discussed against the background of the failure of marker-assisted selection (MAS) and the recent availability of large panels of single nucleotide polymorphisms (SNPs) that have improved the search for mutations underlying variation in complex traits resulting in modern genomic selection.

Genetic and Environmental Influences on Stuttering and Tics in Japanese Twin Children

The purpose of this study was to clarify the genetic contribution to stuttering and tics in childhood using the largest databases of Japanese twins. The subjects were 1896 pairs of twin children consisting of 1849 males and 1943 females with a mean age of 11.6 years (3 years to 15 years). All data were gathered by questionnaire. The prevalence of stuttering was 6.7% in males and 3.6% in females (p < .0001). The prevalence of tics was 6.8% in males and 4.1% in females (p = .0021). Concordance rates and polychoric correlations were all higher in monozygotic pairs than in dizygotic pairs irrespective of sex combination. Structural equation modeling showed that the proportion of total phenotypic variance attributable to genetic influences was 80% in males and 85% in females for stuttering, and 28% in males and 29% in females for tics. Moreover, co-occurrence between stuttering and tics was observed in 0.8% of males (tetrachoric correlation: r = .18) and 0.5% of females (r = .31), which was attributed partly (nearly 10% of total genetic variance of each trait) to the common genetic factors, with genetic correlation of r = .32.

ESTIMATING HERITABILITY OF FAMILIES DERIVED FROM SINGLE PLANTS AT AN ADVANCED GENERATION OF SELF-FERTILIZING SPECIES: DEVELOPING GENERAL FORMULAS AND ESTIMATING SPRING WHEAT TRAITS

Genetic expectations of total genetic variance, and between-family and within-family variance components were developed for any given generation (Fn) derived from single selfed plants of an earlier generation (Fk). A formula to estimate the heritability (h2) in any desired generation (Fn) was developed on the basis of these expectations. This formula estimates the value of the genetic variance from the phenotypic variance adjusted to the F2 generation. Heritability estimates of culm length, heading date, and mean grain weight from two populations of F6 families, each derived from a single F5 plant, were computed using this formula, and a formula which estimates the value of the genetic variance from the phenotypic variance in the Fn generation (“Fn estimates”). The FN h2 estimates at F6 were always higher than those adjusted to F2 variance, due to the increase in additive variance and the reduction in dominance variance.

Identification of Sources and Inheritance of Resistance to Sphaceloma Scab in Cowpea

Resistance in cowpea to Sphaceloma scab was characterized based on foliar and pod infection. Disease severity on cowpea plants was rated on a scale of 1 to 5, as follows: 1 = no symptoms, 2 = less than 10% infection, 3 = 10 to 20% infection, 4 = 20 to 50% infection, and 5 = more than 50% infection. Mean severity scores were used to calculate areas under the disease progress curve. Of the 75 cowpea lines evaluated, 10 were resistant, 30 were moderately resistant, and 35 were susceptible based on foliar infection. For pod infection, 24 lines were resistant, 40 were either moderately resistant or susceptible, and 11 were very susceptible. Local lines were less infected than plant introductions. In a separate experiment, 25 lines previously considered resistant were evaluated in the field with infested cowpea crop debris and susceptible rows as sources of inocula. Only 3 lines (39, KVu/175, and 46) maintained their high levels of resistance to Sphaceloma scab. Five cowpea lines were subsequently diallel-crossed, and parents and F2 were evaluated in the field to determine the nature of inheritance of resistance to Sphaceloma scab. The majority of the crosses between the resistant and susceptible lines showed intermediate reaction to scab, and high variation was obtained due to genotype and combining abilities. Partitioning of the variance into components due to general and specific combining ability revealed that additive genetic variation constituted the major portion of the total genetic variance for resistance to scab in cowpea.

THE INHERITANCE OF GOSSYPOL LEVEL IN GOSSYPIUM II: INHERITANCE OF SEED GOSSYPOL IN TWO STRAINS OF CULTIVATED GOSSYPIUM BARBADENSE L

ABSTRACT Two strains of cultivated Gossypium barbadense L., Sea Island AS-2 and Pima S-4, were used to study the effects of alleles at two loci on the production and/or storage of gossypol in mature embryos. The normal alleles, Gl 2 and Gl 3, are "native" to G. barbadense, whereas the mutant alleles, gl 2 and gl 3, were introduced from Gossypium hirsutum L. through backcrossing. Each strain was grown in three replications per trial, and one, Sea Island AS-2, was grown in three environments. Each experiment consisted of all possible crosses, including reciprocals, of the four true-breeding genotypes, plus parents. Additive effects accounted for more than 90% of the total genetic variance for seed gossypol level in all trials. Epistatic effects, though small, were frequently significant. In G. barbadense Gl 2 and Gl 3 were associated with the production of similar amounts of gossypol, whereas previous trials with cultivated varieties of G. hirsutum showed that Gl 2 was more than twice as expressive as Gl 3. The greater average productivity of seed gossypol in cultivated G. barbadense, as compared with G. hirsutum, was attributed to greater activity at the Gl 3 locus in the former species.