Estimated breeding values and association mapping for persistency and total milk yield using natural cubic smoothing splines

BackgroundFor dairy producers, a reliable description of lactation curves is a valuable tool for management and selection. From a breeding and production viewpoint, milk yield persistency and total milk yield are important traits. Understanding the genetic drivers for the phenotypic variation of both these traits could provide a means for improving these traits in commercial production.MethodsIt has been shown that Natural Cubic Smoothing Splines (NCSS) can model the features of lactation curves with greater flexibility than the traditional parametric methods. NCSS were used to model the sire effect on the lactation curves of cows. The sire solutions for persistency and total milk yield were derived using NCSS and a whole-genome approach based on a hierarchical model was developed for a large association study using single nucleotide polymorphisms (SNP).ResultsEstimated sire breeding values (EBV) for persistency and milk yield were calculated using NCSS. Persistency EBV were correlated with peak yield but not with total milk yield. Several SNP were found to be associated with both traits and these were used to identify candidate genes for further investigation.ConclusionNCSS can be used to estimate EBV for lactation persistency and total milk yield, which in turn can be used in whole-genome association studies.Klara L. Verbyla and Arunas P. Verbyl

Archives of psychiatry and psychotherapy

The effects were studied of potassium sulfate and potassium chloride applied at rates up to 640 kg/ha K on tuber specific gravity, size and susceptibility to internal bruising. The field experiments from which these data were obtained were conducted during the 1982-83 and 1983-84 seasons throughout the main potato-growing areas of South Australia. For the deficient and marginal site groupings, there was a consistent positive trend in specific gravity as potassium sulfate rates increased up to 640 kg/ha K. There was a slight negative trend when potassium chloride was used. Potassium fertiliser had no consistent effect on specific gravity at sites in the non-responsive grouping. Petiole or tuber potassium concentrations were poorly correlated with specific gravity. In the deficient and marginal groups increasing rates of potassium increased the yield of 80-350, 350-450, 450-680 and greater than 680-g tubers. The percentage increase in yield was greatest for the larger size grades (350-450 g or larger). At sites in the non-responsive group potassium had no effect on tuber size. At 2 out of 9 sites the effect of potassium chloride on tuber size was significantly different from that of potassium sulfate. Potassium chloride at rates of 160 and 320 kg/ha K reduced the susceptibility of tubers to internal bruising at 3 out of 4 sites. Potassium sulfate was effective at 3 out of 6 sites but only at the highest rate tested (640 kg/ ha K). Susceptibility to internal bruising was significantly (P t 0.01) negatively correlated with both petiole and tuber potassium concentrations. Prognostic critical potassium concentrations above which internal bruising was minimised were 8.30% in petioles or 1.84% in tubers. These values were calculated using the Cate-Nelson separation

(Co)variance structures for linear models in the analysis of plant improvement data

Plant improvement programs involve the evaluation of a large number of genotypes (varieties) in a series of designed experiments known as multi-environment trials (MET). The combined analysis of MET data is a complex statistical problem which requires extensions to the standard linear mixed model. The analysis must accommodate spatial correlation structures for the plot errors from each trial and appropriate genetic covariance structures. ASReml (Gilmour, Cullis, Welham & Thompson, 1998) provides a broad range of variance structures for both the errors and the random effects in a linear mixed model. The gains in statistical efficiency resulting from the use of more complex but more realistic variance structures are large. With ASReml they can be achieved at very little extra cost since the algorithm and use of sparse matrix methods ensures timely analyses. In this paper the computational strategy of ASReml will be described and some of the scope of the program will be demonstrated in the analysis of a MET data set

Global adaptation patterns of Australian and CIMMYT spring bread wheat

The International Adaptation Trial (IAT) is a special purpose nursery designed to investigate the genotype-by-environment interactions and worldwide adaptation for grain yield of Australian and CIMMYT spring bread wheat (Triticum aestivum L.) and durum wheat (T. turgidum L. var. durum). The IAT contains lines representing Australian and CIMMYT wheat breeding programs and was distributed to 91 countries between 2000 and 2004. Yield data of 41 reference lines from 106 trials were analysed. A multiplicative mixed model accounted for trial variance heterogeneity and inter-trial correlations characteristic of multi-environment trials. A factor analytic model explained 48% of the genetic variance for the reference lines. Pedigree information was then incorporated to partition the genetic line effects into additive and non-additive components. This model explained 67 and 56% of the additive by environment and non-additive by environment genetic variances, respectively. Australian and CIMMYT germplasm showed good adaptation to their respective target production environments. In general, Australian lines performed well in south and west Australia, South America, southern Africa, Iran and high latitude European and Canadian locations. CIMMYT lines performed well at CIMMYT's key yield testing location in Mexico (CIANO), north-eastern Australia, the Indo-Gangetic plains, West Asia North Africa and locations in Europe and Canada. Maturity explained some of the global adaptation patterns. In general, southern Australian germplasm were later maturing than CIMMYT material. While CIANO continues to provide adapted lines to northern Australia, selecting for yield among later maturing CIMMYT material in CIANO may identify lines adapted to southern and western Australian environments

Patterns of genotype-by-environment interaction in diameter at breast height at age 3 for eucalypt hybrid clones grown for reafforestation of lands affected by salinity

The commercial viability of plantations established for the recovery of saline lands may be supported by the deployment of improved genetic material matched to these particularly challenging environments. Patterns of genotype-by-environment interaction were investigated in a highly unbalanced data set of diameter at breast height at approximately 3 years for a total of 841 genotypes from ten Eucalyptus camaldulensis x Eucalyptus globulus and Eucalyptus camaldulensis x Eucalyptus grandis hybrid families assessed across 21 trials grown on a range of saline and non-saline low rainfall sites from southeast Queensland through central NSW, Victoria, Tasmania and southeast South Australia to southwest Western Australia using factor-analytic mixed-model methods. There was significant heterogeneity among trials in estimates of family variance, genotype-within-family variance, the ratio of family variance to total genetic variance and individual broad-sense heritability. Cluster analyses indicated that family effects were highly correlated across a main group of 19 trials and that most trials fell into two major groups for genotype-within-family effects, with an average correlation among trials within these groups of 0.55. There was, however, no obvious geographical or other explanation for the patterns, suggesting that genotypes should be deployed on the basis of broad-scale adaptation