1977 performance of commercial soybeans in Illinois / 1152

Chiefly tables.Cover title

A QTL for osteoporosis detected in an F2 population derived from White Leghorn chicken lines divergently selected for bone index

Osteoporosis, resulting from progressive loss of structural bone during the period of egg-laying in hens, is associated with an increased susceptibility to bone breakage. To study the genetic basis of bone strength, an F cross was produced from lines of hens that had been divergently selected for bone index from a commercial pedigreed White Leghorn population. Quantitative trait loci (QTL) affecting the bone index and component traits of the index (tibiotarsal and humeral strength and keel radiographic density) were mapped using phenotypic data from 372 F individuals in 32 F families. Genotypes for 136 microsatellite markers in 27 linkage groups covering ∼80% of the genome were analysed for association with phenotypes using within-family regression analyses. There was one significant QTL on chromosome 1 for bone index and the component traits of tibiotarsal and humeral breaking strength. Additive effects for tibiotarsal breaking strength represented 34% of the trait standard deviation and 7.6% of the phenotypic variance of the trait. These QTL for bone quality in poultry are directly relevant to commercial populations

MITOCHONDRIAL DNA POLYMORPHISMS AND FERTILITY IN BEEF CATTLE

Two regions of mitochondrial DNA, D-loop and ND-5 were characterized using polymerase chain reaction – restriction fragment length polymorphism (PCR-RFLP) involving 422 beef cattle of Hereford and composite breeds from Wokalup’s research station. ANOVA models (model I, II) were used to estimate associations between molecular haplotypes and quantitative traits. The phenotypic data used were records on calving rate, defined as the mean number of live calves born over four years, while the genotypic data used were the result of PCR-RFLP analysis in both regions of mitochondrial DNA using 7 restriction enzymes. The results of the present study have provided evidence that mitochondrial polymorphisms in the D-loop and ND-5 regions are associated significantly with fertility. This is the first report of a correlation between mitochondrial polymorphism in D-loop and ND-5 on fertility in beef cattle. Key words: PCR-RFLP, bovine mitochondrial DNA, D-loop, ND-5

Milk whey protein concentration and mRNA associated with β-lactoglobulin phenotype

Two common genetic variants of β-lactoglobulin (β-lg), A and B, exist as co- dominant alleles in dairy cattle (Aschaffenburg, 1968). Numerous studies have shown that cows homozygous for β-lg A have more β-lg and less α-lactalbumin (α-la) and casein in their milk than cows expressing only the B variant of β-lg (Ng-Kwai-Hang et al. 1987; Graml et al. 1989; Hill, 1993; Hill et al. 1995, 1997). These differences have a significant impact on the processing characteristics of the milk. For instance, the moisture-adjusted yield of Cheddar cheese is up to 10% higher using milk from cows of the β-lg BB phenotype compared with milk from cows expressing only the A variant (Hill et al. 1997). All these studies, however, describe compositional differences associated with β-lg phenotype in established lactation only. No information is available on the first few weeks of lactation, when there are marked changes in the concentrations of β-lg and α-la (Pérez et al. 1990)

Genome-wide association study identifies common and low-frequency variants at the AMHgene locus that strongly predict serum AMH levels in males

Anti-Müllerian hormone (AMH) is an essential messenger of sexual differentiation in the foetus and is an emerging biomarker of postnatal reproductive function in females. Due to a paucity of adequately sized studies, the genetic determinants of circulating AMH levels are poorly characterized. In samples from 2815 adolescents aged 15 from the ALSPAC study, we performed the first genome-wide association study of serum AMH levels across a set of ∼9 M ‘1000 Genomes Reference Panel’ imputed genetic variants. Genetic variants at the AMH protein-coding gene showed considerable allelic heterogeneity, with both common variants [rs4807216 (PMale = 2 × 10−49, Beta: ∼0.9 SDs per allele), rs8112524 (PMale = 3 × 10−8, Beta: ∼0.25)] and low-frequency variants [rs2385821 (PMale = 6 × 10−31, Beta: ∼1.2, frequency 3.6%)] independently associated with apparently large effect sizes in males, but not females. For all three SNPs, we highlight mechanistic links to AMH gene function and demonstrate highly significant sex interactions (PHet 0.0003–6.3 × 10−12), culminating in contrasting estimates of trait variance explained (24.5% in males versus 0.8% in females). Using these SNPs as a genetic proxy for AMH levels, we found no evidence in additional datasets to support a biological role for AMH in complex traits and diseases in men

Are current ecological restoration practices capturing natural levels of genetic diversity? A New Zealand case study using AFLP and ISSR data from mahoe (Melicytus ramiflorus)

Sourcing plant species of local provenance (eco-sourcing) has become standard practice in plant community restoration projects. Along with established ecological restoration practices, knowledge of genetic variation in existing and restored forest fragments is important for ensuring the maintenance of natural levels of genetic variation and connectivity (gene flow) among populations. The application of restoration genetics often employs anonymous ‘fingerprinting’ markers in combination with limited sample sizes due to financial constraints. Here, we used two such marker systems, AFLPs and ISSRs, to estimate population-level genetic variation of a frequently used species in restoration projects in New Zealand, māhoe (Melicytus ramiflorus, Violaceae). We examined two rural and two urban forest fragments, as potential local source populations, to determine whether the māhoe population at the recently (re)constructed ecosystem at Waiwhakareke Natural Heritage Park (WNHP), Hamilton, New Zealand reflects the genetic variation observed in these four potential source populations. Both marker systems produced similar results and indicated, even with small population sizes, that levels of genetic variation at WNHP were comparable to in situ populations. However, the AFLPs did provide finer resolution of the population genetic structure than ISSRs. ISSRs, which are less expensive and technically less demanding to generate than AFLPs, may be sufficient for restoration projects where only a broad level of genotypic resolution is required. We recommend the use of AFLPs when species with a high conservation status are being used due to the greater resolution of this technique

Biomarker Detection in Association Studies: Modeling SNPs Simultaneously via Logistic ANOVA

In genome-wide association studies, the primary task is to detect biomarkers in the form of Single Nucleotide Polymorphisms (SNPs) that have nontrivial associations with a disease phenotype and some other important clinical/environmental factors. However, the extremely large number of SNPs comparing to the sample size inhibits application of classical methods such as the multiple logistic regression. Currently the most commonly used approach is still to analyze one SNP at a time. In this pa- per, we propose to consider the genotypes of the SNPs simultaneously via a logistic analysis of variance (ANOVA) model, which expresses the logit transformed mean of SNP genotypes as the summation of the SNP effects, effects of the disease phenotype and/or other clinical variables, and the interaction effects. We use a reduced-rank representation of the interaction-effect matrix for dimensionality reduction, and employ the L1-penalty in a penalized likelihood framework to filter out the SNPs that have no associations. We develop a Majorization-Minimization algorithm for computational implementation. In addition, we propose a modified BIC criterion to select the penalty parameters and determine the rank number. The proposed method is applied to a Multiple Sclerosis data set and simulated data sets and shows promise in biomarker detection

Long-term rearrangement of retinal structures in a novel mutation of X-linked retinoschisis

The aim of the present study was to report a novel mutation in the retinoschisin 1 (RS1) gene in a Caucasian family affected by X-linked juvenile retinoschisis (XLRS) and to describe the long-term modification of retinal structure. Two brothers with an early onset maculopathy were diagnosed with XLRS. Fundus photography, fluorescein angiography, spectral domain optical coherence tomography and electroretinogram analyses were performed. Their sister was also examined. All subjects were screened for mutations in the RS1 gene. XLRS patients demonstrated a marked reduction of best-corrected visual acuity. SD-OCT scans reported a cystic degeneration primarily involving the inner nuclear layer, though some cysts were detected in the outer plexiform layer and in the ganglion cell layer. During the ten-year follow-up, a progressive retinal thickening and coalescence of the cysts was observed. Genetic testing revealed a novel mutation (p.Ile212Asn) in the RS1 gene in both XLRS patients, whereas their sister was not a genetic carrier. Several mutations of the RS1 gene were recognized to be responsible for XLRS. Although the correspondence between genotype and phenotype is still under debate, is reasonable that siblings affected by XLRS could share other genetic and/or epigenetic factors capable to influence clinical course of the disease