Genetic Parameters for Physiological Characters in Merino Rams in Central and North West Queensland

Genetic and phenotypic parameters for respiration rate (RR) and rectal temperature (RT) are presented for weaner and hogget Merino rams, at Longreach and Julia Creek, Queensland. Heritability estimates for RT and RR at both sites and at both ages ranged from moderate to very high. Phenotypic and genetic correlations between these characters are also reported. AAABG 14th Conference; Proceedings of the Association for the Advancement of Animal Breeding and Genetics. AAABG

A physiological framework to explain genetic and environmental regulation of tillering in sorghum

Tillering determines the plant size of sorghum (Sorghum bicolor) and an understanding of its regulation is important to match genotypes to prevalent growing conditions in target production environments. The aim of this study was to determine the physiological and environmental regulation of variability in tillering among sorghum genotypes, and to develop a framework for this regulation. * Diverse sorghum genotypes were grown in three experiments with contrasting temperature, radiation and plant density to create variation in tillering. Data on phenology, tillering, and leaf and plant size were collected. A carbohydrate supply/demand (S/D) index that incorporated environmental and genotypic parameters was developed to represent the effects of assimilate availability on tillering. Genotypic differences in tillering not explained by this index were defined as propensity to tiller (PTT) and probably represented hormonal effects. * Genotypic variation in tillering was associated with differences in leaf width, stem diameter and PTT. The S/D index captured most of the environmental effects on tillering and PTT most of the genotypic effects. * A framework that captures genetic and environmental regulation of tillering through assimilate availability and PTT was developed, and provides a basis for the development of a model that connects genetic control of tillering to its phenotypic consequences.

Genetic Parameters for Production Traits in Queensland Merinos

Genetic and phenotypic parameters are presented for production traits, greasy fleece weight (GFW), yield (YLD), clean fleece weight (CFW), average fibre diameter (DIAM) and liveweight (LWT), in 15 month old medium Peppin Merino sheep at Longreach and Julia Creek, Queensland. Heritabilities for GFW, YLD, CFW, DIAM and LWT were respectively 0.35, 0.62, 0.34, 0.74, and 0.37 for Longreach and 0.23, 0.52, 0.20, 0.67 and 0.56 for Julia Creek. Most estimates were consistent with other reported values. AAABG 13th Conference; Proceedings of the Association for the Advancement of Animal Breeding and Genetics.

Assessing for genetic and environmental effects on ruminant feed quality in barley ( Hordeum vulgare )

Grain samples from a combined intermediate and advanced stage barley breeding trial series, grown at two sites in two consecutive years were assessed for detailed grain quality and ruminant feed quality. The results indicated that there were significant genetic and environmental effects for “feed” traits as measured using grain hardness, acid detergent fibre (ADF), starch and in-sacco dry matter digestibility (ISDMD) assays. In addition, there was strong genotypic discrimination for the regressed feed performance traits, namely Net Energy (NE) and Average Daily Gain (ADG). There was considerable variation in genetic correlations for all traits based on variance from the cultivars used, sites or laboratory processing effects. There was a high level of heritability ranging from 89% to 88% for retention, 60% to 80% for protein and 56% to 68% for ADF. However, there were only low to moderate levels of heritability for the feed traits, with starch 30–39%, ISDMD 55–63%, ADF 56–68%, particle size 47–73%, 31–48% NE and ADG 44–51%. These results suggest that there were real differences in the feed performance of barleys and that selection for cattle feed quality is potentially a viable option for breeding programs.

Measurement of genetic and environmental variation in barley (Hordeum vulgare) grain hardness

In this study, we assessed a broad range of barley breeding lines and commercial varieties by three hardness methods (two particle size methods and one crush resistance method (SKCS—Single-Kernel Characterization System), grown at multiple sites to see if there was variation in barley hardness and if that variation was genetic or environmentally controlled. We also developed near-infrared reflectance (NIR) calibrations for these three hardness methods to ascertain if NIR technology was suitable for rapid screening of breeding lines or specific populations. In addition, we used this data to identify genetic regions that may be associated with hardness. There were significant (p<0.05) genetic effects for the three hardness methods. There were also environmental effects, possibly linked to the effect of protein on hardness, i.e. increasing protein resulted in harder grain. Heritability values were calculated at >85% for all methods. The NIR calibrations, with R2 values of >90%, had Standard Error of Prediction values of 0.90, 72 and 4.0, respectively, for the three hardness methods. These equations were used to predict hardness values of a mapping population which resulted in genetic markers being identified on all chromosomes but chromosomes 2H, 3H, 5H, 6H and 7H had markers with significant LOD scores. The two regions on 5H were on the distal end of both the long and short arms. The region that showed significant LOD score was on the long arm. However, the region on the short arm associated with the hardness (hordoindoline) genes did not have significant LOD scores. The results indicate that barley hardness is influenced by both genotype and environment and that the trait is heritable, which would allow breeders to develop very hard or soft varieties if required. In addition, NIR was shown to be a reliable tool for screening for hardness. While the data set used in this study has a relatively low variation in hardness, the tools developed could be applied to breeding populations that have large variation in barley grain hardness.

Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog

The mountain yellow-legged frog Rana muscosa sensu lato, once abundant in the Sierra Nevada of California and Nevada, and the disjunct Transverse Ranges of southern California, has declined precipitously throughout its range, even though most of its habitat is protected. The species is now extinct in Nevada and reduced to tiny remnants in southern California, where as a distinct population segment, it is classified as Endangered. Introduced predators (trout), air pollution and an infectious disease (chytridiomycosis) threaten remaining populations. A Bayesian analysis of 1901 base pairs of mitochondrial DNA confirms the presence of two deeply divergent clades that come into near contact in the Sierra Nevada. Morphological studies of museum specimens and analysis of acoustic data show that the two major mtDNA clades are readily differentiated phenotypically. Accordingly, we recognize two species, Rana sierrae, in the northern and central Sierra Nevada, and R. muscosa, in the southern Sierra Nevada and southern California. Existing data indicate no range overlap. These results have important implications for the conservation of these two species as they illuminate a profound mismatch between the current delineation of the distinct population segments (southern California vs. Sierra Nevada) and actual species boundaries. For example, our study finds that remnant populations of R. muscosa exist in both the southern Sierra Nevada and the mountains of southern California, which may broaden options for management. In addition, despite the fact that only the southern California populations are listed as Endangered, surveys conducted since 1995 at 225 historic (1899-1994) localities from museum collections show that 93.3% (n=146) of R. sierrae populations and 95.2% (n=79) of R. muscosa populations are extinct. Evidence presented here underscores the need for revision of protected population status to include both species throughout their ranges.

High resolution genetic and physical mapping of the I-3 region of tomato chromosome 7 reveals almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with duplications on Arabidopsis chromosomes 1, 2 and 3

The tomato I-3 gene introgressed from the Lycopersicon pennellii accession LA716 confers resistance to race 3 of the fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici. We have improved the high-resolution map of the I-3 region of tomato chromosome 7 with the development and mapping of 31 new PCR-based markers. Recombinants recovered from L. esculentum cv. M82 × IL7-2 F2 and (IL7-2 × IL7-4) × M82 TC1F2 mapping populations, together with recombinants recovered from a previous M82 × IL7-3 F2 mapping population, were used to position these markers. A significantly higher recombination frequency was observed in the (IL7-2 × IL7-4) × M82 TC1F2 mapping population based on a reconstituted L. pennellii chromosome 7 compared to the other two mapping populations based on smaller segments of L. pennellii chromosome 7. A BAC contig consisting of L. esculentum cv. Heinz 1706 BACs covering the I-3 region has also been established. The new high-resolution map places the I-3 gene within a 0.38 cM interval between the molecular markers RGA332 and bP23/gPT with an estimated physical size of 50-60 kb. The I-3 region was found to display almost continuous microsynteny with grape chromosome 12 but interspersed microsynteny with Arabidopsis thaliana chromosomes 1, 2 and 3. An S-receptor-like kinase gene family present in the I-3 region of tomato chromosome 7 was found to be present in the microsyntenous region of grape chromosome 12 but was absent altogether from the A. thaliana genome.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05-7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

A genome-wide association study of tick burden and milk composition in cattle.

To study the genetic basis of tick burden and milk production and their interrelationship, we collected a sample of 1961 cattle with multiple tick counts from northern Australia of which 973 had dairy production data in the Australian Dairy Herd Information Service database. We calculated heritabilities, genetic and phenotypic correlations for these traits and showed a negative relationship between tick counts and milk and milk component yield. Tests of polymorphisms of four genes associated with milk yield, ABCG2, DGAT1, GHR and PRLR, showed no statistically significant effect on tick burden but highly significant associations to milk component yield in these data and we confirmed separate effects for GHR and PRLR on bovine chromosome 20. To begin to identify some of the molecular genetic bases for these traits, we genotyped a sample of 189 of these cattle for 7397 single nucleotide polymorphisms in a genome-wide association study. Although the allele effects for adjusted milk fat and protein yield were highly correlated (r = 0.66), the correlations of allele effects of these milk component yields and tick burden were small (|r| <= 0.10). These results agree in general with the phenotypic correlations between tick counts and milk component yield and suggest that selection on markers for tick burden or milk component yield may have no undesirable effect on the other trait.

Geographic and Phenotypic Variation in Heartwood and Essential-Oil Characters in Natural Populations of Santalum austrocaledonicum in Vanuatu.

Phenotypic variation in heartwood and essential-oil characters of Santalum austrocaledonicum was assessed across eleven populations on seven islands of Vanuatu Trees differed significantly in their percentage heartwood cross-sectional area and this varied independently of stem diameter The concentrations of the four major essential-oil constituents (alpha-santalol, beta-santalol. (Z)-beta-curcumen-12-ol, and cis-nuciferol) of alcohol-extracted heartwood exhibited at least tenfold and continuous tree-to-tree variation Commercially important components alpha- and beta-santalol found in individual trees ranged from 0 8-47% and 0-24 1%, respectively, across all populations, and significant (P < 0 05) differences for each were found between Individual populations. The Erromango population was unique in that the mean concentrations of its monocyclic ((Z)-beta-curcumen-12-ol and cis-nuciferol) sesquiterpenes exceeded those of Its bi- and tricyclic (alpha- and beta-santalol) sesquiterpenes Heartwood colour varied between trees and spanned 65 colour categories, but no identifiable relationships were found between heartwood colour and alpha- and beta-santalol, although a weak relationship was evident between colour saturation and total oil concentration These results indicate that the heartwood colour is not a reliable predictive trait for oil quality The results of this study highlight the knowledge gaps in fundamental understanding of heartwood biology in Santalum genus The intraspecific variation in heartwood cross-sectional area. oil concentration. and oil quality traits is of considerable importance to the domestication of sandalwood and present opportunities for the development of highly superior S austrocaledonicum cultivars that conform to the industry's International Standards used for S album.

Genetic and Malt Quality Diversity of East Asian Two-Rowed Barley Accessions in Relationship to North American Malting Barley.

Because of epidemics of Fusarium head blight (FHB; caused by Fusarium graminearum Schwabe [teleomorph Gibberella zeae (Schwein.) Petch]) in the northern Great Plains of the United States and Canada in the past two decades, malting barley breeders have been forced to use nonadapted barley (Hordeum vulgare L.) accessions as sources of FHB resistance. Many of the resistant accessions are from East Asia, and limited information is available on their genetic diversity and malt quality. The objectives of this study were to determine the genetic diversity among 30 East Asian accessions and two North American cultivars. Genetic diversity was based on 49 simple-sequence repeat markers. All accessions were tested for barley grain brightness; protein content; 1,000-kernel weight; malting loss; fine-grind malt extract; content of plump kernels, free amino nitrogen, soluble protein, and wort beta-glucan; the Kolbach index (i.e., the ratio of malt soluble protein to malt total protein); a-amylase activity; diastatic power; won color; and wort viscosity. A few accessions had equal quality compared with Harrington and Conlon barley for individual traits but not for all. Qing 2, Mokkei 93-78, and Nitakia 48 could be excellent sources for increased malt extract; Nitakia 48 is a possible source for low wort viscosity; and Mokkei 93-78 and Nitakia 48 are putative sources of low beta-glucan content. The cluster analyses also implied that the malt quality of an accession cannot be predicted based on the country where it was developed.

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

Use of part records in Merino breeding programs - The inheritance of wool growth and fibre traits during different times of the year to determine their value in Merino breeding programs

Fibre diameter can vary dramatically along a wool staple, especially in the Mediterranean environment of southern Australia with its dry summers and abundance of green feed in spring. Other research results have shown a very low phenotypic correlation between fibre diameter grown between seasons. Many breeders use short staples to measure fibre diameter for breeding purposes and also to promote animals for sale. The effectiveness of this practice is determined by the relative response to selection by measuring fibre traits on a full 12 months wool staple as compared to measuring them only on part of a staple. If a high genetic correlation exists between the part record and the full record, then using part records may be acceptable to identify genetically superior animals. No information is available on the effectiveness of part records. This paper investigated whether wool growth and fibre diameter traits of Merino wool grown at different times of the year in a Mediterranean environment, are genetically the same trait, respectively. The work was carried out on about 7 dyebanded wool sections/animal.year, on ewes from weaning to hogget age, in the Katanning Merino resource flocks over 6 years. Relative clean wool growth of the different sections had very low heritability estimates of less than 0.10, and they were phenotypically and genetically poorly correlated with 6 or 12 months wool growth. This indicates that part record measurement of clean wool growth of these sections will be ineffective as indirect selection criteria to improve wool growth genetically. Staple length growth as measured by the length between dyebands, would be more effective with heritability estimates of between 0.20 and 0.30. However, these measurements were shown to have a low genetic correlation with wool grown for 12 months which implies that these staple length measurements would only be half as efficient as the wool weight for 6 or 12 months to improve total clean wool weight. Heritability estimates of fibre diameter, coefficient of variation of fibre diameter and fibre curvature were relatively high and were genetically and phenotypically highly correlated across sections. High positive phenotypic and genetic correlations were also found between fibre diameter, coefficient of variation of fibre diameter and fibre curvature of the different sections and similar measurements for wool grown over 6 or 12 months. Coefficient of variation of fibre diameter of the sections also had a moderate negative phenotypic and genetic correlation with staple strength of wool staples grown over 6 months indicating that coefficient of variation of fibre diameter of any section would be as good an indirect selection criterion to improve stable strength as coefficient of variation of fibre diameter for wool grown over 6 or 12 months. The results indicate that fibre diameter, coefficient of variation of fibre diameter and fibre curvature of wool grown over short periods of time have virtually the same heritability as that of wool grown over 12 months, and that the genetic correlation between fibre diameter, coefficient of variation of fibre diameter and fibre curvature on part and on full records is very high (rg > 0.85). This indicates that fibre diameter, coefficient of variation of fibre diameter and fibre curvature on part records can be used as selection criteria to improve these traits. However, part records of greasy and clean wool growth would be much less efficient than fleece weight for wool grown over 6 or 12 months because of the low heritability of part records and the low genetic correlation between these traits on part records and on wool grown for 12 months.

An evaluation of genetic analyses, skull morphology and visual appearance for assessing dingo purity: implications for dingo conservation

The introgression of domestic dog genes into dingo populations threatens the genetic integrity of 'pure' dingoes. However, dingo conservation efforts are hampered by difficulties in distinguishing between dingoes and hybrids in the field. This study evaluates consistency in the status of hybridisation (i.e. dingo, hybrid or dog) assigned by genetic analyses, skull morphology and visual assessments. Of the 56 south-east Queensland animals sampled, 39 (69.6%) were assigned the same status by all three methods, 10 (17.9%) by genetic and skull methods, four (7.1%) by genetic and visual methods; and two (3.6%) by skull and visual methods. Pair-wise comparisons identified a significant relationship between genetic and skull methods, but not between either of these and visual methods. Results from surveying 13 experienced wild dog managers showed that hybrids were more easily identified by visual characters than were dingoes. A more reliable visual assessment can be developed through determining the relationship between (1) genetics and phenotype by sampling wild dog populations and (2) the expression of visual characteristics from different proportions and breeds of domestic dog genes by breeding trials. Culling obvious hybrids based on visual characteristics, such as sable and patchy coat colours, should slow the process of hybridisation.

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.