A simplified protocol for molecular sexing in the emu (Dromaius novaehollandiae)

New primers for sex identification in the Chukar partridges (Alectoris chukar)

1. Male and female Chukar partridges are difficult to differentiate based on their morphology or by the Chromobox-Helicase-DNA binding (CHD) during early growth.2. The current study developed a novel, simple, low-cost and rapid sexing protocol for Chukar partridges based on the newly defined sexing gene ubiquitin-associated protein 2 (UBAP2).3. The length of polymorphism between UBAP2-W and UBAP2-Z homologous genes allows for easy sex discrimination in this species. Molecular sexing analysis was based on the simultaneous amplification of both genes, resulting in two distinct amplicons (947 bp and 535 bp) in heterogametic females and only a single band (535 bp) in homogametic males, which is easy to detect with agarose gel electrophoresis.4. This technique is simple and convenient for genetic sex determination in Chukar partridges.

Sex identification of birds in Taipei Zoo

As a conservation and breeding institution for birds, Taipei Zoo plays an important role in restoring endangered species. As approximately half of all bird species are monomorphic, precisely confirming the sex of individuals is critical for the management of ex-situ conservation breeding populations, as well as for understanding the sex ratio of those in the wild. Generally, PCR is used more reliably for sex determination versus traditional methods such as plumage, behavior or hormone levels. Nevertheless, the various primer sets and annealing temperatures vary between species, and so inaccurate sexing can occasionally happen due to inadequate PCR conditions. To reduce the probability of misidentification, and to establish a PCR condition database for sex determination across the diverse range of avian taxa, we tested multiple primer sets and annealing temperatures for amplification of the bird sex-specific gene fragments (CHD1) for each captive or rescued avian species held at Taipei Zoo since 2014. A total of 162 species across 22 orders were tested using one or two primer sets. One hundred and fifty-five species were successfully sexed by the primer set 2550F/2718R and the success rate of sex typing reached over 90% of species tested in each order. Most species have suitable PCR annealing temperatures between 45°C and 55°C, and the species in the same avian taxa showed similar results in temperature. This indicates that it is possible to select the annealing temperature of other species in the same family when the species had not been tested before. We expect this study will improve the success rate of identifying sex by using applicable PCR conditions and reduce the time for searching references every time before attempts to PCR sex birds.

A new method for molecular sex identification in the emu (Dromaius novaehollandiae)

1. Sex chromosomes of emus are largely homomorphic. Therefore, the standard methodology for molecular sexing is based on screening intron length variations in sex-linked genes is not applicable. However, emu sexing requires costly and time-consuming PCR-RFLP or multiplex PCR methods.2. This experiment used a directed PCR amplification and capillary electrophoresis sexing protocol. Two distinct peaks were observed in females (ZW), while only one peak was observed in males (ZZ).3. This sexing technique proved to be rapid, non-invasive, and highly sensitive and may be useful for verifying the sex ratio and breeding management of emus.

Carcass traits and fat quality of breeding emu (Dromaius novaehollandiae) in northern Japan

Characterization of carcass traits and fat quality is important to effectively produce and genetically improve emus. We investigated carcass traits in 309 emus. The meat production of female emus showed a significantly higher value than that of males (P < 0.01). The fat weight of male (9.232 ± 3.156 kg) was larger than that of the female (7.772 ± 2.697 kg). The fat yield (fat weight per kg of body weight) was strongly correlated to body weight (r = 0.79 and r = 0.75 in male and female, respectively). The fat melting points of females and males were 19.19 ± 3.39°C and 19.39 ± 3.39°C, respectively, without significant difference. Since the fat melting point did not correlate to body and fat weights, we predicted that it was an independent trait from body growth and was highly influenced by genetic elements. Percentages of palmitic, stearic, oleic, linoleic, and α-linolenic acids were 22.27 ± 3.50%, 9.37 ± 1.90%, 54.11 ± 5.17%, 13.54 ± 7.80% and 0.71 ± 0.59%, respectively. Among them, linoleic acid contents showed a wide individual difference (range 0.3–19.9%). The oleic/stearic acid ratio showed a negative correlation to the fat melting point. These results suggest that the fat melting point is a good indicator of C18:1/C18:0 ratio in emu fat.

Chemical Characterization and In Vivo Toxicological Safety Evaluation of Emu Oil

In this study, the physicochemical properties, fatty acid composition, antioxidant activities, and in vitro as well as in vivo toxicological safety of emu oil were investigated. Emu oil was shown to have a low acid and peroxide value, low amounts of carotenoid and phenolic compounds, and high doses of oleic acid and linoleic acid. Furthermore, in a bacterial reverse mutation assay, emu oil demonstrated no change in the amount of revertant colonies for all strains. In a chromosomal assay, no aberrations occurred in any of the emu oil treatment groups (1.25, 2.5, and 5 μg/mL). In the bone marrow micronucleus test, emu oil up to 20 mL/kg showed no significant increase in the incidence of micronucleated polychromatic erythrocytes. Moreover, emu oil up to 19.3 mg/kg body weight did not affect body weight in an acute oral toxicity study. These results are crucial for the adoption of emu oil as an alternative source of edible oil.

The Length Polymorphism of the 9th Intron in the Avian CHD1 Gene Allows Sex Determination in Some Species of Palaeognathae

In palaeognathous birds, several PCR-based methods and a range of genes and unknown genomic regions have been studied for the determination of sex. Many of these methods have proven to be unreliable, complex, expensive, and time-consuming. Even the most widely used PCR markers for sex typing in birds, the selected introns of the highly conserved CHD1 gene (primers P2/P8, 1237L/1272H, and 2550F/2718R), have rarely been effective in palaeognathous birds. In this study we used eight species of Palaeognathae to test three PCR markers: CHD1i9 (CHD1 gene intron 9) and NIPBLi16 (NIPBL gene intron 16) that performed properly as Psittaciformes sex differentiation markers, but have not yet been tested in Palaeognathae, as well as the CHD1iA intron (CHD1 gene intron 16), which so far has not been used effectively to sex palaeognathous birds. The results of our research indicate that the CHD1i9 marker effectively differentiates sex in four of the eight species we studied. In Rhea americana, Eudromia elegans, and Tinamus solitarius, the electrophoretic patterns of the amplicons obtained clearly indicate the sex of tested individuals, whereas in Crypturellus tataupa, sexing is possible based on poorly visible female specific bands. Additionally, we present and discuss the results of our in silico investigation on the applicability of CHD1i9 to sex other Palaeognathae that were not tested in this study.

Sexing chickens (Gallus gallus domesticus) with high-resolution melting analysis using feather crude DNA

Identification of sex in broiler chickens allows researchers to reduce the level of variation in an experiment caused by the sex effect. Broiler breeds commonly used in research are no longer feather sexable because of the change in their genetics. Other alternate sexing methods are costly and difficult to apply on a large scale. Therefore, a sexing method is required that is both cost effective and highly sensitive as well as having the ability to offer high throughput genotyping. In this study, high-resolution melting (HRM) analysis was used to detect DNA variations present in the gene chromodomain helicase DNA binding 1 protein (CHD1) on the Z and W chromosomes (CHD1Z and CHD1W, respectively) of chickens. In addition, a simplified DNA extraction protocol, which made use of the basal part of chicken feathers, was developed to speed up the sexing procedure. Three pairs of primers, that is, CHD1UNEHRM1F/R, CHD1UNEHRM2F/R, and CHD1UNEHRM3F/R, flanking the polymorphic regions between CHD1Z and CHD1W were used to differentiate male and female chickens via distinct melting curves, typical of homozygous or heterozygous genotypes. The assay was validated by the HRM-sexing of 1,318 broiler chicks and verified by examining the sex of the birds after dissection. This method allows for the sexing of birds within a couple of days, which makes it applicable for use on a large scale such as in nutritional experiments.

Development of 49 novel microsatellite markers from Next-generation sequencing data and a robust method for parentage tests in the emu (Dromaius novaehollandiae)

The emu is a useful and new breed of poultry, but their genetic improvement has not advanced yet due to their very recent domestication. Pedigree information is difficult to record because of their complex reproduction system (polyandry). To identify parent-offspring relationships in the emu, parentage test based on polymorphic DNA markers have to be developed. In this study, we isolated more than 25,000 microsatellite (simple sequence repeat, SSR) regions from Next-generation sequencing data via the QDD pipeline and developed 49 SSR markers with polymorphism in the Japanese farmed emu. The dinucleotide motifs, (AC)_n, (AT)_n and (AG)_n, were the most frequently detected and were found on 10,167 (38.55%), 8,114 (30.76%) and 4,796 (18.18%) contigs, respectively. Forty-nine novel SSR markers were characterized in 20 individuals and showed N_A ranged from 2 to 12, with an average of 4.2. H_E/H_O ranged from 0.389/0.071 to 0.702/1.000 with an average of 0.601/0.515. PIC value ranged from 0.059 to 0.886 with an average of 0.528, and 17 of 49 markers showed a higher polymorphism than 0.500. Thirty-four individuals were genotyped using 12 markers, and CERVUS simulations based on genotype showed that parents of all offspring were identified with 0.9995-1.0 probability. Thus, 49 novel SSR markers and a robust method for parentage test for the Japanese emu were developed.

Development and characterization of ten novel microsatellite loci for the emu (Dromaius novaehollandiae) and genetic diversity of Japanese farm populations

The emu (Dromaius novaehollandiae) is a useful poultry animal farmed for fat, meat, and eggs. Genetic structure and relationships among farmed emu populations in Japan are unknown and the number of microsatellite markers for genetic analysis of the emu is insufficient. In this study, we isolated 16 microsatellites from the emu genome and developed ten new microsatellite markers. These microsatellite markers were used to characterize three farm emu populations in Japan. The number of alleles ranged from 3 to 13 and the expected (H_E) and observed heterozygosity (H_O) of these microsatellite loci was 0.187-0.802 and 0.179-0.647, respectively. The polymorphic information content ranged from 0.176 to 0.786. Positive inbreeding coefficient (F_IS) values were detected in all tested populations, and they ranged from 0.027 to 0.540. These results suggest that farm populations of the emu in Japan resulted from inbreeding. The fixation index (F_ST) values ranged from 0.026 to 0.061, and phylogenetic trees and population structure analysis confirmed no definitive genetic differentiation among the three populations. Therefore, these populations are at a relatively low level of genetic differentiation at present. The microsatellite markers developed in our study can be utilized for genetic analysis and preservation of genetic resources in the emu.