Gallus Gallus Research Articles

Comparison of haemosporidian infection between wild red junglefowls and domestic chickens

Comparison of haemosporidian infection between wild red junglefowls and domestic chickens

Mapping genome-wide diversity and population dynamics in Indian chicken breeds for targeted conservation and breeding

ABSTRACT 1. Genetic improvement and widespread use of artificial selection may have impacted the genetic make-up of Indian chicken breeds. The genetic architecture of contemporary chicken population of India needs to be assessed for future improvement and conservation programmes. This study utilised whole-genome sequences in 180 chicken samples from 16 indigenous breeds, along with the Red Jungle Fowl and the commercial White Leghorn. 2. A panel of 76 978 genome-wide single-nucleotide polymorphisms (SNP) was selected for comparative genome analysis after stringent screening. Breeds originating from the eastern regions of India exhibited higher genomic diversity, indicative of a rich repository of distinct germplasm. Conversely, the Uttara breed, from the northern hilly areas, display considerable genetic differentiation with diminished diversity compared to others, underscoring conservation concerns. The average coefficient (FIS) of 0.084 caution the need to mitigate risks associated with inbreeding. 3. The study revealed that the analysis of 76 978 genome-wide SNP will serve as a cornerstone in refining conservation strategies, to design interventions with greater precision. 4. The contribution of Red Jungle Fowl to the gene pool of all native breeds was supported by this study. Genetic structuring indicated a relationship among breeds based on geographical proximity, underscored by varying levels of admixture.

Purposive breeding strategies drive genetic differentiation in Thai fighting cock breeds.

Fighting cock breeds have considerable historical and cultural place in Thailand. Breeds such as Lueng Hang Khao (LHK) and Pradu Hang Dam (PDH) are known for their impressive plumage and unique meat quality, suggesting selection for fighting and other purposes. However, information regarding the genetic diversity and clustering in indigenous and local Thai chickens used for cockfighting is unclear. To investigates the genetic diversity and differentiation in Thai fighting cock breeds, including populations for cockfighting, ornamental aspects, and consumption. Thai fighting cook breeds, including LHK and PDH chickens were analyzed using genotyping with 28 microsatellite loci. Data were compared to a gene pool library from "The Siam Chicken Bioresource Project" to understand the impact of human selection on genetic differentiation. Fighting cock strains from different breeds may cluster owing to shared breeding goals. The analysis of several chicken breeds showed subpopulation differentiation driven by artificial selection and genetic drift, affecting the genetic landscape and causing genetic hitchhiking. Eleven of 28 microsatellite loci showed hitchhiking selection, indicating directional selection in fighting cocks. Additionally, analyses revealed admixture with domestic chicken breeds and minimal influence of red junglefowl in the gene pool of Thai fighting chickens. These findings inform breed improvement, selection strategies, genetic resource management, and maintaining genetic diversity in fighting cocks. Analysis of Thai Fighting chicken breeds revealed a correlation between utilization and subpopulation differentiation. Specifically, selection for cockfighting and ornamental traits appears to explain the observed genetic structure within these breeds.

The female red jungle fowl (Gallus gallus gallus) reproductive investment stimulated by male attractiveness

Abstract. Lelono A, Riedstra B, Groothuis T. 2024. The female red jungle fowl (Gallus gallus gallus) reproductive investment stimulated by male attractiveness. Biodiversitas 25: 2931-2936. To maximize their capacity for reproduction, mothers are expected to modify their investment in offspring based on the quality of their mates. A recent study showed that females in female-care only species do so by investing more in egg mass when mated with attractive males rather than in other reproductive traits. In our study, we investigated how red jungle fowl (Gallus gallus gallus) mothers invest in clutch production based on the size of the male's comb, a trait signaling attractiveness. We randomly paired 14 females with 14 males of either large or small combs and monitored their egg laying, clutch completion, and brood rearing. Following the initial clutch, we exchanged male partners and permitted females to establish up second generation. We found that females who were partnered with males who had bigger combs laid down their eggs earlier after pairing compared to those paired with males with smaller combs. However, there were no variations in egg mass or clutch size that we could find. Furthermore, the size of the male's comb influenced the growth and body condition of female chicks, with those sired by males with larger combs being heavier and in better condition at twenty-four weeks old. These data support the premise of the positive Differential Allocation (DA) hypothesis, where maternal investment varies with mate quality, rather than the negative DA, where females more investment in offspring from lower quality mates.

Exploring Evolutionary Adaptations and Genomic Advancements to Improve Heat Tolerance in Chickens.

Climate change poses a significant threat to the poultry industry, especially in hot climates that adversely affect chicken growth, development, and productivity through heat stress. This literature review evaluates the evolutionary background of chickens with the specific genetic characteristics that can help chickens to cope with hot conditions. Both natural selection and human interventions have influenced the genetic characteristics of the breeds used in the current poultry production system. The domestication of chickens from the Red junglefowl (Gallus gallus) has resulted in the development of various breeds with distinct genetic differences. Over the past few years, deliberate breeding for desirable traits (such as meat production and egg quality) in chickens has resulted in the emergence of various economically valuable breeds. However, this selective breeding has also caused a decrease in the genetic diversity of chickens, making them more susceptible to environmental stressors like heat stress. Consequently, the chicken breeds currently in use may possess a limited ability to adapt to challenging conditions, such as extreme heat. This review focuses on evaluating potential genes and pathways responsible for heat tolerance, including heat shock response, antioxidant defense systems, immune function, and cellular homeostasis. This article will also discuss the physiological and behavioral responses of chicken varieties that exhibit genetic resistance to heat, such as the naked neck and dwarf traits in different indigenous chickens. This article intends to review the current genomic findings related to heat tolerance in chickens that used methods such as the genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping, offering valuable insights for the sustainability of poultry in the face of global warming.

Space use of free-range laying hens on two outdoor ranges with different amounts of vegetation cover

Consumers’ awareness of animal welfare in farm animal husbandry – including laying hen systems – increased in the last few decades. As a result, more and more farmers in Austria changed from barn systems to free-range husbandry. However, lack of structure and protective cover in the outdoor area might cause poor use of major parts of the outdoor range. Since the ancestor of domestic chicken – the red junglefowl – inhabits dense jungle forests with manifold ground vegetation, the structural design of an outdoor area might be of high importance for laying hens. To examine this assumption, a 15×15 m grid of barrier tape was brought out on the ground of the outdoor ranges of two commercial free-range laying hen farms that differed in the amount of vegetation cover they provided. Using action cams, we took pictures of each quadrant in ten-minute intervals from 09:00 h to 21:00 h for a total of three full days. We ran GAMs for each farm separately with number of hens per quadrant and interval as dependent variable, and vegetation cover (yes/no) and position (edge/centre) of the quadrant, distance to the shed (in m), as well as temperature (in °C) as predictors. Date, time, and quadrant ID were included as smooth terms. We found a more even and widespread use of space of hens on the outdoor range with a large amount of vegetation cover (farm 1) compared to the range with a small amount of vegetation cover (farm 2). However, the number of hens decreased with increasing distance to the shed on both farms. Hens preferred edge over centre quadrants on the range of farm 1, but preferred centred quadrants with vegetation cover over those without cover on the range of farm 2. On the ranges of both farms, the number of hens decreased with increasing temperature on quadrants without vegetation cover, whereas no such effect was found for covered quadrants. These findings suggest vegetation cover to be a key factor for extensive range use, particularly in view of the expected increase in temperature due to climate change. Therefore, we recommend farmers to provide hens with highly structured outdoor ranges, not only to improve range use but also to offer hens a more species-appropriate environment, which is assumed to increase the hens’ welfare as well.

Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data.

Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected the RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified, and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as "upregulated", "downregulated", or "unchanged" based on their DW-ratio, and the DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.

Samae Dam chicken: a variety of the Pradu Hang Dam breed revealed from microsatellite genotyping data.

The remarkable adaptability to the environment, high growth rate, meat with good taste and aroma, and ornamental appearance of the Pradu Hang Dam (PDH) and Samae Dam (SD) chickens make them valuable for improvement of poultry production to enhance food security. However, despite their close phenotypic similarity, distinct classification of PDH and SD chickens remains controversial. Thus, this study aimed to clarify genetic origins and variation between PDH and SD chickens, genetic diversity and structures of PDH and SD chickens. This study analyzed 5 populations of PDH and 2 populations of SD chickens using 28 microsatellite markers and compared with those of other indigenous and local chicken breeds using Thailand's "The Siam Chicken Bioresource Project" database. Considerably high genetic variability was observed within PDH (370 total alleles; 4.086±0.312 alleles/locus) and SD chickens (179 total alleles; 3.607±0.349 alleles/locus). A partial overlap of gene pools was observed between SD chickens from the Department of Livestock, Uthai Thani (SD1) and PDH chickens, suggesting a potentially close relationship between the two chicken breeds. A gene pool that partially overlapped with that of the red junglefowl was observed in the SD chicken population from the Sanhawat Farm Uthai Thani population (SD2). Distinct subclusters were observed within SD chickens, indicating the possibility that genetic differentiation occurred early in the process of establishment of SD chickens. These findings could offer valuable insights into genetic verification of Thai local chicken breeds and their sustainable conservation and utilization.

Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand

High levels of purine and uric acid, which are associated with health issues such as gout and cardiovascular disease, are found in the meat of fast-growing broiler chickens, which raises concerns about the quality of chicken meat and the health of the consumers who consume it. High genetic homogeneity and uniformity, particularly in genes involved in the synthesis of inosine monophosphate (IMP) and subsequent process of purine synthesis, which are associated with the meat quality, are exhibited in commercial broiler chickens owing to intensive inbreeding programs. Adenosine succinate lyase (ADSL) is a key enzyme involved in de novo purine biosynthetic pathway and its genetic polymorphisms affect IMP metabolism and purine content. In this study, we investigated the polymorphism of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand, using metabarcoding and genetic diversity analyses. Five alleles with 73 single nucleotide polymorphisms in exon 2, including missense and silent mutations, which may act on the synthesis efficiency of IMP and purine. Their protein structures revealed changes in amino acid composition that may affect ADSL enzyme activity. Weak purifying selection in these ADSL alleles was observed in the chicken population studied, implying that the variants have minor fitness impacts and a greater probability of fixation of beneficial mutations than strong purifying selection. A potential selective sweep was observed in Mae Hong Son chickens, whose purine content was lower than that in other breeds. This suggests a potential correlation between variations of the ADSL gene and reduced purine content and an impact of ADSL expression on the quality of chicken meat. However, further studies are required to validate its potential availability as a genetic marker for selecting useful traits that are beneficial to human health and well-being.

Artificial selection footprints in indigenous and commercial chicken genomes

BackgroundAlthough many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China.ResultsWe found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds.ConclusionWe identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs.

Sexual differences in bite force are not related to testosterone level in the wild-derived red junglefowl

Abstract Bite force is an important performance indicator of individual fitness that is closely related to food acquisition, male competition, and mating selection. It is also affected by a variety of factors and different mechanisms. Therefore, it is relatively difficult to understand the evolutionary driving forces of changes in bite force. In this study, the driving factors affecting the bite force of wild-derived red junglefowl (Gallus gallus jabouillei) were investigated from the aspects of morphological indicators and physiological characteristics. Results showed that the bite force of wild-derived red junglefowl was directly related to sex, showing obvious sexual differences. However, there was no correlation between the plasma testosterone level and bite force. The bite force of males was significantly greater than that of females, and the body index (i.e., PC1 of five body measures, namely body mass, body length, wing length, tail length, and tarsus length), the grasp index (i.e., tomial length × bill width) of males were significantly greater than those of females. Sexual selection may have played a key role in the evolution of bite force in the red junglefowl. Future studies should examine other key factors affecting changes in bite force to verify the correlation between secondary sexual characteristics and bite force in red junglefowls.

High quality assemblies of four indigenous chicken genomes and related functional data resources

Many lines of evidence indicate that red jungle fowl (RJF) is the primary ancestor of domestic chickens. Although multiple versions of RJF (galgal2-galgal5 and GRCg6a) and commercial chickens (GRCg7b/w and Huxu) genomes have been assembled since 2004, no high-quality indigenous chicken genomes have been assembled, hampering the understanding of chicken domestication and evolution. To fill the gap, we sequenced the genomes of four indigenous chickens with distinct morphological traits in southwest China, using a combination of short, long and Hi-C reads. We assembled each genome (~1.0 Gb) into 42 chromosomes with chromosome N50 90.5–90.9 Mb, amongst the highest quality of chicken genome assemblies. To provide resources for gene annotation and functional analysis, we also sequenced transcriptomes of 10 tissues for each of the four chickens. Moreover, we corrected many mis-assemblies and assembled missing micro-chromosomes 29 and 34–39 for GRCg6a. Our assemblies, sequencing data and the correction of GRCg6a can be valuable resources for studying chicken domestication and evolution.

Analysis of the mitochondrial genome and phylogenetic relationships of Mong chicken

In this study, the complete nucleotide sequence of the mitochondrial genome of the Mong chicken and an indigenous chicken breed of Vietnam, was determined by the Sanger sequencing method, structurally analysed and used to evaluate the phylogenetic relationship with different chicken breeds. The complete nucleotide sequence data of the Mong chicken’ mitochondrial genome was registered on GenBank with the accession number OR643716. The Mong chicken’ mitochondrial genome has a size of 16785 base pair (bp) and includes 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and one non-coding control region (D-loop). A, T, G, and C nucleotide proportions were 30.28, 23.76, 13.48, and 32.48%, respectively. Results of the analysis of phylogenetic relationships based on 33 complete mitochondrial genome sequences showed that the Mong chicken has evolutional origin from the red junglefowl subspecies Gallus gallus spadiceus. The Mong chicken is in close relationship with the Dong Tao chicken and Cao Son dwarf chicken in Vietnam, Rugao yellow chicken and Xiaoxiang chicken in China.

A Comparison of Telencephalon Composition among Chickens, Junglefowl, and Wild Galliforms

Introduction: Domestication is the process of modifying animals for human benefit through selective breeding in captivity. One of the traits that often diverges is the size of the brain and its constituent regions; almost all domesticated species have relatively smaller brains and brain regions than their wild ancestors. Although the effects of domestication on the brain have been investigated across a range of both mammal and bird species, almost nothing is known about the neuroanatomical effects of domestication on the world’s most common bird: the chicken (Gallus gallus). Methods: We compared the quantitative neuroanatomy of the telencephalon of white leghorn chickens with red junglefowl, their wild counterpart, and several wild galliform species. We focused specifically on the telencephalon because telencephalic regions typically exhibit the biggest differences in size in domesticate-wild comparisons. Results: Relative telencephalon size was larger in chickens than in junglefowl and ruffed grouse (Bonasa umbellus). The relative size of telencephalic regions did not differ between chickens and junglefowl, but did differ in comparison with ruffed grouse. Ruffed grouse had larger hyperpallia and smaller entopallial, nidopallial, and striatal volumes than chickens and junglefowl. Multivariate analyses that included an additional three wild grouse species corroborated these findings: chicken and junglefowl have relatively larger nidopallial and striatal volumes than grouse. Conversely, the mesopallial and hyperpallial volumes tended to be relatively smaller in chickens and junglefowl. Conclusion: From this suite of comparisons, we conclude that chickens do not follow a pattern of widespread decreases in telencephalic region sizes that is often viewed as typical of domestication. Instead, chickens have undergone a mosaic of changes with some regions increasing and others decreasing in size, and there are few differences between chickens and junglefowl.

Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls

The thermal stress caused by global climate change adversely affects the welfare, productivity, and reproductive performance of farm animals, including chickens, and causes substantial economic losses. However, the understanding of the genetic basis of the indigenous chicken adaptation to high ambient temperatures is limited. Hence, to reveal the genetic basis of thermal stress adaptation in chickens, this study investigated polymorphisms in the heat shock protein 70 (HSP70) and HSP90 genes, known mechanisms of cellular defense against thermal stress in indigenous and local chicken breeds and red junglefowls in Thailand. The result revealed seven alleles of the HSP70 gene. One allele exhibited a missense mutation, where an amino acid changed from Asn to His in the substrate-binding and peptide-binding domains, which is exclusive to the Lao Pa Koi chicken breed. Twenty new alleles with silent mutations in the HSP90 gene highlighted its greater complexity. Despite this diversity, distinct population structures were not found for either HSP70 or HSP90, which suggests incomplete impact on the domestication process and selection. The low genetic diversity, shown by the sharing of alleles between red junglefowls and Thai indigenous and local chicken breeds, aligns with the hypothesis that these alleles have undergone selection in tropical regions, such as Thailand. Selection signature analysis suggests the purifying selection of HSP70 for thermotolerance. This study provides valuable insights for enhancing the conservation of genetic resources with thermotolerant traits, which are essential for developing breeding programs to increase poultry production in the context of global climate change.

Molecular Characterization of Nepalese Indigenous Chicken, Sakini, Based on Mitochondrial DNA Displacement (D)-loop Sequences

This study is the first time to perform molecular characterization in indigenous chickens, Sakini, of Nepal for studying genetic diversity and its relationship with its assumed progenitors. The first 522 nucleotides of hypervariable I (HVI) segment of the D-loop from 33 individuals were PCR amplified and subsequently sequenced. Fourteen haplotypes out of 33 sequences were identified from 20 polymorphic sites. Haplotype (gene) diversity (Hd) is 0.813 with SD 0.065 and nucleotide diversity (Pi) is 0.00525 with SD 0.00091. The neighbour joining tree indicated that Red Jungle Fowl from India is the progenitor of the Nepalese Sakini chicken. NETWORK analysis revealed that it can be grouped into four distinct Haplogroups (A1, E1, E2, and E3) respectively. Seventeen individuals belonged to E1, eight to E3, seven to E2, and one to A1. The high mitochondrial D-loop diversity in Nepalese Sakini chicken with multiple maternal origins serves the scientific basis for the development of rational policies supporting conservation efforts and provides directions for future research for developing sustainable genetic improvement approaches.

DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA

Abstract. Utama AF, Jarulis, Sipriyadi, Jannah IM. 2023. DNA barcoding of Burgo chicken from Bengkulu, Indonesia, based on the cytochrome oxidase gene sub unit I mitochondria DNA. Biodiversitas 24: 6268-6275. The Burgo chicken provides a genetic source of one crossbreed chicken in Bengkulu Province. However, genetic information on Burgo chickens is not yet available, while the population of this chicken continues to decline. Research on DNA barcoding using the cytochrome oxidase subunit I mtDNA gene was conducted to obtain DNA barcodes and the relationship between Burgo chickens and other chicken species based on the COI mtDNA gene. Blood samples were obtained from Burgo chickens belonging to the Bengkulu Burgo chicken hobbyist community. Collected blood was isolated following the dneasy® blood and tissue kit protocol based on the spin-column protocol procedure, Qiagen. Amplification of genomic DNA using Polymerase Chain Reaction. The product was electrophoresed on a 1.2% agarose gel and visualized under UV light using Gel Documentation System, Axygen. Samples with bright DNA bands proceeded to the sequencing process. Sequencing results were analyzed using MEGA 11.0 software. The results showed that the target length of the Burgo chicken band was in accordance with the primer design used (752pb). SNPs were obtained at 10 specific sites in Burgo chickens and had a species barcode at site 746. The intraspecies genetic distance was 0.6%, interspecies 1.2%, and with the outgroup 14.5%, there were 12 haplotypes from all samples (n=15). Based on the result, we can conclude that the Burgo chicken is closely related to the red jungle fowl compared to other chicken species.

Comparative chromosome painting in three Pelecaniformes species (Aves): Exploring the role of macro and microchromosome fusions in karyotypic evolution.

Pelecaniformes is an order of waterbirds that exhibit diverse and distinct morphologies. Ibis, heron, pelican, hammerkop, and shoebill are included within the order. Despite their fascinating features, the phylogenetic relationships among the families within Pelecaniformes remain uncertain and pose challenges due to their complex evolutionary history. Their karyotypic evolution is another little-known aspect. Therefore, to shed light on the chromosomal rearrangements that have occurred during the evolution of Pelecaniformes, we have used whole macrochromosome probes from Gallus gallus (GGA) to show homologies on three species with different diploid numbers, namely Cochlearius cochlearius (2n = 74), Eudocimus ruber (2n = 66), and Syrigma sibilatrix (2n = 62). A fusion between GGA6 and GGA7 was found in C. cochlearius and S. sibilatrix. In S. sibilatrix the GGA8, GGA9 and GGA10 hybridized to the long arms of biarmed macrochromosomes, indicating fusions with microchromosomes. In E. ruber the GGA7 and GGA8 hybridized to the same chromosome pair. After comparing our painting results with previously published data, we show that distinct chromosomal rearrangements have occurred in different Pelecaniformes lineages. Our study provides new insight into the evolutionary history of Pelecaniformes and the chromosomal changes involving their macrochromosomes and microchromosomes that have taken place in different species within this order.

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

BackgroundThe red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.MethodsWe present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.ResultsWe demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.ConclusionsWe expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

Abundance and factors affecting the appearance of Siamese fireback and Red junglefowl in the lowland forest of Thailand

Abstract. Sukmasuang R, Chaisomboon P, Paansri P, Trisurat Y, Kanka P, Khiowsree N, Kaewdee B, Siripattanukul K, Chankhao A. 2023. Abundance and factors affecting the appearance of Siamese fireback and Red junglefowl in the lowland forest of Thailand. Biodiversitas 24: 5718-5730. Pheasants are indeed important species in various ecosystems. Studies of the abundance and factors influencing the presence of pheasant species have been conducted in the lowland areas of the Khao Ang Rue Nai Wildlife Sanctuary, Thailand, using camera trapping and species distribution models. A total of 23 factors, 2 bio-physiological, 2 geophysical, and 19 climate factors, were used to analyze in this study. The study revealed the presence of only two species of pheasants in the surveyed area, namely the Siamese fireback (Lophura diardi) and the Red junglefowl (Gallus gallus). The encounter rates were calculated as 1.74 photos per 100 trap nights for the Siamese fireback and 2.28 photos per 100 trap nights for the Red junglefowl. The factors influencing the presence of both Siamese fireback and the Red junglefowl were climate factors followed by biophysical and topography factors, respectively. The study's results highlight the importance of climate factors to the appearance of the pheasants, even in lowland areas. The results showed that the both pheasants responded more positively to the secondary forests, the grassland followed by dry dipterocarp forest than to other forest types. Therefore, conservation efforts to protect the areas inside are crucial for conserving the species' population.