Genome-wide association study exploring the genetic architecture of eggshell speckles in laying hens.

BACKGROUND: Eggshell speckle phenotype is an important trait in poultry production because they affect eggshell quality. However, the genetic architecture of speckled eggshells remains unclear. In this study, we determined the heritability of eggshell speckles and conducted a genome-wide association study (GWAS) on purebred Rhode Island Red (RIR) hens at 28 weeks to detect potential genomic loci and candidate genes associated with eggshell speckles. RESULTS: The heritability of eggshell speckles was 0.35 at 28 weeks, and the speckle level is not related to other eggshell quality traits in terms of phenotypic correlation. We detected 311 SNPs (6 significantly, and 305 suggestively associated) and 39 candidate genes associated with eggshell speckles. Based on the pathway analysis, the 39 candidate genes were mainly involved in alpha-linolenic acid metabolism, linoleic acid metabolism, ether lipid metabolism, GnRH signaling pathway, vascular smooth muscle contraction, and MAPK signaling pathway. Ultimately, ten genes, LOC423226, SPTBN5, EHD4, LOC77155, TYRO3, ITPKA, DLL4, PLA2G4B, PLA2G4EL5, and PLA2G4EL6 were considered the most promising genes associated with eggshell speckles that were implicated in immunoregulation, calcium transport, and phospholipid metabolism, while its function in laying hens requires further studies. CONCLUSIONS: This study provides new insights into understanding the genetic basis of eggshell speckles and has practical application value for the genetic improvement of eggshell quality.

Effects of farmland residual mulch film-derived microplastics on the structure and function of soil and earthworm Metaphire guillelmi gut microbiota.

Microplastics derived from polyethylene (PE) mulch films are widely found in farmland soils and present considerable potential threats to agricultural soil ecosystems. However, the influence of microplastics derived from PE mulch films, especially those derived from farmland residual PE mulch films, on soil ecosystems remains unclear. In this study, we analyzed the bacterial communities attached to farmland residual transparent PE mulch film (FRMF) collected from peanut fields and the different ecological effects of unused PE mulch film-derived microplastics (MPs) and FRMF-derived microplastics (MPs-aged) on the soil and earthworm Metaphire guillelmi gut microbiota, functional traits, and co-occurrence patterns. The results showed that the assembly and functional patterns of the bacterial communities attached to the FRMF were clearly distinct from those in the surrounding farmland soil, and the FRMF enriched some potential plastic-degrading and pathogenic bacteria, such as Nocardioidaceae, Clostridiaceae, Micrococcaceae, and Mycobacteriaceae. MPs substantially influenced the assembly and functional traits of soil bacterial communities; however, they only significantly changed the functional traits of earthworm gut bacterial communities. MPs-aged considerably affected the assembly and functional traits of both soil and earthworm gut bacterial communities. Notably, MPs had a more remarkable effect on nitrogen-related functions than the MPs-aged in numbers for both soil and earthworm gut samples. Co-occurrence network analysis revealed that both MPs and MPs-aged enhanced the synergistic interactions among operational taxonomic units (OTUs) of the composition networks for all samples. For community functional networks, MPs and MPs-aged enhanced the antagonistic interactions for soil samples; however, they exhibited contrasting effects for earthworm gut samples, as MPs enhanced the synergistic interactions among the functional contents. These findings broaden and deepen our understanding of the effects of FRMF-derived microplastics on soil ecosystems, suggesting that the harmful effects of aged plastics on the ecological environment should be considered.

Polyethylene mulch film-derived microplastics enhance the bioaccumulation of atrazine in two earthworm species (Eisenia fetida and Metaphire guillelmi) via carrier effects.

Microplastics (MPs) may significantly affect the bioavailability of coexisting pollutants in soil by adsorption-desorption behavior. However, the mechanisms underlying these interaction remain unclear. Herein, the influence of unused polythylene mulch film-derived MPs (MFMPs) and farmland residual polyethylene mulch film-derived MPs (MFMPs-aged) on the adsorption-desorption behavior and bioavailability of atrazine (ATZ) in soil were investigated. The adsorption kinetics and the adsorption isotherms of ATZ on soil, MFMPs, and MFMPs-aged fitted well by the pseudo-second-order model and the Langmuir model, respectively. ATZ were easier to desorb from soil, MFMPs, and MFMPs-aged in the simulated earthworm digestive fluid than that in the CaCl2 solution. The adsorption and desorption capacities of MFMPs and MFMPs-aged for ATZ were higher than those of soil, especially for MFMPs-aged. The existence of MPs in soil strengthened the adsorption and desorption capacities of ATZ, and the strengthened effects were promoted by the addition amount and aging process of MPs. Moreover, the occurrence of MPs significantly increased the bioaccumulation of ATZ in earthworms, especially for MFMPs-aged. This study deepens the knowledge of the interaction mechanisms of mulch film-derived MPs and pesticide pollution.

The Genetic Architecture of Early Body Temperature and Its Correlation With Salmonella Pullorum Resistance in Three Chicken Breeds.

New-born chicks are vulnerable to bacterial infections and not good at regulating body temperature. There is a close relationship between thermal regulation and immunity, however, the underlying mechanism is not well understood. Salmonella Pullorum (SP) is a major concern in developing countries and causes significant economic losses in poultry industry. Early body temperature (EBT) has previously shown to be correlated with host immunity and resistance to pullorum disease. In this study, we challenged three independent chick populations (Beijing You, Dwarf and Rhode Island Red) with SP at 4 days of age, and rectal temperature was measured before and after the SP attack from 2 to 7 days of age. Host defense to SP was evaluated by survival and spleen SP carrier status. The results showed that chicks with higher EBT before SP infection tend to have higher resistance to later SP attack in two populations (Dwarf and Beijing You). The association between EBT before SP attack and SP resistance was non-significant in Rohde Island Red population (P = 0.06), but the trend was consistent with the other two populations. We also found low to moderate heritability in all three populations for EBT before and after the SP attack ranging from 0.14 to 0.20. Genome-wide association studies identified several genomic regions and biological pathways determining EBT before SP attack, which provides candidate functional genes of this trait. Our results reveal the genetic determination of EBT, and the relationship between EBT and SP resistance, providing an alternative strategy for improving SP resistant activities in chicken.

Genetic parameters and characterization of egg content spreading area in White Leghorn chickens.

Uncharacteristically large spreading area on a flat surface of broken egg negatively affects egg quality assessment and reduces eggs' economic value. In this study, we investigated the heredity of the egg content spreading area as well as the relationships between the egg content spreading area and egg quality traits and properties. We measured the total egg content spreading area (TECA), outer thin albumen area (OTAA), inner thick albumen area (ITAA), yolk area (YA), and egg quality traits for 1414 newly laid eggs from 487 27-wk-old White Leghorn pure line pullets. The genetic parameters of egg content spreading areas were estimated. The phenotypic and genetic correlations between egg content spreading area and egg quality traits were analyzed. The differences in the properties of eggs with similar egg weight but markedly different TECA were also analyzed. The heritability estimates for TECA, OTAA, ITAA, and YA were low to moderate, with values of 0.214, 0.176, 0.340, and 0.280, respectively. Egg weight was related to TECA with a phenotypic correlation of 0.450 (P < 0.01) and a genetic correlation of 0.349. A high genetic correlation (-0.731) was found between TECA and Haugh unit. In eggs with larger TECA, the weight and total solid content of outer thin albumen (OTA) and moisture content of inner thick albumen (ITA) were significantly higher, whereas the weight and total solid content of ITA was markedly lower, but no differences (P > 0.05) were found in the pH of OTA and ITA, moisture content of OTA, as well as the eggshell strength, thickness, and non-destruction and fracture deformation between eggs with similar egg weight but markedly different TECA. These results suggest that the egg content spreading area can be regulated via the direct selection strategy or indirect selection of the ratio of OTA to ITA in the breeding program.

Population genomic data reveal genes related to important traits of quail.

Background: Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies. Results: Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHß), which is correlated with different FSHß levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. Conclusions: This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.

Quantitative expression of candidate genes affecting eggshell color.

There are three pigments that affect the color of an eggshell: protoporphyrin, biliverdin and biliverdin-zinc chelate. Protoporphyrin is the main pigment in brown and light-brown eggshells, whereas very little protoporphyrin is found in white eggshells. Eggshell protoporphyrin is derived from the heme formation in birds. Coproporphyrinogen III oxidase (CPOX) and ferrochelatase (FECH) represent rate-limiting enzymes for the heme-biosynthetic pathway. Breast cancer resistance protein (BCRP), feline leukemia virus receptor (FLVCR), and heme-responsive gene-1 (HRG1) serve as primary transporters for both protoporphyrinogen and heme. Finally, four organic anion transporting polypeptide family members (including solute carrier organic anion transporter family, SLCO1C1, SLCO1A2, SLCO1B3 and LOC418189) may affect pigment transport within eggshells. Here we measured gene expression levels in key tissues of egg-producing hens. We analyzed three different types of hens that generated distinct eggshell colors: white, pink or brown. Our data revealed three ways in which eggshell color was genetically influenced. First, high-level expression of CPOX generated more protoporphyrinogen and a brown eggshell color. In contrast, high expression of FECH likely converted more protoporphyrinogen into heme, reduced protoporphyrinogen levels within the eggshell and generated a light color. Second, heme transporters also affected eggshell color. High-level expression of BCRP, HRG1 and FLVCR were associated with brown, white and generally lighter eggshell colors, respectively. Finally, protoporphyrin precipitation also affected eggshell color, as high expression of both SLCO1A2 and SLCO1C1 were associated with brown eggshell color. As such, we have identified seven genes in which expression levels in different tissues were associated with eggshell color.