Genome-wide association study revealed putative SNPs and candidate genes associated with growth and meat traits in Japanese quail

The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F 2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement

Genotyping-by-sequencing strategy for integrating genomic structure, diversity and performance of various Japanese quail (Coturnix japonica) breeds

Simple Summary: Artificial selection has been applied to domesticated birds for many decades. More recently, this selection has made use of so-called single-nucleotide polymorphism (SNP) markers—simple variants in a DNA sequence. These SNPs can be used for whole-genome screening to detect the unique traces of areas of the genome that are subject to selection. Doing this may help to shed light on the evolutionary and family history (phylogeny) of domestic Japanese quails of different breeds and utility types (e.g., egg, meat or dual-purpose breeds). In this study, 99 birds were used, representing eight breeds (11% of the world’s quail gene pool) and various purposes of use to gather genetic (whole-genome) data in the first-ever analysis of its kind performed on domestic quails. We thereby uncovered evolutionary relationships and points of divergence of individual quail breeds, gleaning important insights into the genetic diversity of domestic quail breeds and their future breeding potential. Abstract: Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies

The natural behavior of Drosera: Sundews do not catch insects on purpose

Volume: 38Start Page: 114End Page: 12

Phylogeography of the European rock rose Helianthemum nummularium s.l. (Cistaceae) : western richness and eastern poverty

Helianthemum nummularium s.l. is a young, morphologically diverse species distributed from western Europe to the Caucasus and the Southern Urals in the east. We analysed the rps16-trnK plastid intergenic spacer sequences from 85 localities covering most of the range of H. nummularium. Thirteen haplotypes were very unevenly distributed throughout the range of the species, and exhibited a strong phylogeographic signal. The results confirm range expansions of H. nummularium from Mediterranean refugia northwards, but also show the major role of eastern European (the Caucasus and the Southern Urals) refugia in rapid postglacial colonization of east, north and central Europe. The plastid haplotypes form distinct clades, one representing an eastern European lineage with few haplotypes and the other representing a western European lineage with many haplotypes. Parallel to this split in haplotype diversity is the pronounced differentiation in morphological variation displayed by the taxa found in west and east Europe. We discuss the role of topography in generating differences in morphological and genetic diversity between these two groups. We also discuss the taxonomical status of Helianthemum arcticum, which is regarded as an endangered local endemic of the Kola Peninsula. Helianthemum arcticum appears to represent an outlying peripheral population of H. nummularium preserved since the last postglacial major range expansion of this species, and bears the same plastid haplotype as the bulk of east and north European populations

Identification of SNPs and candidate genes associated with abdominal fat deposition in quails (Coturnix japonica) [Идентификация SNPs и генов-кандидатов, ассоциированных с отложением абдоминального жира у перепелов Coturnix japonica]

The rate of fat deposition, including abdominal fat, is one of the important indicators characterizing both meat performance and product quality, as well as the poultry welfare in general. This trait positively correlates with the bird’s rapid growth and largely depends not only on feeding and housing conditions, but also on genetic factors. Mostly, data on the genetic mechanisms that determine fat metabolism and fat deposition rate have been obtained in chickens; SNPs and candidate genes that determine the deposition of both intramuscular and abdominal fat have been identified. The number of similar studies on quail is relatively small. To date, there is not enough information in the specialized literature about quantitative trait loci (QTLs) that are reliably associated with fat metabolism indices in quails. The present work reports for the first time the identified SNPs that are highly significantly (p < 0.00001) associated with the intensity of abdominal fat deposition in 8-week-old quails from the F2 model resource population. In the region of identified SNPs, candidate genes reliably associated with this trait were established. The objective of the study was to search for SNPs and identify candidate genes associated with abdominal fat deposition in quails. The studies were carried out on F2 males of the model resource population (n = 146) obtained by crossing two quail breeds contrasting in growth rate and meat quality, Japanese (slow growth) and Texas (fast growth). F2 individuals were genotyped using the GBS (genotyping-by-sequencing) method. To identify associations between genome-wide genotyping data and the amount of abdominal fat, PLINK 1.9 software was used with accepted filter settings (geno 0.1, mind 0.1, maf 0.05). The threshold significance criterion was set to p < 0.00001. The resultant F2 resource population of quail was characterized by high variability in the content of abdominal fat in the carcass. At the age of 56 days, this indicator varied from 0.01 to 10.46 g and averaged 2.41±0.16 g. Based on the GWAS (genome-wide association study) analysis, we identified 29 SNPs and 11 candidate genes located in the regions of these SNPs that were associated with abdominal fat deposition in quail. The determined SNPs are localized on chromosomes 1, 2, 7, 8, 17, 19, 21, 24 and 28. The candidate genes identified (CNTN5, GNAL, PDE1A, RBMS1, PTPRF, SH3GLB2, SLC27A4, TRIM62, IGSF9B, USHBP1, and NR2F6) were established on chromosomes CJA1 (1 gene), CJA2 (1 gene), CJA7 (2 genes), CJA8 (1 gene), CJA17 (2 genes), CJA21 (1 gene), CJA24 (1 gene) and CJA28 (2 genes). The detected SNPs and candidate genes can serve as genetic markers in breeding programs to improve the meat quality of quails and reduce the fat content in carcasses. Волкова, Н.А., Герман, Н.Ю., Ларионова, П.В., Ветох, А.Н., Романов М.Н., & Зиновьева, Н.А. Интенсивность отложения жира, в том числе абдоминального, — один из важных показателей, характеризующих как мясную продуктивность и качество продукции, так и общее здоровье сельскохозяйственной птицы. Этот признак положительно коррелирует с быстрым ростом птицы и в значительной степени зависит не только от условий кормления и содержания, но и от генетических факторов. В основном данные о генетических механизмах, обусловливающих жировой обмен и интенсивность отложения жира, получены на курах, идентифицированы SNPs и геныкандидаты, детерминирующие отложение как внутримышечного, так и брюшного (абдоминального) жира. Число подобных исследований на перепелах относительно невелико. К настоящему времени в специальной литературе недостаточно информации о локусах количественных признаков (QTL), достоверно связанных с показателями жирового обмена у перепелов. В представленной работе впервые сообщается о выявленных SNPs, с высокой достоверностью (p < 0,00001) ассоциированных с интенсивностью отложения абдоминального жира у 8-недельных перепелов из F2 модельной ресурсной популяции. В области выявленных SNPs установлены гены-кандидаты, достоверно связанные с этим признаком. Целью работы были поиск SNPs и идентификация генов-кандидатов, связанных с отложением абдоминального жира у перепелов. Исследования проводили на самцах F2 модельной ресурсной популяции (n = 146), полученной при скрещивании двух контрастных по скорости роста и мясным качествам пород — японских (медленный рост) и техасских (быстрый рост) перепелов. Особей F2 генотипировали методом GBS (genotyping-by-sequencing, генотипирование посредством секвенирования). Для выявления ассоциаций между данными полногеномного генотипирования и количеством абдоминального жира использовали программное обеспечение PLINK 1.9 с принятыми ограничениями (geno 0,1; mind 0,1; maf 0,05). В качестве порогового критерия достоверности установили p < 0,00001. Полученная F2 ресурсная популяция перепелов характеризовалась высокой вариабельностью по содержанию абдоминального жира в туше. В возрасте 56 сут этот показатель варьировал от 0,01 до 10,46 г и составил в среднем 2,41±0,16 г. На основании проведенного GWAS-анализа (genome-wide association study) идентифицировали 29 SNPs и 11 генов-кандидатов, находящихся в областях расположения этих SNPs, которые ассоциированы с отложением абдоминального жира у перепелов. Обнаруженные SNPs локализуются на хромосомах 1, 2, 7, 8, 17, 19, 21, 24 и 28. Установленные гены-кандидаты (CNTN5, GNAL, PDE1A, RBMS1, PTPRF, SH3GLB2, SLC27A4, TRIM62, IGSF9B, USHBP1, NR2F6) идентифицированы на хромосомах CJA1 (1), CJA2 (1), CJA7 (2), CJA8 (1), CJA17 (2), CJA21 (1), CJA24 (1) и CJA28 (2). Детектированные SNP и гены-кандидаты могут послужить генетическими маркерами в программах селекции на улучшение мясных качеств перепелов и снижение содержания жира в тушках

Early response of barley embryos to low- and high-dose gamma irradiation of seeds triggers changes in the transcriptional profile and an increase in hydrogen peroxide content in seedlings

International audienceAt low intensity, certain stress conditions may have a positive effect on growth and development of plants (eustress). Growth stimulation of barley plants after gamma irradiation of seeds in low doses was observed as an increase in root and shoot lengths. Hydrogen peroxide concentrations in shoots of irradiated plants were significantly higher than in control, while the opposite effect was observed in the roots. To elucidate the molecular basis of growth stimulation after gamma irradiation of barley seeds, we performed the transcriptomic analysis of barley embryos at different stages of seed germination. The transcriptomic data were correlated with morphological parameters and the hydrogen peroxide levels in irradiated and control plants. These data indicate that the growth stimulation by low-dose irradiation involves the transcriptional control of genes related to phytohormones, antioxidant system, late embryogenesis abundant proteins and cell wall components, with possible involvement of jasmonate and ABA signalling. Gamma irradiation of seeds at dose 100 Gy caused significant growth inhibition and promoted expression changes in transcripts related to cell cycle arrest, DNA damage repair and antioxidant system

Effect of extended defects on phonon confinement in polycrystalline Si and Ge films

We present Raman spectroscopy of the polycrystalline Si and Ge films deposited by molecular beam deposition on a dielectric substrate. The Raman study has been made using lasers with different wavelengths. Structural properties of the poly-films have been studied by XRD and TEM. The Raman spectra are characterized by appearance of the additional wide peaks around 500 cm–1 and 290 cm–1 in the main vibrational bands of TO(c-Si) and TO(c-Ge) phonons, respectively. It is shown that these peaks correspond to scattering in grain boundary area. For the poly–Si films, both a downward shift and an asymmetrical broadening of the vibrational band of TO(c-Si) near 520 cm–1 are observed, whereas there is only a symmetric broadening in the spectra of poly-Ge. The Raman line shape has been modeled within the framework of the phonon confinement theory taking into account the sizes of coherent scattering domains obtained using XRD. The model includes a symmetrical band broadening observed in polycrystalline films. It is shown that confinement of phonon propagation might be in the poly–Si films. The phonon dispersion and the density of phonon states have been simulated using density functional theory. It has been found that phonon confinement relates to grain boundaries rather than other extended defects such as twins (multiple twins, twin boundaries), the appearance of which does not lead to significant changes in phonon dispersion and density of phonon states

Anisotropy of mechanical properties and hardening mechanism in ZrO2–Y2O3 solid solution crystals

The anisotropy of the mechanical properties of crystalline ZrO2 – 2.8 mol.% Y2O3 solid solutions has been studied. The crystals have been grown by skull melting technique. The microhardness and fracture toughness for different crystallographic planes have been tested by indentation with different indenter diagonal orientations. We show that the microhardness of the material depends on the crystallographic orientation but slightly whereas the fracture toughness varies for different planes. The maximum fracture toughness has been observed in the specimen cut out from the crystal laterally to the orientation. We have studied the microhardness anisotropy for different indenter diagonal orientations. The maximum fracture toughness has been obtained for the {100} plane and the indenter diagonal orientation. The phase composition inside and outside the indents on the {100}, {110} and {111} surfaces for 20, 3 and 1 N loads has been studied using local Raman spectroscopy. The degree of the tetragonal-monoclinic transition has been assessed for different crystallographic planes and different indenter diagonal orientations. We show that the tetragonal-monoclinic transition is anisotropic, this affecting the transformation hardening mechanism. The maximum amount of the monoclinic phase has been detected in the vicinity of the indent in the {100} plane for the indenter diagonal orientation. The highest fraction toughness has also been observed in {100} plane for the indenter diagonal orientation. Probably, this indenter diagonal orientation provides for the maximum stress orientation along the coherent conjugation planes between the tetragonal and the monoclinic phases during the tetragonal-monoclinic transition, i.e. (100)t || (100)m and [001]t || [010]m