[Genome-wide association study of testes development indicators in roosters (Gallus gallus L.)] Полногеномные ассоциативные исследования показателей развития семенников у петухов (Gallus gallus L.)

Reproductive ability is one of the main indicators of the male breeding value that depends primarily on the functional state of testes cells. Male fertility is defined by complex physiological processes affecting the formation of mature germ cells, i.e., spermatozoa in the process of spermatogenesis. The forming and accumulation of germ cells occur in the seminiferous tubules of the testes, therefore the gonad development can serve as an indicator characterizing spermatogenesis and the reproductive potential of males. A number of studies on farm animals, including poultry, have shown the genetic determinacy of this trait, with identification of respective single nucleotide polymorphisms (SNPs) and genes determining the male gonad growth and development. In the present investigation, a genome-wide association study (GWAS) of the testes development parameters in roosters (Gallus gallus L.) of the F2 resource population were conducted. For the first time, new significant SNPs and candidate genes (р < 1.05½104) determining gonad growth and development in roosters were identified. The aim of the research was to seek SNPs and identify genes associated with testes growth parameters in roosters. The object of the study were F2 roosters from a model resource population (n = 115) that was obtained by interbreeding two breeds, Russian White and White Cornish. DNA was extracted from feather pulp using a commercial kit DNK Extran-2 (OOO NPF Sintol, Russia) in accordance with the manufacturer’s protocol. Genotyping was carried out using the medium-density Illumina Chicken 60K SNP iSelect BeadChip chip. At the age of 63 days, the experimental birds were slaughtered and the mass and morphometric indices of testes (length and thickness) were examined. Based on the obtained genotypic and phenotypic data, the GWAS analysis was performed in F2 resource population roosters using PLINK 1.9 software. The examined population was characterized by a high coefficient of variation in the measured indices, 96.1 % for the testes mass and 39.1 % for the linear measurements. The mass and linear measurements of the left testis were 5-14 % higher (р 0.05) compared to the right testis. The GWAS analysis revealed 36 significant SNPs (р < 1.05½104) associated with testes growth and development parameters in 63-day-old cockerels, in particular with the mass, length and thickness of the testes, 3, 26 and 7 SNPs, respectively. SNPs were localized on chromosomes GGA1, GGA3, GGA6, GGA7, GGA12, GGA15, and GGA18. A total of 156 genes were identified in the regions of the detected SNPs, including 16 genes that coincided with the positions of these SNPs. In particular, the latter were one gene (WNT7A) associated with the testis mass, 13 genes (LHFPL1, GALNT3, TMEM198, CACNA2D3, CCDC66, CACNA1D, DENND6A, CELSR3, WNT7A, IP6K2, ERC2, ABHD6, and DEPDC5) associated with the testis length, and three genes (ESR1, POLE, and RNFT2) associated with the testis thickness. These data can be used in genomic selection of roosters aimed at increasing their reproductive potential

Genome-wide association study reveals the genetic architecture of growth and meat production traits in a chicken F2 resource population

Background/Objectives: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a chicken F2 resource population (n = 152). Methods: The population was obtained by crossing two breeds with contrasting phenotypes for performance indicators, i.e., Russian White (slow-growing) and Cornish White (fast-growing). The birds were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. After LD filtering of the data, 54,188 SNPs were employed for the GWAS analysis that allowed us to reveal significant specific associations for phenotypic traits of interest and economic importance. Results: At the threshold value of p < 9.2 × 10−7, 83 SNPs associated with body weight at the age of 28, 42, and 63 days were identified, as well as 171 SNPs associated with meat qualities (average daily gain, slaughter yield, and dressed carcass weight and its components). Moreover, 34 SNPs were associated with a group of three or more traits, including 15 SNPs significant for a group of growth traits and 5 SNPs for a group of meat productivity indicators. Relevant to these detected SNPs, nine prioritized candidate genes associated with the studied traits were revealed, including WNT2, DEPTOR, PPA2, UNC80, DDX51, PAPPA, SSC4D, PTPRU, and TLK2. Conclusions: The found SNPs and candidate genes can serve as genetic markers for growth and meat performance characteristics in chicken breeding in order to achieve genetic improvement in broiler production

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

Emotional intelligence as a psychological resource and the features of its development in intellectually gifted school students

The article touches upon the relevant problems of modern psychological and pedagogical science: support for and development of gifted school students, psychological resources of personality, and emotional intelligence. At present, the problem of the features of emotional intelligence development in gifted students is theoretically and empirically underexplored within the framework of the resource approach. The goal of the study is to research the features of the development of emotional intelligence as a psychological resource in gifted adolescent school students. The following methods were used: emotional intelligence questionnaire, resilience test, D. Raven’s Progressive Matrix Scale; methods of mathematical statistics (analysis of variation, correlation analysis, etc.). The first part of the article presents an overview of studies on the problem of psychological resources and emotional intelligence, the current state of research in these fields is outlined, and the understudies issues and prospects for further studies are indicated. The empirical part presents the study results, the analysis of which reveals the specific features of emotional intelligence development in gifted adolescents compared to regular students. The obtained data indicate certain problems associated with the underdevelopment of emotional intelligence and its components in gifted adolescents which calls for further research and consideration in practical work with gifted students. The provided results of correlation analysis demonstrate a statistically significant association between the indicators of emotional intelligence and resilience. The obtained results point to the need for further study of the specifics of emotional intelligence and the opportunities for its development in gifted and non-gifted school students

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

Expression of M2 macrophage markers YKL-39 and CCL18 in breast cancer is associated with the effect of neoadjuvant chemotherapy

Purpos

Expression of M2 macrophage markers YKL-39 and CCL18 in breast cancer is associated with the effect of neoadjuvant chemotherapy

Purpos

Tumor-associated macrophages in human breast cancer produce new monocyte attracting and pro-angiogenic factor YKL-39 indicative for increased metastasis after neoadjuvant chemotherapy

In breast cancer, the tumor microenvironment plays a critical role in the tumor progression and responses to therapy. Tumor-associated macrophages (TAMs) are major innate immune cells in tumor microenvironment that regulate intratumoral immunity and angiogenesis by secretion of cytokines, growth factors as well as chitinase-like proteins (CLPs), that combine properties of cytokines and growth factors. YKL-39 is a chitinase-like protein found in human and absent in rodents, and its expression in TAMs and role in breast cancer progression was not studied to date. Here for the first time we demonstrate that YKL-39 is expressed on TAMs, predominantly positive for stabilin-1, but not by malignant cells or other stromal cells in human breast cancer. TGF-beta in combination with IL-4, but not IL-4 alone was responsible of the stimulation of the production of YKL-39 in human primary macrophages. Mechanistically, stabilin-1 directly interacted with YKL-39 and acted as sorting receptor for targeting YKL-39 into the secretory pathway. Functionally, purified YKL-39 acted as a strong chemotactic factor for primary human monocytes, and induced angiogenesis in vitro. Elevated levels of YKL-39 expression in tumors after neoadjuvant chemotherapy (NAC) were predictive for increased risk of distant metastasis and for poor response to NAC in patients with nonspecific invasive breast carcinoma. Our findings suggest YKL-39 as a novel therapeutic target, and blocking of its activity can be combined with NAC in order to reduce the risk of metastasis in breast cancer patients

Tumor-associated macrophages in human breast cancer produce new monocyte attracting and pro-angiogenic factor YKL-39 indicative for increased metastasis after neoadjuvant chemotherapy

In breast cancer, the tumor microenvironment plays a critical role in the tumor progression and responses to therapy. Tumor-associated macrophages (TAMs) are major innate immune cells in tumor microenvironment that regulate intratumoral immunity and angiogenesis by secretion of cytokines, growth factors as well as chitinase-like proteins (CLPs), that combine properties of cytokines and growth factors. YKL-39 is a chitinase-like protein found in human and absent in rodents, and its expression in TAMs and role in breast cancer progression was not studied to date. Here for the first time we demonstrate that YKL-39 is expressed on TAMs, predominantly positive for stabilin-1, but not by malignant cells or other stromal cells in human breast cancer. TGF-beta in combination with IL-4, but not IL-4 alone was responsible of the stimulation of the production of YKL-39 in human primary macrophages. Mechanistically, stabilin-1 directly interacted with YKL-39 and acted as sorting receptor for targeting YKL-39 into the secretory pathway. Functionally, purified YKL-39 acted as a strong chemotactic factor for primary human monocytes, and induced angiogenesis in vitro. Elevated levels of YKL-39 expression in tumors after neoadjuvant chemotherapy (NAC) were predictive for increased risk of distant metastasis and for poor response to NAC in patients with nonspecific invasive breast carcinoma. Our findings suggest YKL-39 as a novel therapeutic target, and blocking of its activity can be combined with NAC in order to reduce the risk of metastasis in breast cancer patients