scholarly journals Genetic Parameters and Genome-Wide Association Studies for Anti-Müllerian Hormone Levels and Antral Follicle Populations Measured After Estrus Synchronization in Nellore Cattle

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1185
Author(s):  
Laís Grigoletto ◽  
Miguel Henrique Almeida Santana ◽  
Fabiana Fernandes Bressan ◽  
Joanir Pereira Eler ◽  
Marcelo Fábio Gouveia Nogueira ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genetic Parameters ◽  
Association Studies ◽  
Antral Follicle ◽  
Genome Wide Association Studies ◽  
Hormone Levels ◽  
Estrous Synchronization ◽  
Nellore Cattle ◽  
Genomic Regions ◽  
Indicator Traits

Reproductive efficiency plays a major role in the long-term sustainability of livestock industries and can be improved through genetic and genomic selection. This study aimed to estimate genetic parameters (heritability and genetic correlation) and identify genomic regions and candidate genes associated with anti-Müllerian hormone levels (AMH) and antral follicle populations measured after estrous synchronization (AFP) in Nellore cattle. The datasets included phenotypic records for 1099 and 289 Nellore females for AFP and AMH, respectively, high-density single nucleotide polymorphism (SNP) genotypes for 944 animals, and 4129 individuals in the pedigree. The heritability estimates for AMH and AFP were 0.28 ± 0.07 and 0.30 ± 0.09, and the traits were highly and positively genetically correlated (rG = 0.81 ± 0.02). These findings indicated that these traits can be improved through selective breeding, and substantial indirect genetic gains are expected by selecting for only one of the two traits. A total of 31 genomic regions were shown to be associated with AMH or AFP, and two genomic regions located on BTA1 (64.9–65.0 Mb and 109.1–109.2 Mb) overlapped between the traits. Various candidate genes were identified to be potentially linked to important biological processes such as ovulation, tissue remodeling, and the immune system. Our findings support the use of AMH and AFP as indicator traits to genetically improve fertility rates in Nellore cattle and identify better oocyte donors.

scholarly journals Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

2018 ◽  
Author(s):  
Satish K Nandakumar ◽  
Sean K McFarland ◽  
Laura Marlene Mateyka ◽  
Caleb A Lareau ◽  
Jacob C Ulirsch ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Target Genes ◽  
Association Studies ◽  
Human Diseases ◽  
Genome Wide Association Studies ◽  
Loss Of Function ◽  
Genome Wide ◽  
Causal Variants ◽  
Genomic Regions

Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding genomic regions and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1-2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in relevant biological pathways, allowing regulators of human erythropoiesis and blood disease modifiers to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits.

scholarly journals Genetic Mapping Reveals Complex Architecture and Candidate Genes Involved in Common Bean Response to Meloidogyne Incognita Infection

2021 ◽  
Author(s):  
Willian Giordani ◽  
Henrique Castro Gama ◽  
Alisson Fernando Chiorato ◽  
João Paulo Rodrigues Marques ◽  
Luis Eduardo Aranha Camargo ◽  
...  
Keyword(s):  
Common Bean ◽  
Candidate Genes ◽  
Resistance Genes ◽  
Meloidogyne Incognita ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Crop Species ◽  
Egg Masses ◽  
Genomic Regions

Abstract Root-knot nematodes (RKN), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crop species, including common bean. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging since little has been done to discover resistance genes or find markers to assist selection. In this study, we performed genome-wide association studies and QTL mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and root-galling index were evaluated 30 days after inoculation. Complex genetic architecture and independent genomic regions were associated with each trait according to the Fixed and random model Circulating Probability Unification. SNPs located on chromosomes Pv06, Pv07, Pv08 and Pv11 were associated with the number of egg masses, and on Pv01, Pv02, Pv05 and Pv10 with root-galling. A total of 215 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA-seq analysis. The histochemical analysis indicated that the reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance in common bean, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

scholarly journals Identification of Loci Controlling the Dwarfism Trait in the White Sailfin Molly (Poecilia latipinna) Using Genome-Wide Association Studies Based on Genotyping-By-Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 418
Author(s):  
Fan Shao ◽  
Jing Liu ◽  
Mengyuan Ren ◽  
Junying Li ◽  
Haigang Bao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Expression Level ◽  
Genome Wide Association Studies ◽  
Sailfin Molly ◽  
Genome Wide ◽  
Genomic Regions ◽  
Sailfin Mollies

Dwarfism is a condition defined by low harvest weight in fish, but also results in strange body figures which may have potential for the selective breeding of new ornamental fish strains. The objectives of this study are to reveal the physiological causes of dwarfism and identify the genetic loci controlling this trait in the white sailfin molly. Skeletons of dwarf and normal sailfin mollies were observed by X-ray radioscopy and skeletal staining. Genome-wide association studies based on genotyping-by-sequencing (n = 184) were used to map candidate genomic regions associated with the dwarfism trait. Quantitative real-time PCR was performed to determine the expression level of candidate genes in normal (n = 8) and dwarf (n = 8) sailfin mollies. We found that the dwarf sailfin molly has a short and dysplastic spine in comparison to the normal fish. Two regions, located at NW_015112742.1 and NW_015113621.1, were significantly associated with the dwarfism trait. The expression level of three candidate genes, ADAMTS like 1, Larp7 and PPP3CA, were significantly different between the dwarf and normal sailfin mollies in the hepatopancreas, with PPP3CA also showing significant differences in the vertebrae and Larp7 showing significant differences in the muscle. This study identified genomic regions and candidate genes associated with the dwarfism trait in the white sailfin molly and would provide a reference to determine dwarf-causing variations.

scholarly journals Single-step genome-wide association studies (GWAS) and post-GWAS analyses to identify genomic regions and candidate genes for milk yield in Brazilian Girolando cattle

2020 ◽  
Vol 103 (11) ◽  
pp. 10347-10360
Author(s):  
Pamela I. Otto ◽  
Simone E.F. Guimarães ◽  
Mario P.L. Calus ◽  
Jeremie Vandenplas ◽  
Marco A. Machado ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Milk Yield ◽  
Association Studies ◽  
Single Step ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Genomic Regions

scholarly journals Genome-wide associations for immune traits in two maternal pig lines

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christina M. Dauben ◽  
Maren J. Pröll-Cornelissen ◽  
Esther M. Heuß ◽  
Anne K. Appel ◽  
Hubert Henne ◽  
...  
Keyword(s):  
Immune System ◽  
Candidate Genes ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Production Traits ◽  
Biological Relevance ◽  
Genome Wide ◽  
Major Interest ◽  
Immune Traits ◽  
Genomic Regions

Abstract Background In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. Results In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. Conclusion In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system.

scholarly journals Genome-scale comparative analysis for host resistance against sea lice between Atlantic salmon and rainbow trout

2019 ◽  
Author(s):  
Pablo Cáceres ◽  
Agustín Barría ◽  
Kris A. Christensen ◽  
Liane N. Bassini ◽  
Katharina Correa ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Atlantic Salmon ◽  
Candidate Genes ◽  
Association Studies ◽  
Sea Lice ◽  
Genome Wide Association Studies ◽  
Standing Variation ◽  
Breeding Populations ◽  
Genomic Regions ◽  
Genome Scale

AbstractSea lice (Caligus rogercresseyi) are ectoparasites that cause major production losses in the salmon aquaculture industry worldwide. Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) are two of the most susceptible salmonid species to sea lice infestation. The goal of this study was to identify common candidate genes involved in resistance against sea lice. For this, 2,626 Atlantic salmon and 2,643 rainbow trout from breeding populations were challenged with sea lice and genotyped with a 50k and 57k SNP panel. We ran two independent genome-wide association studies for sea lice resistance on each species and identified 7 and 13 windows explaining 3% and 2.7% respectively the genetic variance. Heritabilities were observed with values of 0.19 for salmon and 0.08 for trout. We identified genes associated with immune responses, cytoskeletal factors and cell migration. We found 15 orthogroups which allowed us to identifydust8anddust10as candidate genes in orthogroup 13. This suggests that similar mechanisms can regulate resistance in different species; however, they most likely do not share the same standing variation within the genomic regions and genes that regulate resistance. Our results provide further knowledge and may help establish better control for sea lice in fish populations.

scholarly journals Genome-wide association studies for growth traits in broilers

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Dachang Dou ◽  
Linyong Shen ◽  
Jiamei Zhou ◽  
Zhiping Cao ◽  
Peng Luan ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Candidate Genes ◽  
Rapid Growth ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Multiple Methods ◽  
Genome Wide

Abstract Background The identification of markers and genes for growth traits may not only benefit for marker assist selection /genomic selection but also provide important information for understanding the genetic foundation of growth traits in broilers. Results In the current study, we estimated the genetic parameters of eight growth traits in broilers and carried out the genome-wide association studies for these growth traits. A total of 113 QTNs discovered by multiple methods together, and some genes, including ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, APCDD1, GPR39, and GATA4, were identified as important candidate genes for rapid growth in broilers. Conclusions The results of this study will provide important information for understanding the genetic foundation of growth traits in broilers.

scholarly journals Genetic Parameters and Genome-Wide Association Studies of Eight Longevity Traits Representing Either Full or Partial Lifespan in Chinese Holsteins

2021 ◽  
Vol 12 ◽  
Author(s):  
Hailiang Zhang ◽  
Aoxing Liu ◽  
Yachun Wang ◽  
Hanpeng Luo ◽  
Xinyi Yan ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Candidate Genes ◽  
Genetic Parameters ◽  
Association Studies ◽  
Genetic Correlations ◽  
Good Alternative ◽  
Early Selection ◽  
Genome Wide Association Studies ◽  
Productive Life ◽  
Genome Wide

Due to the complexity of longevity trait in dairy cattle, two groups of trait definitions are widely used to measure longevity, either covering the full lifespan or representing only a part of it to achieve an early selection. Usually, only one group of longevity definition is used in breeding program for one population, and genetic studies on the comparisons of two groups of trait definitions are scarce. Based on the data of eight traits well representing the both groups of trait definitions, the current study investigated genetic parameters and genetic architectures of longevity in Holsteins. Heritabilities and correlations of eight longevity traits were estimated using single-trait and multi-trait animal models, with the data from 103,479 cows. Among the cows with phenotypes, 2,630 cows were genotyped with the 150K-SNP panel. A single-trait fixed and random Circuitous Probability Unification model was performed to detect candidate genes for eight longevity traits. Generally, all eight longevity traits had low heritabilities, ranging from 0.038 for total productive life and herd life to 0.090 for days from the first calving to the end of first lactation or culling. High genetic correlations were observed among the traits within the same definition group: from 0.946 to 0.997 for three traits reflecting full lifespan and from 0.666 to 0.997 for five traits reflecting partial productive life. Genetic correlations between two groups of traits ranged from 0.648 to 0.963, and increased gradually with the extension of lactations number regarding the partial productive life traits. A total of 55 SNPs located on 25 chromosomes were found genome-wide significantly associated with longevity, in which 12 SNPs were associated with more than one trait, even across traits of different definition groups. This is the first study to investigate the genetic architecture of longevity representing both full and the partial lifespan simultaneously, which will assist the selection of an appropriate trait definition for genetic improvement of longevity. Because of high genetic correlations with the full lifespan traits and higher heritability, the partial productive life trait measured as the days from the first calving to the end of the third lactation or culling could be a good alternative for early selection on longevity. The candidate genes identified by this study, such as RPRM, GRIA3, GTF2H5, CA5A, CACNA2D1, FGF10, and DNAJA3, could be used to pinpoint causative mutations for longevity and further benefit the genomic improvement of longevity in dairy cattle.

scholarly journals Uncovering Novel Genomic Regions and Candidate Genes for Senescence-Related Traits by Genome-Wide Association Studies in Upland Cotton (Gossypium hirsutum L.)

2022 ◽  
Vol 12 ◽  
Author(s):  
Qibao Liu ◽  
Libei Li ◽  
Zhen Feng ◽  
Shuxun Yu
Keyword(s):  
Candidate Genes ◽  
Upland Cotton ◽  
Genetic Basis ◽  
Association Studies ◽  
White Flower ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
High Positive Correlation ◽  
Genome Wide ◽  
Genomic Regions

Senescence in plants is a complex trait, which is controlled by both genetic and environmental factors and can affect the yield and quality of cotton. However, the genetic basis of cotton senescence remains relatively unknown. In this study, we reported genome-wide association studies (GWAS) based on 185 accessions of upland cotton and 26,999 high-quality single-nucleotide polymorphisms (SNPs) to reveal the genetic basis of cotton senescence. To determine cotton senescence, we evaluated eight traits/indices. Our results revealed a high positive correlation (r>0.5) among SPAD value 20 days after topping (SPAD20d), relative difference of SPAD (RSPAD), nodes above white flower on topping day (NAWF0d), nodes above white flower 7 days after topping (NAWF7d), and number of open bolls on the upper four branches (NB), and genetic analysis revealed that all traits had medium or high heritability ranging from 0.53 to 0.86. Based on a multi-locus method (FASTmrMLM), a total of 63 stable and significant quantitative trait nucleotides (QTNs) were detected, which represented 50 genomic regions (GWAS risk loci) associated with cotton senescence. We observed three reliable loci located on chromosomes A02 (A02_105891088_107196428), D03 (D03_37952328_38393621) and D13 (D13_59408561_60730103) because of their high repeatability. One candidate gene (Ghir_D03G011060) was found in the locus D03_37952328_38393621, and its Arabidopsis thaliana homologous gene (AT5G23040) encodes a cell growth defect factor-like protein (CDF1), which might be involved in chlorophyll synthesis and cell death. Moreover, qRT-PCR showed that the transcript level of Ghir_D03G011060 was down-regulated in old cotton leaves, and virus-induced gene silencing (VIGS) indicated that silencing of Ghir_D03G011060 resulted in leaf chlorosis and promoted leaf senescence. In addition, two candidate genes (Ghir_A02G017660 and Ghir_D13G021720) were identified in loci A02_105891088_107196428 and D13_59408561_60730103, respectively. These results provide new insights into the genetic basis of cotton senescence and will serve as an important reference for the development and implementation of strategies to prevent premature senescence in cotton breeding programs.

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