scholarly journals Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication

2018 ◽  
Author(s):  
Julie Baker Phillips ◽  
Samuel A. Smith ◽  
Maddison L. Johnson ◽  
Patrick Abbot ◽  
John A. Capra ◽  
...  
Keyword(s):  
Cesarean Section ◽  
Litter Size ◽  
Reproductive Traits ◽  
Genome Wide Association ◽  
Domestic Dog ◽  
Cesarean Section Rate ◽  
Gestation Length ◽  
Stillbirth Rate ◽  
Phenotypic Data ◽  
Genome Wide

AbstractThe diversity of eutherian reproductive strategies has led to variation in many traits, such as number of offspring, age of reproductive maturity, and gestation length. While reproductive trait variation has been extensively investigated and is well established in mammals, the genetic loci contributing to this variation remain largely unknown. The domestic dog, Canis lupus familiaris is a powerful model for studies of the genetics of inherited disease due to its unique history of domestication. To gain insight into the genetic basis of reproductive traits across domestic dog breeds, we collected phenotypic data for four traits – cesarean section rate (n = 97 breeds), litter size (n = 60), stillbirth rate (n = 57), and gestation length (n = 23) – from primary literature and breeders’ handbooks. By matching our phenotypic data to genomic data from the Cornell Veterinary Biobank, we performed genome wide association analyses for these four reproductive traits, using body mass and kinship among breeds as co-variates. We identified 14 genome-wide significant associations between these traits and genetic loci, including variants near CACNA2D3 with gestation length, MSRB3 with litter size, SMOC2 with cesarean section rate, MITF with litter size and still birth rate, KRT71 with cesarean section rate, litter size, and stillbirth rate, and HTR2C with stillbirth rate. Some of these loci, such as CACNA2D3 and MSRB3, have been previously implicated in human reproductive pathologies. Many of the variants that we identified have been previously associated with domestication-related traits, including brachycephaly (SMOC2), coat color (MITF), coat curl (KRT71), and tameness (HTR2C). These results raise the hypothesis that the artificial selection that gave rise to dog breeds also shaped the observed variation in their reproductive traits. Overall, our work establishes the domestic dog as a system for studying the genetics of reproductive biology and disease.

scholarly journals Genome-Wide Association Study for Reproductive Traits in a Duroc Pig Population

Animals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 732 ◽  
Author(s):  
Zhang ◽  
Chen ◽  
Ye ◽  
He ◽  
Huang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Litter Size ◽  
Production Efficiency ◽  
Genome Wide Association Study ◽  
Reproductive Traits ◽  
Genome Wide Association ◽  
Litter Weight ◽  
Genome Wide ◽  
A Genome

In the pig industry, reproductive traits constantly influence the production efficiency. To identify markers and candidate genes underlying porcine reproductive traits, a genome-wide association study (GWAS) was performed in a Duroc pig population. In total, 1067 pigs were genotyped using single-nucleotide polymorphism (SNP) chips, and four reproductive traits, including litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), and litter weight at weaning (LWW), were examined. The results showed that 20 potential SNPs reached the level of suggestive significance and were associated with these traits of interest. Several important candidate genes, including TXN2, KCNA1, ENSSSCG00000003546, ZDHHC18, MAP2K6, BICC1, FAM135B, EPHB2, SEMA4D, ST3GAL1, KCTD3, FAM110A, TMEM132D, TBX3, and FAM110A, were identified and might compose the underlying genetic architecture of porcine reproductive traits. These findings help to understand the genetic basis of porcine reproductive traits and provide important information for molecular breeding in pigs.

scholarly journals Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1386
Author(s):  
Ana Paula Sbardella ◽  
Rafael Nakamura Watanabe ◽  
Rebeka Magalhães da Costa ◽  
Priscila Arrigucci Bernardes ◽  
Larissa Graciano Braga ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Phenotypic Variability ◽  
Additive Genetic Variance ◽  
Reproductive Traits ◽  
Genome Wide Association ◽  
Gestation Length ◽  
Data Set ◽  
Breeding Programs ◽  
Genome Wide ◽  
Nelore Cattle

The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.

scholarly journals A genome-wide association study for prolificacy in three Polish sheep breeds

2021 ◽  
Author(s):  
Grzegorz Smołucha ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Aldona Kawęcka ◽  
Anna Miksza-Cybulska
Keyword(s):  
Association Study ◽  
Litter Size ◽  
Functional Data ◽  
Genome Wide Association Study ◽  
Reproductive Traits ◽  
Phenotypic Selection ◽  
Genome Wide Association ◽  
Sheep Breeds ◽  
Genome Wide ◽  
A Genome

AbstractReproductive traits (especially litter size) are usually characterized by low heritability, and thus, phenotypic selection is often ineffective and slow. In order to improve fertility characteristics such as ovulation rate and litter size, it seems more effective to select breeding animals based on their genotype. The aim of the study was to use genome-wide association study (GWAS) in three sheep breeds to identify the genetic variants affecting the litter size in sheep. The study allowed us to identify one genome-wide significant SNP (rs402032081—located in ephrin type-A receptor 6, EPHA6) showing an association with litter size in Polish Mountain Sheep. We suggest that the EPHA6 gene can be a candidate gene for prolificacy trait in selected breeds of sheep; however, it needs further functional data for validation.

scholarly journals The impact of maternal genetic merit and country of origin on ewe reproductive performance, lambing performance and ewe survival

2021 ◽  
Author(s):  
N Fetherstone ◽  
N McHugh ◽  
T M Boland ◽  
F M McGovern
Keyword(s):  
New Zealand ◽  
Birth Weight ◽  
Litter Size ◽  
Country Of Origin ◽  
Reproductive Traits ◽  
Gestation Length ◽  
Genetic Merit ◽  
Genetic Groups ◽  
One Year ◽  
The Impact

Abstract The objective of this study was to investigate the impact of the ewe’s maternal genetic merit and country of origin (New Zealand or Ireland) on ewe reproductive, lambing and productivity traits. The study was performed over a four year period (2016 to 2019) and consisted of three genetic groups: high maternal genetic merit New Zealand (NZ), high maternal genetic merit Irish (High Irish) and low maternal genetic merit Irish (Low Irish) ewes. Each group contained 30 Suffolk and 30 Texel ewes, selected based on the respective national maternal genetic indexes; i.e. either the New Zealand Maternal Worth (New Zealand group) or the €uro-star Replacement index (Irish groups). The impact of maternal genetic merit on reproductive traits such as litter size; lambing traits such as gestation length, birth weight, lambing difficulty, mothering ability, and productivity traits such as the number of lambs born and weaned were analyzed using linear mixed models. For binary traits, the impact of maternal genetic merit on reproductive traits such as conception to first AI service; lambing traits such as dystocia, perinatal lamb mortality and productivity traits such as ewe survival were analyzed using logistic regression. New Zealand ewes outperformed Low Irish ewes for conception to first AI (P<0.05) and litter size (P=0.05). Irish ewes were more likely to suffer from dystocia (6.84 (High Irish) and 8.25 (Low Irish) times) compared to NZ ewes (P<0.001); birth weight and perinatal mortality did not differ between groups (P>0.05). Lambs born from NZ ewes were 4.67 (95% CI: 1.89 to 11.55; P<0.001) and 6.54 (95% CI: 2.56 to 16.71; P<0.001) times more likely to stand up and suckle unassisted relative to lambs born from High or Low Irish ewes, respectively. New Zealand and High Irish ewes had a greater number of lambs born and weaned throughout the duration of the study compared to their Low Irish counterparts (P<0.001). New Zealand ewes tended to be more likely to survive from one year to the next compared to Low Irish ewes (P=0.07). Irish ewes of high maternal genetic merit outperformed their Low counterparts in total number of lambs born and weaned per ewe, but performance did not differ across other traits investigated. This highlights the importance of continuous development of the Irish maternal sheep index to ensure favourable improvements in reproductive, lambing and productivity traits at farm level. Overall, results demonstrate the suitability of NZ genetics in an Irish production system.

INTERRELATIONS BETWEEN SOME REPRODUCTIVE TRAITS IN SWINE

1972 ◽  
Vol 52 (1) ◽  
pp. 39-45 ◽  
Author(s):  
M. H. FAHMY ◽  
C. S. BERNARD
Keyword(s):  
Litter Size ◽  
Survival Rates ◽  
Reproductive Traits ◽  
The Other ◽  
Gestation Length ◽  
Percentage Survival ◽  
Weaning Pig ◽  
Highly Correlated ◽  
Daily Gain ◽  
Size At Birth

The associations between 15 preweaning traits in pigs were studied to determine which had the most important effects on litter weights at birth and weaning. The traits were litter size at birth and weaning, number born alive, percentage survival to birth and weaning, pig and litter weights at birth and weaning, daily gain from birth to weaning, gestation length, number of teats, weights of dam at farrowing and at weaning, and the change in dam weight during lactation. Of the 105 correlations, 66 were statistically significant, though many were markedly low. Litter weights at birth and weaning were significantly and relatively highly correlated with most of the other traits, whereas number of teats was correlated only with survival rates at birth and weaning and pig birth weight. The results showed that the importance of litter size was almost twice that of pig weight in determining litter weights at birth and weaning. The results in general indicated that most of the economically important traits related to swine reproductivity are favorably associated.

scholarly journals Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

scholarly journals Testing hypotheses of marsupial brain size variation using phylogenetic multiple imputations and a Bayesian comparative framework

2021 ◽  
Vol 288 (1947) ◽  
Author(s):  
Orlin S. Todorov ◽  
Simone P. Blomberg ◽  
Anjali Goswami ◽  
Karen Sears ◽  
Patrik Drhlík ◽  
...  
Keyword(s):  
Litter Size ◽  
Brain Size ◽  
Size Variation ◽  
Reproductive Traits ◽  
Mammalian Brain ◽  
Gestation Length ◽  
High Coverage ◽  
Ecological Predictors ◽  
Size Evolution ◽  
Relative Brain Size

Considerable controversy exists about which hypotheses and variables best explain mammalian brain size variation. We use a new, high-coverage dataset of marsupial brain and body sizes, and the first phylogenetically imputed full datasets of 16 predictor variables, to model the prevalent hypotheses explaining brain size evolution using phylogenetically corrected Bayesian generalized linear mixed-effects modelling. Despite this comprehensive analysis, litter size emerges as the only significant predictor. Marsupials differ from the more frequently studied placentals in displaying a much lower diversity of reproductive traits, which are known to interact extensively with many behavioural and ecological predictors of brain size. Our results therefore suggest that studies of relative brain size evolution in placental mammals may require targeted co-analysis or adjustment of reproductive parameters like litter size, weaning age or gestation length. This supports suggestions that significant associations between behavioural or ecological variables with relative brain size may be due to a confounding influence of the extensive reproductive diversity of placental mammals.

scholarly journals Genome-wide identification of a regulatory mutation in BMP15 controlling prolificacy in sheep

2019 ◽  
Author(s):  
Louise Chantepie ◽  
Loys Bodin ◽  
Julien Sarry ◽  
Florent Woloszyn ◽  
Florence Plisson-Petit ◽  
...  
Keyword(s):  
Association Study ◽  
Litter Size ◽  
X Chromosome ◽  
Genome Wide Association Study ◽  
Ovulation Rate ◽  
Genome Wide Association ◽  
Heterozygous State ◽  
Sheep Population ◽  
Massif Central ◽  
Genome Wide

AbstractThe search for the genetic determinism of prolificacy variability in sheep has evidenced several major mutations in genes playing a crucial role in the control of ovulation rate. In the Noire du Velay (NV) sheep population, a recent genetic study has evidenced the segregation of such a mutation named FecLL. However, based on litter size (LS) records of FecLL non-carrier ewes, the segregation of a second prolificacy major mutation was suspected in this population. In order to identify this mutation, we have combined case/control genome-wide association study with ovine 50k SNP chip genotyping, whole genome sequencing and functional analyses. A new single nucleotide polymorphism (OARX:50977717T>A, NC_019484) located on the X chromosome upstream of the BMP15 gene was evidenced highly associated with the prolificacy variability (P =1.93E-11). The variant allele was called FecXN and shown to segregate also in the Blanche du Massif Central (BMC) sheep population. In both NV and BMC, the FecXN allele frequency was estimated close to 0.10, and its effect on LS was estimated at +0.20 lamb per lambing at heterozygous state. Homozygous FecXN carrier ewes were fertile with increased prolificacy in contrast to numerous mutations affecting BMP15. At the molecular level, FecXN was shown to decrease BMP15 promoter activity and to impact BMP15 expression in oocyte. This regulatory action was proposed as the causal mechanism for the FecXN mutation to control ovulation rate and prolificacy in sheep.Author SummaryIn the genetic etiology of women infertility syndromes, a focus was done on the oocyte-expressed BMP15 and GDF9 genes harboring several mutations associated with ovarian dysfunctions. In sheep also, mutations in these two genes are known to affect the ovarian function leading to sterility or, on the opposite, increasing ovulation rate and litter size constituting the prolificacy trait genetically selected in this species. Through a genome-wide association study with the prolificacy phenotype conducted in the French Noire du Velay sheep breed, we describe a novel mutation located in the regulatory region upstream of the BMP15 gene on the X chromosome. This mutation increases litter size by +0.2 lamb per lambing at the heterozygous state, possibly through an inhibition of BMP15 expression within the oocyte. Our findings suggest a novel kind of BMP15 variant responsible for high prolificacy, in contrast to all other BMP15 variants described so far in the coding sequence.

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