Rice yield is a complex trait affected by many related traits. Traditional single-trait genome-wide association studies (GWAS) have limitations when studying complex traits, as they cannot account ...for the genetic relationships among multiple traits. Multi-trait GWAS, which can consider the relationships among multiple traits and identify pleiotropic loci, is more suitable for complex traits such as rice yield than single-trait GWAS. In this study, we conducted a multi-trait GWAS on 11 two-trait combinations of yield and yield-related traits with 575 hybrid rice varieties across two environments. All of these yield-related traits showed significant genetic correlation with yield (YD), including filled grains per panicle (FGPP), kilo-grain weight (KGW), tillers per plant (TP), primary branch number (PB), secondary branch number (SB) and main panicle length (MPL). In total we identified 44 pleiotropic quantitative trait loci (pQTLs), including 29 new pQTLs not found in single-trait GWAS. We then screened 23 pQTLs showing common effects in two traits as key pQTLs. These key pQTLs were subsequently analyzed for haplotype analysis and identified 13 pleiotropic candidate genes. Finally, we identified two optimal yield-enhancing allele combinations by pyraming superior haplotypes: GS3-GL3.1-OsCIPK17 for the YD-KGW combination and GNP12 for the YD-FGPP and YD-SB combinations. This study provides pleiotropic candidate genes and allele combinations that exhibit superior differences in both yield and yield-related traits, offering valuable information for future high-yielding rice breeding.
The aim of this study was to estimate the growth trait parameters in grass carp, Ctenopharyngodon idella, which is one of the major freshwater aquaculture species in China. The heritability, genetic ...and phenotypic correlations were estimated for body weight, standard length, body height and body thickness measurements of 10 and 18month old fish. Analyses were performed on a total of 41 and 104 full-sib families of grass carp including 937 and 2454 individuals at 10 (first spring) and 18months (second winter) of age, respectively. The families were reconstructed using the molecular pedigree based on twelve microsatellite loci, and 97.6% of the offspring were unambiguously assigned to single parent pairs. Unbalanced contributions to progeny were found among families and parents (P<0.01). Variance components and genetic parameters were estimated using the restricted maximum-likelihood algorithm with animal models. For all growth traits across two stages of grass carp, the common environment/maternal effect in proportion to phenotypic variance was very low (0.00–0.06), and not significant (P>0.05). The heritability estimates for growth traits ranged from 0.24 to 0.38, and were significantly different from zero (P<0.01). These results indicated that the breeding population had considerable additive genetic variation in growth traits, and the ongoing selective breeding program should produce considerable genetic improvement in the growth traits of the grass carp. High genetic and phenotypic correlations were found among growth traits (0.81–0.99, P<0.01). These data indicate that selection for improved standard length will have a favorable effect on body weight in grass carp which is the key economic parameter for production yield. High and positive genetic correlations between growth traits at 10 and 18months of age were also detected in grass carp (0.87–0.95, P<0.01), which indicated that individuals with higher growth performance at 10months also grew to be better at 18months. The results showed that genetic differences in growth traits among grass carp progeny could be determined earlier by measuring indicator traits predictive of long-term genetically determined growth.
Our article comply with the Policy Statement for submission of manuscripts to the Genetic Section.
In this study, we aim to estimate the genetic parameters of growth traits in grass carp, Ctenopharyngodon idella, which is one of the major freshwater aquaculture species in China.
The heritability, genetic, and phenotypic correlations were estimated for growth traits of grass carp at 10 and 18months. Our study is an essential report on the quantitative genetic analysis of growth traits in sub-adult grass carp.
This paper has not been submitted to any other journal for publication. The authors can confirm that the study has no actual or potential conflicts of interest to report. All authors have read and agreed the contents of the manuscript and consent to its publication.
•Genetic parameters estimated for growth of grass carp at 10 and 18months of age.•High genetic correlation between body weight and other length traits found in this study.•High genetic correlation between growth traits across different stages of grass carp detected in the current study.•This study can help in developing and optimizing a selective breeding program.
Molecular genetic assessments are modern selection tools that provide accurate information to producers seeking to improve the health, well-being, and profitability of their herd. The aim of the ...present study was to elaborate the genomic profile of Holstein cows from the semiarid region of Pernambuco through the Genomic Predicted Transmission Ability values, to correlate milk production characteristics with conformation and reproduction characteristics, and to evaluate information on carriers for genetic diseases. Thirty-nine Holstein cows were used to obtain the Genomic Predicted Transmission Ability-GPTA, a 12k chip (12 thousand genetic markers – CLARIFIDE®) by Zoetis. The averages of GPTA in this study were higher than those of American average, namely 384 pounds of milk production, 17.9 pounds of fat, and 12.9 pounds of protein. For CCS, females showed moderate susceptibility to mastitis. The volume and fat content were considered the most indicated selection criteria to improve the gains in quantity and concentration of solids in milk. Carriers for VMC and CHD were identified. It appeared that the Holstein herd from the semiarid region presented a genetic profile with the potential to improve the productive characteristics, allowing the identification of animals with genetic anomalies before entering the reproductive phase
Background: Garden pea is one of the principal vegetable crops cultivated in the temperate and sub- tropical areas of the world for its green pods. It is an important food legume worldwide after ...Phaseolus vulgaris. The knowledge about the interdependence of characters in a particular crop can effectively be employed to breed desirable cultivars and to challenge the consequences of the unprecedented biological, physical and chemical stresses of the future growing conditions. The regression and path analysis further has significance for the assured selection of the varieties with desirable traits and hence adaptation of species in different agro-climatic conditions; hence it is also one of the prerequisites for crop improvement programmes. Correlation and path analysis in garden pea explained that among all the yield contributing traits, number of pods per plant and pod weight have significant contribution in increasing the green pod yield per plant.
Methods: 14 heterotic recombinant inbred lines and 17 existing cultivars of garden pea, were put to experimentation for working out the association of the yield and yield contributing component characters under the open field conditions of Regional Horticultural Research and Training Station, Bajaura Kullu, Himachal Pradesh, India. This association was further elaborated through the coefficient of correlation and regression analysis and path coefficient analysis.
Result: The genotypic correlation coefficients were found higher than the phenotypic correlation coefficients for all the characters studied. The correlation coefficients revealed that green pod yield per plant had highly significant and positive association with pod weight and number of pods per plant. The path coefficient analysis also revealed that the maximum positive direct effect on green pod yield per plant was exerted by the number of pods per plant, pod weight and 100-seed weight. Through regression equation analysis it became clear that number of pods per plant, pod weight contributed significantly in increasing the green pod yield per plant. With a unit increase in these independent characters, the green pod yield per plant will increase by 2.34 and 33.45 per cent. It can thus be concluded that despite of the positive correlation of almost all the characters with green pod yield per plant, only number of pods per plant and pod weight are important and significant independent characters for increasing the green pod yield per plant.
Although genetic correlations between complex traits provide valuable insights into epidemiological and etiological studies, a precise quantification of which genomic regions disproportionately ...contribute to the genome-wide correlation is currently lacking. Here, we introduce ρ-HESS, a technique to quantify the correlation between pairs of traits due to genetic variation at a small region in the genome. Our approach requires GWAS summary data only and makes no distributional assumption on the causal variant effect sizes while accounting for linkage disequilibrium (LD) and overlapping GWAS samples. We analyzed large-scale GWAS summary data across 36 quantitative traits, and identified 25 genomic regions that contribute significantly to the genetic correlation among these traits. Notably, we find 6 genomic regions that contribute to the genetic correlation of 10 pairs of traits that show negligible genome-wide correlation, further showcasing the power of local genetic correlation analyses. Finally, we report the distribution of local genetic correlations across the genome for 55 pairs of traits that show putative causal relationships.
The aim of this study was to estimate genetic parameters of milk urea concentration (MUC) and the relationships with milk yield (MY) in the first lactation of Holstein Friesian cows. Data consisted ...of 952 test day records of MY and MUC on 52 first lactation Holstein Friesian cows calving from 2015 and 2016 at Agricultural Research and Development Station (ARDS) Simnic-Craiova, Romania. Random regression models were used to estimate genetic parameters and associations between traits. The coefficient of variation for MUC in the first parity was 38.34%. Average daily heritability of MUC was 0.20. In the first parity, genetic correlation between MUC and MY was positive and increased with days in milk from 0,18 to 0,38.This results confirm that MUC, used for management purposes, may slightly increase due to selection for milk production trait.
•Loneliness is a strong risk factor for various health problems.•Personality is useful in understanding why people differ in loneliness.•It is largely unclear why certain personality traits are ...associated with loneliness.•We found evidence of genetic and environmental influences in the associations.•This may suggest several traits being involved in the development of loneliness.
As a strong risk factor for mortality, individual differences in loneliness are of clear public health significance. Four of the Big Five traits have emerged as cross-sectional correlates, but the etiology of these links is unclear, as are relations with more specific personality facets. Thus, we estimated phenotypic, genetic, and environmental associations between loneliness and both broader and narrower personality dimensions. Traits that indexed Negative Emotionality (e.g., Neuroticism, Stress Reactivity, Alienation) and low Positive Emotionality (e.g., low Extraversion, low Well-Being) had the strongest associations with loneliness, though low Conscientiousness, low Agreeableness, and high Aggression were also implicated. These associations were explained by both genetic (0.30 < |rg| < 0.80) and unique environmental (0.10 < |re| < 0.35) influences, consistent with an etiology of loneliness involving several personality domains.
Neuroimaging studies examining the effects of aging and neuropsychiatric disorders on the cerebral cortex have largely been based on measures of cortical volume. Given that cortical volume is a ...product of thickness and surface area, it is plausible that measures of volume capture at least 2 distinct sets of genetic influences. The present study aims to examine the genetic relationships between measures of cortical surface area and thickness. Participants were men in the Vietnam Era Twin Study of Aging (110 monozygotic pairs and 92 dizygotic pairs). Mean age was 55.8 years (range: 51–59). Bivariate twin analyses were utilized in order to estimate the heritability of cortical surface area and thickness, as well as their degree of genetic overlap. Total cortical surface area and average cortical thickness were both highly heritable (0.89 and 0.81, respectively) but were essentially unrelated genetically (genetic correlation = 0.08). This pattern was similar at the lobar and regional levels of analysis. These results demonstrate that cortical volume measures combine at least 2 distinct sources of genetic influences. We conclude that using volume in a genetically informative study, or as an endophenotype for a disorder, may confound the underlying genetic architecture of brain structure.
Faot MM, Zubaidah S, Kuswantoro H. 2019. Genetic correlation and path analysis of agronomical traits of soybean (Glycine max) lines infected by CpMMV. Biodiversitas 20: 1496-1503. CpMMV is a virus ...that can decrease soybean production. The virus vector is an insect where the control is carried out using a chemical insecticide that is less environmentally friendly. Developing a superior variety of soybean that is resistant to CpMMV is one of the solutions to solve such a problem. This research aimed to study the relationship of agronomical traits to the yield of soybean line infected by CpMMV. Ten lines and two varieties of soybean with four replications was used in this study in a randomized complete block design. Bemisia tabaci was used in CpMMV infestation as the vector of the disease. Rearing Bemisia tabaci was done forty days before sowing the main experiment, and it placed surrounding the main experiment plots. The observation variables were disease severity, days to flowering and maturity, plant height, length, width and ratio of the leaf, number of branches and reproductive nodes, number of filled and unfilled pods, number of seeds, 100 seeds weight, and seed yield per plant. The data was analyzed for genotypic and phenotypic correlation, and the path analysis for direct and indirect effects of disease severity, and agronomical characters. The results showed that CpMMV infestation caused disease severity by about 20-28.5%. A significant positive phenotypic correlation to the seed yield per plant was shown by the number of reproductive nodes and the 100 seeds weight. Meanwhile, a significant positive genotypic correlation to the seed yield per plant was shown by the days to maturity and the number of branches. The number of reproductive nodes, the 100 seeds weight, and the number of seeds per plant showed a high direct effect to the seed yield per plant. The high positive indirect effect was also shown by the number of filled pods, days to flowering, plant height, leaf length, leaf width, the number of reproductive nodes, and the number of branches through the number of seeds per plant was also. Therefore, the selection criteria for high yielding CpMMV-resistant soybean lines can be based on the number of reproductive nodes and 100 seeds weight.
Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and ...genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 67 traits evaluated on heifers and first-lactation Canadian Holstein cows. The data consisted of approximately 500,000 records with pedigree information collected from 1980 to 2019. Genetic parameters were estimated using bivariate linear animal models under a Bayesian approach. Analyses for the 67 traits resulted in 2,211 bivariate combinations, from which the estimated genetic parameters are reported here. The most highly heritable traits were fat percent (0.66) and protein percent (0.69), followed by stature (0.47). Lowest heritabilities (0.01) were observed for disease-related traits, such as lameness and toe ulcer, and calf survival. The genetic correlations between gestation length, calf size, and calving ease measured on both heifer and cows were close to unity. On the other hand, traits such as body condition score and pin width, cystic ovaries and sole ulcer, rear teat placement, and toe ulcer were genetically unrelated. This study reports genetic parameters that have not been previously published for Canadian Holstein cows, and provides updates of those previously estimated. These estimates are useful for building new indexes, updating existing selection indexes, and for predicting correlated responses due to inclusion of novel traits in the breeding programs.
PDF
