scholarly journals E-index Method for Identifying Dynamic Growth Traits of Poplar

2021 ◽  
Author(s):  
Luman Wang ◽  
Jianxin Wang ◽  
Huiying Qi
Keyword(s):  
Growth Curve ◽  
Growth Process ◽  
Growth Traits ◽  
Permutation Test ◽  
Spline Interpolation ◽  
Mapping Method ◽  
Nucleotide Polymorphisms ◽  
Growth Data ◽  
Index Method ◽  
Significant Qtls

Abstract To detect the mechanism of growth, volume is important to uncover the genetic basis of dynamic complex quantitative traits. Unfortunately, it is difficult to construct the unique simple growth curve to accurately describe the growth process of all trees by the conventional GWAS based on the functional mapping method, which reduces the power of statistics for the growth model. To address this issue, this work adopted a novel approach about the Earliness degree index (E-index). First, it adopted the method of spline interpolation to fit the growth data to acquire the growth curves for each tree. Second, an innovative calculation model based on E-index was used to measure the earliness degree for each growth curve and to identify the potential relationship between QTL effects and traits by a series of hypothesis tests. Besides, a permutation test could be used to estimate the threshold for p values and to screen out significant QTLs from SNPs related to the growth process. To verify the validity and practicability of our model, we applied this method on the data about the volumes of 64 poplar trees chosen randomly from the progeny of two poplar species I-69 and I-45 with 156362 single nucleotide polymorphisms (SNPs). Through the E-index method, 13 significant markers were identified for testcross and 10 for intercross related to the growth process. Overall, this study could help elucidate the underlying genetic mechanisms of complex dynamic traits and perform marker-assisted selection in poplar.

scholarly journals Function of the Porcine TRPC1 Gene in Myogenesis and Muscle Growth

Cells ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 147
Author(s):  
Yu Fu ◽  
Peng Shang ◽  
Bo Zhang ◽  
Xiaolong Tian ◽  
Ruixue Nie ◽  
...  
Keyword(s):  
Transient Receptor Potential ◽  
Growth Traits ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Receptor Potential ◽  
Transient Receptor Potential Channel ◽  
Nucleotide Polymorphisms ◽  
Pig Breeds ◽  
Muscle Tissues ◽  
Transient Receptor

In animals, muscle growth is a quantitative trait controlled by multiple genes. Previously, we showed that the transient receptor potential channel 1 (TRPC1) gene was differentially expressed in muscle tissues between pig breeds with divergent growth traits base on RNA-seq. Here, we characterized TRPC1 expression profiles in different tissues and pig breeds and showed that TRPC1 was highly expressed in the muscle. We found two single nucleotide polymorphisms (SNPs) (C-1763T and C-1604T) in TRPC1 that could affect the promoter region activity and regulate pig growth rate. Functionally, we used RNAi and overexpression to illustrate that TRPC1 promotes myoblast proliferation, migration, differentiation, fusion, and muscle hypertrophy while inhibiting muscle degradation. These processes may be mediated by the activation of Wnt signaling pathways. Altogether, our results revealed that TRPC1 might promote muscle growth and development and plays a key role in Wnt-mediated myogenesis.

scholarly journals Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 192
Author(s):  
Xinghai Duan ◽  
Bingxing An ◽  
Lili Du ◽  
Tianpeng Chang ◽  
Mang Liang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Growth Curve ◽  
Growth And Development ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Coefficient Of Determination ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

scholarly journals Fast genetic mapping using insertion-deletion polymorphisms in Caenorhabditis elegans

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ho-Yon Hwang ◽  
Jiou Wang
Keyword(s):  
Caenorhabditis Elegans ◽  
Genetic Mapping ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Material ◽  
Mapping Method ◽  
Forward Genetics ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Large Populations

AbstractGenetic mapping is used in forward genetics to narrow the list of candidate mutations and genes corresponding to the mutant phenotype of interest. Even with modern advances in biology such as efficient identification of candidate mutations by whole-genome sequencing, mapping remains critical in pinpointing the responsible mutation. Here we describe a simple, fast, and affordable mapping toolkit that is particularly suitable for mapping in Caenorhabditis elegans. This mapping method uses insertion-deletion polymorphisms or indels that could be easily detected instead of single nucleotide polymorphisms in commonly used Hawaiian CB4856 mapping strain. The materials and methods were optimized so that mapping could be performed using tiny amount of genetic material without growing many large populations of mutants for DNA purification. We performed mapping of previously known and unknown mutations to show strengths and weaknesses of this method and to present examples of completed mapping. For situations where Hawaiian CB4856 is unsuitable, we provide an annotated list of indels as a basis for fast and easy mapping using other wild isolates. Finally, we provide rationale for using this mapping method over other alternatives as a part of a comprehensive strategy also involving whole-genome sequencing and other methods.

Additive and non-additive genetic effects of growth-curve parameters of Holstein, Ayrshire and crossbred females

1994 ◽  
Vol 74 (3) ◽  
pp. 401-409 ◽  
Author(s):  
D. Perotto ◽  
R. I. Cue ◽  
A. J. Lee ◽  
A. J. McAllister ◽  
J. R. Batra ◽  
...  
Keyword(s):  
Growth Rate ◽  
Dairy Cattle ◽  
Growth Curve ◽  
Growth Traits ◽  
Individual Performance ◽  
Breeding Value ◽  
Average Lifetime ◽  
Additive Effects ◽  
Positive Effects ◽  
Maternal Performance

Crossbreeding parameters (line additive, dominance and additive × additive epistatic effects for individual and for maternal performance) on growth traits of females from a crossbreeding experiment between Holstein-based (HS) and Ayrshire-based (AS) lines were estimated by individual animal models, incorporating all known additive genetic relationships among animals, through restricted maximum likelihood and mixed-model methodologies. The growth traits [asymptotic weight (A), rate parameter (k), inflection parameter (m), average lifetime absolute growth rate (AGR), average lifetime absolute maturing rate (AMR) and average lifetime relative growth rate (RGR)] were estimated by fitting the Richards function to the observed growth curve of 3076 individuals. The statistical model included the random effect of the animal breeding value and the fixed effects of genetic group and station–year–season of birth. Results indicated that the HS exceeded (P < 0.001) the AS in additive effects for individual performance for both A and AGR. The HS exceeded (P < 0.05) the AS in additive effects for maternal performance for A. Individual heterosis was positive for A (P < 0.001) and for AGR (P < 0.01). Maternal heterosis was negative for A (P < 0.05) and positive for AMR (P < 0.05). Total heterosis (TH) had positive effects on both AGR and AMR (P < 0.05). Heterosis retained in advanced crossbred generations was not significant (P > 0.05) for any of the studied traits. The results suggest that crossbreeding designed to exploit TH can alter the shape of the growth curve of dairy cattle. Key words: Crossbreeding, dairy cattle, growth curve

Association of Interleukin 23 Receptor Variants with Psoriatic Arthritis

2009 ◽  
Vol 36 (1) ◽  
pp. 137-140 ◽  
Author(s):  
PROTON RAHMAN ◽  
ROBERT D. INMAN ◽  
WALTER P. MAKSYMOWYCH ◽  
JEFF P. REEVE ◽  
LYNETTE PEDDLE ◽  
...  
Keyword(s):  
Psoriatic Arthritis ◽  
Permutation Test ◽  
Psoriatic Skin ◽  
Nucleotide Polymorphisms ◽  
Marker Haplotype ◽  
Sliding Windows ◽  
Genome Wide ◽  
Canadian Population ◽  
Interleukin 23 ◽  
Coding Snp

Objective.A recent genome-wide pooling study noted a significant association of interleukin 23 receptor (IL-23R) and psoriasis. Overxpression of IL-23 has been detected in lesional psoriatic skin, and induces epidermal proliferation. Given the interplay between psoriasis and PsA, we examined the association of IL-23R variants in 2 independent Canadian Caucasian cohorts of patients with psoriatic arthritis (PsA).Methods.We examined 496 PsA probands and 476 controls. Cases and controls were genotyped for a panel of 11 single-nucleotide polymorphisms (SNP) in IL-23R. Allele and haplotype associations were calculated using WHAP software. P values for haplotype associations were calculated using a permutation test.Results.The 381Gln allele of the coding SNP Arg381Gln (rs11209026) was found to be protective in the Canadian population (p = 0.004; corrected p = 0.044).A 2-marker haplotype from SNP rs7530511 and rs11209026 was associated with PsA (p = 0.011). All 3-marker sliding windows containing SNP rs11209026 were associated with PsA (p = 0.02 for all 3 windows). The magnitude of effect of IL-23R association in PsA appears to be similar to that reported in uncomplicated psoriasis.Conclusion.Significant associations between Arg381Gln SNP and haplotypes encoding this variant were noted in PsA. It remains to be determined what contribution of this association, if any, is specifically due to the inflammatory arthritis (PsA) rather than psoriasis.

scholarly journals Testing a continuous variation in preweaning expression of muscular hypertrophy in beef cattle using field data

2002 ◽  
Vol 45 (2) ◽  
pp. 139-149 ◽  
Author(s):  
F. Goyache ◽  
L. J. Royo ◽  
I. Alvarez ◽  
J. P. Gutierrez
Keyword(s):  
Field Data ◽  
Growth Traits ◽  
Major Gene ◽  
Continuous Variation ◽  
Muscular Hypertrophy ◽  
Index Method ◽  
Factors Affecting ◽  
Calving Season ◽  
Phenotypical Variability ◽  
Growth Ability

Abstract. The hypothesis of a continuous variation in the expression of muscular hypertrophy has been tested using field data. A modification of NEUVY and VISSAC's cularity index method (Culard Index) was assayed. Expression of muscular hypertrophy showed a broad phenotypical variability. Environmental factors affecting expression of muscular hypertrophy characterised by Culard Index were calving season, age of dam, sex of calf, muscularity of dam, muscularity of sire and age of calf at weaning. In addition, Culard Index influences significantly preweaning growth traits confirming double muscled calves’ higher preweaning growth ability. Culard Index score showed moderate heritability. Expression of muscular hypertrophy could be a relatively different trait with respect to latent muscular hypertrophy that would be, in turn, determined by a partially dominant major gene. Culard Index could be an interesting tool to make use of the observable differences in expression of muscular hypertrophy.

Genetic parameters and responses to selection for pre-weaning growth in suffolk and texel sheep

1995 ◽  
Vol 1995 ◽  
pp. 48-48
Author(s):  
I.W. Purvis ◽  
J.P. Hanrahan
Keyword(s):  
Growth Rate ◽  
Genetic Variation ◽  
Genetic Gain ◽  
Genetic Parameters ◽  
Growth Traits ◽  
Present Report ◽  
Growth Data ◽  
Genetic Trend ◽  
Breeding Objective ◽  
Selection For

In order to evaluate genetic gain in populations under selection it is necessary to be able to partition the observed response into genetic and environmental components. This requires estimates of the appropriate genetic and environmental (co)variances unless appropriate genetic controls are available. Growth rate is an important component of the breeding objective for sheep breeds used as terminal sires and, whereas older estimates of the contribution of genetic variation to differences in preweaning growth indicated heritabilities of the order of 0.1, more recent studies have indicated considerably higher values. The present report concerns analyses of preweaning growth data on purebred Suffolk and Texel sheep to estimate genetic parameters for preweaning growth traits and genetic trend in growth rate from birth to weaning.

scholarly journals Melanocortin-4 Receptor (MC4R) gene polymorphism and its effect on growth traits in Madura cattle

2019 ◽  
Vol 44 (1) ◽  
pp. 38
Author(s):  
P. W. Prihandini ◽  
S. Sumadi ◽  
G. Suparta ◽  
D. Maharani
Keyword(s):  
Growth Traits ◽  
Balance Control ◽  
Direct Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Mc4r Gene ◽  
Melanocortin 4 Receptor ◽  
Pcr Rflp ◽  
Reverse Primer ◽  
Selection For

Melanocortin-4 receptor (MC4R) gene has an important role in the regulation of feed intake and energy balance control. The objective of this study was to identify the single nucleotide polymorphisms (SNPs) of MC4R gene and their association with growth traits in Madura cattle. A total of 198 calves were used in this study.Forward primer: 5’-GTCGGGCGTCTTGTTCATC-3’and reverse primer: 5’-GCTTGTGTTTAGCATCGCGT-3’ were used to amplify approximately 493 bp of MC4R gene. The results showed that two SNPs, g.1133C>G and g.1108C>T were identified by direct sequencing. The PCR-RFLP method was performed to genotype all individuals studied based on SNP g.1133C>G, and its SNP was significantly associated with shoulder height (SH) at yearling age (P<0.05). Animals with GG genotype had a higher SH (110.35±6.40cm) than those with CC (102.00±8.00 cm) and CG genotype (105.96±6.23 cm). The SNP g.1133 C>G changed amino acid from valine to leucine. In conclusion, the SNP g.1133C>G of the MC4R gene may be used as a marker-assisted selection for SH trait in Madura cattle.

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