UNIVERSIDAD ESTATAL DE MILAGRO

FACULTY OF ENGINEERING SCIENCE

BIOTECHNOLOGY ENGINEERING

FIFTH SEMESTER

FUNCTIONAL AND STRUCTURAL GENOMIC

WORKSHOP # 3

TOPIC:
“LOCALIZATION HERITABILITY BY LINKAGE ANALYSIS”

STUDENT:
Mariuxi Andrea Guzmán Loaiza

THEACHER:
MSc. Luis Eduardo Cagua Montaño

DATE:

June 18th of 2021

Milagro – Ecuador

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 UNIVERSIDAD ESTATAL DE MILAGRO

FACULTY OF ENGINEERING SCIENCE

BIOTECHNOLOGY ENGINEERING

FIFTH SEMESTER

FUNCTIONAL AND STRUCTURAL GENOMIC

STUDENT: Mariuxi Andrea Guzmán Loaiza

TOPIC: “Localization heritability by linkage analysis”

INTRODUCTION

Heritability is the variance partition of variable characteristics that can be attributed to

an interindividual genotypic variation. Its variance will arise from different causes and is

described as the phenotypic variance. Heritability is determined by both the genes of an

organism and the environment between individuals (Brookfield, 2012).

In genetic studies, multiple correlated phenotypes are often measured to better

characterize a complex disease. As well the correlation between the differences measurements

can be induced by the genetic mechanisms and the environmental factors. By the way, the

principal components analysis (PC) helps us with the linkage analysis (Liang et al., 2016).

Liang et al. (2016) say that “the traditional PCs are the linear combination of traits

calculated by maximizing the variance with the assumption of independent subjects, which we

termed PCVs. When family data are available, the linear combinations of traits can be obtained

by maximizing heritability, which we termed PCHs” (p. 2).

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DEVELOPMENT

Genetic engineering is a set of techniques to identify, separate, alter, reintroduce, or

transfer a gene from a derived organism to another organism. This means changing the genetic

inheritance of living cells' DNA, allowing them to produce more or different products or perform

entirely new functions (Camarena, Chura, & Blas, 2014).

Heritability is the degree to which the phenotype reflects the genotype in the broad

sense. in a restricted or narrow sense, it is the portion of the genetic variance due to additive

effects expressed as a percentage of the phenotypic variance (Camarena et al., 2014).

In the same way, estimating the heritability of single nucleotide polymorphisms

(SNPs) is an important topic in several research fields, including animal, plant, and human

genetics, as well as ecology (Mathew, Léon, & Sillanpää, 2018).

SNP-heritability (the proportion of genetic factors explaining total variance) is

typically estimated using a linear mixed model, in which the random effect covariance structure

between individuals is replaced with a sample covariance matrix estimated from genome-wide

SNP-marker sets. This model is known as the genomic best linear unbiased prediction (G-BLUP)

model (Mathew et al., 2018).

Mathew et al. (2018) say that “It is also possible to estimate SNP-heritability by fitting

thousands of SNPs simultaneously to the whole-genome regression (WGR) model and applying

variable selection for them” (p.356).

In 2018, Mathew et al. conclude that in the case of low LD, their observed LD

approach provided the same estimation accuracy as the competing methods (VanRaden and

GCTA). Furthermore, LDAK's estimation accuracy was slightly higher than theirs approach,

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VanRaden, and GCTA. This is most likely because LDAK has been optimized for low LD

situations (p.361).

Many studies have highlighted the significance of understanding the patterns and

distributions of LD in humans as well as other species such as animals and plants. Meanwhile, it

is clear that the patterns of LD in a population are heavily influenced by the population

substructure (Mathew et al., 2018).

In association mapping studies, various methods for correcting for population structure

have been proposed. However, there has been less emphasis placed on the significance of

accounting for population structures in the estimation of genomic breeding values and

heritability. In addition, the relationship between epistasis and LD in the estimation of genomic

breeding values and heritability must be clarified (Mathew et al., 2018).

CONCLUSION

Gene detection method in which the distribution of a disease in high-risk families is

investigated. This method attempts to locate a disease-causing gene by identifying genetic

markers with the known chromosomal location that are inherited along with the trait of interest.

Also called linkage analysis.

REFERENCES

Brookfield J. F. (2012). Heritability. Current biology: CB, 22(7), R217–R219.

https://doi.org/10.1016/j.cub.2012.02.035

Camarena F., Chura J. & Blas R. (2014). Mejoramiento genético y biotecnológico de

plantas. Lima, Perú: UNALM/AGROBANCO. https://www.agrobanco.com.pe/wp-

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 content/uploads/2017/07/MEJORAMIENTO_GENETICO_Y_BIOTECNOLOGICO_DE_

PLANTAS.pdf

Liang, J., Cade, B. E., Wang, H., Chen, H., Gleason, K. J., Larkin, E. K., Saxena, R., Lin, X.,

Redline, S., & Zhu, X. (2016). Comparison of Heritability Estimation and Linkage

Analysis for Multiple Traits Using Principal Component Analyses. Genetic

epidemiology, 40(3), 222–232. https://doi.org/10.1002/gepi.21957

Mathew, B., Léon, J., & Sillanpää, M. J. (2018). A novel linkage-disequilibrium corrected

genomic relationship matrix for SNP-heritability estimation and genomic

prediction. Heredity, 120(4), 356–368. https://doi.org/10.1038/s41437-017-0023-4

Kaczmarek, Z., Surma, M., Adamski, T., & Czajka, S. (2004). Numerical method for

detection of linkage between genes for two metrical traits. Journal of applied

genetics, 45(1), 27–35.

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