668. How ssGBLUP became suitable for national dairy cattle evaluations

Misztal, I.; Lourenço, Daniela; Tsuruta, S.; Aguilar, Ignácio; Masuda, Yutaka; Bermann, Matias; Cesarani, Alberto; Legarra, Andrés

doi:10.3920/978-90-8686-940-4_668

Cited by 14 publications

(20 citation statements)

References 15 publications

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“…Genetic (co)variance components of acute hyperthermia resistance and body weight at 275 dpf were estimated with AIREML algorithm in BLUPF90 software (Misztal et al, 2002) using the following animal model:…”

Section: Discussionmentioning

confidence: 99%

579. Genetic parameters and genome-wide association study of resistance to acute hyperthermia in rainbow trout

Lagarde

Lallias

Patrice

et al. 2022

Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)

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Selective breeding is a promising solution to reduce fish farms vulnerability to heat peaks. Objectives of this study were to give a new insight on the genetic architecture of resistance to acute hyperthermia stress in rainbow trout. At 275 days post-fertilization, 1,384 fish were phenotyped for acute hyperthermia resistance and body weight. Challenged fish were genotyped for 57K SNP and their genotypes were imputed at high-density thanks to their parents being genotyped on a 665K SNP array. Heritability estimate of resistance to acute hyperthermia was 0.32 ± 0.04. This trait was genetically negatively correlated with body weight (-0.58 ± 0.17). The genome-wide association study revealed that resistance to acute hyperthermia is highly polygenic as altogether the 5 detected QTLs explained less than 5% of the genetic variance. The main QTL region explained 3% of the genetic variance and contained two candidate genes previously described to be associated with temperature resistance.

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Section: Discussionmentioning

confidence: 99%

579. Genetic parameters and genome-wide association study of resistance to acute hyperthermia in rainbow trout

Lagarde

Lallias

Patrice

et al. 2022

Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP)

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“…Misztal and Perez-Enciso proposed an efficient strategy which calculated only those elements of the inverse that belong to the sparse pattern of the original matrix ( 20 ), and then the fast sparse solver package FSPAK was developed and released to the public ( 21 ), making the traditional breeding evaluation superefficient. FSPAK has been implemented in various software packages, such as DMU ( 10 ) and BLUPF90 ( 11 ).…”

Section: Methodsmentioning

confidence: 99%

“…This is because the algorithm implemented in most software tools [e.g. DMU ( 10 ), BLUPF90 ( 11 ) and ASReml ( 12 )] requires several rounds of inversion of an increasingly dense coefficient matrix of MMEs; the benefits from traditional sparse technologies are limited and have encountered a bottleneck. Nowadays, much effort has been placed on developing faster and computationally feasible strategies to improve the ability to handle a larger number of genotyped individuals for MME-based algorithms ( 13 , 14 ).…”

Section: Introductionmentioning

confidence: 99%

HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data

Yin

Zhang

Tang

et al. 2023

Nucleic Acids Research

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Human diseases and agricultural traits can be predicted by modeling a genetic random polygenic effect in linear mixed models. To estimate variance components and predict random effects of the model efficiently with limited computational resources has always been of primary concern, especially when it involves increasing the genotype data scale in the current genomic era. Here, we thoroughly reviewed the development history of statistical algorithms used in genetic evaluation and theoretically compared their computational complexity and applicability for different data scenarios. Most importantly, we presented a computationally efficient, functionally enriched, multi-platform and user-friendly software package named ‘HIBLUP’ to address the challenges that are faced currently using big genomic data. Powered by advanced algorithms, elaborate design and efficient programming, HIBLUP computed fastest while using the lowest memory in analyses, and the greater the number of individuals that are genotyped, the greater the computational benefits from HIBLUP. We also demonstrated that HIBLUP is the only tool which can accomplish the analyses for a UK Biobank-scale dataset within 1 h using the proposed efficient ‘HE + PCG’ strategy. It is foreseeable that HIBLUP will facilitate genetic research for human, plants and animals. The HIBLUP software and user manual can be accessed freely at https://www.hiblup.com.

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“…Alpha (0.90) and beta (0.10) parameters were used to construct the H matrix. For the genetic correlations, the Gibbs sampling method was applied using the software GIBBS1F90 or THRGIBBS1F90 [ 82 ] for linear or categorical traits, respectively. For all the heritability and genetic correlation estimates, their respective standard errors (SE) were calculated using the standard deviation ( ) of their sample distribution divided by the square root of the number of records (N) present in a given dataset: SE = .…”

Section: Methodsmentioning

confidence: 99%

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle

et al. 2023

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Background Given the economic relevance of fertility and reproductive traits for the beef cattle industry, investigating their genetic background and developing effective breeding strategies are paramount. Considering their late and sex-dependent phenotypic expression, genomic information can contribute to speed up the rates of genetic progress per year. In this context, the main objectives of this study were to estimate variance components and genetic parameters, including heritability and genetic correlations, for fertility, female precocity, and semen production and quality (andrological attributes) traits in Nellore cattle incorporating genomic information. Results The heritability estimates of semen quality traits were low-to-moderate, while moderate-to-high estimates were observed for semen morphological traits. The heritability of semen defects ranged from low (0.04 for minor semen defects) to moderate (0.30 for total semen defects). For seminal aspect (SMN_ASPC) and bull reproductive fitness (BULL_FIT), low (0.19) and high (0.69) heritabilities were observed, respectively. The heritability estimates for female reproductive traits ranged from 0.16 to 0.39 for rebreeding of precocious females (REBA) and probability of pregnancy at 14 months (PP14), respectively. Semen quality traits were highly genetically correlated among themselves. Moderate-to-high genetic correlations were observed between the ability to remain productive in the herd until four years of age (stayability; STAY) and the other reproductive traits, indicating that selection for female reproductive performance will indirectly contribute to increasing fertility rates. High genetic correlations between BULL_FIT and female reproductive traits related to precocity (REBA and PP14) and STAY were observed. The genetic correlations between semen quality and spermatic morphology with female reproductive traits ranged from -0.22 (REBA and scrotal circumference) to 0.48 (REBA and sperm vigor). In addition, the genetic correlations between REBA with semen quality traits ranged from -0.23 to 0.48, and with the spermatic morphology traits it ranged from -0.22 to 0.19. Conclusions All male and female fertility and reproduction traits evaluated are heritable and can be improved through direct genetic or genomic selection. Selection for better sperm quality will positively influence the fertility and precocity of Nellore females. The findings of this study will serve as background information for designing breeding programs for genetically improving semen production and quality and reproductive performance in Nellore cattle.

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668. How ssGBLUP became suitable for national dairy cattle evaluations

Cited by 14 publications

References 15 publications

579. Genetic parameters and genome-wide association study of resistance to acute hyperthermia in rainbow trout

579. Genetic parameters and genome-wide association study of resistance to acute hyperthermia in rainbow trout

HIBLUP: an integration of statistical models on the BLUP framework for efficient genetic evaluation using big genomic data

Genetic parameters for various semen production and quality traits and indicators of male and female reproductive performance in Nellore cattle

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