NDLI: Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers

Content Provider	Springer Nature : BioMed Central
Author	Da, Yang
Abstract	Background The amount of functional genomic information has been growing rapidly but remains largely unused in genomic selection. Genomic prediction and estimation using haplotypes in genome regions with functional elements such as all genes of the genome can be an approach to integrate functional and structural genomic information for genomic selection. Towards this goal, this article develops a new haplotype approach for genomic prediction and estimation. Results A multi-allelic haplotype model treating each haplotype as an ‘allele’ was developed for genomic prediction and estimation based on the partition of a multi-allelic genotypic value into additive and dominance values. Each additive value is expressed as a function of h − 1 additive effects, where h = number of alleles or haplotypes, and each dominance value is expressed as a function of h(h − 1)/2 dominance effects. For a sample of q individuals, the limit number of effects is 2q − 1 for additive effects and is the number of heterozygous genotypes for dominance effects. Additive values are factorized as a product between the additive model matrix and the h − 1 additive effects, and dominance values are factorized as a product between the dominance model matrix and the h(h − 1)/2 dominance effects. Genomic additive relationship matrix is defined as a function of the haplotype model matrix for additive effects, and genomic dominance relationship matrix is defined as a function of the haplotype model matrix for dominance effects. Based on these results, a mixed model implementation for genomic prediction and variance component estimation that jointly use haplotypes and single markers is established, including two computing strategies for genomic prediction and variance component estimation with identical results. Conclusion The multi-allelic genetic partition fills a theoretical gap in genetic partition by providing general formulations for partitioning multi-allelic genotypic values and provides a haplotype method based on the quantitative genetics model towards the utilization of functional and structural genomic information for genomic prediction and estimation.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-015-0301-1.pdf
Ending Page	12
Page Count	12
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/s12863-015-0301-1
Journal	BMC Genomic Data
Issue Number	1
Volume Number	16
Language	English
Publisher	BioMed Central
Publisher Date	2015-12-18
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Haplotype Genomic selection Variance component Heritability BLUP REML
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers

GVCHAP: A Computing Pipeline for Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

Multi-population genomic prediction using a multi-task Bayesian learning model

Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits

Genetic parameters for milk fatty acids in Danish Holstein cattle based on SNP markers using a Bayesian approach

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

Genomic selection in sugar beet breeding populations

Comparison of single-trait and multiple-trait genomic prediction models

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers

Similar Documents

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers

GVCHAP: A Computing Pipeline for Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers

Evaluation of approaches for estimating the accuracy of genomic prediction in plant breeding

Multi-population genomic prediction using a multi-task Bayesian learning model

Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits

Genetic parameters for milk fatty acids in Danish Holstein cattle based on SNP markers using a Bayesian approach

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

Genomic selection in sugar beet breeding populations

Comparison of single-trait and multiple-trait genomic prediction models

Multi-allelic haplotype model based on genetic partition for genomic prediction and variance component estimation using SNP markers