A Ranking Approach to Genomic Selection

PloS One
Mathieu BlondelNaonori Ueda

Abstract

Genomic selection (GS) is a recent selective breeding method which uses predictive models based on whole-genome molecular markers. Until now, existing studies formulated GS as the problem of modeling an individual's breeding value for a particular trait of interest, i.e., as a regression problem. To assess predictive accuracy of the model, the Pearson correlation between observed and predicted trait values was used. In this paper, we propose to formulate GS as the problem of ranking individuals according to their breeding value. Our proposed framework allows us to employ machine learning methods for ranking which had previously not been considered in the GS literature. To assess ranking accuracy of a model, we introduce a new measure originating from the information retrieval literature called normalized discounted cumulative gain (NDCG). NDCG rewards more strongly models which assign a high rank to individuals with high breeding value. Therefore, NDCG reflects a prerequisite objective in selective breeding: accurate selection of individuals with high breeding value. We conducted a comparison of 10 existing regression methods and 3 new ranking methods on 6 datasets, consisting of 4 plant species and 25 traits. Our experimental ...Continue Reading

References

Feb 13, 2003·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·O. LoudetF. Daniel-Vedele
May 2, 2003·Bioinformatics·Karl W BromanGary A Churchill
Apr 12, 2005·Plant Molecular Biology·Pushpendra K GuptaPawan L Kulwal
Dec 14, 2007·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·M E Goddard, B J Hayes
May 29, 2008·Genetics·Nengjun Yi, Shizhong Xu
Jan 24, 2009·Journal of Dairy Science·Ben J HayesM E Goddard
Feb 10, 2009·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Mar 19, 2009·Genetics·Gustavo de Los CamposJosé Miguel Cotes
Oct 21, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Robenzon E Lorenzana, Rex Bernardo
Jan 23, 2010·BMC Genetics·Takeshi Hayashi, Hiroyoshi Iwata
Feb 17, 2010·Briefings in Functional Genomics·Jean-Luc JanninkHiroyoshi Iwata
Mar 2, 2010·Biotechnology Advances·G Ram KumarM S Madhav
May 25, 2011·BMC Bioinformatics·David HabierDorian J Garrick
Jan 1, 2013·G3 : Genes - Genomes - Genetics·Paulino Pérez-RodríguezS Dreisigacker
Feb 1, 2014·Neural Computation·Ching-Pei Lee, Chih-Jen Lin
Mar 7, 2014·Frontiers in Neuroinformatics·Alexandre AbrahamGaël Varoquaux

Citations

Sep 23, 2017·Molecular Breeding : New Strategies in Plant Improvement·Jiayin SongCharles Chen
Sep 20, 2019·G3 : Genes - Genomes - Genetics·Christina B AzodiShin-Han Shiu
Jul 11, 2019·The Plant Genome·Po-Ya WuChen-Tuo Liao
Jun 29, 2018·Frontiers in Genetics·Daniel GianolaChris-Carolin Schön
Jul 20, 2018·G3 : Genes - Genomes - Genetics·Bartolode Jesús Villar-HernándezJuan Burgueño
Jan 2, 2021·Journal of Plant Physiology·Hao Tong, Zoran Nikoloski

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Hereditary Sensory Autonomic Neuropathy

Hereditary Sensory Autonomic Neuropathies are a group of inherited neurodegenerative disorders characterized clinically by loss of sensation and autonomic dysfunction. Here is the latest research on these neuropathies.

Spatio-Temporal Regulation of DNA Repair

DNA repair is a complex process regulated by several different classes of enzymes, including ligases, endonucleases, and polymerases. This feed focuses on the spatial and temporal regulation that accompanies DNA damage signaling and repair enzymes and processes.

Glut1 Deficiency

Glut1 deficiency, an autosomal dominant, genetic metabolic disorder associated with a deficiency of GLUT1, the protein that transports glucose across the blood brain barrier, is characterized by mental and motor developmental delays and infantile seizures. Follow the latest research on Glut1 deficiency with this feed.

Separation Anxiety

Separation anxiety is a type of anxiety disorder that involves excessive distress and anxiety with separation. This may include separation from places or people to which they have a strong emotional connection with. It often affects children more than adults. Here is the latest research on separation anxiety.

KIF1A Associated Neurological Disorder

KIF1A associated neurological disorder (KAND) is a rare neurodegenerative condition caused by mutations in the KIF1A gene. KAND may present with a wide range and severity of symptoms including stiff or weak leg muscles, low muscle tone, a lack of muscle coordination and balance, and intellectual disability. Find the latest research on KAND here.

Regulation of Vocal-Motor Plasticity

Dopaminergic projections to the basal ganglia and nucleus accumbens shape the learning and plasticity of motivated behaviors across species including the regulation of vocal-motor plasticity and performance in songbirds. Discover the latest research on the regulation of vocal-motor plasticity here.

Related Papers

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Akio OnogiHiroyoshi Iwata
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Torben Schulz-StreeckHans-Peter Piepho
IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Ke LuLing Shao
© 2021 Meta ULC. All rights reserved