Genomic prediction offers the most effective marker assisted breeding approach for ability to prevent arsenic accumulation in rice grains.

08:00 EDT 13th June 2019 | BioPortfolio

Summary of "Genomic prediction offers the most effective marker assisted breeding approach for ability to prevent arsenic accumulation in rice grains."

The high concentration of arsenic (As) in rice grains, in a large proportion of the rice growing areas, is a critical issue. This study explores the feasibility of conventional (QTL-based) marker-assisted selection and genomic selection to improve the ability of rice to prevent As uptake and accumulation in the edible grains. A japonica diversity panel (RP) of 228 accessions phenotyped for As concentration in the flag leaf (FL-As) and in the dehulled grain (CG-As), and genotyped at 22,370 SNP loci, was used to map QTLs by association analysis (GWAS) and to train genomic prediction models. Similar phenotypic and genotypic data from 95 advanced breeding lines (VP) with japonica genetic backgrounds, was used to validate related QTLs mapped in the RP through GWAS and to evaluate the predictive ability of across populations (RP-VP) genomic estimate of breeding value (GEBV) for As exclusion. Several QTLs for FL-As and CG-As with a low-medium individual effect were detected in the RP, of which some colocalized with known QTLs and candidate genes. However, less than 10% of those QTLs could be validated in the VP without loosening colocalization parameters. Conversely, the average predictive ability of across populations GEBV was rather high, 0.43 for FL-As and 0.48 for CG-As, ensuring genetic gains per time unit close to phenotypic selection. The implications of the limited robustness of the GWAS results and the rather high predictive ability of genomic prediction are discussed for breeding rice for significantly low arsenic uptake and accumulation in the edible grains.


Journal Details

This article was published in the following journal.

Name: PloS one
ISSN: 1932-6203
Pages: e0217516


DeepDyve research library

PubMed Articles [15971 Associated PubMed Articles listed on BioPortfolio]

Opportunities for genomic selection in American mink: A simulation study.

Genomic selection can be considered as an effective tool for developing breeding programs in American mink. However, the genetic gains for economically important traits can be influenced by the accura...

Multigenerational prediction of genetic values using genome-enabled prediction.

The identification of elite individuals is a critical component of most breeding programs. However, the achievement of this goal is limited by the high cost of phenotyping and experimental research. A...

Selection of trait-specific markers and multi-environment models improve genomic predictive ability in rice.

Developing high yielding rice varieties that are tolerant to drought stress is crucial for the sustainable livelihood of rice farmers in rainfed rice cropping ecosystems. Genomic selection (GS) promis...

Modelling G×E with historical weather information improves genomic prediction in new environments.

Interaction between the genotype and the environment (G×E) has a strong impact on the yield of major crop plants. Although influential, taking G×E explicitly into account in plant breeding has remai...

Genomic Prediction for Crossbred Performance using Metafounders.

Future genomic evaluation models to be used routinely in breeding programs for pigs and poultry need to be able to optimally use information of crossbred animals to predict breeding values for crossbr...

Clinical Trials [5108 Associated Clinical Trials listed on BioPortfolio]

Pan-genome Analysis of Neuroblastoma by Comparative Genomic Hybridization and Correlation With Pathology for the Diagnostic and the Prognostic Classification

Neuroblastoma (NB) is characterized by its wide heterogeneity in clinical presentation and evolution. Recent retrospective studies have revealed by CGH-array that the overall genomic patte...

Urinary Marker for Oxidative Stress in Human Cisplatin- Induced Renal Injury

We previously reported early measurement of urinary MDA might be a useful marker for the prediction of CDDP-induced renal damage in rat. The purpose of this clinical study is to test wheth...

Copeptin in Outcome Prediction of an Acute Psychotic Episode

An acute psychotic episode is a severe psychiatric syndrome which might occur in different psychiatric diagnoses. The outcome prediction of relapse rate of a psychotic episode within a ce...

Treatment of Breast Cancer Related Lymphedema With Cell-assisted Lipotransfer

Breast cancer is the most common cancer type among women. Treatment in many cases involves axillary lymphadenectomy followed by radiation therapy. This increases the risk of lymphedema dev...

Targeted Genomic Analysis of Blood and Tissue Samples From Patients With Cancer

This research trial studies the use of targeted genomic analysis of blood and tissue samples from patients with cancer. Genomic sequencing is a laboratory method that is used to determine ...

Medical and Biotech [MESH] Definitions

Methods pertaining to the generation of new individuals, including techniques used in selective BREEDING, cloning (CLONING, ORGANISM), and assisted reproduction (REPRODUCTIVE TECHNIQUES, ASSISTED).

Therapy assisted by the use of a horse and/or its movement, including equine-assisted psychotherapy, horseback riding, and hippotherapy.

Predicting the time of OVULATION can be achieved by measuring the preovulatory elevation of ESTRADIOL; LUTEINIZING HORMONE or other hormones in BLOOD or URINE. Accuracy of ovulation prediction depends on the completeness of the hormone profiles, and the ability to determine the preovulatory LH peak.

Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.

The systematic study of annotated genomic information to global protein expression in order to determine the relationship between genomic sequences and both expressed proteins and predicted protein sequences.

Quick Search


DeepDyve research library

Searches Linking to this Article