QTL Mapping and Candidate Gene Analysis for Alkali Tolerance in Japonica Rice at the bud Stage Based on Linkage Mapping and Genome-Wide Association Study

Rice
Xianwei LiHongwei Zhao

Abstract

Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in japonica rice at the bud stage. A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage, qAT11, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in qAT11 that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (LOC_Os11g37300, LOC_Os11g37320 and LOC_Os11g37390). In addition, we perfor...Continue Reading

References

Feb 15, 2001·Trends in Plant Science·J K Zhu
Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Aug 10, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jennifer M GagneRichard D Vierstra
Sep 13, 2005·Nature Genetics·Zhong-Hai RenHong-Xuan Lin
Sep 29, 2006·Current Opinion in Plant Biology·Esther LechnerPascal Genschik
Jan 16, 2007·Annals of Botany·Kate Dreher, Judy Callis
Jun 26, 2007·Bioinformatics·Peter J BradburyEdward S Buckler
May 24, 2008·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Dongling QiLongzhi Han
Oct 10, 2009·Plant Signaling & Behavior·Yu'e Zhang, Yongbiao Xue
Jun 9, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Zhoufei WangHongsheng Zhang
May 21, 2013·Plant Physiology and Biochemistry : PPB·Yunhong ZhangBao Liu
Jan 30, 2015·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Vinod KumarTrilochan Mohapatra
Feb 17, 2018·Journal of Plant Physiology·Tino KresziesKosala Ranathunge

❮ Previous
Next ❯

Citations

Mar 26, 2021·Breeding Science·Ichirou Karahara, Tomoaki Horie

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
PCR

Software Mentioned

TASSEL
DnaSP
R package ‘ qqman

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.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

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.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

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.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.