scholarly journals Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dan Wang ◽  
Zhuo Liu ◽  
Yinghui Xiao ◽  
Xionglun Liu ◽  
Yue Chen ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Gene Knockout ◽  
Micro Rna ◽  
Negative Regulator ◽  
Bud Burst ◽  
Rab Protein ◽  
Genome Wide ◽  
Direct Seeded

AbstractCold tolerance at the bud burst stage (CTB) is a key trait for direct-seeded rice. Although quantitative trait loci (QTL) affecting CTB in rice have been mapped using traditional linkage mapping and genome-wide association study (GWAS) methods, the underlying genes remain unknown. In this study, we evaluated the CTB phenotype of 339 cultivars in the Rice Diversity Panel II (RDP II) collection. GWAS identified four QTLs associated with CTB (qCTBs), distributed on chromosomes 1–3. Among them, qCTB-1-1 overlaps with Osa-miR319b, a known cold tolerance micro RNA gene. The other three qCTBs have not been reported. In addition, we characterised the candidate gene OsRab11C1 for qCTB-1-2 that encodes a Rab protein belonging to the small GTP-binding protein family. Overexpression of OsRab11C1 significantly reduced CTB, while gene knockout elevated CTB as well as cold tolerance at the seedling stage, suggesting that OsRab11C1 negatively regulates rice cold tolerance. Molecular analysis revealed that OsRab11C1 modulates cold tolerance by suppressing the abscisic acid signalling pathway and proline biosynthesis. Using RDP II and GWAS, we identified four qCTBs that are involved in CTB and determined the function of the candidate gene OsRab11C1 in cold tolerance. Our results demonstrate that OsRab11C1 is a negative regulator of cold tolerance and knocking out of the gene by genome-editing may provide enhanced cold tolerance in rice.

scholarly journals Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

2021 ◽  
Author(s):  
Caijing Li ◽  
Jindong Liu ◽  
Jianxin Bian ◽  
Tao Jin ◽  
Baoli Zou ◽  
...  
Keyword(s):  
Low Temperature ◽  
Association Study ◽  
Cold Tolerance ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

scholarly journals Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

2018 ◽  
Vol 37 (3) ◽  
pp. 529-539 ◽  
Author(s):  
Mengchen Zhang ◽  
Jing Ye ◽  
Qun Xu ◽  
Yue Feng ◽  
Xiaoping Yuan ◽  
...  
Keyword(s):  
Association Study ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Indica Rice ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

scholarly journals Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Leila Nayyeripasand ◽  
Ghasem Ali Garoosi ◽  
Asadollah Ahmadikhah
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Salinity Tolerance ◽  
Genome Wide Association Study ◽  
Dry Weight ◽  
Genome Wide Association ◽  
Vegetative Stage ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

scholarly journals Genome-wide association study identifies PERLD1 as asthma candidate gene

2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Ramani Anantharaman ◽  
Anand Kumar Andiappan ◽  
Pallavi Parate Nilkanth ◽  
Bani Kaur Suri ◽  
De Yun Wang ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

Genome-wide association study reveals the genetic basis of cold tolerance in wheat

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Yong Zhao ◽  
Jiahao Li ◽  
Ruiling Zhao ◽  
Ke Xu ◽  
Yirao Xiao ◽  
...  
Keyword(s):  
Association Study ◽  
Cold Tolerance ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Comprehensive Identification of Drought Tolerance QTL-Allele and Candidate Gene Systems in Chinese Cultivated Soybean Population

2020 ◽  
Vol 21 (14) ◽  
pp. 4830
Author(s):  
Wubin Wang ◽  
Bin Zhou ◽  
Jianbo He ◽  
Jinming Zhao ◽  
Cheng Liu ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Genetic System ◽  
Phenotypic Variance ◽  
Quantitative Real Time Pcr ◽  
Plant Weight ◽  
Factors Affecting ◽  
Genome Wide ◽  
Cultivated Soybean

Drought is one of the most important factors affecting plant growth and productivity. The previous results on drought tolerance (DT) genetic system in soybean indicated a complex of genes not only few ones were involved in the trait. This study is featured with a relatively thorough identification of QTL-allele/candidate-gene system using an efficient restricted two-stage multi-locus multi-allele genome-wide association study, on two comprehensive DT indicators, membership index values of relative plant weight (MPW) and height (MPH), instead of a single biological characteristic, in a large sample (564 accessions) of the Chinese cultivated soybean population (CCSP). Based on 24,694 multi-allele markers, 75 and 64 QTL with 261 and 207 alleles (2–12/locus) were detected for MPW and MPH, explaining 54.7% and 47.1% of phenotypic variance, respectively. The detected QTL-alleles were organized into a QTL-allele matrix for each indicator, indicating DT is a super-trait conferred by two (even more) QTL-allele systems of sub-traits. Each CCSP matrix was separated into landrace (LR) and released cultivar (RC) sub-matrices, which showed significant differentiation in QTL-allele constitutions, with 58 LR alleles excluded and 16 new ones emerged in RC. Using the matrices, optimal crosses with great DT transgressive recombinants were predicted. From the detected QTL, 177 candidate genes were annotated and validated with quantitative Real-time PCR, and grouped into nine categories, with ABA and stress responders as the major parts. The key point of the above results is the establishment of relatively full QTL-allele matrices composed of numerous gene functions jointly conferring DT, therefore, demonstrates the complexity of DT genetic system and potential of CCSP in DT breeding.

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