scholarly journals Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa) during germination

3 Biotech ◽  
2018 ◽  
Vol 8 (5) ◽  
Author(s):  
Heng Wang ◽  
Ah-Rim Lee ◽  
So-Yeon Park ◽  
Sang-Hyeon Jin ◽  
Joohyun Lee ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Low Temperature ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Temperature Tolerance ◽  
Genome Wide Association ◽  
Low Temperature Tolerance ◽  
Genome Wide

scholarly journals Identification of candidate genes for low temperature tolerance during germination of maize using a genome-wide association study and RNA-sequencing

2020 ◽  
Author(s):  
Hong Zhang ◽  
Jiayue Zhang ◽  
Qingyu Xu ◽  
Dandan Wang ◽  
Hong Di ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Temperature Tolerance ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Agricultural Crop ◽  
Low Temperature Tolerance ◽  
Genome Wide

Abstract Background: Maize ( Zea mays L.) is the largest agricultural crop in the world based on acreage and yield, however, it is inherently sensitive to low temperatures. The growth and yield of maize can be affected by low temperature during its whole growth period, particularly during germination. Therefore, it is urgent to identify the new gene(s) related to the low temperature tolerance during maize germination. Results: In this study, 14 phenotypic traits related to seed germination were used to explore the genetic architecture of maize through genome-wide association analysis (GWAS). A total of 30 single nucleotide polymorphisms (SNPs) associated with low temperature tolerance were detected (–log10( P ) > 4); 14 candidate genes were detected as being directly associated with these SNPs and 81 candidate genes were identified when the screen was extended to a distance of 30 kb from these SNPs. The candidate genes were predicted by conjoint analysis with RNA-sequencing (RNA-seq) to evaluate whole-genome gene expression levels. A total of nine differentially expressed genes (DEGs) (|log2foldchange|≥0.585， P <0.05) were found within distance of 30 kb, including two DEGs ( GRMZM2G101383 and GRMZM2G402584 ), which were associated with SNPs directly. The differential expression of these candidate genes was verified using qRT-PCR. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of DEGs GRMZM2G052129 and GRMZM2G038964 were, ‘fatty acid metabolic process’, ‘Mitogen-activated protein kinase (MAPK) signal transduction’, and so on, which are related to the fluidity of the cell membrane and low temperature signal transduction. Conclusion: Therefore, further functional analysis of GRMZM2G052129 and GRMZM2G038964 will provide valuable information for understanding the genetic mechanism of low temperature tolerance during germination in maize.

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 Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

scholarly journals Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Bingru Zhao ◽  
Hanpeng Luo ◽  
Xixia Huang ◽  
Chen Wei ◽  
Jiang Di ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Growth Traits ◽  
Fibre Diameter ◽  
Single Step ◽  
Genome Wide Association ◽  
Six Traits ◽  
Genome Wide

Abstract Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

scholarly journals Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans

2010 ◽  
Vol 125 (2) ◽  
pp. 321-327.e13 ◽  
Author(s):  
Hao Wu ◽  
Isabelle Romieu ◽  
Min Shi ◽  
Dana B. Hancock ◽  
Huiling Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Childhood Asthma ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinyue Shu ◽  
Aijun Wang ◽  
Bo Jiang ◽  
Yuqi Jiang ◽  
Xing Xiang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Bacterial Leaf Blight ◽  
Significant Differential Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB. Results Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (–log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice. Conclusions Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

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.

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