scholarly journals Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice

2021 ◽  
Vol 22 (9) ◽  
pp. 4445
Author(s):  
Hedia Tnani ◽  
Dmytro Chebotarov ◽  
Ranjita Thapa ◽  
John Carlos I. Ignacio ◽  
Walter K. Israel ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Sugar Metabolism ◽  
Differential Regulation ◽  
Cell Wall Modification ◽  
Pigmented Rice ◽  
Novel Approach ◽  
Genome Wide ◽  
Anaerobic Germination ◽  
Direct Seeded

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.

scholarly journals Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ling Su ◽  
Jing Yang ◽  
Dandan Li ◽  
Ziai Peng ◽  
Aoyun Xia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Oxygen Deficiency ◽  
Direct Seeding ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Anaerobic Germination ◽  
Dynamic Genome ◽  
Rice Seeds

Abstract Background In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. Results In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (−log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19–1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG. Conclusion The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.

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 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 for Maize Leaf Cuticular Conductance Identifies Candidate Genes Involved in the Regulation of Cuticle Development

2020 ◽  
Vol 10 (5) ◽  
pp. 1671-1683 ◽  
Author(s):  
Meng Lin ◽  
Susanne Matschi ◽  
Miguel Vasquez ◽  
James Chamness ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Crop Productivity ◽  
Genome Wide Association ◽  
Cell Wall Modification ◽  
Major Barrier ◽  
Maize Leaf ◽  
Genome Wide ◽  
A Genome

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA, in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.

scholarly journals Genome-wide association study for maize leaf cuticular conductance identifies candidate genes involved in the regulation of cuticle development

2019 ◽  
Author(s):  
Meng Lin ◽  
Susanne Matschi ◽  
Miguel Vasquez ◽  
James Chamness ◽  
Nicholas Kaczmar ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Cell Wall Modification ◽  
Major Barrier ◽  
Maize Leaf ◽  
Genome Wide ◽  
Genome Prediction ◽  
A Genome

AbstractThe cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed at night and under water-limited conditions. Elucidating the genetic architecture of natural variation for leaf cuticular conductance (gc) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we conducted a genome-wide association study of gc of adult leaves in a maize inbred association panel that was evaluated in four environments (Maricopa, AZ, and San Diego, CA in 2016 and 2017). Five genomic regions significantly associated with gc were resolved to seven plausible candidate genes (ISTL1, two SEC14 homologs, cyclase-associated protein, a CER7 homolog, GDSL lipase, and β-D-XYLOSIDASE 4). These candidates are potentially involved in cuticle biosynthesis, trafficking and deposition of cuticle lipids, cutin polymerization, and cell wall modification. Laser microdissection RNA sequencing revealed that all these candidate genes, with the exception of the CER7 homolog, were expressed in the zone of the expanding adult maize leaf where cuticle maturation occurs. With direct application to genetic improvement, moderately high average predictive abilities were observed for whole-genome prediction of gc in locations (0.46 and 0.45) and across all environments (0.52). The findings of this study provide novel insights into the genetic control of gc and have the potential to help breeders more effectively develop drought-tolerant maize for target environments.Article summaryThe cuticle serves as the major barrier to water loss when stomata are closed at night and under water-limited conditions and potentially relevant to drought tolerance in crops. We performed a genome-wide association study to elucidate the genetic architecture of natural variation for maize leaf cuticular conductance. We identified epidermally expressed candidate genes that are potentially involved in cuticle biosynthesis, trafficking and deposition, cutin polymerization, and cell wall modification. Finally, we observed moderately high predictive abilities for whole-genome prediction of leaf cuticular conductance. Collectively, these findings may help breeders more effectively develop drought-tolerant maize.

scholarly journals Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice

2020 ◽  
Author(s):  
Ling Su ◽  
Jing Yang ◽  
Dandan Li ◽  
Ziai Peng ◽  
Aoyun Xia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Expression Profiles ◽  
Oxygen Deficiency ◽  
Direct Seeding ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Anaerobic Germination ◽  
Dynamic Genome ◽  
Rice Seeds

Abstract Background: In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding.Results: In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (−log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19-1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG.Conclusion: The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.

scholarly journals Loci and natural alleles for cadmium-mediated growth responses revealed by a genome wide association study and transcriptome analysis in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jianping Yu ◽  
Chaolei Liu ◽  
Hai Lin ◽  
Bin Zhang ◽  
Xiaoxia Li ◽  
...  
Keyword(s):  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Growth Responses ◽  
Cd Stress ◽  
New Genes ◽  
Genome Wide ◽  
A Genome ◽  
Natural Variations

Abstract Background Cadmium (Cd) is a toxic heavy metal that is harmful to the environment and human health. Cd pollution threatens the cultivation of rice (Oryza sativa L.) in many countries. Improving rice performance under Cd stress could potentially improve rice productivity. Results In this study, 9 growth traits of 188 different cultivated rice accessions under normal and Cd stress conditions were found to be highly variable during the seedling stage. Based on ~3.3 million single nucleotide polymorphisms (SNPs), 119 Cd-mediated growth response (CGR) quantitative trait loci (QTL) were identified by a genome-wide association study (GWAS), 55 of which have been validated by previously reported QTL and 64 were new CGR loci. Combined with the data from the GWAS, transcriptome analysis, gene annotations from the gene ontology (GO) Slim database, and annotations and functions of homologous genes, 148 CGR candidate genes were obtained. Additionally, several reported genes have been found to play certain roles in CGRs. Seven Cd-related cloned genes were found among the CGR genes. Natural elite haplotypes/alleles in these genes that increased Cd tolerance were identified by a haplotype analysis of a diverse mini core collection. More importantly, this study was the first to uncover the natural variations of 5 GST genes that play important roles in CGRs. Conclusion The exploration of Cd-resistant rice germplasm resources and the identification of elite natural variations related to Cd-resistance will help improve the tolerance of current major rice varieties to Cd, as well as provide raw materials and new genes for breeding Cd-resistant varieties.

scholarly journals Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sushil Raj Subedi ◽  
Nitika Sandhu ◽  
Vikas Kumar Singh ◽  
Pallavi Sinha ◽  
Santosh Kumar ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Cultivation Condition ◽  
Genome Wide ◽  
Direct Seeded ◽  
Genomic Regions

Food intake‐related genes in chicken determined through combinatorial genome‐wide association study and transcriptome analysis

2020 ◽  
Vol 51 (5) ◽  
pp. 741-751 ◽  
Author(s):  
Xuemin Cao ◽  
Yuzhe Wang ◽  
Dingming Shu ◽  
Hao Qu ◽  
Chenglong Luo ◽  
...  
Keyword(s):  
Food Intake ◽  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Combined genome‐wide association study and transcriptome analysis reveal candidate genes for resistance to Fusarium ear rot in maize

2020 ◽  
Vol 62 (10) ◽  
pp. 1535-1551 ◽  
Author(s):  
Lishan Yao ◽  
Yanmei Li ◽  
Chuanyu Ma ◽  
Lixiu Tong ◽  
Feili Du ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Genome Wide
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