scholarly journals Genome-wide association study-based identification genes influencing agronomic traits in rice (Oryza sativa L.)

Genomics ◽  
2021 ◽  
Author(s):  
Aijun Wang ◽  
Yuqi Jiang ◽  
Xinyue Shu ◽  
Zhongping Zha ◽  
Desuo Yin ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

2020 ◽  
Vol 21 (14) ◽  
pp. 4930
Author(s):  
Mingnan Qu ◽  
Jemaa Essemine ◽  
Ming Li ◽  
Shuoqi Chang ◽  
Tiangen Chang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Natural Variation ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Dark Respiration ◽  
Genome Wide Association ◽  
Strong Positive Correlation ◽  
Diversity Panel ◽  
Genome Wide

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

scholarly journals Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study

2014 ◽  
Vol 66 (1) ◽  
pp. 293-306 ◽  
Author(s):  
Yoshiaki Ueda ◽  
Felix Frimpong ◽  
Yitao Qi ◽  
Elsa Matthus ◽  
Linbo Wu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genetic Dissection ◽  
Genome Wide ◽  
A Genome ◽  
Ozone Tolerance

Genome Wide Association Study of Rice (Oryza sativa L.) during Heading Stage under a High Temperature

2021 ◽  
Vol 9 (2) ◽  
pp. 104-111
Author(s):  
Yebin Kwon ◽  
Tae-Ho Ham ◽  
JeeHye Kim ◽  
Gileung Lee ◽  
Yoonjung Lee ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
High Temperature ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Genome Wide Association ◽  
Genome Wide ◽  
Heading Stage

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.

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