scholarly journals Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi

2019 ◽  
Vol 20 (10) ◽  
pp. 2598 ◽  
Author(s):  
Do-Yu Kang ◽  
Kyeong-Seong Cheon ◽  
Jun Oh ◽  
Hyoja Oh ◽  
Song Lim Kim ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rice Variety ◽  
Rice Genome ◽  
Chromosome 9 ◽  
Dna Polymorphisms ◽  
Fusarium Fujikuroi ◽  
Japonica Rice ◽  
Bakanae Disease ◽  
Trait Locus

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, ‘Samgwang’ and ‘Junam’, respectively. Resequencing of ‘Junam’ and ‘Samgwang’ genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24–7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the ‘Junam’ and ‘Samgwang’ genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.

scholarly journals Detection of a novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah

2011 ◽  
Vol 61 (1) ◽  
pp. 61-68 ◽  
Author(s):  
Masahiko Mori ◽  
Kazumitsu Onishi ◽  
Yoshiro Tokizono ◽  
Hiroshi Shinada ◽  
Toru Yoshimura ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Cold Tolerance ◽  
Quantitative Trait ◽  
Rice Variety ◽  
Japonica Rice ◽  
Booting Stage ◽  
Tropical Japonica ◽  
Trait Locus ◽  
Japonica Rice Variety

scholarly journals Mapping and characterization of a quantitative trait locus resistance to the brown planthopper in the rice variety IR64

Hereditas ◽  
2019 ◽  
Vol 156 (1) ◽  
Author(s):  
Meng Yang ◽  
Ling Cheng ◽  
Liuhui Yan ◽  
Wan Shu ◽  
Xinyi Wang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Rice Variety ◽  
Brown Planthopper ◽  
Trait Locus

scholarly journals A Deletion Downstream of the CHCHD7 Gene Is Associated with Growth Traits in Sheep

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1472
Author(s):  
Hongwei Xu ◽  
Haixia Li ◽  
Zhen Wang ◽  
Ayimuguli Abudureyimu ◽  
Jutian Yang ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Growth And Development ◽  
Major Quantitative Trait Locus ◽  
Growth Traits ◽  
Coiled Coil ◽  
Chromosome 9 ◽  
Wild Type ◽  
Tan Sheep ◽  
Trait Locus

In sheep, the coiled-coil-helix-coiled-coil-helix domain containing 7 (CHCHD7) gene and the pleiomorphic adenoma gene 1 (PLAG1) are on the same growth-related major quantitative trait locus, positioned head-to-head approximately 420 bp apart on chromosome 9. PLAG1 affects sheep growth, but the effects of CHCHD7 have not been determined. In this study, an 8-bp deletion downstream of CHCHD7 was analyzed in 2350 sheep from seven breeds. The associations between the deletion and growth traits of Tan sheep were also determined. Both genotypes (homozygous wild-type and heterozygous) for the 8-bp deletion were found in Tan (TS), Luxi Blackhead (LXBH), Small-Tail Han (STHS), and Lanzhou Fat-Tail (LFTS) sheep. However, there were no polymorphic sites for the mutation in Hu (HS), Sartuul (SS), and Australian White (AUW) sheep. In TS, LXBH, STHS, and LFTS sheep, the deletion genotype was less frequent than the wild-type genotype, and the allele frequencies of the deletion variant were 0.007 (TS), 0.011 (LBXH), 0.008 (STHS), and 0.010 (LFTS). The 8-bp deletion was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) in Tan sheep. Thus, the 8-bp deletion downstream of the CHCHD7 gene might be associated with growth and development traits of sheep.

scholarly journals Defining a rat blood pressure quantitative trait locus to a <81.8 kb congenic segment: comprehensive sequencing and renal transcriptome analysis

2010 ◽  
Vol 42A (2) ◽  
pp. 153-161 ◽  
Author(s):  
K. Gopalakrishnan ◽  
J. Saikumar ◽  
C. G. Peters ◽  
S. Kumarasamy ◽  
P. Farms ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Transcriptome Analysis ◽  
Quantitative Trait ◽  
Congenic Strain ◽  
Association Studies ◽  
Chromosome 9 ◽  
Genome Wide Association Studies ◽  
Congenic Strains ◽  
Trait Locus

Evidence from multiple linkage and genome-wide association studies suggest that human chromosome 2 (HSA2) contains alleles that influence blood pressure (BP). Homologous to a large segment of HSA2 is rat chromosome 9 (RNO9), to which a BP quantitative trait locus (QTL) was previously mapped. The objective of the current study was to further resolve this BP QTL. Eleven congenic strains with introgressed segments spanning <81.8 kb to <1.33 Mb were developed by introgressing genomic segments of RNO9 from the Dahl salt-resistant (R) rat onto the genome of the Dahl salt-sensitive (S) rat and tested for BP. The congenic strain with the shortest introgressed segment spanning <81.8 kb significantly lowered BP of the hypertensive S rat by 25 mmHg and significantly increased its mean survival by 45 days. In contrast, two other congenic strains had increased BP compared with the S. We focused on the <81.8 kb congenic strain, which represents the shortest genomic segment to which a BP QTL has been mapped to date in any species. Sequencing of this entire region in both S and R rats detected 563 variants. The region did not contain any known or predicted rat protein coding genes. Furthermore, a whole genome renal transcriptome analysis between S and the <81.8 kb S.R congenic strain revealed alterations in several critical genes implicated in renal homeostasis. Taken together, our results provide the basis for future studies to examine the relationship between the candidate variants within the QTL region and the renal differentially expressed genes as potential causal mechanisms for BP regulation.

Mapping of a major quantitative trait locus for bakanae disease resistance in rice by genome resequencing

2017 ◽  
Vol 293 (3) ◽  
pp. 579-586 ◽  
Author(s):  
Hyeonso Ji ◽  
Tae-Ho Kim ◽  
Gang-Seob Lee ◽  
Hyun-Ju Kang ◽  
Seung-Bum Lee ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Disease Resistance ◽  
Quantitative Trait ◽  
Major Quantitative Trait Locus ◽  
Genome Resequencing ◽  
Bakanae Disease ◽  
Trait Locus
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