A multiple near isogenic line (multi-NIL) RNA-seq approach to identify candidate genes underpinning QTL

2017 ◽  
Vol 131 (3) ◽  
pp. 613-624 ◽  
Author(s):  
Ahsan Habib ◽  
Jonathan J. Powell ◽  
Jiri Stiller ◽  
Miao Liu ◽  
Sergey Shabala ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Isogenic Line ◽  
Near Isogenic Line ◽  
Rna Seq

scholarly journals RNA-Seq Analysis of a Soybean Near-Isogenic Line Carrying Bacterial Leaf Pustule-Resistant and -Susceptible Alleles

DNA Research ◽  
2011 ◽  
Vol 18 (6) ◽  
pp. 483-497 ◽  
Author(s):  
K. H. Kim ◽  
Y. J. Kang ◽  
D. H. Kim ◽  
M. Y. Yoon ◽  
J.-K. Moon ◽  
...  
Keyword(s):  
Isogenic Line ◽  
Near Isogenic Line ◽  
Rna Seq

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

scholarly journals Lipoxygenase activities during development of root and nodule of soybean

2004 ◽  
Vol 39 (7) ◽  
pp. 625-630 ◽  
Author(s):  
Tatiana Góes Junghans ◽  
Maria Goreti de Almeida Oliveira ◽  
Maurilio Alves Moreira
Keyword(s):  
Growth And Development ◽  
Root Formation ◽  
Lipoxygenase Activity ◽  
Post Inoculation ◽  
Isogenic Line ◽  
Near Isogenic Line ◽  
Near Isogenic Lines ◽  
Isogenic Lines ◽  
Bradyrhizobium Elkanii ◽  
Over Time

The objective of this work was to evaluate root and nodule soybean lipoxygenases in Doko cultivar and in a near isogenic line lacking seed lipoxygenases, inoculated and uninoculated with Bradyrhizobium elkanii. The lipoxygenase activities from roots collected at 3, 5, 9, 13, 18 and 28 days post-inoculation and from nodules collected at 13, 18 and 28 days post-inoculation were measured. The pH-activity profiles from root and nodules suggested that the lipoxygenases pool expressed in these organs from Doko cultivar and triple-null near isogenic lines are similar. The root lipoxygenase activity of Doko and triple-null lines, inoculated and uninoculated, reduced over time. The highest lipoxygenase activity observed at the beginning of root formation suggests the involvement of this enzyme in growth and development of this organ. However, for nodules an expressive increase of lipoxygenase activity was noticed 28 days post-inoculation. Root and nodule showed, at least, two mobility groups for lipoxygenases in immunoblottings, with approximately 94 and 97 kDa.

A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq

2018 ◽  
Vol 132 (2) ◽  
pp. 515-529 ◽  
Author(s):  
Minjeong Park ◽  
Joung-Ho Lee ◽  
Koeun Han ◽  
Siyoung Jang ◽  
Jiwoong Han ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Rna Seq ◽  
Capsicum Chinense ◽  
Major Qtl ◽  
Capsaicinoid Biosynthesis

scholarly journals Development of a near isogenic line of ‘Koshihikari’ with a seed dormancy gene and an evaluation of its resistance to heat-induced quality decline

2016 ◽  
Vol 18 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Asako Kobayashi ◽  
Kazuhiko Sugimoto ◽  
Takeshi Hayashi ◽  
Motohiko Kondo ◽  
Junya Sonoda ◽  
...  
Keyword(s):  
Seed Dormancy ◽  
Isogenic Line ◽  
Near Isogenic Line ◽  
Resistance To Heat

scholarly journals Tissue-specific cis-regulatory divergence implicates a fatty acid elongase necessary for inhibiting interspecies mating in Drosophila

2018 ◽  
Author(s):  
Peter A. Combs ◽  
Joshua J. Krupp ◽  
Neil M. Khosla ◽  
Dennis Bua ◽  
Dmitri A. Petrov ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Sister Species ◽  
F1 Hybrids ◽  
Rna Seq ◽  
Fatty Acid Elongase ◽  
Tissue Specific ◽  
Regulatory Changes ◽  
Wide Range

AbstractPheromones known as cuticular hydrocarbons are a major component of reproductive isolation in Drosophila. Individuals from morphologically similar sister species produce different sets of hydrocarbons that allow potential mates to identify them as a suitable partner. In order to explore the molecular mechanisms underlying speciation, we performed RNA-seq in F1 hybrids to measure tissue-specific cis-regulatory divergence between the sister species D. simulans and D. sechellia. By focusing on cis-regulatory changes specific to female oenocytes, we rapidly identified a small number of candidate genes. We found that one of these, the fatty acid elongase eloF, broadly affects both the complement of hydrocarbons present on D. sechellia females and the propensity of D. simulans males to mate with those females. In addition, knockdown of eloF in the more distantly related D. melanogaster led to a similar shift in hydrocarbons as well as lower interspecific mate discrimination by D. simulans males. Thus, cis-regulatory changes in eloF appear to be a major driver in the sexual isolation of D. simulans from multiple other species. More generally, our RNA-seq approach proved to be far more efficient than QTL mapping in identifying candidate genes; the same framework can be used to pinpoint cis-regulatory drivers of divergence in a wide range of traits differing between any interfertile species.

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