Identification of Candidate Genes Related to Stem Development in Brassica napus Using RNA-Seq

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.

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Identification of candidate genes involved in fatty acids degradation at the late maturity stage in Brassica napus based on transcriptomic analysis

Plant Growth Regulation ◽

10.1007/s10725-017-0305-0 ◽

2017 ◽

Vol 83 (3) ◽

pp. 385-396 ◽

Cited By ~ 3

Author(s):

Longhua Zhou ◽

Haoyi Wang ◽

Xin Chen ◽

Yuling Li ◽

Nazim Hussain ◽

...

Keyword(s):

Fatty Acids ◽

Brassica Napus ◽

Candidate Genes ◽

Transcriptomic Analysis ◽

Maturity Stage ◽

Late Maturity

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

Theoretical and Applied Genetics ◽

10.1007/s00122-018-3238-8 ◽

2018 ◽

Vol 132 (2) ◽

pp. 515-529 ◽

Cited By ~ 7

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

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RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening

Scientia Horticulturae ◽

10.1016/j.scienta.2019.04.018 ◽

2019 ◽

Vol 254 ◽

pp. 26-34 ◽

Cited By ~ 3

Author(s):

Dante Travisany ◽

Anibal Ayala-Raso ◽

Alex Di Genova ◽

Liliam Monsalve ◽

Maricarmen Bernales ◽

...

Keyword(s):

Candidate Genes ◽

Fruit Development ◽

Transcriptome Assembly ◽

Rubus Idaeus ◽

Rna Seq ◽

Fruit Development And Ripening

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

10.1101/344754 ◽

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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QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Plants ◽

10.3390/plants11020214 ◽

2022 ◽

Vol 11 (2) ◽

pp. 214

Author(s):

Qinghui Han ◽

Qingxiang Zhu ◽

Yao Shen ◽

Michael Lee ◽

Thomas Lübberstedt ◽

...

Keyword(s):

Transcription Factor ◽

Low Temperature ◽

Candidate Genes ◽

Temperature Tolerance ◽

Bhlh Transcription Factor ◽

Rna Seq ◽

Dh Population ◽

Low Temperature Tolerance ◽

Germination Ability ◽

Upregulated Genes

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

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