scholarly journals Combined QTL mapping and RNA-Seq profiling reveals candidate genes associated with cadmium tolerance in barley

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0230820 ◽  
Author(s):  
Behnam Derakhshani ◽  
Hossein Jafary ◽  
Bahram Maleki Zanjani ◽  
Karim Hasanpur ◽  
Kohei Mishina ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Cadmium Tolerance ◽  
Rna Seq

Detection of a Major QTL and Development of KASP Markers for Seed Weight by Combining QTL-seq, QTL-mapping and RNA-seq in Peanut

2021 ◽  
Author(s):  
Zhihui Wang ◽  
Liying Yan ◽  
Yuning Chen ◽  
Xin Wang ◽  
Dongxin Huai ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Seed Development ◽  
Seed Weight ◽  
Molecular Mechanisms ◽  
Large Contribution ◽  
Phenotypic Variance ◽  
Rna Seq ◽  
Late Stages ◽  
Kasp Markers

Abstract Seed weight is a major target of peanut breeding as an important component of seed yield. However, relatively little is known about QTLs and candidate genes associated with seed weight in peanut. In this study, three major QTLs on chromosomes A05, B02 and B06 were determined by applying NGS-based QTL-seq approach for a RIL population. These three QTL regions have been successfully narrowed down through newly developed SNP and SSR markers based on traditional QTL mapping. Among these three QTL regions, qSWB06.3 exhibited stable expression with large contribution to phenotypic variance across all environments. Furthermore, RNA-seq were applied for early, middle and late stages of seed development, and differentially expression genes (DEGs) were identified in ubiquitin-proteasome pathway, serine/threonine protein pathway and signal transduction of hormones and transcription factors. Notably, DEGs at early stage were majorly related to regulating cell division, whereas DEGs at middle and late stages were mainly associated with cell expansion during seed development. Through integrating SNP variation, gene expression and functional annotation, candidate genes related to seed weight in qSWB06.3 were predicted and distinct expression pattern of those genes were exhibited using qRT-PCR. In addition, KASP-markers in qSWB06.3 were successfully validated in diverse peanut varieties and the alleles of parent Zhonghua16 in qSWB06.3 was associated with high seed weight. This suggested that qSWB06.3 was reliable and the markers in qSWB06.3 could be deployed in marker-assisted breeding to enhance seed weight. This study provided insights into the understanding of genetic and molecular mechanisms of seed weight in peanut.

Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice (Oryza sativa L.)

2019 ◽  
Vol 39 (6) ◽  
Author(s):  
Tao Guo ◽  
Jing Yang ◽  
Dongxiu Li ◽  
Kai Sun ◽  
Lixin Luo ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Oryza Sativa L ◽  
Seed Vigor ◽  
Rna Seq

scholarly journals Identification of heat-tolerance QTLs and high-temperature stress-responsive genes through conventional QTL mapping, QTL-seq and RNA-seq in tomato

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Junqin Wen ◽  
Fangling Jiang ◽  
Yiqun Weng ◽  
Mintao Sun ◽  
Xiaopu Shi ◽  
...  
Keyword(s):  
High Temperature ◽  
Qtl Mapping ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Heat Tolerance ◽  
Fine Mapping ◽  
High Temperature Stress ◽  
Rna Seq ◽  
Major Qtls ◽  
Mapping Qtl

Abstract Background High temperature is one of the major abiotic stresses in tomato and greatly reduces fruit yield and quality. Identifying high-temperature stress-responsive (HSR) genes and breeding heat-tolerant varieties is an effective way to address this issue. However, there are few reports on the fine mapping of heat-tolerance quantitative trait locus (QTL) and the identification of HSR genes in tomato. Here, we applied three heat tolerance-related physiological indexes, namely, relative electrical conductivity (REC), chlorophyll content (CC) and maximum photochemical quantum efficiency (Fv/Fm) of PSII (photosystem II), as well as the phenotypic index, the heat injury index (HII), and conventional QTL analysis combined with QTL-seq technology to comprehensively detect heat-tolerance QTLs in tomato seedlings. In addition, we integrated the QTL mapping results with RNA-seq to identify key HSR genes within the major QTLs. Results A total of five major QTLs were detected: qHII-1-1, qHII-1-2, qHII-1-3, qHII-2-1 and qCC-1-5 (qREC-1-3). qHII-1-1, qHII-1-2 and qHII-1-3 were located, respectively, in the intervals of 1.43, 1.17 and 1.19 Mb on chromosome 1, while the interval of qHII-2-1 was located in the intervals of 1.87 Mb on chromosome 2. The locations observed with conventional QTL mapping and QTL-seq were consistent. qCC-1-5 and qREC-1-3 for CC and REC, respectively, were located at the same position by conventional QTL mapping. Although qCC-1-5 was not detected in QTL-seq analysis, its phenotypic variation (16.48%) and positive additive effect (0.22) were the highest among all heat tolerance QTLs. To investigate the genes involved in heat tolerance within the major QTLs in tomato, RNA-seq analysis was performed, and four candidate genes (SlCathB2, SlGST, SlUBC5, and SlARG1) associated with heat tolerance were finally detected within the major QTLs by DEG analysis, qRT-PCR screening and biological function analysis. Conclusions In conclusion, this study demonstrated that the combination of conventional QTL mapping, QTL-seq analysis and RNA-seq can rapidly identify candidate genes within major QTLs for a complex trait of interest to replace the fine-mapping process, thus greatly shortening the breeding process and improving breeding efficiency. The results have important applications for the fine mapping and identification of HSR genes and breeding for improved thermotolerance.

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 QTL Mapping by SLAF-seq and Expression Analysis of Candidate Genes for Aphid Resistance in Cucumber

2016 ◽  
Vol 7 ◽  
Author(s):  
Danna Liang ◽  
Minyang Chen ◽  
Xiaohua Qi ◽  
Qiang Xu ◽  
Fucai Zhou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Genes ◽  
Expression Analysis ◽  
Aphid Resistance

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 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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