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.

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.

scholarly journals Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

2019 ◽  
Vol 20 (17) ◽  
pp. 4303 ◽  
Author(s):  
Hongyou Li ◽  
Qiuyu Lv ◽  
Jiao Deng ◽  
Juan Huang ◽  
Fang Cai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Development ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fagopyrum Esculentum ◽  
Rna Seq ◽  
Common Buckwheat ◽  
Size Change ◽  
Key Genes

Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

scholarly journals Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shan Lin ◽  
Zhicheng Zou ◽  
Cuibing Zhou ◽  
Hancheng Zhang ◽  
Zhiming Cai
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Purine Metabolism ◽  
Expression Data ◽  
Rna Seq ◽  
Metabolism Pathway ◽  
Caterpillar Fungus ◽  
Regulated Gene Expression ◽  
Late Stages

Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p≤0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.

scholarly journals Genome-wide transcriptome analysis between Small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing

Reproduction ◽  
2013 ◽  
Vol 145 (6) ◽  
pp. 587-596 ◽  
Author(s):  
Xiangyang Miao ◽  
Qingmiao Luo
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Complex Trait ◽  
Future Research ◽  
Rna Seq ◽  
Molecular Biology Technique ◽  
High Fecundity ◽  
Next Generation Sequencing Technology ◽  
Genome Wide ◽  
Generation Sequencing

The Small-tail Han sheep and the Surabaya fur sheep are two local breeds in North China, which are characterized by high-fecundity and low-prolificacy breed respectively. Significant genetic differences between these two breeds have provided increasing interests in the identification and utilization of major prolificacy genes in these sheep. High prolificacy is a complex trait, and it is difficult to comprehensively identify the candidate genes related to this trait using the single molecular biology technique. To understand the molecular mechanisms of fecundity and provide more information about high prolificacy candidate genes in high- and low-fecundity sheep, we explored the utility of next-generation sequencing technology in this work. A total of 1.8 Gb sequencing reads were obtained and resulted in more than 20 000 contigs that averaged ∼300 bp in length. Ten differentially expressed genes were further verified by quantitative real-time RT-PCR to confirm the reliability of RNA-seq results. Our work will provide a basis for the future research of the sheep reproduction.

scholarly journals Tissue-Specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum purpureum Schum.)

2020 ◽  
Author(s):  
Wenqing Zhang ◽  
Shengkui Zhang ◽  
Xianqin Lu ◽  
Can Li ◽  
Xingwang Liu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Lignin Content ◽  
Pennisetum Purpureum ◽  
Cellulose Synthesis ◽  
Elephant Grass ◽  
Rna Seq ◽  
Lignin Synthesis

Abstract Background: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered.Results: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes.Conclusions: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

scholarly journals Comparative Transcriptomic Analysis Revealed Complex Molecular Mechanisms Underlying Pests, Pathogens Resistance and Seed Development in Wild and Cultivated Blackgram

2020 ◽  
Author(s):  
Avi Raizada ◽  
Souframanien Jegadeesan
Keyword(s):  
Seed Development ◽  
Molecular Mechanisms ◽  
Callosobruchus Maculatus ◽  
Transmembrane Protein ◽  
Mosaic Disease ◽  
Molecular Networks ◽  
Wild Accession ◽  
Rna Seq ◽  
Legume Production ◽  
Related Proteins

AbstractBlackgram is a widely cultivated pulse crop in Asia. Bruchid pests and yellow mosaic disease (YMD) causes huge loss in legume production including blackgram. Blackgram wild accession (Vigna mungo var. silvestris), Trombay wild urd (INGR10133) conferred resistance to bruchids especially Callosobruchus maculatus, through antibiosis. However, the mechanisms still remains uncharacterized. We performed the comparative transcriptome analysis of the developing seeds of wild and cultivated blackgram with contrasting phenotypes for 3 traits, bruchids infestation, YMD and seed size. In this study,715differentially expressed genes(DEGs) were re-annotated with reference to NCBI nr database. RNA-Seq was validated by quantitative real-time PCR for 22 DEGs. In Trombay wild, defense related components such as acid phosphatase, vicilins, trypsin inhibitor, brassinosteroid signalling components were found up-regulated. While in cultivar, transcripts for LEA, cysteine protease, autophagy related proteins(ATG3, ATG5, ATG8C and ATG1t), DnaJ, tobamovirus multiplication protein, downy mildew resistance protein, LRR/F-box proteins were found up-regulated. In TW, three transcripts were found common for both bruchids pest and geminivirus resistance (LRR receptor kinase, transmembrane protein 87b and thaumatin like protein).Our study is the first report on transcriptomic differences between wild and cultivated blackgram with new insights into the molecular networks underlying seed development, resistance to pests and pathogens.

scholarly journals Tissue-Specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum purpureum Schum.)

2020 ◽  
Author(s):  
Wenqing Zhang ◽  
Shengkui Zhang ◽  
Xianqin Lu ◽  
Can Li ◽  
Xingwang Liu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Lignin Content ◽  
Pennisetum Purpureum ◽  
Cellulose Synthesis ◽  
Elephant Grass ◽  
Rna Seq ◽  
Lignin Synthesis

Abstract Background: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered.Results: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes.Conclusions: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

scholarly journals Tissue-Specific Transcriptome Analysis Reveals Lignocellulose Synthesis Regulation in Elephant Grass (Pennisetum purpureum Schum.)

2020 ◽  
Author(s):  
Wenqing Zhang ◽  
Shengkui Zhang ◽  
Xianqin Lu ◽  
Can Li ◽  
Xingwang Liu ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Lignin Content ◽  
Pennisetum Purpureum ◽  
Cellulose Synthesis ◽  
Elephant Grass ◽  
Rna Seq ◽  
Lignin Synthesis

Abstract Background: The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered.Results: In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a ‘blue’ module highly associated with cellulose synthesis and a ‘turquoise’ module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes.Conclusions: This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.

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

scholarly journals Into the Seed: Auxin Controls Seed Development and Grain Yield

2020 ◽  
Vol 21 (5) ◽  
pp. 1662 ◽  
Author(s):  
Jinshan Cao ◽  
Guoji Li ◽  
Dejie Qu ◽  
Xia Li ◽  
Youning Wang
Keyword(s):  
Grain Yield ◽  
Seed Development ◽  
Seed Weight ◽  
Molecular Mechanisms ◽  
Crop Yields ◽  
Molecular Regulation ◽  
Research Progress ◽  
Comprehensive Review ◽  
Cellular Processes

Seed development, which involves mainly the embryo, endosperm and integuments, is regulated by different signaling pathways, leading to various changes in seed size or seed weight. Therefore, uncovering the genetic and molecular mechanisms of seed development has great potential for improving crop yields. The phytohormone auxin is a key regulator required for modulating different cellular processes involved in seed development. Here, we provide a comprehensive review of the role of auxin biosynthesis, transport, signaling, conjugation, and catabolism during seed development. More importantly, we not only summarize the research progress on the genetic and molecular regulation of seed development mediated by auxin but also discuss the potential of manipulating auxin metabolism and its signaling pathway for improving crop seed weight.

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