Meta‐analysis and overview analysis of quantitative trait locis associated with fatty acid content in soybean for candidate gene mining

Qin, Hui; Liu, Zhangxiong; Wang, Yuyang; Xu, Mingyue; Mao, Xinrui; Qi, Hongbo; Yin, Zhan; Li, Yongliang; Jiang, Hongwei; Hu, Zhenbang; Wu, Xiaoxia; Zhu, Rong; Liu, Chunyan; Chen, Qingshan; Xin, Dawei; Qi, Zhaoming

doi:10.1111/pbr.12562

Cited by 14 publications

(16 citation statements)

References 68 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…They detected 20 “Meta‐QTLs” and identified genes controlling oil contents (Qi et al, ). Additionally, Qin et al () integrated the QTL information for soybean fatty acids and conducted a meta‐analysis and an overview analysis, during which they obtained consistent results. Three genes controlling fatty acid content were discovered in the “common” QTL range (Qin et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, Qin et al () integrated the QTL information for soybean fatty acids and conducted a meta‐analysis and an overview analysis, during which they obtained consistent results. Three genes controlling fatty acid content were discovered in the “common” QTL range (Qin et al, ). Collinearity analysis represents a new way to integrate QTL data.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Identification of soybean genes related to fatty acid content based on a soybean genome collinearity analysis

Wang

Zhang

et al. 2019

Plant Breeding

Self Cite

View full text Add to dashboard Cite

Seed fatty acid content is an important consideration for soybean produced for food, feed, and industrial applications. In this study, MCScanX was used to analyze the entire soybean genome to generate a collinearity block, which was then used to assess the collinearity among the soybean fatty acid quantitative trait loci (QTL) in the SoyBase database. The hub‐QTLs located in the Gm06, Gm07, and Gm10 segments were identified. The Kyoto Encyclopedia of Genes and Genomes and gene ontology databases were used to analyze the genes in hub‐QTL regions, resulting in the identification of 17 candidate genes related to soybean fatty acid content. Two lines with different fatty acid contents and a recurrent parent were selected from a chromosome segment substitution line library for a subsequent quantitative real‐time polymerase chain reaction (qRT‐PCR) assay to verify the candidate gene expression patterns. Four genes were related to the total soybean fatty acid content, while three genes were related to the content of specific fatty acid types. The results of this study may be relevant for the fine mapping of soybean fatty acid QTLs/genes.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identification of soybean genes related to fatty acid content based on a soybean genome collinearity analysis

Wang

Zhang

et al. 2019

Plant Breeding

Self Cite

View full text Add to dashboard Cite

show abstract

“…Meta-analysis is a scientific quantitative method that can integrate and analyze results of similar studies to reveal the consistency of some research [34,35]. Currently, meta-analysis has been improved to offer a reliable and effective new analytical method for genetic breeding, and combining meta-analysis with research is a very meaningful approach [20,36]. From the Meta-QTL mentioned in Qi (2018) [11], the genes Glyma.13G035200 and Glyma.14G156400 related to oil are contained in MQTLSA-2 and MQTLLNA-1, respectively.…”

Section: Discussionmentioning

confidence: 99%

“…The specific primer for the gene was designed by the software Primer 5, and the internal reference gene was GmActin4 [20].…”

Section: Methodsmentioning

confidence: 99%

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Zhang

Huang

et al. 2019

Genes

View full text Add to dashboard Cite

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

show abstract

“…2016), fatty acid content in soybean (Qin et al 2018) and root-related traits in bread wheat (Soriano and Alvaro 2019).…”

Section: Estimation Of Qtl-overview Index For Rsa Qtls In Ricementioning

confidence: 99%

Pinpointing Genomic Regions Associated with Root System Architecture in Rice Through an Integrative Meta-Analysis Approach

Daryani

Ramandi

Dezhsetan

et al. 2021

Preprint

View full text Add to dashboard Cite

Root system architecture (RSA) is an important factor for facilitating water and nutrient uptake from deep soils and adaptation to drought stress conditions. In the present research, an integrated meta-analysis approach was employed to find candidate genes and genomic regions involved in rice RSA traits. A whole-genome meta-analysis was performed for 425 initial QTLs reported in 34 independent experiments controlling RSA traits under control and drought stress conditions in the previous twenty years. Sixty-four consensus meta-QTLs (MQTLs) were detected, unevenly distributed on twelve rice chromosomes. The confidence interval (CI) of the identified MQTLs was obtained as 0.11-14.23 cM with an average of 3.79 cM, which was 3.88 times narrower than the mean CI of the original QTLs. Interestingly, 52 MQTLs were co-located with SNP peak positions reported in rice genome-wide association studies (GWAS) for root morphological traits. The genes located in these RSA related MQTLs were detected, and explored to find the drought-responsive genes in the rice root based on the RNA-seq and microarray data. Multiple RSA and drought tolerance associated genes were found in the MQTLs including the genes involved in auxin biosynthesis or signaling (e.g. YUCCA, WOX, AUX/IAA, ARF), root angle (DRO1-related genes), lateral root development (e.g. DSR, WRKY), root diameter (e.g. OsNAC5), plant cell wall (e.g. EXPA) and lignification (e.g. C4H, PAL, PRX and CAD). The genes located both in the SNP peak positions and in the high-overview-index MQTLs for root architecture traits are suggested as novel candidate genes for further functional analysis.. The promising candidate genes and MQTLs would be applicable to genetic engineering and MQTL-assisted breeding of root phenotypes aimed at improving yield potential, stability and performance in a water-stressed environment.

show abstract

Meta‐analysis and overview analysis of quantitative trait locis associated with fatty acid content in soybean for candidate gene mining

Cited by 14 publications

References 68 publications

Identification of soybean genes related to fatty acid content based on a soybean genome collinearity analysis

Identification of soybean genes related to fatty acid content based on a soybean genome collinearity analysis

Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Pinpointing Genomic Regions Associated with Root System Architecture in Rice Through an Integrative Meta-Analysis Approach

Contact Info

Product

Resources

About