Linkage and Association Analyses Reveal That Hub Genes in Energy-flow and Lipid Biosynthesis Pathways Form a Cluster in Upland Cotton

Overview

Journal Comput Struct Biotechnol J

Specialty Biotechnology

Date 2022 May 6

PMID 35521543

Authors

Juwu Gong

Yan Peng

Jiwen Yu

Wenfeng Pei

Zhen Zhang

Daoran Fan

Linjie Liu

Xianghui Xiao

Ruixian Liu

Quanwei Lu

Pengtao Li

Haihong Shang

Yuzhen Shi

Junwen Li

Qun Ge

Aiying Liu

Xiaoying Deng

Senmiao Fan

Jingtao Pan

Quanjia Chen

Youlu Yuan

Wankui Gong

Affiliations

Soon will be listed here.

Abstract

Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In 'CCRI70' RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In '0-153' RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, , , , and , formed hub genes and two of them, and , formed the key genes in the interaction network. Sequence variations in the coding regions of , , , , and genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.

Citing Articles

Genomic and co-expression network analyses reveal candidate genes for oil accumulation based on an introgression population in Upland cotton (Gossypium hirsutum).

Ma J, Jia B, Bian Y, Pei W, Song J, Wu M Theor Appl Genet. 2024; 137(1):23.

PMID: 38231256 DOI: 10.1007/s00122-023-04527-3.

Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways.

Alam B, Liu R, Gong J, Li J, Yan H, Ge Q Int J Mol Sci. 2023; 24(23).

PMID: 38068920 PMC: 10706765. DOI: 10.3390/ijms242316595.

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies.

Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G Sci China Life Sci. 2023; 66(10):2214-2256.

PMID: 36899210 DOI: 10.1007/s11427-022-2278-0.

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