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Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L.

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Abstract

Key message

Based on the integration of QTL-mapping and regulatory network analyses, five high-confidence stable QTL regions, six candidate genes and two microRNAs that potentially affect the cottonseed oil content were discovered.

Abstract

Cottonseed oil is increasingly becoming a promising target for edible oil with its high content of unsaturated fatty acids. In this study, a recombinant inbred line (RIL) cotton population was constructed to detect quantitative trait loci (QTLs) for the cottonseed oil content. A total of 39 QTLs were detected across eight different environments, of which five QTLs were stable. Forty-three candidate genes potentially involved in carbon metabolism, fatty acid synthesis and triacylglycerol biosynthesis processes were further obtained in the stable QTL regions. Transcriptome analysis showed that nineteen of these candidate genes expressed during  the developing cottonseed ovules and may affect the cottonseed oil content. Besides, transcription factor (TF) and microRNA (miRNA) co-regulatory network analyses based on the nineteen candidate genes suggested that six genes, two core miRNAs (ghr-miR2949b and ghr-miR2949c), and one TF GhHSL1 were considered to be closely associated with the cottonseed oil content. Moreover, four vital genes were validated by quantitative real-time PCR (qRT-PCR). These results provide insights into the oil accumulation mechanism in developing cottonseed ovules through the construction of a detailed oil accumulation model.

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Data availability

Supplementary tables S1 to S9 were submitted to the online open access repository Figshare with a link https://doi.org/10.6084/m9.figshare.16536627.v1. Additional Files List: Table S1. ANOVA and broad-sense heritability analysis for cottonseed oil content. Table S2. QTLs related to cottonseed oil content identified in eight environments. Table S3. 832 genes in the five stable QTL regions. Table S4. KEGG pathway enrichment analysis of 832 genes in stable QTLs regions. Table S5. Genes list identified by BLAST with Arabidopsis thaliana oil-related genes. Table S6. The expression level (FPKM values) of candidate oil genes during developing ovules of G. hirsutum L. Table S7. Four transcription factors related to cottonseed lipid content. Table S8. The microRNA-target gene regulatory network of G. hirsutum L. Table S9. The designed primers of genes encoding the key enzymes involved in lipid biosynthesis for qRT-PCR.

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Acknowledgements

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Funding

This study was supported by the National Natural Science Foundation of China (31621005), the National Agricultural Science and Technology Innovation project for CAAS (CAAS-ASTIP-2016-ICR) and the Central Level of the Scientific Research Institutes for Basic R & D Special Fund Business (1610162019010101).

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  1. Zhibin Zhang and Juwu Gong contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China

    Zhibin Zhang, Juwu Gong, Zhen Zhang, Wankui Gong, Junwen Li, Yuzhen Shi, Aiying Liu, Qun Ge, Jingtao Pan, Senmiao Fan, Xiaoying Deng, Shaoqi Li, Youlu Yuan & Haihong Shang

  2. Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450000, China

    Zhibin Zhang, Youlu Yuan & Haihong Shang

  3. Xinjiang Research Base, State Key Laboratory of Cotton Biology, Xinjiang Agricultural University, Ürümqi, 830001, China

    Juwu Gong, Quanjia Chen & Youlu Yuan

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Contributions

ZZ, SH and YY conceived the study; ZZ contributed to the data processing and analysis and wrote the manuscript; GJ collected and analyzed the phenotype data; ZZ, GW, LJ and SY managed the RIL population; LA, GQ and PJ collected the phenotype data in Anyang and Shihezi; FS and DX managed and collected the phenotype data in Kuerle and Alaer; LS and CQ helped with manuscript reviewing; SH and YY provided the resources, designed the experiment and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Youlu Yuan or Haihong Shang.

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Communicated by Tianzhen Zhang.

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Zhang, Z., Gong, J., Zhang, Z. et al. Identification and analysis of oil candidate genes reveals the molecular basis of cottonseed oil accumulation in Gossypium hirsutum L.. Theor Appl Genet 135, 449–460 (2022). https://doi.org/10.1007/s00122-021-03975-z

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