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The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton

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Abstract

Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium raimondii, as well as tetraploid Gossypium hirsutum (‘TM-1’) and Gossypium barbadense (‘Hai-7124’ and ‘3-79’), was divided into 6 groups and 15 sub-groups, with each group containing two to five homologous genes. Most CesA genes in the four species are highly collinear. Among the five cotton genomes, 440 and 1929 single nucleotide polymorphisms (SNPs) in the CesA gene family were identified in exons and introns, respectively, including 174 SNPs resulting in amino acid changes. In total, 484 homeologous SNPs between the A and D genomes were identified in diploids, while 142 SNPs were detected between the two tetraploids, with 32 and 82 SNPs existing within G. hirsutum and G. barbadense, respectively. Additionally, 74 quantitative trait loci near 18 GhCesA genes were associated with fiber quality. One to four GhCesA genes were differentially expressed (DE) in ovules at 0 and 3 days post anthesis (DPA) between two backcross inbred lines having different fiber lengths, but no DE genes were identified between these lines in develo** fibers at 10 DPA. Twenty-seven SNPs in above DE CesA genes were detected among seven cotton lines, including one SNP in Ghi_A08G03061 that was detected in four G. hirsutum genotypes. This study provides the first comprehensive characterization of the cotton CesA gene family, which may play important roles in determining cotton fiber quality.

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Abbreviations

SNP:

Single nucleotide polymorphisms

QTL:

Quantitative trait loci

SNP:

Single nucleotide polymorphism

DPA:

Day post-anthesis

CesAs :

Cellulose synthase genes

MAS:

Marker-assisted selection

Gb:

Gossypium barbadense.

Gh:

Gossypium hirsutum L.

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Acknowledgments

We thank Lesley Benyon, PhD, from Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of an early draft of this manuscript.

Funding

This work was supported by New Mexico Agricultural Experiment Station and a USDA-Hatch Project. It was financially supported by Cotton Heterosis Utilization Technology and Superior Hybrid Seed Creation Project (2016YFD0101415), the Hebei Province "Giant Plan" Innovation and Entrepreneurship Team, and the State Key Laboratory of Cotton Biology Open Fund (CB2018A15).

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Authors and Affiliations

  1. Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, Hebei, China

    Sujun Zhang, **a Chi, **angyun Zhang & Jianhong Zhang

  2. Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, 88003, USA

    Sujun Zhang, Jie Chen, Zongfu Han, **a Chi & **fa Zhang

  3. Hebei Academy of Governance, Hebei, 050031, China

    Zhenxing Jiang

  4. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Jie Chen

  5. Cotton Research Center, Shandong Academy of Agricultural Sciences, **an, 250100, China

    Zongfu Han

  6. State Key Laboratory of Cotton Biology, Institute of Cotton Research (ICR), Chinese Academy of Agricultural Sciences (CAAS), Anyang, 455000, China

    **hua Li, Jiwen Yu, Chaozhu **ng & Jianyong Wu

  7. Department of Computer Science, New Mexico State University, Las Cruces, 88003, USA

    Mingzhou Song & Feng Liu

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  1. Sujun Zhang
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Contributions

SZ performed the study and drafted the manuscript. ZJ shared the work of verifying the existence of SNP. JC and ZH helped in screening of differential sites and software use, JC helped ZJ in the verifying the existence of SNP. XL was was responsible for RNA-Seq data. JY and CX collected flowering buds, extracted RNA and analyzed RNA-Seq data. MS searched the QTLs near the target genes, JW helped to add detailed information on RNA-seq experiment, FL assisted MS to find the physical location of the QTLs, JZ was responsible for screening representative materials for sequencing to verify the authenticity of SNPs. XZ helped to conceive the project. JZ conceived and oversaw the project and revised the manuscript. All authors read and approved the manuscript.

Corresponding authors

Correspondence to **angyun Zhang, **fa Zhang or Jianhong Zhang.

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The authors declare that they have no competing interests.

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Communicated by Stefan Hohmann.

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Supplementary Information

Below is the link to the electronic supplementary material.

Seven cotton lines in which SNPs were detected using Sanger sequencing (XLSX 11 KB)

Primer sequences used to amplify SNPs in the CesA gene family (XLSX 12 KB)

Exon sequence variations in the CesA gene family among homologous genes in four cotton species (XLSX 72 KB)

Intron sequence variations in the CesA gene family among homologous genes in four cotton species (XLSX 109 KB)

438_2020_1758_MOESM5_ESM.xlsx

Sequence variations in the CesA gene family among homologous genes in different species identified in the NCBI databases (XLSX 35 KB)

438_2020_1758_MOESM6_ESM.xlsx

Detection of SNPs located in the coding sequences of five CesA genes in seven cotton lines using Sanger sequencing (XLSX 14 KB)

QTLs related to fiber quality near the CesA genes in Upland cotton (PDF 624 KB)

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Zhang, S., Jiang, Z., Chen, J. et al. The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton. Mol Genet Genomics 296, 355–368 (2021). https://doi.org/10.1007/s00438-020-01758-7

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