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Elucidation of sequence polymorphism in fuzzless-seed cotton lines

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Abstract

Most commercially produced cotton cultivars have two types of fibers on the seed coat, short fuzz and long lint. Lint fiber is used in the textile industry, while fuzz is considered an undesirable trait. Both types of fibers are believed to be controlled by the same regulators; however, their mechanisms of actions are still obscure. Cotton fiber mutants provide an excellent system to study the genes that regulate fiber development. Here we described four uncharacterized and three previously reported cotton mutants with fuzzless seed phenotypes. To evaluate whether or not the genes previously associated with fuzzless seed phenotypes have mutations we sequenced whole genomic DNA of seven mutants and wild type varieties. We identified multiple polymorphic changes among the tested genes. Non-synonymous SNPs in the coding region of the MML3-A gene was common in the six mutant lines tested in this study, showing both dominant and recessive fuzzless phenotypes. We have mapped the locus of the causative mutation for one of the uncharacterized fuzzless lines using an F2 population that originated from a cross between the dominant fuzzless mutant and a wild type. Further, we have clarified the current knowledge about the causative n2 mutations by analyzing the sequence data and previously reported mapping data. The key genes and possible mechanisms of fiber differentiation are discussed in this study.

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Acknowledgements

We are grateful to Dr. Bechere for providing n4t mutant line. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture, which is an equal opportunity provider and employer.

Funding

This research was funded by the United States Department of Agriculture-Agricultural Research Service CRIS project 6054-21000-018-00D.

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Authors and Affiliations

  1. Cotton Fiber Bioscience Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center (SRRC), 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA

    Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Ping Li & Christopher B. Florane

  2. Cotton Chemistry and Utilization Research Unit, USDA-ARS-SRRC, 1100 Robert E. Lee Blvd, New Orleans, LA, 70124, USA

    Gregory N. Thyssen

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  1. Marina Naoumkina
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  2. Gregory N. Thyssen
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  3. David D. Fang
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  4. Ping Li
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  5. Christopher B. Florane
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Contributions

MN conceived the research, designed experiments and drafted the manuscript. DDF provided NCVT data and oversee mapping experiment. GNT performed bioinformatics analysis. LP and CBF conducted the experiments. All authors read and approved the manuscript.

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Correspondence to Marina Naoumkina.

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Communicated by Stefan Hohmann.

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Supplementary file1 Figure S1. Flowers. a, SC9023; b, SA-143 (n2); c, SA-9 and d, SA-13 (JPG 298 kb)

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Supplementary file2 Figure S2. Expression level of homeologous RDL1 genes. The expression data was obtained from ccNET database (You et al. 2017) (JPG 82 kb)

Supplementary file3 Figure S3. Lint phenotype of segregating F2 plants (SC9023 x SA-68) (JPG 352 kb)

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Supplementary file4 Figure S4. Expression level of genes from SA68fzl locus. The expression data was obtained from ccNET database (You et al. 2017) (TIF 2557 kb)

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Supplementary file5 Figure S5. Alignment of nucleotide sequences of the promoter region, 969 bp before ATG start (a), or 3’UTR region, 1480 bp after stop codon (b), of Ghir_A12G017450 (MML3-A) gene of fuzzy TM1, Sc9024 and fuzzless SA9, SA13, SA51, SA68, SA143, SA243, n4 lines (DOCX 16 kb)

438_2020_1736_MOESM6_ESM.docx

Supplementary file6 Figure S6. (a) Alignment of nucleotide sequences of Ghir_A12G017460, Ghir_D12G017670, Gbar_D12G017700, Gorai.008G179800, MF974183 G. hirsutum isolate n2_NSM_Dt, and Ghir_D12G017680. Asterisks (*) highlighted by yellow indicate the stop codon in Ghir_D12G017670. Signs ‘>’ or ‘<’ on top of sequence indicate positions and directions of primers. (b) Alignment of amino acid sequences of listed above genes (DOCX 15 kb)

438_2020_1736_MOESM7_ESM.xlsx

Supplementary file7 Table S1. Analysis of SNPs found in MML3-A, MML4-D, HD1-A and RDL1-A genes on diversity panel of 377 G. hirsutum cultivars, reference G. hirsutum TM-1, reference G. barbadense 3-79 and seven mutants (XLSX 28 kb)

Supplementary file8 Table S2. Description of phenotypic traits of seven naked mutant lines (XLSX 10 kb)

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Supplementary file9 Table S3. Evaluation of polymorphism in previously reported genes associated with naked seed phenotype in mutant and wild type lines. Names for eleven MAGIC parental lines are: 551—Acala Ultima; 552—Tamcot Pyramid; 553—Coker 315; 554—Stoneville 825; 555—Fibermax 966; 556—M240RNR; 557—Paymaster HS26; 558—Deltapine Acala 90; 559 Suregrow 747; 560—Phytogen PCS 355; 561—Stoneville 474. Line 3-79 is Gossypium barbadense species, data were obtained from CottonGen database (Yu et al. 2013). Polymorphism detected in mutant lines is indicated with red font; nd—not detected (XLSX 16 kb)

Supplementary file10 Table S4. Primers used in this study (XLSX 13 kb)

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Supplementary file11 Table S5. Evaluation of one or two genes phenotypic ratios by Goodness of Fit using Chi-Square tests of naked seed segregation of F2 population (XLSX 11 kb)

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Supplementary file12 Table S6. Table S6. Evaluation of polymorphism in SA68fzl locus in a sequence of mutant and wild type varieties. Names for eleven MAGIC parental lines are: 551—Acala Ultima; 552—Tamcot Pyramid; 553—Coker 315; 554—Stoneville 825; 555—Fibermax 966; 556—M240RNR; 557—Paymaster HS26; 558—Deltapine Acala 90; 559 Suregrow 747; 560—Phytogen PCS 355; 561—Stoneville 474. Sequence of each line compared to the sequence of TM-1 reference (Wang et al. 2019); (0/0) indicates the same nucleotide as in TM-1 in the homozygous state, whereas (1/1) is alternative nucleotide in the homozygous state; (0/1) is a heterozygous state, and (./.) indicates missing data (XLSX 430 kb)

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Naoumkina, M., Thyssen, G.N., Fang, D.D. et al. Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Mol Genet Genomics 296, 193–206 (2021). https://doi.org/10.1007/s00438-020-01736-z

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