Abstract
Cotton fiber mutants are valuable resources for studying functions of altered genes and their roles in fiber development. The n4t is a recessive tufted-fuzzless seed mutant created through chemical mutagenesis with ethyl methanesulfonate. Genetic analysis indicated that the tufted-fuzzless phenotype is controlled by a single recessive locus. In this study, we developed an F2 population of 602 progeny plants and sequenced the genomes of the parents and two DNA bulks from F2 progenies showing the mutant phenotype. We identified DNA sequence variants between the tufted-fuzzless mutant and wild type by aligning the sequence reads to the reference TM-1 genome and designed subgenome-specific SNP markers. We mapped the n4t locus on chromosome D04 within a genomic interval of about 411 kb. In this region, seven genes showed significant differential expression between the tufted-fuzzless mutant and wild type. Possible candidate genes are discussed in this study. The utilization of the n4t mutant along with other fiber mutants will facilitate our understanding of the molecular mechanisms of cotton fiber cell growth and development.
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References
Bechere E, Auld DL (2014) Registration of a tufted-naked seed upland cotton germplasm, 9023n4t. J Plant Regist 8(1):63–67
Bechere E, Boykin JC et al (2011) Evaluation of cotton genotypes for ginning energy and ginning rate. J Cotton Sci 15(1):11–21
Bechere E, Turley RB et al (2012) A new fuzzless seed locus in an upland cotton (Gossypium hirsutum L.) mutant. Am J Plant Sci 3(06):799
Cosgrove DJ (2005) Growth of the plant cell wall. Nat Rev Mol Cell Biol 6(11):850–861. https://doi.org/10.1038/nrm1746
Dettmer K, Aronov PA et al (2007) Mass spectrometry-based metabolomics. Mass Spectrom Rev 26(1):51–78
Fang DD, Xiao J et al (2010) A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.). Theor Appl Genet 120(5):943–953. https://doi.org/10.1007/s00122-009-1223-y
Feng X, Cheng H et al (2019) Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum). Theor Appl Genet 132(8):2169–2179
Islam MS, Fang DD et al (2016) Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne. BMC Plant Biol 16(1):1–19
Jordan DB, Bacot KO et al (1999) Plant riboflavin biosynthesis: cloning, chloroplast localization, expression, purification, and partial characterization of spinach lumazine synthase. J Biol Chem 274(31):22114–22121
Kearney TH, Harrison GJ (1927) Inheritance of smooth seeds in cotton. J Agric Res 35:193–217
Kim HJ, Triplett BA (2001) Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol 127(4):1361–1366
Liu X, Moncuquet P et al (2020) Genetic identification and transcriptome analysis of lintless and fuzzless traits in Gossypium arboreum L. Int J Mol Sci 21(5):1675
Michelmore RW, Paran I et al (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci 88(21):9828–9832
Naoumkina M, Thyssen GN et al (2020) Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Mol Genet Genom. https://doi.org/10.1007/s00438-020-01736-z
Obata T, Fernie AR (2012) The use of metabolomics to dissect plant responses to abiotic stresses. Cell Mol Life Sci 69(19):3225–3243. https://doi.org/10.1007/s00018-012-1091-5
Ohmiya Y, Nakai T et al (2003) The role of PopCel1 and PopCel2 in poplar leaf growth and cellulose biosynthesis. Plant J 33(6):1087–1097
Park YW, Tominaga R et al (2003) Enhancement of growth by expression of poplar cellulase in Arabidopsis thaliana. Plant J 33(6):1099–1106
Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT–PCR. Nucleic Acids Res 29(9):e45–e45
Song L, Guo WZ et al (2010) Genetic analysis and molecular validation of chromosome assignment for fuzzless genes N1 and n2 in cotton. J Nanjing Agric Univ 33:21–26
Steward JM (1975) Fiber initiation on the cotton ovule (Gossypium hirsutum). Am J Bot 62:723–730
Takagi H, Abe A et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74(1):174–183
Taliercio EW, Boykin D (2007) Analysis of gene expression in cotton fiber initials. BMC Plant Biol 7(1):22
Thyssen GN, Fang DD et al (2014) Next generation genetic mapping of the Ligon-lintless-2 (Li2) locus in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 127(10):2183–2192. https://doi.org/10.1007/s00122-014-2372-1
Turley R, Kloth R (2002) Identification of a third fuzzless seed locus in upland cotton (Gossypium hirsutum L.). J Hered 93(5):359–364
Walford SA, Wu Y et al (2011) GhMYB25-like: a key factor in early cotton fibre development. Plant J 65(5):785–797. https://doi.org/10.1111/j.1365-313X.2010.04464.x
Wan Q, Guan X et al (2016) Small interfering RNAs from bidirectional transcripts of GhMML3_A12 regulate cotton fiber development. New Phytol 210(4):1298–1310
Wang M, Tu L et al (2019) Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 51(2):224–229
Ware JO, Benedict LI et al (1947) A recessive naked-seed character in upland cotton. J Hered 38(10):313–320
Wu H, Tian Y et al (2017) Genetics and evolution of MIXTA genes regulating cotton lint fiber development. New Phytol 217(2):883–895. https://doi.org/10.1111/nph.14844
You Q, Xu W et al (2017) ccNET: database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic Acids Res 45(D1):D1090–D1099
Yu L, Sun J et al (2013) PtrCel9A6, an endo-1, 4-β-glucanase, is required for cell wall formation during xylem differentiation in Populus. Mol Plant 6(6):1904–1917
Zhang D, Zhang T et al (2007) Comparative development of lint and fuzz using different cotton fiber-specific developmental mutants in Gossypium hirsutum. J Integr Plant Biol 49(7):1038–1046. https://doi.org/10.1111/j.1672-9072.2007.00454.x
Zhu Q-H, Yuan Y et al (2018) Genetic dissection of the fuzzless seed trait in Gossypium barbadense. J Exp Bot 69(5):997–1009. https://doi.org/10.1093/jxb/erx459
Zhu Q-H, Stiller W et al (2020) Genetic mapping and transcriptomic characterisation of a new fuzzless-tufted cottonseed mutant. G3 Genes Genomes Genet 11:1–14
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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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MN conceived the research, designed experiments, and drafted the manuscript. GNT performed bioinformatics analysis. DDF oversaw the mapping experiment. EB developed the n4t mutant. LP and CBF conducted the experiments. All authors read and approved the manuscript.
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438_2021_1802_MOESM1_ESM.xlsx
Figure S1. Histogram of SNPs and indel distribution between the WT and the n4t tufted-fuzzless mutant across 26 chromosomes of G. hirsutum. Two major peaks on Chr. D04 and Chr. D07 represents SNPs and indels, both homozygous and heterozygous for an alternative allele in F2 bulks. (TIF 1498 kb)
438_2021_1802_MOESM2_ESM.tif
Table S1. Sequences of primers for SNP markers. Table S2. Sequences of primers used for RT-qPCR analysis. Table S3. Positions of the polymorphic changes in the n4t locus. Genomic sequence of parents (SC9023 and the n4t) and two bulks of F2 individuals showing the mutant phenotype were compared to the sequence of the TM-1 reference (Wang, Tu et al. 2019): (0/0) indicates the same nucleotide as in TM-1 in homozygous state, whereas (1/1) is same nucleotide as in the n4t in homozygous state and (0/1) is heterozygous. (XLSX 37 kb)
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Naoumkina, M., Thyssen, G.N., Fang, D.D. et al. Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton. Mol Genet Genomics 296, 1041–1049 (2021). https://doi.org/10.1007/s00438-021-01802-0
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DOI: https://doi.org/10.1007/s00438-021-01802-0