Theoretical and Applied Genetics

, Volume 133, Issue 1, pp 271–282 | Cite as

An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the liy short fiber phenotype in cotton

  • David D. FangEmail author
  • Marina Naoumkina
  • Gregory N. Thyssen
  • Efrem Bechere
  • Ping Li
  • Christopher B. Florane
Original Article


Key message

The EMS-induced threonine/isoleucine substitution in a tetratricopeptide repeat-like superfamily protein encoded by gene Ghir_A12G008870 is responsible for the Ligon-lintless-y (liy) short fiber phenotype in cotton.


A short fiber mutant Ligon-lintless-y was created through treating the seeds of the cotton line MD15 with ethyl methanesulfonate. Genetic analysis indicated that the short fiber phenotype is controlled by a single recessive locus designated liy. From F2 populations derived from crosses between the mutant and its wild type (WT), we selected 132 short fiber progeny (liy/liy) and made two DNA bulks. We sequenced these DNA bulks along with the two parents of the population. The liy locus was located on chromosome A12. Using multiple F2 populations and F3 progeny plants, we mapped the liy locus within a genomic region of 1.18 Mb. In this region, there is only one gene, i.e., Ghir_A12G008870 encoding a tetratricopeptide repeat-like superfamily protein that has a non-synonymous mutation between the liy mutant and its WT. Analysis of a SNP marker representing this gene in the F2 and F3 progeny plants demonstrated its complete linkage with the liy short fiber phenotype. We further analyzed this SNP marker in a panel of 384 cotton varieties. The mutant allele is absent in all varieties analyzed. RNAseq and RT-qPCR analysis of the gene Ghir_A12G008870 during fiber development showed a significant expression difference between the liy mutant and its WT in developing fiber cells beginning at 12 days post-anthesis. Virus-induced gene silencing of the gene Ghir_A12G008870 significantly reduced the fiber length of the WT cotton line MD15. Taken together, our results suggest that the gene Ghir_A12G008870 is involved in the cotton fiber cell elongation process and is a promising candidate gene responsible for the liy short fiber phenotype.


Cotton EMS Ligon-lintless-y mutation Mapping-by-sequencing Short fiber mutation Tetratricopeptide repeat (TPR)-like superfamily protein 



This research was funded by the USDA-Agricultural Research Service CRIS projects 6054-21000-018-00D and 6066-21000-052-00D. We thank Mr. Chris Delhom and Mrs. Holly King at Cotton Structure and Quality Research Unit in New Orleans for measuring the fiber quality attributes using a high volume instrument. 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 USDA which is an equal opportunity provider and employer.

Authors’ contributions

DDF conceived and coordinated the project and wrote the manuscript. MN made crosses for part of the mapping populations, conducted RNAseq and RT-qPCR analysis, and designed and executed the VIGS experiment. GNT analyzed DNA sequences, designed primers, and co-wrote the manuscript. EB created the liy mutant, developed and grew F2 populations. PL isolated DNAs and conducted DNA marker genotyping. CBF assisted growing the experimental materials, conducted VIGS experiment and RNA isolation. All authors read, edited, and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

122_2019_3456_MOESM1_ESM.jpg (155 kb)
Fig. S1F2 plants growing in a New Orleans, LA, USA field (JPEG 155 kb)
122_2019_3456_MOESM2_ESM.jpg (91 kb)
Fig. S2Expression of the gene Ghir_A12G008870 in virus induced gene silencing plants (NC = negative control) (JPEG 91 kb)
122_2019_3456_MOESM3_ESM.pdf (385 kb)
Fig. S3One Way ANOVA analysis of fiber quality traits in virus-induced gene silencing plants (NC = negative control).No significant difference was observed for uniformity (UI), strength (STR), elongation (ELO), short fiber content (SFC), or maturity between VIGS plants containing empty vector (NC) and containing gene constructs (p = 0.05) (PDF 384 kb)
122_2019_3456_MOESM4_ESM.tif (315 kb)
Fig. S4RNAseq reads of the gene Ghir_A12G008870 and Ghir_D12G008610 at 3, 8, and 16 days post-anthesis (DPA) fibers (TIFF 315 kb)
122_2019_3456_MOESM5_ESM.xlsx (11 kb)
Supplementary material 5 (XLSX 11 kb)
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Supplementary material 6 (XLSX 21 kb)
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Supplementary material 8 (XLSX 18 kb)
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Supplementary material 9 (XLSX 12 kb)
122_2019_3456_MOESM10_ESM.xlsx (12 kb)
Supplementary material 10 (XLSX 12 kb)


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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection  2019

Authors and Affiliations

  1. 1.Cotton Fiber Bioscience Research UnitUSDA-ARS-SRRCNew OrleansUSA
  2. 2.Cotton Chemistry and Utilization Research UnitUSDA-ARS-SRRCNew OrleansUSA
  3. 3.Crop Genetics Research UnitUSDA-ARSStonevilleUSA

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