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
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.
KeywordsCotton 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.
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.
- Gilbert MK, Bland JM, Shockey JM, Cao H, Hinchliffe DJ, Fang DD, Naoumkina M (2013a) A transcript profiling approach reveals an abscisic acid-specific glycosyltransferase (UGT73C14) induced in developing fiber of Ligon lintless-2 mutant of cotton (Gossypium hirsutum L.). PLoS One 8:e75268PubMedPubMedCentralCrossRefGoogle Scholar
- Kearney TH, Harrison GJ (1927) Inheritance of smooth seeds in cotton. J Agric Res 35:193–217Google Scholar
- Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997
- Snider JL, Oosterhuis DM (2015) Physiology. In: Fang DD, Percy RG (eds) Cotton, 2nd edn. ASA-SSSA-CSSA, Madison, pp 339–400Google Scholar
- Thyssen GN, Fang DD, Turley RB, Florane C, Li P, Naoumkina M (2015) Mapping-by-sequencing of Ligon-lintless-1 (Li1) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 128:1703–1712PubMedCrossRefGoogle Scholar
- Thyssen GN, Fang DD, Zeng L, Song X, Delhom CD, Condon TL et al (2016) The immature fiber mutant phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondria targeted pentatricopeptide repeat gene. G3 Genes Genomes Genetics 6:1627–1633PubMedPubMedCentralGoogle Scholar
- Zhang TZ, Pan JJ (1991) Genetic analysis of a fuzzless-lintless mutant in Gossypium hirsutum L. Jiangsu J Agr Sci 7:13–16Google Scholar