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A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li₃ of Tetraploid Cotton.

ABSTRACT: Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li₃ was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li₃ is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene's expression. The genetic loci n₂ and n₃ underlying the recessive fuzzless phenotype in Gossypium hirsutum were also mapped. The genomic location of n₃ overlapped with that of the dominant fuzzless locus N₁ , and n₃ appeared to be a loss-of-function allele caused by a single nucleotide polymorphism (SNP) mutation in the coding region of GhMML3_A12. The n₂ allele was found to be co-located with li₃ and originated from G. babardense. n₂ and li₃ are possibly the multiple alleles of the GhMML3_D12 gene. Genetic analysis showed that Li₃ and N₃ are a pair of homologs with additive effects for the initiation of fibers (fuzz or lint). In addition, the presence of another locus was speculated, and it appeared to show an inhibitory effect on the expression of GhMML3. These findings provide new information about the genetic factors affecting the initiation of fibers in cotton.

SUBMITTER: Chen W

PROVIDER: S-EPMC7725795 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li3 of Tetraploid Cotton.

Chen Wei W Li Yan Y Zhu Shouhong S Fang Shengtao S Zhao Lanjie L Guo Yan Y Wang Junyi J Yuan Li L Lu Youjun Y Liu Fang F Yao Jinbo J Zhang Yongshan Y

Frontiers in plant science 20201126

Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li3 was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li3 is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene's expression. ...[more]

PMID: 33324436

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Project description:BackgroundCotton fiber length is a key determinant of fiber quality for the textile industry. Understanding the molecular basis of fiber elongation would provide a means for improvement of fiber length. Ligon lintless-1 (Li 1 ) and Ligon lintless-2 (Li 2 ) are monogenic and dominant mutations, that result in an extreme reduction in the length of lint fiber to approximately 6 mm on mature seeds. In a near-isogenic state with wild type (WT) cotton these two short fiber mutants provide an excellent model system to study mechanisms of fiber elongation.ResultsWe used next generation sequencing (RNA-seq) to identify common fiber elongation related genes in developing fibers of Li 1 and Li 2 mutants growing in the field and a greenhouse. We found a large number of differentially expressed genes common to both mutants, including 531 up-regulated genes and 652 down-regulated genes. Major intrinsic proteins or aquaporins were one of the most significantly over-represented gene families among common down-regulated genes in Li 1 and Li 2 fibers. The members of three subfamilies of aquaporins, including plasma membrane intrinsic proteins, tonoplast intrinsic proteins and NOD26-like intrinsic proteins were down-regulated in short fiber mutants. The osmotic concentration and the concentrations of soluble sugars were lower in fiber cells of both short fiber mutants than in WT, whereas the concentrations of K+ and malic acid were significantly higher in mutants during rapid cell elongation.ConclusionsWe found that the aquaporins were the most down-regulated gene family in both short fiber mutants. The osmolality and concentrations of soluble sugars were less in saps of Li 1 - Li 2 , whereas the concentrations of malic acid, K+ and other detected ions were significantly higher in saps of mutants than in WT. These results suggest that higher accumulation of ions in fiber cells, reduced osmotic pressure and low expression of aquaporins, may contribute to the cessation of fiber elongation in Li 1 and Li 2 short-fiber mutants. The research presented here provides new insights into osmoregulation of short fiber mutants and the role of aquaporins in cotton fiber elongation.

Project description:BackgroundCotton is the leading fiber crop worldwide. Gossypium barbadense is an important species of cotton because of its extra-long staple fibers with superior luster and silkiness. However, a systematic analysis and utilization of cDNA sequences from G. barbadense fiber development remains understudied.ResultsA total of 21,079 high quality sequences were generated from two non-normalized cDNA libraries prepared by using a mixture of G. barbadense Hai7124 fibers and ovules. After assembly processing, a set of 8,653 unigenes were obtained. Of those, 7,786 were matched to known proteins and 7,316 were assigned to functional categories. The molecular functions of these unigenes were mostly related to binding and catalytic activity, and carbohydrate, amino acid, and energy metabolisms were major contributors among the subsets of metabolism. Sequences comparison between G. barbadense and G. hirsutum revealed that 8,245 unigenes from G. barbadense were detected the similarity with those released publicly in G. hirsutum, however, the remaining 408 sequences had no hits against G. hirsutum unigenes database. Furthermore, 13,275 putative ESTs InDels loci involved in the orthologous and/or homoeologous differences between/within G. barbadense and G. hirsutum were discovered by in silico analyses, and 2,160 InDel markers were developed by ESTs with more than five insertions or deletions. By gel electrophoresis combined with sequencing verification, 71.11% candidate InDel loci were reconfirmed orthologous and/or homoeologous loci polymorphisms using G. hirsutum acc TM-1 and G. barbadense cv Hai7124. Blastx result showed among 2,160 InDel loci, 81 with significant function similarity with known genes associated with secondary wall synthesis process, indicating the important roles in fiber quality in tetraploid cultivated cotton species.ConclusionSequence comparisons and InDel markers development will lay the groundwork for promoting the identification of genes related to superior agronomic traits, genetic differentiation and comparative genomic studies between G. hirsutum and G. barbadense.

Project description:BackgroundCotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (Gossypium hirsutum L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (Li2) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, Li2 is a model system with which to study fiber elongation.ResultsTwo near-isogenic lines of Ligon lintless-2 (Li2) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC5). An F2 population was developed from a cross between the two Li2 near-isogenic lines and used to develop a linkage map of the Li2 locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the Li2 locus region with two of the markers flanking the Li2 locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the Li2 mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the Li2 locus.ConclusionsIn the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the Li2 locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the Li2 gene.

Dataset Information

A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li₃ of Tetraploid Cotton.

Publications

A Retrotransposon Insertion in <i>GhMML3_D12</i> Is Likely Responsible for the Lintless Locus <i>li<sub>3</sub></i> of Tetraploid Cotton.

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