The <i>Ligon lintless</i><i>-2</i> Short Fiber Mutation Is Located within a Terminal Deletion of Chromosome 18 in Cotton

Patel, Jinesh; Huang, Xianzhong; Lin, Lifeng; Das, Sayan; Chandnani, Rahul; Khanal, Sameer; Adhikari, Jeevan; Shehzad, Tariq; Guo, Hui; Roy-Zokan, Eileen M.; Rong, Junkang; Paterson, Andrew H.

doi:10.1104/pp.19.01531

Cited by 20 publications

(26 citation statements)

References 84 publications

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“…Enrichment of DEGs at the N 5 locus and its flanking regions indicates the existence of a cluster of co-regulated and functionally related genes associated with the mutant phenotype. A similar phenomenon has been reported for the genomic region with the Ligon lintless-2 mutation ( Patel et al 2020 ). One possibility for co-regulation of functionally related genes is the presence of shared cis -regulatory elements in their promoters.…”

Section: Resultssupporting

confidence: 85%

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Zhu

Stiller

Moncuquet

et al. 2020

G3 Genes|Genomes|Genetics

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Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

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Section: Resultssupporting

confidence: 85%

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Zhu

Stiller

Moncuquet

et al. 2020

G3 Genes|Genomes|Genetics

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“…However, this compensation may not be highly effective because the yield traits of E6015‐3S, which lacked TaHST1 and carried extensive deletions in 4AL distal terminus, were decreased under control conditions in the field relative to those of E6015‐4T (Table S1). In line with this proposition, a recent study in tetraploid cotton shows that the functional deficiency of two glycosyltransferase genes, caused by a terminal deletion in the short arm of chromosome 18, could not be compensated by their homoeologs, thus leading to a defective short fibre phenotype (Patel et al, 2020). From this finding and the contrasting performance of E6015‐3S and E6015‐4T under field conditions (Figure 2), we reckon that the deletions in 4AL distal end should be corrected timely so as to enhance wheat tolerance to more severe HS episodes that are likely to occur in the coming years because of global warming (Lesk et al, 2016; Reinman, 2013).…”

Section: Discussionmentioning

confidence: 89%

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Zhai

Jiang

Zhao

et al. 2021

Plant Biotechnology Journal

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Heat stress (HS) causes substantial damages to worldwide crop production. As a cool season crop, wheat (Triticum aestivum) is sensitive to HS-induced damages. To support the genetic improvement of wheat HS tolerance (HST), we conducted fine mapping of TaHST1, a locus required for maintaining wheat vegetative and reproductive growth under elevated temperatures. TaHST1 was mapped to the distal terminus of 4AL chromosome arm using genetic populations derived from two BC 6 F 6 breeding lines showing tolerance (E6015-4T) or sensitivity (E6015-3S) to HS. The 4AL region carrying TaHST1 locus was approximately 0.949 Mbp and contained the last 19 high confidence genes of 4AL according to wheat reference genome sequence. Resequencing of E6015-3S and E6015-4T and haplotype analysis of 3087 worldwide wheat accessions revealed heightened deletion polymorphisms in the distal 0.949 Mbp region of 4AL, which was confirmed by the finding of frequent gene losses in this region in eight genomesequenced hexaploid wheat cultivars. The great majority (86.36%) of the 3087 lines displayed different degrees of nucleotide sequence deletions, with only 13.64% of them resembling E6015-4T in this region. These deletions can impair the presence and/or function of TaHST1 and surrounding genes, thus rendering global wheat germplasm vulnerable to HS or other environmental adversities. Therefore, conscientious and urgent efforts are needed in global wheat breeding programmes to optimize the structure and function of 4AL distal terminus by ensuring the presence of TaHST1 and surrounding genes. The new information reported here will help to accelerate the ongoing global efforts in improving wheat HST.

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“…The Li 1 mutation is caused by a Gly65Val substitution in an actin gene on chromosome D04, which disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants [ 15 ]. The Li 2 mutation is located within a terminal deletion of chromosome 18 (also called chromosome D13) [ 18 ]. A comparative study shows that at least seven of the 10 putative fiber development genes in the deletion region showed a higher expression in the wild type than in a Li 2 mutant during the fiber development stages.…”

Section: Introductionmentioning

confidence: 99%

“…However, no statistically significant ( p > 0.05) difference in the parameter of micronaire is observed between the two cotton fibers. Those morphological characterizations helped the genomic studies shed novel light on cotton fiber elongation, suggesting multiple genes coordinately regulated processes involving cell wall development and cell elongation [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Surface and Thermal Characterization of Cotton Fibers of Phenotypes Differing in Fiber Length

Nam

Fang

et al. 2021

Polymers

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Cotton is one of the most important and widely grown crops in the world. Understanding the synthesis mechanism of cotton fiber elongation can provide valuable tools to the cotton industry for improving cotton fiber yield and quality at the molecular level. In this work, the surface and thermal characteristics of cotton fiber samples collected from a wild type (WT) and three mutant lines (Li1, Li2-short, Li2-long, Li2-mix, and liy) were comparatively investigated. Microimaging revealed a general similarity trend of WT ≥ Li2-long ≈ Li2-mix > Li1 > Li2 short ≈ liy with Ca detected on the surface of the last two. Attenuated total reflectance Fourier transform infrared (ATR FT-IR) spectroscopy and thermogravimetric measurements also showed that Li2-short and liy were more similar to each other, and Li2-long and Li2-mix closer to WT while Li1 was quite independent. FT-IR results further demonstrated that wax and amorphous cellulose were co-present in fiber structures during the fiber formation processes. The correlation analysis found that the FT-IR-based maturity parameter was well correlated (p ≤ 0.05) to the onset decomposition temperature and all three weight-loss parameters at onset, peak, and end decomposition stages, suggesting that the maturity degree is a better parameter than crystallinity index (CI) and other FT-IR parameters that reflect the thermal stability of the cotton fiber. In summary, this work demonstrated that genetic mutation altered the surface and thermal characteristics in the same way for Li2-short and liy, but with different mechanisms for the other three mutant cotton fiber samples.

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The Ligon lintless-2 Short Fiber Mutation Is Located within a Terminal Deletion of Chromosome 18 in Cotton

Cited by 20 publications

References 84 publications

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Surface and Thermal Characterization of Cotton Fibers of Phenotypes Differing in Fiber Length

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