Elsevier

Industrial Crops and Products

Volume 184, 15 September 2022, 115034
Industrial Crops and Products

Fine mapping and characterization of the Crinkled Dwarf gene in cotton

https://doi.org/10.1016/j.indcrop.2022.115034Get rights and content

Highlights

  • The Crinkled Dwarf (cr) mutant was controlled by a major recessive locus.

  • The cr phenotype was sensitive to environmental factors such as light intensity.

  • The cr gene was mapped to a 35.8-kbp genomic interval on chromosome D03.

  • Ttranscriptome analysis showed that stress/disease resistance was enhanced in the cr mutation.

  • The plant height of cr was sensitive to most of exogenous phytohormones treatments.

Abstract

Cotton (Gossypium) is an important natural fiber crop worldwide. Plant height, which is an important commercial cotton breeding trait, is also useful for plant architecture research. Crinkled Dwarf (cr), a natural mutant of Sea Island cotton (Gossypium barbadense L.), simultaneously displays crinkled leaves and dwarfing. However, the genes controlling cr have not been characterized, and the molecular mechanism of the trait remains unknown. In this study, genetic analysis indicated that cr was likely controlled by a major recessive gene, although the cr phenotype was sensitive to environmental factors, including light intensity. Using bulked-segregant analysis and recombinant methods, the cr gene was mapped to a 35.8-kbp genomic interval on chromosome D03 that contained three annotated protein-coding genes. Comparative transcriptome analysis showed that cr enhanced stress/disease resistance and repressed plant development/growth. Endogenous phytohormone measurements showed that most auxin compounds were decreased in the cr mutant. Although the cr mutation was insensitive to exogenous auxin, gibberellin and cytokinin treatments promoted and repressed main stem elongation, respectively. However, no hormone treatment could fully rescue the crinkled leaf phenotype. These findings will contribute to the breeding of cotton lines with improved plant architecture or yield, and aid in the dissection of the genetic basis of cr.

Introduction

Plant architecture is an important agronomic trait that comprises several components, including plant height, number of branches/tillers, and internode length (Wang et al., 2018). Dwarf mutants, which are good germplasm resources for the study of plant architecture, usually carry beneficial agronomic characters for crop breeding, such as lodging resistance, higher harvest index, and improved tolerance of dense planting (Akter et al., 2015). In cereal crops, semi-dwarf varieties were produced during the agricultural green revolution of the 1960s (Hedden, 2003). Many dwarf mutants have been studied in detail (Nakazawa et al., 2001, Tanabe et al., 2005, Dai et al., 2006, Wang et al., 2017), and they usually result from mutations of genes involved in phytohormone biosynthesis or transduction pathways(Winkler and Helentjaris, 1995; Choe et al., 1998; Helliwell et al., 2001).

Cotton is an important textile crop. Cultivated cotton usually has a tall and incompact plant type, because it was domesticated from tree-like wild species (Paterson et al., 2012, Wendel and Grover, 2015). To control the plant height of cotton, the application of chemical reagents such as chlormequat chloride is popular in cotton planting, a practice that leads to rising labor costs and the potential environmental pollution (Vahl et al., 1998, Guo et al., 2010). Appropriate plant height is important for the cultivation of high-yield cotton suitable for high planting density (Dong et al., 2018). Thus, dwarf mutants of cotton have been widely studied. The Crinkled Dwarf (cr) mutant of Sea Island cotton (Gossypium barbadense L.) was discovered in 1916 (Harland, 1918). This mutation displays crinkled leaves and dwarfing, and varying degrees of abnormality are exhibited under different environmental conditions. This mutation occurs comparatively frequently in cotton. Morphologically similar mutants have been reported several times with different genetic backgrounds, and they have all been found to be allelic with cr, including 'controta', 'Wrinkled Leaf', and 'rugose'. The cr phenotype appears to be due to a single-locus recessive mutation, with some “modifiers” (minor genes) affecting the degree of the mutant phenotype. Normal alleles with complete dominance (crB) have been found in G. barbadens (Gb), G. darwinii and G. tomentosum, and low normal alleles with partial dominance (crH) have been identified in G. hirsutum (Gh) and G. thurberi (Harland, 1933, Harland, 1935; Harland and Atteck, 1941, Harland and Atteck, 1941; Hutchinson, 1946).

In the past few decades, many novel dwarf mutants appearing to be nonallelic with cr have been reported, including dwarf-red (red plants with dwarfing) (McMichael, 1942), Aizao-1(a dwarf with early flowering) (He et al., 1996), du (an ultra-dwarf) (Chen et al., 2007), AiSheng98 (an ultra-dwarf) (Zhang et al., 2011), Lu-ai-1 (a semi-dwarf) (Liu et al., 2008), sd (a semi-dwarf) (Zhou et al., 2018), sda (a sterile-dwarf) and pagoda1 (an ultra-dwarf) (Wu et al., 2009, Yang et al., 2014). Most of these mutants have been found to be controlled by one to two major loci, and are usually sensitive to certain exogenous hormones (Chen et al., 2007, Yang et al., 2014, Zhou et al., 2018). Recently, some underlying mutations for these phenotypes have been identified. The mutant pagoda1 is caused by the increased transcription of a CYP734A1/BAS1 gene that promotes brassinosteroid (BR) catabolism (Yang et al., 2014). In the Aisheng98 mutant, the overexpression of a dehydration-responsive element-binding (DREB) transcription factor resulting from the doubling of gene copy number leads to the dwarfing phenotype (Ji et al., 2021). Interestingly, Aisheng98 also displayed improved chilling tolerance in cotton seedlings due to the elevation of DREB transcription (Wang et al., 2021).

In the present study, phenotypic characterization and genetic analysis of the cr mutant were conducted, and map-based cloning was performed to identify the underlying mutations. In addition, comparisons of the transcriptome and endogenous phytohormones between cr and normal lines were also conducted to identify the underlying mechanisms for this mutation.

Section snippets

Plant materials and field experiment

A cr Sea Island cotton line named NAM has been planted for more than 10 generations with continuous selfing. NAM also contains the nulliplex-branch (nb) mutation that causes determinate sympodial branches (Chen et al., 2019). Xinhai-18 and Xinhai-43 are nb-type lines with normal plant height and leaves (crB). Line 9078 N is another wild-type (WT, crB) line with normal sympodial branches (NB genotype). In 2018, F1 plants of the crosses NAM × Xinhai-18 and 9078 N × NAM were self-pollinated to

cr phenotype

In the field, the cr mutant usually displayed relatively normal plant height before the bud stage, although the cotyledons and all true leaves were deformed (Fig. 1a, b). The cotyledons of cr were mildly curled, and the true leaves were usually smaller, with shallow clefts. After blooming, the later differentiated leaves became more crinkled, and the upper internode of the main shoot became progressively shorter (Fig. 1c, d). The final length was usually less than 10 mm after the 16th

Discussion

The cr mutant was first reported more than 100 years ago, but its underlying molecular mechanism remains unknown. In this study, the cr locus was restricted to a ~35 kb interval through fine mapping, and the transcriptomic profile was analyzed using RNA-seq. The precise knowledge of the location of cr provides a foundation for cloning of this important gene, and the detailed transcriptomic profile will help researchers to elucidate the function and regulatory mechanism of the trait.

In the final

Conclusions

In this study, phenotypic characterization, genetic analysis, molecular marker mapping, transcriptome analysis and phytohormone treatment were conducted on the cr mutant in cotton. Although the cr phenotype is sensitive to planting environments, cr is most likely controlled by a major recessive gene. This gene was mapped to 35.8-kbp genomic interval on chromosome D03. Comparative transcriptome analysis and measurements of endogenous phytohormones showed that stress/disease resistance was

CRediT authorship contribution statement

Shengtao Fang: Conceptualization, Methodology, Investigation, Writing – original draft, Writing - review & editing. Jinbo Yao: Conceptualization, Methodology, Data curation, Writing - review & editing. Yan Li: Data curation, Investigation. Shouhong Zhu: Methodology, Validation. Jingwen Pan: Investigation, Validation. Qiulin Li: Investigation, Data curation. Weiran Wang: Investigation, Visualization. Jie Kong: Methodology, Validation. Liangrong He: Investigation, Resources. Yongshan Zhang:

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgments

This research was funded by the National Natural Science Foundation of China (31871680).

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    These authors contributed equally to this work

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