Genetic mapping, transcriptomic sequencing and metabolic profiling indicated a glutathione S-transferase is responsible for the red-spot-petals in Gossypium arboreum

Identification of the cysteine-rich transmembrane module CYSTM family in upland cotton and functional analysis of GhCYSTM5_A in cold and drought stresses

Abiotic stress poses adverse impacts on cotton production, raising demands for a better understanding of stress-response mechanisms and developing strategies to improve plant performance to cope with stress. CYSTM (Cysteine-rich transmembrane module) is a widely distributed and conserved family in eukaryotes that performs potential functions in stress tolerance. However, CYSTM genes and their role in stress response is uncharacterized in cotton. Herein, we identified a total of 23 CYSTM genes from upland cotton. They underwent mainly segmental duplications and experienced purifying selection during evolution. Expression profiles revealed GhCYSTMs were closely related to abiotic stress response. Furthermore, GhCYSTM5_A overexpression enhanced the cold and drought tolerance of cotton, while RNAi-mediated knockdown of GhCYSTM5_A decreased stress tolerance. Transcriptome analysis revealed GhCYSTM5_A may contribute to cold and drought tolerance by regulating the expression of oxidative stress-related genes through MAPK signaling. GhCYSTM5_A, localized in the nucleus and cytoplasm interacted with a secreted cysteine-rich peptide GhGASA14. Moreover, GhGASA14 silencing rendered cotton plants vulnerable to cold and drought. These results suggested the potential functions of GhCYSTM genes in abiotic stress and a positive role of GhCYSTM5_A in cold and drought tolerance. This study sheds light on comprehensive characteristics of GhCYSTM, and provides candidate genes for genetic breeding.

Natural variations in the Cis-elements of GhRPRS1 contributing to petal colour diversity in cotton

The cotton genus comprises both diploid and allotetraploid species, and the diversity in petal colour within this genus offers valuable targets for studying orthologous gene function differentiation and evolution. However, the genetic basis for this diversity in petal colour remains largely unknown. The red petal colour primarily comes from C, G, K, and D genome species, and it is likely that the common ancestor of cotton had red petals. Here, by employing a clone mapping strategy, we mapped the red petal trait to a specific region on chromosome A07 in upland cotton. Genomic comparisons and phylogenetic analyses revealed that the red petal phenotype introgressed from G. bickii. Transcriptome analysis indicated that GhRPRS1, which encodes a glutathione S-transferase, was the causative gene for the red petal colour. Knocking out GhRPRS1 resulted in white petals and the absence of red spots, while overexpression of both genotypes of GhRPRS1 led to red petals. Further analysis suggested that GhRPRS1 played a role in transporting pelargonidin-3-O-glucoside and cyanidin-3-O-glucoside. Promoter activity analysis indicated that variations in the promoter, but not in the gene body of GhRPRS1, have led to different petal colours within the genus. Our findings provide new insights into orthologous gene evolution as well as new strategies for modifying promoters in cotton breeding.

Genetic analysis and molecular validation of gene conferring petal spot phenotype in interspecific crosses of cotton

Cotton (Gossypium species) has received considerable interest from the geneticists, cytologists and evolutionary biologists since the last more than a century. Here, we explore the genetics of petal spot in the interspecific derivatives involving tetraploid and diploid cottons; and confirm the location of gene governing petal spot phenotype on chromosome A7 by demonstrating co-segregation of SSR marker NAU 2186 with petal spot phenotype. The presence of petal spot was observed to be dominant over its absence. Petal spot inheritance showed significant deviation from the expected Mendelian ratio in all the segregating populations indicating segregation distortion. The distortion was biased towards the hirsutum parent which has important implications from introgression point of view. We also report a strong association between petal spot and petal margin coloration phenotypes. Extant American cotton varieties generally lack petal spot and margin coloration phenotypes. These petal characteristics can serve as morphological markers during germplasm characterization.

Aspartyl proteases identified as candidate genes of a fiber length QTL, qFLD05, that regulates fiber length in cotton (Gossypium hirsutum L.)

KEY MESSAGE

GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.

A glutathione S-transferase GhTT19 determines flower petal pigmentation via regulating anthocyanin accumulation in cotton

Anthocyanin accumulations in the flowers can improve seed production of hybrid lines, and produce higher commodity value in cotton fibre. However, the genetic mechanism underlying the anthocyanin pigmentation in cotton petals is poorly understood. Here, we showed that the red petal phenotype was introgressed from Gossypium bickii through recombination with the segment containing the R₃ ^bic region in the A07 chromosome of Gossypium hirsutum variety LR compared with the near-isogenic line of LW with white flower petals. The cyanidin-3-O-glucoside (Cy3G) was the major anthocyanin in red petals of cotton. A GhTT19 encoding a TT19-like GST was mapped to the R₃ ^bic site associated with red petals via map-based cloning, but GhTT19 homologue gene from the D genome was not expressed in G. hirsutum. Intriguingly, allelic variations in the promoters between GhTT19^LW and GhTT19^LR , rather than genic regions, were found as genetic causal of petal colour variations. GhTT19-GFP was found localized in both the endoplasmic reticulum and tonoplast for facilitating anthocyanin transport. An additional MYB binding element found only in the promoter of GhTT19^LR , but not in that of GhTT19^LW , enhanced its transactivation by the MYB activator GhPAP1. The transgenic analysis confirmed the function of GhTT19 in regulating the red flower phenotype in cotton. The essential light signalling component GhHY5 bonded to and activated the promoter of GhPAP1, and the GhHY5-GhPAP1 module together regulated GhTT19 expression to mediate the light-activation of petal anthocyanin pigmentation in cotton. This study provides new insights into the molecular mechanisms for anthocyanin accumulation and may lay a foundation for faster genetic improvement of cotton.