Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in upland cotton

Abstract

Background Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important. Results In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of the GH3 gene family, which are involved in auxin signal transduction, and CKX enzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS), EIN2/3 and ERF in the ethylene signal transduction pathway and genes related to JAR1, COI1 and MYC2 in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. The WRKY, ERF and bHLH TF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77. Conclusions Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, the WRKY, ERF and bHLH TFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches.

CpARF2 and CpEIL1 interact to mediate auxin–ethylene interaction and regulate fruit ripening in papaya

“…For ACC measurements, standard solutions of ACC were prepared with a concentration gradient of 1, 5, 10, 20, 50 and 200 ng ml −1 . ACC concentrations were analyzed as described previously (Ju et al ., 2019).…”

GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton (Gossypium hirsutum L.) Across Multiple Environments

“…Two candidate genes, Gh_D02G1201 and Gh_A10G1233 , showed an association with FE-related hQTNs. Both Gh_D02G1201 and Gh_A10G1233 encode FAR-RED elongated proteins which are involved in light responses and FE development ( Ju et al, 2019 ) along with the positive regulation of chlorophyll biosynthesis ( Tang et al, 2012 ; Miao et al, 2017 ). Gh_A11G1858 , which displayed an association with the hQTN related to FL, encodes a serine-threonine kinase SAPK1 protein that may play a role in the signal transduction of a hyperosmotic response markedly influencing the fiber development process ( Kobayashi et al, 2004 ; Magwanga et al, 2018 ; Li et al, 2019 ).…”

“…Gh_A11G1858 , which displayed an association with the hQTN related to FL, encodes a serine-threonine kinase SAPK1 protein that may play a role in the signal transduction of a hyperosmotic response markedly influencing the fiber development process ( Kobayashi et al, 2004 ; Magwanga et al, 2018 ; Li et al, 2019 ). FU was identified with hQTNs associated with Gh_A01G0481 and Gh_A11G0475 ; the former encodes a cytochrome P450 protein which may have a role in the maturation or aging of tissues ( Ju et al, 2019 ), while the latter encodes the Ras-related protein RAB11A, it detected previously in fiber development and elongation ( Qin et al, 2017 ). The FUI trait was associated with a hQTN related to Gh_A03G0366 , which encodes a scarecrow-like protein that acts as transcription factor and which regulates the development of vegetative and reproductive plant parts ( Cenci and Rouard, 2017 ; Zhang et al, 2018 ).…”

“…The FUI trait was associated with a hQTN related to Gh_A03G0366 , which encodes a scarecrow-like protein that acts as transcription factor and which regulates the development of vegetative and reproductive plant parts ( Cenci and Rouard, 2017 ; Zhang et al, 2018 ). The LP-associated hQTN was related to Gh_A05G0285 , a gene earlier detected in cotton for coding nucleotide binding protein responsible for fiber development ( Ju et al, 2019 ). The MIC-directed association toward hQTNs related to Gh _ A03G1505 , Gh_A03G0332 , Gh_A02G0495 , and Gh_D06G1287 ; these reportedly encode in cotton the production of calcium-dependent proteins related respectively to the kinase family ( Si et al, 2020 ), histones H2B ( Qin et al, 2019 ), phosphatase 2C ( Ju et al, 2019 ; Song et al, 2019 ; Shahzad et al, 2020 ), and cytochrome C oxidase ( Zhang et al, 2019 ).…”

“…The LP-associated hQTN was related to Gh_A05G0285 , a gene earlier detected in cotton for coding nucleotide binding protein responsible for fiber development ( Ju et al, 2019 ). The MIC-directed association toward hQTNs related to Gh _ A03G1505 , Gh_A03G0332 , Gh_A02G0495 , and Gh_D06G1287 ; these reportedly encode in cotton the production of calcium-dependent proteins related respectively to the kinase family ( Si et al, 2020 ), histones H2B ( Qin et al, 2019 ), phosphatase 2C ( Ju et al, 2019 ; Song et al, 2019 ; Shahzad et al, 2020 ), and cytochrome C oxidase ( Zhang et al, 2019 ). Finally, FS was associated with a hQTN related to the Gh_A01G1348 gene known for encoding axial regulator proteins controlling the biomass vigor of hybrid cotton ( Shahzad et al, 2020 ).…”