Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton ( Gossypium hirsutum L.)

Hamid, Rasmieh; Tomar, R. S.; Marashi, Hassan; Malekzadeh-Shafaroudi, Saeid; Golakiya, B. A.; Mohsenpour, M

doi:10.1016/j.gene.2018.03.070

Cited by 25 publications

(18 citation statements)

References 67 publications

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“…Understanding the molecular mechanisms controlling anther development and male sterility is of great importance for heterosis utilization in many crop species, including cotton. In recent years, male sterility lines have been widely studied by transcriptomic analysis in different species, such as wheat [ 56 , 57 ], maize [ 58 ], eggplant [ 59 ] and cotton [ 60 – 63 ]. However, most studies tend to carry out extensive enrichment of DEGs without systematic classification analysis based on different development stages.…”

Section: Discussionmentioning

confidence: 99%

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Zhang

Liu

et al. 2020

BMC Genomics

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Background Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106. Results Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (lUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition. Conclusions We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.

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Section: Discussionmentioning

confidence: 99%

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Zhang

Liu

et al. 2020

BMC Genomics

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“…In addition to its wide application in hybrid production, CMS also provides a window to the world of plant mitochondrial-nuclear interactions. Many of CMS-related genes have been cloned from different crops [15–23], and CMS has been characterized with respect to a number of different features, including mitochondrial genome [6, 24–33], transcriptome [34, 35], proteome [36–38], miRNA [39–42], non-coding RNA [43, 44], circular RNA [45], and RNA editing [46]. Comparative mitochondrial genome sequencing between male sterility and maintainer line in CMS is often performed to elucidate sequence rearrangements by repeats, conduct phylogenetic analysis, and uncover candidate genes for CMS [26, 28, 29, 47].…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

Yan

et al. 2019

BMC Genomics

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Background Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea . Results The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene ( orf108 ) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes. Conclusions On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica . Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5721-2) contains supplementary material, which is available to authorized users.

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“…Understanding the molecular mechanisms controlling anther development and male sterility is of great importance for heterosis utilization in many crop species, including cotton. In recent years, male sterility lines have been widely studied by transcriptomic analysis in different species, such as wheat [56,57], maize [58], eggplant [59] and cotton [60][61][62][63]. However, most studies tend to carry out extensive enrichment of DEGs without systematic classi cation analysis based on different development stages.…”

Section: Discussionmentioning

confidence: 99%

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Zhang

Liu

et al. 2020

Preprint

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Background: Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CCRI040029, was reported of great advantages to cotton heterosis. However, little information concerning the male sterility of CCRI9106 is known. Here, comparative transcriptome analysis of CCRI9106 (the mutant, MT) and CCRI040029 (the wild type, WT) anthers in Anyang (long-day, male sterile condition to CCRI9106) was performed to reveal the potential male sterile mechanism of CCRI9106.Results: Light and electron microscopy revealed that the male sterility phenotype of MT was mainly attributed to irregularly exine, lacking tryphine and immature anther cuticle. Based on the cytological characteristics of MT anthers, anther RNA libraries (18 in total) of tetrad (TTP), late uninucleate (LUNP) and binucleate (BNP) stages in MT and WT were constructed for transcriptomic analysis, therefore revealing a total of 870,4 differentially expressed genes (DEGs). By performing gene expression pattern analysis and protein-protein interaction (PPI) networks construction, we found down-regulation of DEGs, which enriched by the lipid biosynthetic process and the synthesis pathways of several types of secondary metabolites such as terpenoids, flavonoids and steroids, may crucial to the male sterility phenotype of MT, and resulting in the defects of anther cuticle and tryphine, even the irregularly exine. Furthermore, several lipid-related genes together with ABA-related genes and MYB transcription factors were identified as hub genes via weighted gene co-expression network analysis (WGCNA). Additionally, the ABA content of MT anthers was reduced across all stages when compared with WT anthers. At last, genes related to the formation of anther cuticle and tryphine could activated in MT under short-day condition.Conclusions: We propose that the down-regulation of genes related to the assembly of anther cuticle and tryphine may lead to the male sterile phenotype of MT, and MYB transcription factors together with ABA played key regulatory roles in these processes. The conversion of fertility in different photoperiods may closely relate to the functional expression of these genes. These findings contribute to elucidate the mechanism of male sterility in upland cotton.

show abstract

Transcriptome profiling and cataloging differential gene expression in floral buds of fertile and sterile lines of cotton ( Gossypium hirsutum L.)

Cited by 25 publications

References 67 publications

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line

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