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Transcriptome sequencing and de novo analysis of cytoplasmic male sterility and maintenance in JA-CMS cotton.

Yang P, Han J, Huang J - PLoS ONE (2014)

Bottom Line: By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage.Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages.Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China; Department of Rural Development, Shanxi Agricultural University, Taigu, Shanxi, China.

ABSTRACT
Cytoplasmic male sterility (CMS) is the failure to produce functional pollen, which is inherited maternally. And it is known that anther development is modulated through complicated interactions between nuclear and mitochondrial genes in sporophytic and gametophytic tissues. However, an unbiased transcriptome sequencing analysis of CMS in cotton is currently lacking in the literature. This study compared differentially expressed (DE) genes of floral buds at the sporogenous cells stage (SS) and microsporocyte stage (MS) (the two most important stages for pollen abortion in JA-CMS) between JA-CMS and its fertile maintainer line JB cotton plants, using the Illumina HiSeq 2000 sequencing platform. A total of 709 (1.8%) DE genes including 293 up-regulated and 416 down-regulated genes were identified in JA-CMS line comparing with its maintainer line at the SS stage, and 644 (1.6%) DE genes with 263 up-regulated and 381 down-regulated genes were detected at the MS stage. By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage. Quantitative RT-PCR was used to validate 7 randomly selected DE genes. Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages. All these four biological processes play important roles in reactive oxygen species (ROS) homeostasis, which may be an important factor contributing to the sterile trait of JA-CMS. Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS.

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Related in: MedlinePlus

Venn diagram of DE gene counts at the SS and MS stages for JA-CMS and JB floral buds.B2 = SS stage of JA-CMS, K2 = SS stage of JB, K3 = MS stage of JB, B3 = MS stage of JA-CMS (from right to left).
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pone-0112320-g001: Venn diagram of DE gene counts at the SS and MS stages for JA-CMS and JB floral buds.B2 = SS stage of JA-CMS, K2 = SS stage of JB, K3 = MS stage of JB, B3 = MS stage of JA-CMS (from right to left).

Mentions: Gene expression levels at the SS or MS stage for JA-CMS and JB floral buds were quantified and compared using RSEM [21], TMM [22], and DEGseq [23]. At the SS stage, there were 11,111 genes uniquely expressed in JA-CMS plants and 7,811 in JB plants; 40,318 genes were shared between the two lines at this stage. At the MS stage, 8,502 and 8,636 genes were specifically expressed in JA-CMS and JB lines, and the number of commonly expressed genes was 39,967. Regarding gene expression level comparison between the two stages of the same plant material, JA-CMS plants had 9,334 genes uniquely expressed at the SS stage and 6,374 at the MS stage; 42,905 genes were expressed at both stages; and there were 7,366 and 7,840 genes expressed at the SS and MS stages of JB plants, respectively, while 40,763 genes were commonly found at both stages (Figure 1).


Transcriptome sequencing and de novo analysis of cytoplasmic male sterility and maintenance in JA-CMS cotton.

Yang P, Han J, Huang J - PLoS ONE (2014)

Venn diagram of DE gene counts at the SS and MS stages for JA-CMS and JB floral buds.B2 = SS stage of JA-CMS, K2 = SS stage of JB, K3 = MS stage of JB, B3 = MS stage of JA-CMS (from right to left).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4221291&req=5

pone-0112320-g001: Venn diagram of DE gene counts at the SS and MS stages for JA-CMS and JB floral buds.B2 = SS stage of JA-CMS, K2 = SS stage of JB, K3 = MS stage of JB, B3 = MS stage of JA-CMS (from right to left).
Mentions: Gene expression levels at the SS or MS stage for JA-CMS and JB floral buds were quantified and compared using RSEM [21], TMM [22], and DEGseq [23]. At the SS stage, there were 11,111 genes uniquely expressed in JA-CMS plants and 7,811 in JB plants; 40,318 genes were shared between the two lines at this stage. At the MS stage, 8,502 and 8,636 genes were specifically expressed in JA-CMS and JB lines, and the number of commonly expressed genes was 39,967. Regarding gene expression level comparison between the two stages of the same plant material, JA-CMS plants had 9,334 genes uniquely expressed at the SS stage and 6,374 at the MS stage; 42,905 genes were expressed at both stages; and there were 7,366 and 7,840 genes expressed at the SS and MS stages of JB plants, respectively, while 40,763 genes were commonly found at both stages (Figure 1).

Bottom Line: By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage.Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages.Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China; Department of Rural Development, Shanxi Agricultural University, Taigu, Shanxi, China.

ABSTRACT
Cytoplasmic male sterility (CMS) is the failure to produce functional pollen, which is inherited maternally. And it is known that anther development is modulated through complicated interactions between nuclear and mitochondrial genes in sporophytic and gametophytic tissues. However, an unbiased transcriptome sequencing analysis of CMS in cotton is currently lacking in the literature. This study compared differentially expressed (DE) genes of floral buds at the sporogenous cells stage (SS) and microsporocyte stage (MS) (the two most important stages for pollen abortion in JA-CMS) between JA-CMS and its fertile maintainer line JB cotton plants, using the Illumina HiSeq 2000 sequencing platform. A total of 709 (1.8%) DE genes including 293 up-regulated and 416 down-regulated genes were identified in JA-CMS line comparing with its maintainer line at the SS stage, and 644 (1.6%) DE genes with 263 up-regulated and 381 down-regulated genes were detected at the MS stage. By comparing the two stages in the same material, there were 8 up-regulated and 9 down-regulated DE genes in JA-CMS line and 29 up-regulated and 9 down-regulated DE genes in JB maintainer line at the MS stage. Quantitative RT-PCR was used to validate 7 randomly selected DE genes. Bioinformatics analysis revealed that genes involved in reduction-oxidation reactions and alpha-linolenic acid metabolism were down-regulated, while genes pertaining to photosynthesis and flavonoid biosynthesis were up-regulated in JA-CMS floral buds compared with their JB counterparts at the SS and/or MS stages. All these four biological processes play important roles in reactive oxygen species (ROS) homeostasis, which may be an important factor contributing to the sterile trait of JA-CMS. Further experiments are warranted to elucidate molecular mechanisms of these genes that lead to CMS.

Show MeSH
Related in: MedlinePlus