Adaptability and Stability Comparisons of Inbred and Hybrid Cotton in Yield and Fiber Quality Traits

Shahzad, Kashif; Qi, Ting; Guo, Liping; Tang, Huini; Zhang, Xuexian; Wang, Hailin; Qiao, Xin; Zhang, Meng; Zhang, Bingbing; Feng, Juanjuan; Iqbal, Muhammad Shahid; Wu, Jianyong; Xing, Chaozhu

doi:10.3390/agronomy9090516

“…Our previous study of 11 inbred lines and 30 intraspecific hybrids in six environments found that cotton hybrids had better and stable performance compared to inbred lines in yield traits [40]. Here, analysis of heterosis in these hybrids showed majority of hybrids had positive mid parent heterosis (MPH) and better parent heterosis (BPH) for boll weight, seed cotton yield (SCY), lint yield and lint percentage (Additional file 14: Table S1).…”

Section: Identification Of Cotton Hybrids Exhibiting Different Level mentioning

confidence: 80%

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

Shahzad

¹

,

Zhang

²

,

Guo

³

et al. 2020

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Background: Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. Results: In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024,

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“…Cotton ( Gossypium hirsutum L.), as a vital resource for plant fiber and oil, is widely cultivated worldwide [1]. However, its low yield is one of the key factors hindering its further development.…”

Section: Introductionmentioning

confidence: 99%

Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

Zhang

¹

,

Guo

²

,

Qi

³

et al. 2019

IJMS

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DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H2O2 production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.

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“…Our previous study of 11 inbred lines and 30 intraspeci c hybrids in six environments found that cotton hybrids had better and stable performance compared to inbred lines in yield traits [40]. Here, analysis of heterosis in these hybrids showed majority of hybrids had positive mid parent heterosis (MPH) and better parent heterosis (BPH) for boll weight, seed cotton yield (SCY), lint yield and lint percentage (Table S1).…”

Section: Identi Cation Of Cotton Hybrids Exhibiting Different Level Omentioning

confidence: 71%

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

Shahzad

¹

,

Zhang

²

,

Guo

³

et al. 2020

Preprint

Self Cite

0

View full text Add to dashboard Cite

Background: Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. Results: In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. Conclusions: Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

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Adaptability and Stability Comparisons of Inbred and Hybrid Cotton in Yield and Fiber Quality Traits

Cited by 40 publications

References 46 publications

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton

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