Comparative transcriptome analysis provides insights of anti-insect molecular mechanism of Cassia obtusifolia trypsin inhibitor against Pieris rapae

2017 ◽  
Vol 97 (1) ◽  
pp. e21427 ◽  
Author(s):  
Mian Xiang ◽  
Xian Zhang ◽  
Yin Deng ◽  
Yangyang Li ◽  
Jihua Yu ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Trypsin Inhibitor ◽  
Transcriptome Analysis ◽  
Pieris Rapae ◽  
Comparative Transcriptome ◽  
Cassia Obtusifolia ◽  
Comparative Transcriptome Analysis

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

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Efficient Breeding

Abstract 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

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

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Efficient Breeding

Abstract 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.

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

2020 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
Lisheng Bao ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Tissue Expression ◽  
Cotton Yield ◽  
Comparative Transcriptome ◽  
Seed Cotton ◽  
Comparative Transcriptome Analysis ◽  
Seed Cotton Yield ◽  
Field Experimentation

Abstract Background: Utilization of heterosis has greatly enhanced the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization in cotton produces superior yield is critical for efficient plant breeding. Results: With the whole-genome RNA sequencing, here, high, medium, and low hybrids varying in level of yield heterosis were screened based on different years and locations field experimentation. Phenotypically, high Department showed a mean of 14% more seed cotton yield than its better parent. A total of 63 samples comprised of different squaring stage tissues of three hybrids and four their inbred parents were used to perform transcriptomic analysis. A comparison of transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis exposed the majority of hybrids DEGs followed parent like expressions. Functional annotations identified an array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation. Starch and sucrose metabolism 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 raveled genes GhBZR1, GhASK8, At3g43860, GhGBSS1, GhAPL2, GhMPK4, GhPHO1, GhJAZ10, and GhCRR21 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 provides novel insights about phenomics and genomics of heterosis in upland cotton. Our results and data resources will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

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