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.

Seed Cotton Yield and Fibre Properties of F1 and F2 Hybrids of Upland Cotton

2001 ◽  
Vol 1 (1) ◽  
pp. 48-50
Author(s):  
Mohammad Jurial Balo . ◽  
Abdul Rahim Lakho . ◽  
Hidayatullah Butto . ◽  
Rehmatullah Rind .
Keyword(s):  
Upland Cotton ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Fibre Properties ◽  
Seed Cotton Yield ◽  
F2 Hybrids

scholarly journals Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Jianyong Wu ◽  
Meng Zhang ◽  
Bingbing Zhang ◽  
Xuexian Zhang ◽  
Liping Guo ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Upland Cotton ◽  
Comparative Transcriptome ◽  
Comparative Transcriptome Analysis ◽  
Genome Wide

scholarly journals Genetic Variability, Heritability and Correlation Studies in F2 Populations of Upland Cotton

2018 ◽  
Vol 61 (3) ◽  
pp. 136-144
Author(s):  
Muhammad Jurial Baloch ◽  
Rehana Lochi ◽  
Wajid Ali Jatoi ◽  
Abdul Wahid Baloch ◽  
Muhammad Ahmed Arain
Keyword(s):  
Upland Cotton ◽  
Block Design ◽  
Fibre Length ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Node Number ◽  
Plant Seed ◽  
Seed Cotton Yield ◽  
Fibre Traits ◽  
Selection Of

A field experiment was conducted at the experimental area of the Department of Plant Breeding & Genetics, Sindh Agriculture University Tandojam, during the year 2014-2015 in order to carry-out genetic analysis in F2 populations of upland cotton. The trial was laid-out in a Randomized Complete Block Design with four replications. The material was consisted of eight parents and ten F2 populations. The analysis of variance revealed significant differences among the parents and F2 populations for all the traits studied except that fibre length was non-significant in parents.  The results further suggested that maximum heritability, higher genetic variances coupled with more genetic gains were expressed by the F2 populations CRIS-134 ´ CRIS-508 and CRIS-134 ´ CIM-598 for 1st sympodial node number; CRIS-134 ´ Neelum- 121 and CRIS-134 ´ CRIS-508 for sympodial branches/plant;  CRIS-342 ´ FH-113 for boll weight;  CRIS- 342 ´ Neelum-121 for bolls/plant, seed cotton yield/plant, lint % and micronaire value and progenies CRIS-342 ´ MNH-886 followed by CRIS-342 ´ Neelum-121  for staple length.  These results also suggested that a number of F2 populations indicated their potential for various seed cotton yield and fibre traits. The phenotypic correlations revealed that most of the traits were significantly and positively associated with seed cotton yield/plant.  However, higher correlations of sympodial branches/plant (r = 0.69**) and bolls/ plant (r = 0.82**) with seed cotton yield indicated that both the traits are more reliable as compared to other traits for selection of higher seed cotton yields. Very interestingly, fibre traits like lint%, fibre length and micronaire were also significantly correlated with seed cotton yield, suggesting that fibre quality traits can be improved without compromising on seed cotton yield. Thus, the material under study is very promising and worthy of selection to improve many traits simultaneously.

scholarly journals Genetic analysis of yield components and fiber quality parameters in upland cotton

1970 ◽  
pp. 13-19
Author(s):  
Bilal Nawaz, Saira Sattar, Tanwir Ahmad Malik
Keyword(s):  
Upland Cotton ◽  
Phenotypic Correlation ◽  
Cotton Yield ◽  
Seed Cotton ◽  
Seed Cotton Yield ◽  
Maximum Value ◽  
Fiber Fineness ◽  
Significant Difference ◽  
Boll Weight ◽  
Seed Index

The experiment was laid to analyze genetic features, genotypic and phenotypic correlation coefficients, path analysis with regression analysis among yield contributing traits in a selected F3 populations of upland cotton including parents. In this research experiment ANOVA showed significant difference among all individual plants in F3 populations. Monopodia per plant and bolls per plant possessed maximum value of PCV% and GCV%. Maximum broad sense heritability (≥ 90) was found in all recorded traits except seeds per boll, fiber length and lint percentage. Correlation studies revealed that Seed cotton yield positively correlated with all yield contributing traits i.e. plant height, monopodial branches per plant, Number of bolls per plant, boll weight, lint weight, seed index, lint index, seeds per boll, fiber fineness, fiber strength and fiber uniformity at both genotypic and phenotypic level whereas it depicted negative relationship with staple length. Path coefficient analysis showed that maximum direct positive effect was found of lint weight (2.6005) on seed cotton yield followed fiber fineness (1.2628), seed index (1.1449) and bolls per plant (1.0027). Regression study exhibited that maximum value of R2 for lint weight (0.9509) and boll weight (0.3735) depicted that 95.09% and 37.35% variation in the seed cotton yield, due to its relationship with lint weight and boll weight. It is concluded that there is a great genetic potential in F3 populations for mostly yield contributing traits for further enhancing yield. So those traits should be used as selection criteria during breeding for yield.

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