Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization View Full Text


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Article Info

DATE

2022-06-30

AUTHORS

Kashif Shahzad, Xuexian Zhang, Meng Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Hailin Wang, Iqra Mubeen, Xiuqin Qiao, Renhai Peng, Jianyong Wu, Chaozhu Xing

ABSTRACT

Hybridization is useful to enhance the yield potential of agronomic crops in the world. Cotton has genome doubling due to the allotetraploid process and hybridization in coordination with duplicated genome can produce more yield and adaptability. Therefore, the expression of homoeologous gene pairs between hybrids and inbred parents is vital to characterize the genetic source of heterosis in cotton. Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (an average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton. More... »

PAGES

757-768

References to SciGraph publications

  • 2018-08-06. Homoeolog expression bias and expression level dominance in resynthesized allopolyploid Brassica napus in BMC GENOMICS
  • 2019-09-06. Genetic analysis of yield and fiber quality traits in upland cotton (Gossypium hirsutum L.) cultivated in different ecological regions of China in JOURNAL OF COTTON RESEARCH
  • 2015-07-08. Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis in NATURE COMMUNICATIONS
  • 2014-03-28. Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana in NATURE COMMUNICATIONS
  • 2002-12-16. Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat in NATURE GENETICS
  • 2020-02-10. Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton in BMC GENOMICS
  • 2010-12-23. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners in GENOME BIOLOGY
  • 2017-10-20. Analyzing homoeolog expression provides insights into the rediploidization event in gynogenetic hybrids of Carassius auratus red var. × Cyprinus carpio in SCIENTIFIC REPORTS
  • 2010-09-17. Homoeolog-specific transcriptional bias in allopolyploid wheat in BMC GENOMICS
  • 2009-09-17. Brassica orthologs from BANYULS belong to a small multigene family, which is involved in procyanidin accumulation in the seed in PLANTA
  • 2008-04-16. Duplicate gene expression in allopolyploid Gossypiumreveals two temporally distinct phases of expression evolution in BMC BIOLOGY
  • 2020-05-27. Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton in BMC PLANT BIOLOGY
  • 2020-04-29. Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus in BMC GENOMICS
  • 2016-06-06. Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae in SCIENTIFIC REPORTS
  • 2009-01. RNA-Seq: a revolutionary tool for transcriptomics in NATURE REVIEWS GENETICS
  • 2019-03-25. Heterotic patterns of primary and secondary metabolites in the oilseed crop Brassica juncea in HEREDITY
  • 2003-11-01. Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags in MOLECULAR GENETICS AND GENOMICS
  • 2012-11-21. Homoeolog expression bias and expression level dominance in allopolyploid cotton in HEREDITY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10142-022-00877-1

    DOI

    http://dx.doi.org/10.1007/s10142-022-00877-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1149107615

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35771309


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