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Open AccessArticle

Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination

1
College of Agronomy, Jilin Agricultural University, Changchun 130118, China
2
Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing 100081, China
3
College of Agronomy, Jilin Agricultural Science and Technology University, Jilin 132101, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(2), 199; https://doi.org/10.3390/genes11020199 (registering DOI)
Received: 28 December 2019 / Revised: 6 February 2020 / Accepted: 12 February 2020 / Published: 15 February 2020
(This article belongs to the Section Plant Genetics and Genomics)
Interspecific hybridization creates genetic variation useful for crop improvement. However, whether pollen from a different genus affects the genomic stability and/or transcriptome of the recipient species during intergeneric pollination has not been investigated. Here, we crossed japonica rice cv. Z12 with the maize accession B73 (pollen donor) and obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number, and increased grain weight compared with Z12. To reveal the genetic basis of these morphological changes in MU1, we performed whole-genome resequencing of MU1 and Z12. Compared with Z12, MU1 showed 107,250 single nucleotide polymorphisms (SNPs) and 23,278 insertion/deletions (InDels). Additionally, 5’-upstream regulatory regions (5’UTRs) of 429 and 309 differentially expressed genes (DEGs) in MU1 contained SNPs and InDels, respectively, suggesting that a subset of these DEGs account for the variation in 5’UTRs. Transcriptome analysis revealed 2190 DEGs in MU1 compared with Z12. Genes up-regulated in MU1 were mainly involved in photosynthesis, generation of precursor metabolites, and energy and cellular biosynthetic processes; whereas those down-regulated in MU1 were involved in plant hormone signal transduction pathway and response to stimuli and stress processes. Quantitative PCR (qPCR) further identified the expression levels of the up- or down-regulated gene in plant hormone signal transduction pathway. The expression level changes of plant hormone signal transduction pathway may be significant for plant growth and development. These findings suggest that mutations caused by intergeneric pollination could be the important reason for changes of MU1 in agronomic traits. View Full-Text
Keywords: rice; intergeneric pollination; genetic variation; hormone signal transduction pathway rice; intergeneric pollination; genetic variation; hormone signal transduction pathway
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Meng, W.-L.; Zhao, M.-J.; Yang, X.-B.; Zhang, A.-X.; Wang, N.-N.; Xu, Z.-S.; Ma, J. Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination. Genes 2020, 11, 199.

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