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

Abstract

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.

Exploration of incompatible crosses in plants for novel and useful variations

“…Inactivation of MMR (DNA mismatch repair system) genes that was observed was suggested as the cause of microsatellites' instability by failing to correct replication errors. Intergeneric cross between rice and maize was shown to bring about genomic rearrangements in the maternal parent even in the absence of evidence for introgression of the male parent (Meng et al, 2020). Intergeneric pollination was found to trigger extensive genomic changes in MU1, a morphologically stable line generated from the intergeneric cross of japonica rice cv.…”

“…Some of these variations are agronomically useful and were evolved as additional source of variation (Meng et al, 2020;Visarada, 2020a;Wang et al, 2005Wang et al, , 2009. Meng et al (2020) obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number and increased grain weight in rice  maize cross. Wang, Zhang, et al (2013) demonstrated that introgressive hybridization between Oryza sativa ssp.…”

“…The extent of variation in F 2 varied between F 1 s. Some of the variants are stable and inherited, whereas others are lost. Some of these variations are agronomically useful and were evolved as additional source of variation (Meng et al, 2020;Visarada, 2020a;Wang et al, 2005Wang et al, , 2009. Meng et al (2020) obtained a morphologically stable line, MU1, exhibiting moderate dwarfism, higher tiller number and increased grain weight in rice  maize cross.…”

“…Whole genome resequencing method is emplooyed to understand the extensive genomic variations arising from interspecififc and intergeneric pollination using next-generation sequencing methods (Meng et al, 2020;Wang, Zhang, et al, 2013) Wide hybridization is known to bring about genome evolution that can lead to speciation. Rather than following Mendelian inheritance principles, many distant crosses result in structural changes in the genome of the organisms involved, epigenetic modifications and variations in gene expression patterns, ultimately leading to infertility or genetic instability of the hybrids.…”

“…In the third course of events, all the paternal genome is eliminated, but it disturbs the maternal DNA leading to permanent genetic changes (Figure 1c). When the genome of the maternal parent is disturbed/shuffled a large de novo variation is generated in the F 2 F I G U R E 1 Pictorial representation of genome changes in incompatible crosses [Color figure can be viewed at wileyonlinelibrary.com] progeny, some of which is stable and inherited, whereas in others it is not inherited (Meng et al, 2020;Visarada, 2020a;Wang et al, 2009;Zou et al, 2018).…”