Sequencing and Genomic Analysis of Sorghum DNA Introgression Variant Line R21 and Recipient Rice Jin Hui 1 Revealed Repetitive Element Variation

Abstract

Transferring the genome of distant species to crops is an efficient way to create new germplasms. However, the molecular mechanisms involved are unclear. In this study, a new rice restorer line R21 with heat tolerance was created by introgressing the genomic DNA of sorghum into the recipient restorer line Jin Hui 1. Assembly of rice R21 and Jin Hui 1 genomes was performed using PacBio sequencing technology. Comparative genome analysis and coverage statistics showed that the repetitive sequence atr0026 was a candidate introgression fragment of sorghum DNA. Sequence similarity analysis revealed that atr0026 was distributed at different copy numbers on the telomeric position of chromosomes 9 or 10 in R21, Jin Hui 1, and several rice varieties, indicating that the repetitive sequence from sorghum was highly conserved in rice. The repeat annotation in Gramineae indicated that ribosomal DNA loci that existed in atr0026 may be cause a rearrangement of chromosomes 9 and 10 of the R21 genome, resulting in a copy number variation at the 5′ end of it. Our study lays the foundation for further elucidation of the molecular mechanisms underlying the heat tolerance of sorghum DNA introgression variant line R21, which is of great significance for guiding crop genetic breeding.

Diversity of Unusual Ribosomal Genes and Ecological Origin of Rice (Oryza spp.)

“…edu/cgis/seq_align.cgi?su=LSU (accessed on 15 July 2022)) and the MultAlin alignment tools (http://prodes.toulouse.inra.fr/multalin/multalin.html (accessed on 15 July 2022)). The alignment producing the shortest tree was used for (equal weighting) maximum parsimony, neighbor-joining, and maximum likelihood analyses with PAUP version 4.0b2a [5]. Parsimony jackknifing (1000 replicates) with TBR branch swapping, 10 random sequence additions, and gaps treated as missing data were used to provide estimates for internal support of clades.…”

“…Species in the genus Oryza and other genera closely related to Oryza have been extensively studied either because of their agronomically useful traits in rice genetic improvement (wild species in Oryza and Porteresia) or because of their economic value as part of cuisine (Zizania) and forage (Leersia) [4]. The origin and diversification of this tribe, in particular the origin of the genus Oryza and its divergence, remains largely unclear [5].…”

Molecular Genetics Enhances Plant Breeding

“…Therefore, coupling hybrid breeding with bridge genotypes and guiding molecular markers unleashes novel opportunities to improve the chances of success, pace, and precision of the target introgression. Such utility has been reinforced in rice by Zhang et al [ 36 ], who bred for heat tolerance by introgressed sorghum ancestry. The authors utilized the rice restorer line ‘R21’ and the recipient restorer line Jin ‘Hui 1’, and were able to demonstrate with WGR that the sorghum introgression in line ‘R21’ confers mobile heat tolerance.…”

“…For original datasets, please refer to the published articles [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 ] within the second Special Issue of IJMS on “Molecular Genetics and Plant Breeding 2.0” ( , as accessed on 6 June 2023).…”