Abstract
Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.
Highlights
As a consequence of adaptation to different habitats, extensive genotypic and phenotypic diversity exists within O. sativa L., resulting in about 120,000 different accessions[20]
We identified 3,960 variations across the landrace and weedy rice accessions, with 203 HQ sites (Supplementary Tables 1 and 2)
3041 variations (76.8% of total) among the 60 rice accessions located in the intergenic regions, while only 23.2% variations are in the gene region (Supplementary Table 1)
Summary
A core set containing 137 rice accessions with diverse types (landrace, weedy, bred) previously generated from worldwide varieties collected from the National Genebank of the Rural Development Administration (RDA-Genebank, Republic of Korea) using the program PowerCore[41,42] was selected for whole genome resequencing[43], in which 60 landrace and weedy type rice accessions were isolated for current mt genome analysis (Supplementary Table 9). 10 wild rice (Oryza rufipogon and Oryza nivara) from the resequencing set developed by Xu, et al.[44] were combined in the present study (Supplementary Table 9). Qualified DNA was used for whole-genome resequencing of the collected rice varieties, with an average coverage of approximately 9×on the Illumina HiSeq 2000 Sequencing Systems Platform (Illumina Inc.)
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