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The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population

Citation

Hanzi, He (2020), The 49,890 SNPgenotype derived from genotyping-by-sequencing strategy for the NIP/9311 backcross inbred lines population, Dryad, Dataset, https://doi.org/10.5061/dryad.sf7m0cg44

Abstract

Transmission ratio distortion (TRD) refers to a widespread phenomenon in which one allele is transmitted by heterozygotes more frequently to the progeny than the opposite allele. TRD is considered as a mark suggesting the presence of reproductive barrier. However, the genetic and molecular mechanisms underlying TRD in rice remain largely unknown. In the present study, a population of backcross inbred lines (BILs) derived from the cross of a japonica cultivar Nipponbare and an indica variety 9311 was utilized to study the genetic base of TRD. A total of eighteen genomic regions were identified for TRD in the BILs. Among them, twelve and six regions showed indica (9311) and japonica (Nipponbare) alleles with preferential transmission, respectively. A series of F2 populations were used to confirm the TRD effects, including six genomic regions that were confirmed by chromosome segment substitution line (CSSL)-derived F2 populations from inter-subspecific allelic combinations. However, none of the regions was confirmed by the CSSL-derived populations from intra-subspecific allelic combination. Furthermore, significant epistatic interaction was found between TRD1.3 and TRD8.1 suggesting that TRD could positively contribute to breaking inter-subspecific reproductive barriers. Our results have laid the foundation for identifying the TRD genes and provide an effective strategy to breakdown TRD for breeding wide-compatible lines, which will be further utilized in the inter-subspecific hybrid breeding programs.

Methods

The BILs were genotyped using a genotyping-by-sequencing (GBS) strategy.  Sequencing was performed on the selected tags using Illumina HiSeq with the paired-end mode and 150-bp read length.  The Burrows Wheeler Aligner software was used to map the clean reads for each sample on the reference genome (MSU7.0) (http://rice.plantbiology.msu.edu/index.shtml).  Single nucleotide polymorphism (SNP) calling was performed by Genome Analysis Toolkit.

 

Funding

National Natural Science Foundation of China, Award: 31671656

National Natural Science Foundation of China, Award: 31971864