Re-sequencing DNA Assembly And SNPs Detection Of CO39 And Its Five Near Isogenic Lines

The development of Next Generation Sequencing (NGS) technologies and the appearance of the 3rd generation sequencing methods have made DNA sequencing high throughput and very cost-effective. Consequently, many opportunities are being opened to explore the relationships between genetic and phenotypic diversity with a resolution never reached before. Re-sequencing, leading to arrays of high-density Single Nucleotide Polymorphisms (SNPs), is allowing whole-genome scans to identify genetic blocks that are significantly correlated with crop quantitative trait variation. In this paper,we used NGS technology to re-sequence the genome DNA of CO39 (Susceptible to blast fungus) and its five near isogenic lines(NILs) varieties, including CN-1, CN-2, CN-3, CN-4a and CN-4b, which were resistant to blast fungus. SOAPaligner was applied to assembly the genome DNA sequence and SOAPsnp was used to detect Single Nucleotide Polymorphisms (SNPs) in five NILs genome. The main results are summarized in the following.1. The results showed that CN-4b resistant to Guyl 1 race, while the other tested rice genotypes was susceptible to GUY11 race. Meanwhile, all the 5 NILs were resistant to 81278ZB15 race. After genome re-sequencing of CO39 and its 5 NILs, SOAPaligner was used to assembly the genome DNA sequence of the 6 tested rice genotypes by using Nipponbare genome as reference. We found the average genome sequence coverage of the 6 tested rice genotypes were all higher than 86% and their sequencing depth was over 50x, indicating that the genome DNA sequences could be used to comparative genomics research.2. SOAPsnp tools was applied to detect SNPs in the 5 NILs genome by using CO39 genome as background.3773/105,2946/54,1459/34,822/18 and 3082/52 nSNPs/nonsense SNPs were detected in the 5 NILsrespectively. nSNPs and nonsense SNPs can cause the change of the gene product, which may lead to produce different agronomic trait between the NILs and its parental line, CO39.3. Totally, we found 397 genes containing 1 or more than 1 o nSNPs in the 4 NILs genomes, among them 128 were NBS-LRR genes. Some genes contain more than 4 nSNPs. The candidate fungus race-resistant genes were screened from the nSNPs containing genes considering the resistant ability of the 4 NILs to different fungus race. In GUY 11-resistant rice genotype, CN-4b genome, we found 63 Guyl 1-resistant genes. Whilst,457 81278ZB15-resistant genes were selected from the 4 NILs. Finally, the structural variation induced by nSNPs in the candidate blast race-resistant genes was predicted.In summary, the candidate fungus race-resistant genes were screened from the blast-resistant rice genotypes by using genome re-sequencing and comparative genomics methods. The result would provide the clue for the further research work on the function of blast-resistant genes in rice.