Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing

Subbaiyan, Gopala K., Waters, Daniel L. E., Katiyar, Sanjay K., Sadananda, Ajanahalli R., Vaddadi, Satyadev and Henry, Robert J. (2012) Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing. Plant Biotechnology Journal, 10 6: 623-634. doi:10.1111/j.1467-7652.2011.00676.x


Author Subbaiyan, Gopala K.
Waters, Daniel L. E.
Katiyar, Sanjay K.
Sadananda, Ajanahalli R.
Vaddadi, Satyadev
Henry, Robert J.
Title Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7644
1467-7652
Publication date 2012-08
Sub-type Article (original research)
DOI 10.1111/j.1467-7652.2011.00676.x
Volume 10
Issue 6
Start page 623
End page 634
Total pages 12
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell
Collection year 2013
Language eng
Abstract Advances in next-generation sequencing technologies have aided discovery of millions of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels), which are an invaluable resource for marker-assisted breeding. Whole-genome resequencing of six elite indica rice inbreds (three cytoplasmic male sterile and three restorer lines) resulted in the generation of 338million 75-bp paired-end reads, which provided 85.4% coverage of the Nipponbare genome. A total of 2819086 nonredundant DNA polymorphisms including 2495052 SNPs, 160478 insertions and 163556 deletions were discovered between the inbreds and Nipponbare, providing an average of 6.8 SNPs/kb across the genome. Distribution of SNPs and InDels in the chromosome was nonrandom with SNP-rich and SNP-poor regions being evident across the genome. A contiguous 4.3-Mb region on chromosome 5 with extremely low SNP density was identified. Overall, 83262 nonsynonymous SNPs spanning 16379 genes and 3620 nonsynonymous InDels in 2625 genes have been discovered which provide valuable insights into the basis underlying performance of the inbreds and the hybrids between these inbred combinations. SNPs and InDels discovered from this diverse set of indica rice inbreds not only enrich SNP resources for molecular breeding but also enable the study of genome-wide variations on hybrid performance.
Keyword Deletions
Genome-wide variations
Insertions
Next-generation sequencing
Rice (Oryza sativa L.)
Single nucleotide polymorphism
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article first published online: 6 January 2012.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2013 Collection
 
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