Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing
Gopala K. Subbaiyan
Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
Search for more papers by this authorDaniel L. E. Waters
Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
Search for more papers by this authorSanjay K. Katiyar
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorAjanahalli R. Sadananda
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorSatyadev Vaddadi
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorCorresponding Author
Robert J. Henry
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, Australia
(Tel +61 7 3346 0551; fax +61 7 3346 0555; email [email protected])Search for more papers by this authorGopala K. Subbaiyan
Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
Search for more papers by this authorDaniel L. E. Waters
Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
Search for more papers by this authorSanjay K. Katiyar
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorAjanahalli R. Sadananda
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorSatyadev Vaddadi
Advanta India Limited, Banjara Hills, Hyderabad, AP, India
Search for more papers by this authorCorresponding Author
Robert J. Henry
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld, Australia
(Tel +61 7 3346 0551; fax +61 7 3346 0555; email [email protected])Search for more papers by this authorSummary
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 338 million 75-bp paired-end reads, which provided 85.4% coverage of the Nipponbare genome. A total of 2 819 086 nonredundant DNA polymorphisms including 2 495 052 SNPs, 160 478 insertions and 163 556 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, 83 262 nonsynonymous SNPs spanning 16 379 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.
Supporting Information
Figure S1 Classification of the reads from the sequence of each of the six elite indica rice inbreds mapped onto the Nipponbare genome genotypes.
Figure S2 Distribution of SNPs identified between each of the six elite indica rice inbreds and Nipponbare in the 12 rice chromosomes.
Figure S3 Distribution of insertions identified between each of the six elite indica rice inbreds and Nipponbare in the 12 rice chromosomes.
Figure S4 Distribution of deletions identified between each of the six elite indica rice inbreds and Nipponbare in the 12 rice chromosomes.
Figure S5 Distribution of InDel polymorphisms in each of the elite indica rice inbreds compared with Nipponbare genome based on their length.
Figure S6 Annotation of SNPs, insertions and deletions identified between each of the six elite rice genotypes and Nipponbare.
Figure S7 Degree of distribution and skewness of nonsynonymous SNPs per kb in genes among each of the six elite inbred lines and Nipponbare.
Tables S1 Coverage of the reads from resequencing of the elite inbred parent 9001 A, 9002 A, 9003 A, 9001 R, 9002 R and 9003 R with Illumina GAIIx to the Nipponbare genome.
Tables S2 Polymorphism in genomic DNA observed in the elite rice inbred 9001 A, 9002 A, 9003 A, 9001 R, 9002 R and 9003 R in comparison with Nipponbare.
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| PBI_676_sm_TableS1-S2-FigS1-S7.docx3.4 MB | Supporting info item |
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