Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica)

Waters, Daniel L. E., Subbaiyan, Gopala Krishnan, Mani, Elangovan, Singh, Sukhpa, Vaddadi, Satyadev, Baten, Abdul and Henry, Robert J. (2015) Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica). Tropical Plant Biology, 8 3-4: 117-125. doi:10.1007/s12042-015-9156-x

Author Waters, Daniel L. E.
Subbaiyan, Gopala Krishnan
Mani, Elangovan
Singh, Sukhpa
Vaddadi, Satyadev
Baten, Abdul
Henry, Robert J.
Title Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica)
Journal name Tropical Plant Biology   Check publisher's open access policy
ISSN 1935-9756
Publication date 2015-11-13
Year available 2015
Sub-type Article (original research)
DOI 10.1007/s12042-015-9156-x
Open Access Status Not Open Access
Volume 8
Issue 3-4
Start page 117
End page 125
Total pages 9
Place of publication New York, NY United States
Publisher Springer New York LLC
Collection year 2016
Language eng
Formatted abstract
The linear relationship between genetic distance and heterosis within maize heterotic groups has inspired efforts to predict heterosis using molecular markers in other species. In this study, three cytoplasmic male sterile and three restorer lines from a hybrid rice breeding program were crossed in all possible (9) combinations and the F1 offspring grown in replicated trials in three locations. Whole genome sequence analyses were used to identify hybrid pair genome-wide polymorphisms and the extent to which these polymorphisms were associated with heterosis estimated. The number of total hybrid pair SNP ranged from 150,823 to 331,876 and mid-parent heterosis from −13.6 % to 18.6 %. Hybrid pair total SNP, total INDEL, gene SNP and gene INDEL counts were generally correlated at the whole genome and chromosome level. There was a close correlation between chromosome SNP and INDEL frequencies while gene presence-absence analysis found little difference between cross combinations. The relationship between whole genome SNP and heterosis was best explained by a second order polynomial of negative sign, suggesting a positive heterotic response may be achieved by maintaining a balance between inbreeding and outbreeding depression, and that genome wide polymorphisms may have a role in predicting heterosis in rice.
Keyword Genome sequence
Genome wide polymorphism
Oryza sativa
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2016 Collection
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