Abstract
Abstract
Background
Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services.
Results
We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines.
Conclusion
One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.
Funder
Louisiana Rice Research Board
National Institute of Food and Agriculture
Publisher
Springer Science and Business Media LLC
Subject
Plant Science,Soil Science,Agronomy and Crop Science
Reference48 articles.
1. Ahn SN, Bollich CN, Tanksley SD (1992) RFLP tagging of a gene for aroma in rice. Theor Appl Genet 84(7–8):825–828. https://doi.org/10.1007/BF00227391
2. Annex (2011) Business process analysis of the export of jasmine rice from thailand to the United States. Buiness Process Anal. Guid. to Simpl. Trade Proced., pp 1–68 http://www.unescap.org/tid/publication/tipub2558.asp (Accessed 2 Feb 2019)
3. Asante MD, Kovach MJ, Huang L, Harrington S, Dartey PK et al (2010) The genetic origin of fragrance in NERICA1. Mol Breed 26(3):419–424. https://doi.org/10.1007/s11032-009-9382-8
4. Baldwin, K., and N. Childs. 2018. USDA Rice Outlook. USDA Rice Outlook. https://www.ers.usda.gov/webdocs/publications/89598/rcs-18g.pdf?v=0 (Accessed 13 Dec 2018).
5. Blanche SB, Linscombe SD, Sha X, Bearb KF, Groth DE et al (2009) Registration of ‘Catahoula’ Rice. J Plant Regist 3(2):146. https://doi.org/10.3198/jpr2008.11.0677crc
Cited by
22 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献