Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 12/1/2003
Publication Date: 6/1/2004
Citation: Fjellstrom, R.G., McClung, A.M., Gibbons, J., Deren, C. 2004. Development of genetic markers for semi-dwarf plant height and photoperiod insensitivity for marker aided selection in u.s. rice. In: Rice Technical Working Group Meeting Proceedings, February 29-March 4, 2004, New Orleans, LA. 2004 CDROM. Interpretive Summary:
Technical Abstract: Plant height and photoperiod sensitivity are important characteristics of rice that have a large effect on cultivar acceptability for crop production in the US. Semi-dwarf cultivars commonly have increased resistance to lodging and photoperiod-insensitive cultivars are able to flower during the long daylength summer growing season of the US. Exotic rice cultivars are often tall and can be day-length sensitive, resulting in susceptibility to lodging and not produce an a lack of seed set due to late fall heading. These characteristics of exotic cultivars make them difficult to use in US rice breeding programs and can overshadow beneficial characteristics they may possess, like disease resistance, high yield potential, and specialty grain quality traits. DNA markers tagging semi-dwarf plant height and photoperiod insensitivity could be used to efficiently select for breeding lines carrying these traits in crosses between exotic lines and US adapted cultivars. The genes encoding semi-dwarf plant height (named sd-1) and photoperiod insensitivity (named hd-1 or, alternatively, se-1), located on rice chromosomes 1 and 6, respectively, have both been cloned. However, knowing the DNA sequences of these cloned genes in itself does not provide markers useful for selection of these traits. We surveyed substantial DNA sequence database information to identify polymorphisms in and around these two genes as sequence data became available through efforts of the International Rice Genome Sequencing Project (IRGSP) and the Beijing Genomics Institute. PCR primers were developed which flanked candidate sequence polymorphisms and were tested for PCR amplification repeatability, straightforward polymorphism scoring, and close linkage with the target gene. Genetic linkage analysis of markers with traits was analyzed in a cross between Khao Dawk Mali 105 (KDM-105), a tall and photoperiod-sensitive cultivar, and Jasmine-85, a semi-dwarf and photoperiod-insensitive cultivar. DNA marker polymorphisms were also analyzed for their association with plant height and flowering date in URRN entries and GRIN accessions. PCR primers developed to amplify polymorphic regions within the sd-1 and hd-1 genes performed unsatisfactory by producing numerous and weak amplification products. However, PCR primers flanking microsatelllite sequences near these genes consistently gave repeatable results and unambiguous scoring. Several polymorphic microsatellites were found close to the sd-1 gene. One tightly linked microsatellite found on the same BAC sequence as the sd-1 gene appears ideal for marker aided selection of this trait. The hd-1 gene also had several microsatellites in its vicinity, but displayed far less polymorphism than those around the sd-1 gene. The measured segregation of plant height and heading date in over 200 early generation progeny from the KDM-105 / Jasmine-85 cross indicates that a large proportion of the variation in these traits is explained by the sd-1 and hd-1 genes, respectively, and the markers linked to them. There was excellent association between plant height and sd-1 microsatellite markers among URRN entries and GRIN accessions, where nearly all shorter cultivars shared a common pool of microsatellite alleles not found in taller cultivars. There was poor association between heading date and hd-1 markers in comparing URRN entries with a sample of 15 photoperiod sensitive GRIN accessions. Nevertheless, hd-1 markers could still be readily used for selection of photoperiod-insensitivity in crosses between US and exotic germplasm.