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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.)

Author
item Sater, Haley
item Pinson, Shannon
item Moldenhauer, Karen
item Siebenmorgen, Terry
item Mason, Richard
item Boyett, Virginia
item Edwards, Jeremy

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/9/2017
Publication Date: 6/2/2017
Citation: Sater, H.M., Pinson, S.R.M., Moldenhauer, K., Siebenmorgen, T.J., Mason, R.E., Boyett, V.A., Edwards, J. 2017. Fine mapping and introgressing qFIS1-2, a major QTL for kernel fissure resistance in rice (Oryza sativa L.). Crop Science. doi:10.2135/cropsci2016.09.08213.

Interpretive Summary: Rice that remains whole after milling is more desired and commands a higher market price than rice that is broken. Incomes for farmers, millers, processors, and international marketers of rice are all improved when rice is prevented from breaking during milling. A primary cause of breakage in the mill is field fissuring which occurs when rice that is mature or nearing maturity in the field is exposed to dew or rain causing the grains to swell and crack. Three quantitative trait loci (QTLs) associated with resistance to rice kernel fissuring were previously identified. In the present study, the largest of these QTLs was mapped more precisely, making it even more amenable for use in marker-assisted selection by breeders. With the more precise location, we were also able to compare genomic sequence between a fissure resistant (FR) parental line and several of its fissure susceptible (FS) progeny lines leading to the identification of three genes as being likely candidates underlying or explaining the FR effects of the target QTL. Prior to the present study, all of the germplasm in which this QTL for fissure resistance was known to exist were of semidwarf height, and the fissure resistance locus appeared to linked to the sd-1 semidwarf gene as the two traits segregated together among cross progeny. This raised concern that the mechanisms for kernel fissure resistance from this QTL might depend in some way on the altered plant canopy that is also associated with the sd-1 gene, which is known to create a unique microclimate that affects other traits (e.g., sheath blight disease resistance). Many but not all rice breeders want to develop semidwarf rice cultivars, making the linkage between sd-1 and the fissure resistance QTL advantageous for many, but not for all, rice breeders. While we were fine-mapping the fissure resistance locus, we found some progeny lines in which the genetic linkage was broken and the fissure resistance trait was recombined instead with the allele for tall plant height (Sd-1). This study documented definitively that kernel fissure resistance can be expressed in rice cultivars that do not have the semidwarf height, and resulted in new germplasm that is of particular interest to breeders who develop rice cultivars of traditional or tall height.

Technical Abstract: Rice (Oryza sativa L.) kernel fissuring increases breakage during milling and decreases the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to rice genotypes of non-semidwarf stature better adapted to some rice production systems. Three QTLs for FR were previously reported, with the FR locus linked with the semidwarf sd-1 locus on chromosome 1 having the strongest effect. For fine mapping, F2 progeny were developed from a cross between U.S. breeding line RU1201108 with non-semidwarf height (Sd-1/Sd-1) and reduced milling yield, and Cybonnet (sd-1/sd-1) with semidwarf height and containing multiple FR loci. Simple sequence repeat (SSR) markers were used to select F2 plants that both retained at least one copy of the Sd-1 allele and showed evidence of genetic recombination in the region of chromosome 1 known to contain Sd-1 and qFIS1-2, a QTL for fissure resistance. Progeny from three F2 individuals with desirable recombination at the qFIS1-2 were phenotyped for kernel fissure resistance. Marker-trait linkages observed in the three populations indicate that the qFIS1-2 locus resides distal to RM1068 on chromosome 1 at 38.44Mb, but anterior to RM3482 at 39.72Mb, or approximately 6 to 10 cM distal to sd-1 on chromosome 1. The recombination documented in this study verifies that the previously identified qFIS1-2 is not pleiotropic with sd-1 and can be recombined with Sd-1 to increase the FR of non-semidwarf rice cultivars.

Last Modified: 08/17/2017
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