Date of Graduation


Document Type


Degree Name

Master of Science in Crop, Soil & Environmental Sciences (MS)

Degree Level



Crop, Soil & Environmental Sciences


Karen A. Moldenhauer

Committee Member

Richard E. Mason

Second Committee Member

Shannon R. Pinson

Third Committee Member

Terry J. Siebenmorgen

Fourth Committee Member

Richard J. Norman


Biological sciences, Breeding, Fissure, Grain quality, Head rice, QTL, Rice


Rice (Oryza sativa L.) kernel fissuring is a major concern of both rice producers and millers. Fissures are small cracks in rice kernels that increase breakage of kernels when milled, and decrease the value of processed rice. This study employed molecular gene tagging methods to fine-map a fissure resistance (FR) locus found in ‘Cybonnet’, a semidwarf tropical japonica cultivar, as well as transfer this trait to rice genotypes of taller, non-semidwarf plant height that are better adapted to some rice production systems. Three QTLs for FR were previously reported; the FR locus with strongest effect resides near the semidwarf sd-1 locus on the long arm of chromosome 1, explaining associations observed between increased FR and reduced plant height. This study began with F2 progeny from a cross between a U.S. inbred breeding line with non-semidwarf (Sd-1/Sd-1) plant height and poor milling yields, and Cybonnet, which is semidwarf (sd-1/sd-1) and noted for having improved milling quality due to increased FR. Simple sequence repeat (SSR) molecular markers were used to select 11 F2 progeny plants that retained at least one copy of the Sd-1 allele, but also contained evidence of genetic recombination in the region of chromosome 1, known to contain Sd-1 and qFIS1-2, so that the positon of qFIS1-2 relative to Sd-1 could be determined more precisely, and so that FR allele could be recombined with the Sd-1 allele. Three of the 11 selected plants were also homozygous at the two known FR QTLs that are not closely linked to sd-1; another four plants were homozygous at one but not both of the two additional FR loci. The F2:3 progeny generated were genotyped prior to being phenotyped; only individuals homozygous for the new recombination underwent extensive evaluation for FR. Progeny from three of 11 populations have been phenotyped. Marker-trait linkages observed in the first two populations indicated that qFIS1-2 resides distal to RM1068. Research efforts were then focused on just those populations whose recombination points were distal to RM1068 (i.e., at a base pair location higher 1:38439184). Results from the three populations observed to date indicate that the qFIS1-2 locus resides distal to RM1068 at 1:38439184 but anterior to RM3482 at 1:39720039, 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 linked to, but not pleiotropic with, sd-1 and thus can be recombined with Sd-1 during introgression breeding to increase the FR of rice cultivars having non-semidwarf stature.