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United States Department of Agriculture

Agricultural Research Service

Research Project: DEVELOPMENT AND CHARACTERIZATION OF GENETIC RESOURCES FOR AGRONOMIC AND QUALITY TRAITS USING GENOMIC TOOLS Title: Three QTLs conferring resistance to kernel fissuring in rice (Oryza sativa L.) identified by selective genotyping in two tropical japonica populations

Authors
item Pinson, Shannon
item Jia, Yulin
item Gibbons, James -

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 21, 2013
Publication Date: October 25, 2013
Citation: Pinson, S.R., Jia, Y., Gibbons, J. 2013. Three QTLs conferring resistance to kernel fissuring in rice (Oryza sativa L.) identified by selective genotyping in two tropical japonica populations. Crop Science. 53:2434-2443.

Interpretive Summary: Unbroken rice kernels have twice as much market value as broken milled rice. A few rice varieties break less than others because their grains resist developing stress fissures (cracks) during pre-milling stages. Identification and molecular-tagging of the genes underlying fissure resistance would speed the development of new varieties improved for this trait. Marker-aided selections (MAS) are based on the principle that when markers linked to a gene affecting a desired trait are selected, the physically linked trait is also in selected individuals. The present study took advantage of the fact that the reverse also holds true, and was accomplished by selecting for fissure resistance (FisR) versus fissure susceptibility (FisS) among the progeny of two populations, then identifying molecular marker alleles that were present in different proportions between the FisR and FisS subgroups. Identification of the same genes in multiple populations and environments increases confidence in those genes, and indicates which genes will be most effective under a variety of genetic and field conditions. Thus it was significant that both populations identified three FisR genes, two on chromosome 1, plus another on chromosome 9. Our first study population segregated for plant height due to the sd1 gene on chromosome 1, while the second other did not (all short height). When association between FisR and short plant height was detected in the first population, it raised concern that FisR could be a result of short plant height. However, verification of two FisR loci on chromosome 1 in the second population, which did not segregate for plant height, indicates that FisR is due to a separate but nearby gene. While semidwarf rice varieties are often preferred, there are some parts of the U.S. and of the world where farmers prefer to plant tall rice varieties. This means that the linkage we found between FisR and the sd1 semidwarf gene is considered desirable by some breeders, but undesired by others. The markers found linked to the FisR genes can be used by breeders to either maintain the linkage, or to instead break it by identifying breeding progeny where natural genetic recombination has switched the linkages, now re-aligning the FisR gene with the Sd1 tall allele.

Technical Abstract: Kernel fissures caused by pre- or post-harvest stresses are the leading cause of breakage among milled rice, causing economic losses for producers, millers, and processors. Being an environmentally sensitive trait, it is difficult to reliably select for rice fissure resistance among breeding progeny. Identification of QTLs and molecular gene-tags is desirable for marker-assisted selection. The present study first identified chromosomal regions containing QTLs associated with fissure resistance (FisR) by molecular markers whose alleles were present in different proportions between selectively genotyped FisR and fissure susceptible (FisS) progeny subgroups of two mapping populations. Three FisR QTLs were identified, two on chromosome 1 and one on chromosome 8, all of which were identified in both populations. Further QTL verification as well as improved estimates of QTL locations and effects were obtained using a set of recombinant inbred lines (RILs) tagged with markers along chromosomes 1 and 8. The QTL with largest effect, qFIS1-2, was found linked to the semidwarf sd1 locus on chromosome 1. This explained earlier reports of putative association between FisR and short plant height. However, semidwarf plant height is not desired for all rice growing regions of the U.S. or the world. The fact that the LOD peak for qFIS1-2 was approximately 25 cM distal to the sd1 locus among the RILs indicates that this linkage can be broken, especially through marker-aided selection. This is the first report of rice FisR QTLs whose effects were verified in multiple mapping populations and seed-production environments.

Last Modified: 11/24/2014
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