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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #326626

Title: Rice fissure resistance QTLs from ‘Saber’ complement those from ‘Cypress’

item Pinson, Shannon
item Jia, Yulin
item GIBBONS, JAMES - Basf Corporation North America

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 3/25/2016
Publication Date: 9/12/2017
Citation: Pinson, S.R.M., Jia, Y., Gibbons, J. 2017. Rice fissure resistance QTLs from ‘Saber’ complement those from ‘Cypress’. Rice Technical Working Group Meeting Proceedings. , p. 171-172. March 1-4, 2016. CDROM.

Interpretive Summary:

Technical Abstract: The economic value of broken rice is about half that of whole milled rice, so one goal of producers, millers, and rice breeders is to reduce grain breakage during the dehusking and milling processes. One of the primary causes of rice breakage is fissuring, or cracking, of the rice before it enters the mill. A common cause of rice fissuring is the exposure of drying, mature kernels to humid field or postharvest conditions that cause the kernels to reabsorb moisture. Fissures may be caused by rain or dew in not-yet-harvested fields. A few rice varieties produce grain more resistant to fissuring than others, and breeders would like to incorporate these genes into improved rice varieties. Unfortunately, evaluating numerous breeding lines for fissure resistance is laborious and the environment in which the seed samples were produced can impact results. Use of molecular gene-tags to accomplish marker-assisted selections (MAS) is particularly desired by breeders for traits such as kernel fissure resistance which are both costly/laborious to measure and environmentally sensitive. Three QTLs for rice kernel fissure resistance (FisR) were previously discovered using selectively genotyped ‘Cypress’ x ‘LaGrue’ F2 progeny, and verified in a set of set of ‘Cybonnet’ x ‘Saber’ recombinant inbred lines (CbSa-RILs). Association between plant height and FisR was first detected among the Cypress x LaGrue F2 progeny, and later shown to be due to close linkage between a FisR QTL and the sd-1 semidwarf locus on the long arm of chromosome 1. A second FisR QTL mapped also to chromosome 1, but was not closely linked (> 50 cM distant) to sd-1. The third FisR QTL mapped to the short arm of chromosome 8. Cybonnet is another FisR cultivar, and its sole FisR parent was Cypress. The same three FisR QTLs originally identified in Cypress were confirmed in the CbSa-RILs, with the FisR alleles now attributed to Cybonnet. The CbSa-RILs, being pure breeding, also provided improved FisR phenotypic data due to replication across years and locations (2 replications each for TX2007, AR2007, TX2009, and TX2011). The three FisR QTLs were initially discovered using selective genotyping, where the population was first phenotyped and only progeny exhibiting extreme phenotypes were molecularly genotyped. Marker-trait linkages were detected as unequal distribution of molecular alleles between the phenotypically divergent groups. Selective genotyping resulted in identification of nine CbSa-RILs that were consistently more FisR than Saber and Cybonnet. While the high FisR of three of these RILs could be explained by their containing all three FisR alleles originally identified from Cypress, the other six FisR RILs contained 2, 1, or even 0 of the known Cypress FisR alleles. Saber is also known to be FisR, and a likely source of FisR alleles yet to be mapped in the CbSa-RILs. To better identify all FisR QTLs segregating among the CbSa-RILs, we needed to collect molecular marker data tagging the whole length of the 12 rice chromosomes. For this, we used a SNP chip designed to identify polymorphisms between japonica genotypes. Of the 384 SNPs, 28 proved noninformative due to both parents being either null or heterozygous at that locus, 212 were polymorphic, and clustering among the 144 monomorphic SNPs suggested several genomic regions to be identical by descent between Cybonnet and Saber, which are known to share ancestors. The QTL regions previously identified on chromosomes 1 and 8 were further saturated with the addition of 20 SSR loci. QTL mapping among the 286 CbSa-RILs confirmed the existence of three FisR alleles originating from Cypress, two on chromosome 1, and one on chromosome 8. Even though the CbSa-RILs were all of semidwarf plant height, they showed linkage between markers linked to sd-1 and FisR. This finding clarified that a FisR gene is