Three Quantitative Trait Loci Conferring Resistance to Kernel Fissuring in Rice Identified by Selective Genotyping in Two Tropical Japonica Populations

Abstract

Kernel fissures in rice (Oryza sativa L.) caused by pre‐ or postharvest stresses are the leading cause of breakage among milled rice, causing economic losses for producers, millers, and processors. The present study identified three quantitative trait loci (QTLs) associated with fissure resistance (FisR) through selective genotyping of two mapping populations, one derived from ‘Cypress’ × ‘LaGrue’ and the other derived from ‘Cybonnet’ × ‘Saber’. Two QTLs were identified on chromosome 1 and one on chromosome 8 in both populations. Further QTL verification as well as improved estimates of QTL locations and effects were obtained using a set of 275 Cybonnet × Saber recombinant inbred lines (RILs) tagged with markers along chromosomes 1 and 8 and phenotyped using seven replications of seed harvested in four environments. Both QTLs on chromosome 1 were statistically significant in all four environments; the chromosome 8 QTL was significant in three. All alleles for FisR originated from Cypress, which was the FisR parent of Cybonnet. The QTL with largest effect, qFIS1‐2, which explained 13% of the RIL variance for FisR, was found linked to the semidwarf sd1 locus on chromosome 1. This explains earlier reports of putative association between FisR and short plant height. This is the first report of rice FisR QTLs whose effects were verified in multiple mapping populations and seed‐production environments.

Novel QTLs Affecting Rice Kernel Fissure Resistance Discovered in the Cultivar ‘Saber’ Augment Those from ‘Cybonnet’

“…Five QTLs affecting rates of kernel fissuring were identified (Table 2). The three with the largest LODs and additive effects among the CS‐RILs ( qFIS1‐1 , qFIS1‐2 , and qFIS8) were the same three FR loci discovered previously in Cypress (Pinson et al, 2013). Cypress is the sole FR parent of Cybonnet, and thus it was not surprising for Cybonnet to have seemingly inherited its three FR alleles from Cypress.…”

“…The next largest marker gap is a 44‐cM gap on chromosome 3, which was also characterized as likely IBD with eight intervening SNP and SSR loci being monomorphic. Although SNP monomorphism supported contentions of IBD in some chromosomal regions, in other regions polymorphic SNPs were now available to support new QTL evaluations in regions previously confounded by SSR monomorphism (Pinson et al, 2013). This was most notable on the short arms of chromosomes 1 and 8, where qFIS1‐1 and qFIS8 were detected with SSRs, but not mapped precisely (Pinson et al, 2013).…”

“…Cypress is the sole FR parent of Cybonnet, and thus it was not surprising for Cybonnet to have seemingly inherited its three FR alleles from Cypress. Although the three FR QTLs originating from Cybonnet among the CS‐RILs were previously known and validated (Pinson et al, 2013), the availability of higher density SNP markers allowed them to be more accurately mapped. The QTL qFIS1‐1 was previously reported to be on or near RM580 (Pinson et al, 2013), with a LOD peak proximal to RM580.…”

“…Cybonnet (PI 636726) and Saber (PI 633624) are both tropical japonica US long grain rice cultivars that have exhibited fissure resistance in past studies (Pinson, 2004; Blanche et al, 2009; Pinson et al, 2013). Both Cybonnet and Saber are sd‐1 semidwarfs (McClung et al, 2004; Gibbons et al, 2006).…”

“…To facilitate the breeding of cultivars with improved FR, a laboratory method for distinguishing fissure‐resistant and ‐susceptible cross‐progeny was developed (Pinson et al, 2012) and used to discover three quantitative trait loci (QTLs) associated with FR in selectively genotyped Cypress × ‘LaGrue’ F 2 plants (Pinson et al, 2013). These three FR QTLs ( qFIS1‐1 , qFIS1‐2 , and qFIS8 ) were subsequently validated among a set of 275 Cybonnet × ‘Saber’ recombinant inbred lines (CS‐RILs) that were genotyped using relatively few (18) simple sequence repeat markers (SSRs) located only in and around the putative QTL regions (Pinson et al, 2013). One FR QTL was later fine‐mapped using F 3 and F 4 progeny derived from a different Cybonnet cross (Sater et al, 2017), which placed qFIS1‐2 in the 1.3‐megabase (Mb) interval between RM1068 and RM3482 on the long arm of chromosome 1.…”