Fine Mapping of qFIS1‐2, a Major QTL for Kernel Fissure Resistance in Rice

Abstract

W hen rice (Oryza sativa L.) is milled to remove the hull and bran layer, the resulting white rice is graded according to physical properties. A key component determining the grade or economic value for a consignment of rice is its milling quality, which is defined by the proportion (in mass) of rice that remains intact (unbroken) after milling. After rice is milled, the broken kernels (defined as having grain length less than three-fourths the sample average) are separated from the unbroken rice (also known 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 to transfer this trait to rice genotypes of non-semidwarf stature that are better adapted to some rice production systems. Three quantitative trait loci (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, F 2 progeny were produced from a cross between US breeding line RU1201108, having non-semidwarf height (Sd-1/Sd-1) and poor milling quality, and Cybonnet (sd-1/sd-1), having semidwarf height and containing multiple FR loci. Simple sequence repeat (SSR) markers were used to select F 2 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 FR. Progeny from three F 2 individuals with desirable recombination at the qFIS1 -2 were phenotyped for kernel FR. Markertrait linkages observed in the three populations indicated that the qFIS1-2 locus resides on chromosome 1 distal to RM1068 at 38.44 Mb, but anterior to RM3482 at 39.72 Mb, placing it ~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 nor reliant on sd-1 and can be recombined with Sd-1 to increase the FR of non-semidwarf rice cultivars.

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

“…An association between taller height and increased kernel fissuring was detected in all four environments. This was unexpected because previous reports of association between PH and FR indicated that their correlations were due to physical linkage between qFIS1‐2 and the sd‐1 semidwarf gene, an association that the qFIS1‐2 fine mapping study (Sater et al, 2017) documented to be due to physical linkage that could be broken by recombination. As both Cybonnet and Saber are sd‐1 semidwarfs (McClung et al, 2004; Gibbons et al, 2006), the CS‐RILs do not segregate for this trait, but they apparently segregate for other PH genes, as evidenced by transgressive segregation among the CS‐RILs (Table 1).…”

“…Although the QTL intervals were long and overlapping, the locations of their LOD peaks varied between the environments by as much as 20 cM (Table 2); variable LOD peak locations between environments was true for all FR QTLs except qFIS5 , which mapped consistently to 22 to 24 cM. The fact that the LOD peak for qFIS1‐2 using across‐environment LSMean data mapped precisely to the known, fine‐mapped location (Sater et al, 2017) indicates confidence in the all QTL estimates based on LSMean data as well, it but underscores the need for numerous replications for proper evaluation of FR.…”

“…However, it is unlikely that mere differences in PH are causing differences in FR based on two findings. First, FR was previously separated from the large sd‐1 PH effects in a previous study (Sater et al, 2017). Second, among the CS‐RILs, FR was not associated with the QTL having largest effect on PH, qPH3‐2 , which explained 20% of the variance in PH among the CS‐RILs but had no effect on FR (LOD < 0.5).…”

“…The three FR QTLs originating here from Cybonnet, and previously identified in Cypress (Pinson et al, 2013), are the only FR QTLs to have been validated, to date, in more than one mapping population, as well as across multiple environments. Although qFIS1‐2 has been fine‐mapped (Sater et al, 2017), previous estimates of qFIS1‐1 and qFIS8 were hindered by marker monomorphism. The ability of SNPs to detect polymorphism undetected by SSRs was most notable on the short arm of chromosome 8 where 14 polymorphic SNP loci were present in the region telomeric to RM404, allowing qFIS8 to be more accurately mapped than before (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. Use of the Michigan State University Rice Genome Annotation Project Rice Genome Browser (MSU7; Kawahara et al, 2013) and the Rice Annotation Project Database (RAP‐DB; Sakai et al, 2013) for gene annotations, combined with information on single‐nucleotide polymorphism (SNP) variants between Cypress, LaGrue, Cybonnet, and several fissure susceptible (FS) relatives of the Cypress cultivar (Duitama et al, 2015a, 2015b) led to the identification of a gene associated with breakdown of seed storage proteins (LOC_Os01g67980) as the most likely, although not only, candidate for qFIS1‐2 (Sater et al, 2017).…”