The genetic and molecular origin of natural variation for the fragrance trait in an elite Malaysian aromatic rice through quantitative trait loci mapping using SSR and gene-based markers

Abstract

MRQ74, a popular aromatic Malaysian landrace, allows for charging considerably higher prices than non-aromatic landraces. Thus, breeding this profitable trait has become a priority for Malaysian rice breeding. Despite many studies on aroma genetics, ambiguities considering its genetic basis remain. It has been observed that identifying quantitative trait loci (QTLs) based on anchor markers, particularly candidate genes controlling a trait of interest, can increase the power of QTL detection. Hence, this study aimed to locate QTLs that influence natural variations in rice scent using microsatellites and candidate gene-based sequence polymorphisms. For this purpose, an F2 mapping population including 189 individual plants was developed by MRQ74 crosses with 'MR84', a non-scented Malaysian accession. Additionally, qualitative and quantitative approaches were applied to obtain a phenotype data framework. Consequently, we identified two QTLs on chromosomes 4 and 8. These QTLs explained from 3.2% to 39.3% of the total fragrance phenotypic variance. In addition, we could resolve linkage group 8 by adding six gene-based primers in the interval harboring the most robust QTL. Hence, we could locate a putative fgr allele in the QTL found on chromosome 8 in the interval RM223-SCU015RM (1.63cM). The identified QTLs represent an important step toward recognition of the rice flavor genetic control mechanism. In addition, this identification will likely accelerate the progress of the use of molecular markers for gene isolation, gene-based cloning, and marker-assisted selection breeding programs aimed at improving rice cultivars.

Opportunities of marker‐assisted selection for rice fragrance through marker–trait association analysis of microsatellites and gene‐based markers

“…; Golestan Hashemi et al . ). In MAS, the highly efficient integration of exogenous gene(s) into receptors requires the simultaneous use of three types of marker: functional, closely linked and genome‐wide SSR markers (Shi et al .…”

“…; Golestan Hashemi et al . ). The fgr locus has been mapped between RM3459 and RM8264, with a physical interval of ∼800 kb.…”

Genetic Analysis of Natural Variation in Antirrhinum Scent Profiles Identifies BENZOIC ACID CARBOXYMETHYL TRANSFERASE As the Major Locus Controlling Methyl Benzoate Synthesis

“…In crops, scent related traits include flavor and aroma and have undergone extensive research in many important plants such as rice (Lorieux et al, 1996; Singh et al, 2007; Golestan Hashemi et al, 2015), tomato (Klee, 2010; Klee and Tieman, 2013), strawberry (Zorrilla-Fontanesi et al, 2012), or trees such as peaches (Eduardo et al, 2013). The use of natural variation has helped first to define the genetic structure of the character and second to identify candidate genes involved in scent and volatile emission.…”

“…The genetic studies on scent and volatiles have been an important part of plant biotechnology as the major compounds involved in flavor and aroma are VOCs. As a result, studies in crops such as tomato, peach, rice or strawberry are well-developed (Zorrilla-Fontanesi et al, 2012; Sánchez et al, 2013; Rambla et al, 2014; Golestan Hashemi et al, 2015). The genetics of scent emission and its control has been studied in a variety of plants with different outcomes.…”

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“…Genetic maps have become significantly important in understanding markers, breeding, association genetics, and map-assisted gene cloning, gene mining and mapping of quantitative trait loci (QTLs) (Golestan Hashemi et al, 2015). In our study we integrated two genetic maps from the D genome of the diploid cotton with mapping size of 188 F 2:3 population, the first genetic map (Map A) was composed of a genetic cross between G. klotzschianum (female parent )and G. davidsonii (male parent) while the second genetic map (Map B) was developed from G. thurberi (female parent) and G. trilobum (male parent).…”