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

Abstract

Developing fragrant rice through marker-assisted/aided selection (MAS) is an economical and profitable approach worldwide for the enrichment of an elite genetic background with a pleasant aroma. The PCR-based DNA markers that distinguish the alleles of major fragrance genes in rice have been synthesised to develop rice scent biofortification through MAS. Thus, the present study examined the aroma biofortification potential of these co-dominant markers in a germplasm panel of 189 F2 progeny developed from crosses between a non-aromatic variety (MR84) and a highly aromatic but low-yielding variety (MRQ74) to determine the most influential diagnostic markers for fragrance biofortification. The SSRs and functional DNA markers RM5633 (on chromosome 4), RM515, RM223, L06, NKSbad2, FMbadh2-E7, BADEX7-5, Aro7 and SCU015RM (on chromosome 8) were highly associated with the 2AP (2-acetyl-1-pyrroline) content across the population. The alleles traced via these markers were also in high linkage disequilibrium (R(2) > 0.70) and explained approximately 12.1, 27.05, 27.05, 27.05, 25.42, 25.42, 20.53, 20.43 and 20.18% of the total phenotypic variation observed for these biomarkers, respectively. F2 plants harbouring the favourable alleles of these effective markers produced higher levels of fragrance. Hence, these rice plants can be used as donor parents to increase the development of fragrance-biofortified tropical rice varieties adapted to growing conditions and consumer preferences, thus contributing to the global rice market.

Allelic variations in aroma gene in cultivated rice varieties

“…Conventional breeding methods combined with selection of DNA markers, so called Marker Assisted Selection (MAS), is a fast and efficient strategy for the introgression of aroma trait (Golestan Hashemi et al, 2015). But this requires correct phenotyping of the breeding materials for aroma and understanding the genetic basis of aroma in these materials.…”

High-resolution quantitative trait locus mapping for rice grain quality traits using genotyping by sequencing

“…Identification of the genes associated with QTLs controlling a trait was challenging owing to the low resolution of early QTL maps with low-density markers. Since the first linkage map constructed using RFLP markers in rice ( McCouch et al., 1988 ), several linkage maps have been produced using SSR ( Golestan Hashemi et al., 2015 ; Bazrkar-Khatibani et al., 2019 ; Bhat et al., 2019 ; Jia et al., 2019 ) and SNP ( Rahman et al., 2017 ; Jewel et al., 2019 ) markers in rice. However, these maps could not overcome the issues of either low-density linkage maps with unreasonable marker coverage or high-density linkage maps requiring considerably more time, manpower, and financial resources.…”

Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

“…The OsGluA2LET allele exhibits lower transcription and is thus a promising target gene for low-PC rice breeding through MAS ( Yang et al., 2019a ; 2019b ). Gene-specific molecular markers such as NKSbad2 , FMbadh2-E7 , BADEX7-5 , Aro7 , and KASP markers (nine SNPs) that are highly associated with elevated 2-AP content have been used for aroma improvement by MAS ( Golestan Hashemi et al., 2015 ; Addison et al., 2020 ). In terms of lipid manipulation, although the four genes PAL6 , LIN6 , MYR2 , and ARA6 have been found to contribute to lipid content variation among rice accessions, there is no evidence for their use in MAB programs.…”