Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice

Abstract

Background: Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services. Results: We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines. Conclusion: One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.

Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs

“…A set of 342 lines, the representative germplasm set (RGS), was genotyped with the 7K array (Morales et al, 2020) (Addison et al, 2020(Addison et al, , 2021Angira et al, 2019). The biparental populations-MPA, MPB, MPC, MPD-originated from eight cultivars representing the elite southern U.S. rice germplasm.…”

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.…”

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

“…After this, one of the fluor-labelled oligo that was quenched until now binds as a tail to the corresponding amplified allele, generating a fluorescent signal. KASP assays have been extensively used in different crops, mainly cereals, becoming very helpful for MAS in wheat [ 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 ], barley [ 100 ], rice [ 101 , 102 , 103 , 104 ], sorghum [ 105 ], pea [ 106 ], watermelon [ 107 , 108 ], faba bean [ 109 ], tomato [ 110 , 111 ], and Brassica oleracea (cabbage, broccoli, kohlrabi, and Chinese kale [ 112 ]).…”