Development and Application of an SNP Marker for High-Throughput Detection and Utilization of the badh2 Gene in Rice Breeding

TL;DR

This study develops efficient genetic tools to detect and utilize the badh2 gene in rice breeding, helping to improve aromatic rice varieties.

Contribution

The development of a multiplex-ready PCR assay and a KASP marker for high-throughput badh2 genotyping in rice.

Findings

Eight japonica aromatic lines had a 7 bp deletion in badh2-E2, while 12 indica lines had an 8 bp deletion in badh2-E7.

A KASP marker enabled successful screening of an elite aromatic rice line with superior agronomic traits.

The PCR assay showed high accuracy in genotyping 200 rice plants, with only one potential heterozygous case.

Abstract

Background: As a key rice breeding resource, aromatic rice is widely cultivated in agriculture due to its unique aroma. Badh2 mutations cause function loss, enabling rice’s characteristic aroma. Methods: In this study, we analyzed several badh2 mutation types across 8 japonica and 16 indica aromatic rice lines. Based on the 7 bp deletion in badh2-E2 identified in japonica aromatic lines, we developed a multiplex-ready PCR assay for badh2 genotyping. Additionally, leveraging the deletion mutation in badh2-E7 from the indica aromatic line Yexiang, we designed a KASP marker. Results: All 8 japonica aromatic lines carried a 7 bp deletion in badh2-E2, while 12 indica aromatic lines harbored an 8 bp deletion in badh2-E7, and 4 additional indica aromatic lines exhibited an 8 bp deletion in badh2-E2. The multiplex-ready PCR assay was used to screen 200 individual plants from the aromatic rice line Jia 58: 199 plants showed the expected results, while the remaining 1 exhibited two fluorescent signal peaks—suggesting that it may be a heterozygous individual. Using the KASP marker, we performed genotyping analysis on F7 progeny individuals derived from the cross between Yexiang (aromatic line) and Yuenongsimiao (non-aromatic line). Combined with phenotypic observations, we successfully screened out an elite aromatic line named Zhexiangzhenhe, which not only possesses aroma but also maintains superior agronomic traits. Conclusions: The multiplex-ready PCR assay and KASP markers facilitate high-throughput genotyping in large-scale breeding populations, providing breeders with a rapid and efficient selection tool to accelerate aromatic trait improvement in rice.

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