THB1, a putative transmembrane protein that causes hybrid breakdown in rice

Area of Science:

• Genetics and Plant Breeding
• Reproductive Biology
• Molecular Evolution

Background:

• Hybrid breakdown is a key post-zygotic reproductive isolation mechanism hindering gene flow between species.
• In rice (Oryza sativa), hybrid breakdown is attributed to two complementary recessive genes: temperature sensitive hybrid breakdown1 (thb1) and thb2.

Purpose of the Study:

• To delimit the THB1 locus and identify the causal mutation responsible for hybrid breakdown.
• To investigate the evolutionary history and distribution of THB1 and THB2 alleles in different rice subgroups.

Main Methods:

• Fine-mapping of the THB1 locus to a 9.1-kb region containing a single gene.
• Haplotype analysis of THB1 in 119 rice accessions.
• Test crosses with thb2 and thb1 carriers to identify functional alleles.
• Identification of a nonsynonymous SNP as the causal mutation for thb1.
• Development of a derived cleaved amplified polymorphic sequence (dCAPS) marker for SNP detection.

Main Results:

• The THB1 locus was delimited, revealing a gene encoding a putative transmembrane protein.
• Haplotype analysis identified 22 distinct haplotypes for THB1, with haplotype 2 (H2) linked to thb1 and restricted to temperate japonica.
• A specific nonsynonymous SNP in H2 was confirmed as the causal mutation for thb1.
• THB2 was found in temperate japonica, tropical japonica, and indica subgroups, suggesting ancient japonica origin and introgression.

Conclusions:

• THB1 likely evolved recently in temperate japonica rice, contributing to reproductive isolation.
• THB2 appears to be an older gene with a broader distribution across rice subgroups.
• The developed dCAPS marker facilitates efficient detection of the thb1 causal SNP, aiding rice breeding efforts.