Identification of candidate genes for panicle length in Oryza sativa L. ssp. japonica via genome-wide association study and linkage mapping

Panicle length is an important trait for improving panicle architecture and grain yield in rice (Oryza sativa L.). Two populations were used to identify QTLs associated with panicle length. Based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs), twenty eight lead SNPs significantly associated with panicle length in 2018 and 2019 were detected on chromosomes 1, 2, 3, 4, 6, 7, 9, 10 and 11 in the natural population consisting of 295 japonica rice varieties collected from Northeast Asia. Eight QTLs for panicle length in 2018 and 2019 were detected on chromosomes 1, 2, 3, 6, 7 and 9 through linkage mapping in the recombinant inbred line population derived from a cross between the cultivars Kongyu131 (short panicle) and Xiaobaijingzi (long panicle). Interestingly, Chr6_7539486 identified by GWAS in both years, was located within the same region as qPL6 identified by the linkage mapping. According to LD decay of the whole genome, a 218-kb region on chromosome 6 was selected for further analysis. After haplotype analysis, quantitative real-time PCR and sequence analysis, LOC_Os06g14200 and LOC_Os06g14370 were initially considered as the candidate genes. Moreover, LOC_Os06g14200 encoding a C3HC4 type zinc finger protein containing RING finger domain plays an important role in the growth and development of plants, which was most likely involved in the regulation of panicle length in rice. This study provides resources for breeding aimed at improving rice high yield potential.