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The tiller angle, which is an important agronomic trait, determines plant architecture and greatly influences the grain yield of rice. In this study, a population of chromosome segment substitution lines derived from a cross between a japonica variety with a compact plant architecture—Koshihikari—and an indica variety with a spread-out plant architecture—Nona Bokra—was used to investigate the genetic basis of the tiller angle. Five quantitative trait loci (qTA1, qTA5, qTA9-1, qTA9-2, and qTA11) for the tiller angle were detected on chromosomes 1, 5, 9, 9, and 11 in two different environments. The phenotypic variation in these QTLs ranged from 3.78% to 8.22%. Two pairs of digenic epistatic QTLs were detected in Lingshui. The epistatic interaction explained 15.19% and 13.60% of the phenotypic variance, respectively. Among the five QTLs, qTA9-2 was detected in both environments. An F2 mapping population containing the qTA9-2 QTL was established. The location of qTA9-2 was narrowed down to a 187 kb region between InDel markers M9 and M10 on chromosome 9. Thirty open reading frames (ORFs), including TAC1, a gene known to regulate the tiller angle, were identified in this region. The gene sequencing results suggested that a base substitution from G to A at position 1557 in the 3′-untranslated region led to a difference in the expression of qTA9-2 in Koshihikari and Nona Bokra. These findings provide a potential gene resource for the improvement of rice plant architecture.

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding.