Identification of a plant height quantitative trait loci and candidate genes in a chromosome segment substitution line population derived from wild rice

Abstract

Plant height is an important agronomic trait in rice and shows marked divergence between wild and cultivated germplasm. To identify loci associated with plant height variation from wild rice, we developed a BC ₄ F ₇ chromosome segment substitution line population of 308 lines derived from Yuanjiang common wild rice ( Oryza rufipogon ) and elite cultivar Youzhan 8 ( Oryza sativa ). Bulked segregant analysis coupled with sequencing identified a 13.6‐Mb quantitative trait loci region on chromosome 7 associated with plant height. Eight prioritized candidate genes were identified within this interval based on sequence polymorphism and functional annotation, including known regulators OsTCP21 and PROG1 . Quantitative RT‐PCR analysis of stem tissues at the jointing stage detected measurable expression for five of these genes. Four genes, OsTCP21 , OsFBL35 , OsFBA2 , and LOC_Os07g08190 , showed significant differential expression between tall and dwarf lines, whereas GID1L2 did not. The other three genes, including PROG1 , showed transcript levels too low for reliable detection. Haplotype analysis further identified coding and promoter variation in OsFBL35 , OsFBA2 , LOC_Os07g08190 , and GID1L2 , as well as promoter haplotypes in OsTCP21 . These results suggest that OsTCP21, OsFBL35 , OsFBA2 , LOC_Os07g08190 , and GID1L2 are potential candidate genes for plant height variation in this wild rice‐derived population. Functional annotation suggested that these candidates may be related to ubiquitination, hormone signaling, and growth regulation. These findings provide insight into the genetic basis of plant height variation derived from wild rice and offer candidate loci and molecular markers for rice improvement.