Hd-q, a novel allele of Ef7 from a Chinese rice landrace, confers weak photoperiod sensitivity and improves local adaptability and yield potential

Abstract

Heading date is a major determinant of adaptability and yield potential in rice (Oryza sativa L.) and is influenced by photoperiod. Among chromosome segment substitution lines, the introgression line C63 contains a segment of the short arm of chromosome 6 from indica Qingluzhan 11 in the japonica Nipponbare background and exhibits a delayed heading date under both long day (LD) and short day (SD) natural field conditions. This study demonstrates that the late heading date of the C63 line is controlled by a single recessive gene, Heading date from Qingluzhan 11 (Hd-q). Hd-q was mapped to a region of less than 43.7 kb. Complementation testing revealed that Ef7 (LOC_Os06g05060), a homolog of Arabidopsis ELF3, is the candidate gene, while Hd-q is a new allele of Ef7. Sequence alignment revealed at least five Ef7 alleles among 11 rice cultivars based on polymorphism in the coding region. Unlike other alleles, Hd-q has a single nucleotide polymorphism (T/A) in exon 2, which leads to premature termination of translation. In addition to delayed heading date, Hd-q has pleiotropic effects on major agronomic characteristics, which were determined by comparing the near-isogenic line, NIL (Hd-q), with its recurrent parent Nipponbare. The Hd-q allele improved grain yield under both LD and SD conditions and in different geographical regions. Finally, a dCAPS (derived cleaved amplified polymorphic sequence) marker was developed based on the T/A polymorphism, and will be useful for introgression of the Hd-q allele via marker-assisted selection. The Hd-q allele is a useful target for the improvement of rice adaptation and production, especially at low latitudes.