Diversification in flowering time due to tandem FT‐like gene duplication, generating novel Mendelian factors in wild and cultivated rice

Abstract

The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se-pat gene. Fine mapping in two of these near-isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly-observed recessive gene (se-pat). Molecular dissection suggested that the tandemly duplicated FT-like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype x environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se-pat(+) alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.

Identification of QTLs controlling heading date on the short arm of chromosome 3 in rice (Oryza sativa L.)

“…Genetic relationships with tight linkage between QTLs controlling heading date in rice have been reported previously (Hagiwara et al 2009, Maas et al 2010, Monna et al 2002, Thomson et al 2006. A QTL for heading date, Hd3, was detected in the F 2 population derived from a cross between japonica and indica varieties (Yano et al 1997).…”

“…High-resolution mapping genetically dissected Hd3 into two tightly linked loci, Hd3a and Hd3b (Monna et al 2002). In the same chromosomal region, at least three QTLs controlling heading date have been identified using introgression lines from indica and a wild accession, O. rufipogon (Hagiwara et al 2009). A QTL for heading date, dth1.1, was detected originally in an advanced backcrossed population derived from the cross between japonica and a wild accession, O. rufipogon (Thomson et al 2003).…”

Development of near-isogenic lines for BPH25(t) and BPH26(t), which confer resistance to the brown planthopper, Nilaparvata lugens (Stal.) in indica rice 'ADR52'

“…T, A, and H indicate loci homozygous for the T65 allele, homozygous for the ADR52 allele, and heterozygous, respectively. chromosome 6 in indica cultivars and O. rufipogon (Hagiwara et al 2009. Among these reported genes and QTLs, hdX(t) is located in the same region as qDF6.3, which is derived from the indica cultivar Patpaku, and qDF6.5, which is derived from O. rufipogon, Acc.…”

“…W593. qDF6.5 repressed heading, whereas qDF6.3 promoted heading (Hagiwara et al 2009). The delay of heading date in the hdX(t) NIL may therefore be associated with the repressed heading caused by qDF6.5.…”

“…Heading date is also an important factor for the adaptation of novel rice cultivars to local environments. However, some rice accessions from tropical and subtropical regions carry recessive alleles for photosensitivity on the short arm of chromosome 6 (Dung et al 1998, Hagiwara et al 2009. Plants carrying the homozygous recessive alleles or QTLs experience delayed heading under natural field conditions in Japan.…”