A novel genotype DATTO5 developed using the five genes exhibits the fastest heading date designed in rice

Abstract

The optimization of heading date is a key aspect for maximizing grain productivity in cereal crops including rice. The combinations of genes for heading date, a quantitative trait, are a major driver in the wide adaptability of cultivated rice worldwide. Here, we identified a novel QTL, qDTH3 (quantitative trait locus for daysto-heading on chromosome 3), for early flowering time in the F 2 population derived from a cross between Hoshinoyume (HS) and Daichinohoshi (DH) among local rice populations with extremely early heading date. The DH allele at qDTH3, qDTH3 DH , headed 2.7 days earlier than the HS allele at qDTH3, qDTH3 HS. We sought to design a genotype for earlier heading date by pyramiding of five heading date genes. We designated this aggregate of the five genes as DATTO5. Plants with DATTO5 were selected from the F 2 population derived from a cross between DH and HShd5, which is a near-isogenic line carrying a loss-of-function of days to heading 8 in a genetic background of HS. Plants with DATTO5 exhibited earlier heading date but reduced fitness, including shorter culm and panicle length and fewer seeds compared with HS, as a representative local rice variety with extremely early heading date.

Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

“…Molecular technologies including MAS and NGS may enhance accurate selection based on the genotype for a desirable phenotype. Previously, we identified QTLs/genes responsible for adaptability to Hokkaido ( Fujino 2003 , Fujino and Sekiguchi 2005a , 2005b , 2008 , Fujino et al 2013 , 2019a , 2019b , 2019c , Fujino and Ikegaya 2020 , Nonoue et al 2008 ). In addition, we demonstrated phenotypic gains in the 100 years of rice breeding programs in Hokkaido ( Fujino et al 2017 ).…”

“…Although the uniqueness of the adaptability and genetic population structure in rice varieties from Hokkaido has been characterized ( Fujino 2003 , Fujino and Sekiguchi 2005a , 2005b , 2008 , Fujino et al 2013 , 2015 , 2017 , 2019a , 2019b , 2019c , Fujino and Ikegaya 2020 , Nonoue et al 2008 , Shinada et al 2014 ), it is unclear whether artificial selection has shaped the genome sequence depending on phenotypes during current rice breeding programs in Hokkaido ( Fujino et al 2019c ). Here, we demonstrated the genetic relationships of current varieties bred in Hokkaido with Koshihikari, a famous rice cultivar in Japan ( Kobayashi et al 2018 ).…”

Days to heading, controlled by the heading date genes, <i>Hd1</i> and <i>DTH8</i>, limits rice yield-related traits in Hokkaido, Japan

“…The genetic role of yield makes their control difficult and complex in rice breeding programs. Previously, associations of DTH with yield-related traits have been demonstrated using series of NILs ( Fujino and Ikegaya 2020 , Fujino et al 2019a ). The higher coefficient values in these studies indicate that the significance of genes/QTLs for the heading date plays a role not only in the control of heading date but also in the regulation of yield.…”

“…These yield-related traits were measured in plants with the four genotypes homozygous in both Hd1 and DTH8 . In addition, the internode length and panicle components were measured according to Fujino and Ikegaya (2020) . The phenotypes were averaged for each line/variety and were compared using Tukey–Kramer HSD test among genotypes.…”

“…However, the genetic base for rice yield in agriculture was still unclear. Pleiotropic effects of the heading date genes on the developmental phase in panicles have been reported ( Endo-Higashi and Izawa 2011 , Fujino and Ikegaya 2020 , Fujino et al 2019a , Wei et al 2010 , Weng et al 2014 , Xue et al 2008 ). Furthermore, it was unclear whether the genotype for heading date regulates the yield-related traits as a genetic background.…”