Abstract
The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.
Highlights
The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown
To characterize the gene responsible for black seed hull coloration and phenotypic variations resulting from the transition from black to straw-white hull, we constructed a set of chromosome segment substitution lines from backcross progeny derived from a cross between cultivated rice variety O. sativa indica cv Guangluai 4 as the recurrent parent and wild rice accession O. rufipogon Griff W1943 as the donor parent
To separate the Shattering4 (Sh4) locus, which controls the seed shattering in wild rice (Li et al, 2006), we developed a near isogenic line (NIL8) that contained a short segment from wild rice in Guangluai 4
Summary
The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. The genetic basis for the transition from the black hull of the wild rice to the straw-white hull of cultivated rice remains unknown. No candidate gene has been cloned for the transition from the black hull of the ancestral wild rice to the straw-white seed hull of cultivated rice, and the genetic basis for this kind of hull color alteration remains unknown. We cloned the Bh4 gene, a member of an amino acid transporter family conditioning for black hull on chromosome 4. Sequence analysis of O. sativa varieties and wild rice accessions revealed that Bh4 has been the selection target and undergoes strong selection
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