Differentiation in wild-type allele of the sd1 locus concerning culm length between indica and japonica subspecies of Oryza sativa (rice)

Abstract

A dwarfing gene (allele) sd1-d has been intensively utilized to develop short-culm indica varieties in southeast Asia up to now. Before the first sd1-d-carrying variety IR8 was released, rice researchers had recognized the general tendency that culm length is higher in indica varieties than in temperate-japonica ones. Inter-subspecific difference of the tall (wild-type) allele SD1 at the sd1 locus was examined on the common genetic background, using five isogenic lines developed by substituting sd1-d of the recurrent parent IR36 by SD1s of two indica varieties, two temperate-japonica varieties and one tropical-japonica variety. The two indica -donor isogenic lines had longer culms than the three japonica-donor isogenic lines consistently in two different environmental conditions. Moreover, nonsynonymous single-nucleotide polymorphism between the two subspecies was detected at two sites in Exon 1 and Exon 3 of the sd1 locus. It is demonstrated that the inter-subspecific differentiation of SD1 contributes height difference between indica and japonica. The indica-originating and japonica-originating alleles at the sd1 locus were designated as SD1-in(t) and SD1-ja(t), respectively.

Genetic architecture underlying the evolutionary change of competitive ability in Asian cultivated and wild rice

“…In the qCA1 region, the QTL for culm length, in which the allele of wild rice (W107) increased the culm length, was detected . In this region, the 'green revolution' gene (sd1 gene) locus, which confers the semi-dwarf trait by the recessive (sd1) allele, is known to be located between RM431 and RM471 (Asano et al 2011;Murai et al 2011). Allelic differentiation among wild-type alleles at the sd1 locus also confers variation of culm length (Asano et al 2011;Murai et al 2011) and is responsible for the reduction in culm length during domestication of japonica rice (Asano et al 2011).…”

“…In this region, the 'green revolution' gene (sd1 gene) locus, which confers the semi-dwarf trait by the recessive (sd1) allele, is known to be located between RM431 and RM471 (Asano et al 2011;Murai et al 2011). Allelic differentiation among wild-type alleles at the sd1 locus also confers variation of culm length (Asano et al 2011;Murai et al 2011) and is responsible for the reduction in culm length during domestication of japonica rice (Asano et al 2011). Generally, lower plant height, such as the semi-dwarf trait, is expected to confer lower competitive ability (Jennings and Aquino 1968;Kawano et al 1974;McDonald and Gill 2009); however, the A58 allele(s) of the qCA1-sd1 region conferred lower culm length but higher competitive ability than the W107 allele(s).…”

Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection

“…Among the subspecies of rice, indica cultivars are generally taller than japonica cultivars [ 15 ]. This height difference between the sub-species was shown to be due to two non-synonymous SNPs in the SD1 gene, present on exon 1 at the 299th nucleotide position (A in japonica and G in indica ) and at the 1099th nucleotide position on exon 3 (A in japonica and G in indica ) [ 16 ]. Based on the whole genome sequence, the japonica cultivar, Nipponbare was found to possess this wild japonica allele.…”

“…However, the allele in Pusa 1652 was similar to that of wild indica subtypes. When introgressed, both the wild indica and japonica SD1 alleles were demonstrated to increase the plant height of IR36, an indica cultivar possessing the sd1-d allele [ 16 ]. The possession of the japonica SD1 allele in Chakhao Poireiton , a tall rice cultivar popularly known as Manipur black rice [ 17 ], could also draw support for the fact that several of the rice cultivars of hill districts of northeast India have japonica lineages [ 18 ].…”

“…Furthermore, a comparison of the SD1 gene sequence in Pusa 1652, with Nipponbare and Chakhao Poireiton , could help identify four SNPs, one on exon 1 and three on exon 3. Among these, the first SNP on exon 1 and the third on exon 3 were already known to be the causal SNPs for plant height difference between indica and japonica genotypes [ 16 ]. This drew our interest towards the remaining two SNPs on exon 3, which were unreported.…”