Paper of the month (June 2006)

An SNP caused loss of seed shattering during Rice domestication

Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M.

Institute of the Society for Techno-Innovation of Agriculture, Forestry,

and Fisheries, 446-1 Ippaizuka, Kamiyokoba Tsukuba, Ibaraki 305-0854,

Japan.

Science 312: 1392 - 1394.

Abstract: Loss of seed shattering was a key event in the domestication of major cereals. We revealed that the qSH1 gene, a major quantitative trait locus of seed shattering in rice, encodes a BEL1-type homeobox gene and demonstrated that a single-nucleotide polymorphism (SNP) in the 5' regulatory region of the qSH1 gene caused loss of seed shattering owing to the absence of abscission layer formation. Haplotype analysis and association analysis in various rice collections revealed that the SNP was highly associated with shattering among japonica subspecies of rice, implying that it was a target of artificial selection during rice domestication.

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In this fascinating article, the authors unravel the molecular basis of loss of seed shattering trait during the course of rice domestication. Selection for this trait is considered to be the most important aspect in the emergence of rice as a cultivated crop; its wild relatives yield less due to seed shattering. The authors used natural variation of among rice cutlivars (by crossing high seed shattering indica cultivar Kaslath with low seed shattering japonica cultivar Nipponbare) to identify several Quantitative trait loci (QTL) linked to this phenotype. Of the five QTLs, the authors analyzed the QTL with the largest effect-qsh1. They demonstrated that only one SNP was found in the 5' regulatory region of a gene that is similar to the Arabdiopsis bel1-type homeobox gene involved in abcission. The gene downstream of qsh1 is expressed in the abscission layer between pedicel and spikelet at the base of a rice seed. In the cultivar that does not contain SNP (Kaslath), abscission layer forms and cause seeds to drop. The single nucleotide change in Nipponbare cultivar leads to absence of abcission layer and as a result the seeds do not fall. This nucleotide therefore seems to be important in the cis-regulatory element, possibly for DNA binding of transcription factor that regulateds the expression of qSH1 in the abscission layer.

The elegant identification of a SNP that resulted in loss of shattering in rice and how this change was incoporated into the domesticated rice cultivars is the reason this paper is our paper of the month. This paper provides a window into the molecular basis of the trait that humans selected based on phenotype. This article was also highlighted by John Doebely in the perspectives section of the same issue of Science in which it appeared.

Remarkably in March, Tao Sang group at MSU published another paper, in which they also used QTL mapping in the F2 population generated from a cross between O. sativa (no seed shattering) and O. nivara (excessive seed shattering) to identify 3 QTL loci that controlled seed shattering. Of these, the major QTL sh4 was mapped and cloned. Guess what! SH4 is a gene of unknown function but contains DNA binding domain and a single nucleotide substitution in this domain in the O. sativa allele undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel!

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