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  • The rice Os01g0848400 was first reported as qSH1 in 2006 by the researchers from Japan [1]. qSH1 encodes a BEL1-type homeobox protein.

Annotated Information

Figure 1.qSH1 is required for formation of the abscission layer at the base of the rice grain.


  • The gene qSH1 is a major quantitative trait locus of seed shattering in rice. 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.


  • The Japanese researchers in 2006 made a near-isogenic line (NIL)that contained a short chromosomal segment from Kasalath at the qSH1 region in a Nipponbare genetic background. The NIL exhibited the formation of a complete abscission layer between pedicel and spikelet at the base of the rice seed and had a stronger seed-shattering phenotype than either Kasalath or Nipponbare.
  • In contrast, no abscission layer was observed in Nipponbare at all (Fig. 1, E to G). This indicated that a mutation in the qSH1 gene alone resulted in complete loss of the abscission layer in the Nipponbare genetic background and that the Kasalath allele of qSH1 could rescue it. Kasalath could form a partial abscission layer only at the peripheries in the transverse plane (Fig. 1, H to K), perhaps because of the pres- ence of the minor QTLs.
  • The Fig. 1A describe Seed-shattering habits of rice panicles. Photos taken after grabbing rice panicles. (Left) Nonshattering-type cultivar, Nipponbare. (Right) Shattering-type cultivar, Kasalath, in which the seed has shattered. The Fig. 1B shwos the Chromosomal locations of QTLs for seed-shattering degree, based on an F 2 population from a cross between Nipponbare and Kasalath. Positions of circles indicate positions of QTLs, and circle size indicates the relative contribution of each QTL. Red circles, Nipponbare alleles contributing to non- shattering habit; blue circles, Kasalath alleles contributing to nonshattering. qSH1 is marked on chromosome 1 with the nearest DNA marker (C434).
  • The Fig. 1c shows the Non–seed-shattering habits of Nipponbare, Kasalath, and NIL(qSH1). Breaking tensile strength upon detachment of seeds from the pedicels by bending and pulling was measured (10). Increase in value indicates loss of shattering. NIL(qSH1), a nearly isogenic line carrying a Kasalath fragment at the qSH1 locus in the Nipponbare background.


Figure 2.Association of qSH1 haplotypes with degree of shattering.
  • A large-scale linkage analysis of 10,388 plants segregating at the qSH1 region was performed for the fine mapping of qSH1. The researchers finally succeeded in mapping the functional natural variation in 612 bp between the flanking markers qSH1-F and qSH1-H and found only one single-nucleotide polymorphism (SNP) within this region (Fig. 2A). They confirmed this result using several recombinant homozygous plants in the progeny (Fig. 2A).
  • Gene prediction for the qSH1 region in both Nipponbare (11) and Kasalath genome sequences showed no distinct open reading frame (ORF) in the SNP region. However, located 12 kb away from the SNP, we found one ORF (locus ID Os01g0848400 in the Rice Annotation Project DataBase) for a rice ortholog of the Arabidopsis REPLUMLESS (RPL) (12, 13) gene (Fig. 2B and).
  • The RPL gene encodes a BEL1-type homeobox (14, 15) and is involved in the for- mation of a dehiscence zone (or abscission layer) alongside the valve in the Arabidopsis fruit (silique). Because the fruit originates from the carpels in Arabidopsis, the botanical origin of the dehiscence zone in Arabidopsis fruit does not correspond to that of the abscission layer in rice seeds. However, it was still possible that this RPL ortholog was the qSH1 gene.

Knowledge Extension

  • Cereal crops such as maize, rice and wheat were domesticated from wild grasses between 7000 and 10 000 yr ago (Doebley et al., 2006). In all cereal crops, the transition to domestication included a dramatic reduction in grain shattering. The mature grains of wild grasses dissociate easily from

the panicle to ensure successful seed dispersal.

  • However, grain shattering makes harvest difficult. Archeological evidence suggests that before domestication, gatherers collected immature grains by cutting off panicles before the onset of shattering (Tanno & Willcox, 2006). The development of nonshattering cultivars substantially improved grain yield and is considered to be the hallmark of cereal domestication [2] .
  • The loss of seed-shattering habit is thought to be one of the most important events in rice domestication, because the Beasy-to-shatter trait in wild relatives results in severe reduction in yield.
  • Over the course of human history, distinct grain-threshing systems have been developed in several different eras in local areas of the world, in accordance with the degree of seed shattering.
  • In current rice-breeding programs, this seed-shattering habit is still a target, especially in the construction of new indica (another subspecies of O. sativa) cultivars. Thus, seed-shattering habit is one of the most important agronomic traits in rice cultivation and breeding.

Labs working on this gene

  • Institute of the Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Ippaizuka, Kamiyokoba Tsukuba, Ibaraki 305-0854, Japan.
  • National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
  • Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan.


  1. Konishi, Saeko, et al. "An SNP caused loss of seed shattering during rice domestication." Science 312.5778 (2006): 1392-1396.
  2. Zhang, Lin‐Bin, et al. "Selection on grain shattering genes and rates of rice domestication." New Phytologist 184.3 (2009): 708-720.

Structured Information