Genetic control of rice plant architecture under domestication

Abstract

The closely related wild rice species Oryza rufipogon is considered the progenitor of cultivated rice (Oryza sativa). The transition from the characteristic plant architecture of wild rice to that of cultivated rice was one of the most important events in rice domestication; however, the molecular basis of this key domestication transition has not been elucidated. Here we show that the PROG1 gene controls aspects of wild-rice plant architecture, including tiller angle and number of tillers. The gene encodes a newly identified zinc-finger nuclear transcription factor with transcriptional activity and is mapped on chromosome 7. PROG1 is predominantly expressed in the axillary meristems, the site of tiller bud formation. Rice transformation experiments demonstrate that artificial selection of an amino acid substitution in the PROG1 protein during domestication led to the transition from the plant architecture of wild rice to that of domesticated rice.

A map of rice genome variation reveals the origin of cultivated rice

“…Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 . However, the well-characterized domestication genes in rice were found to be fixed in both subspecies with the same alleles, thus supporting a single domestication origin [6][7][8][9]16 . Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 .…”

“…We noticed that many loci with strong signals of selection were nearly identical in both indica and japonica where F ST between indica and japonica was extremely low, indicating that introduction of traits during domestication has in many cases involved introgression events. We noted that most well-characterized domestication genes, including Bh4 (hull colour 9 ), PROG1 (tiller angle 7,8 ), sh4 (seed shattering 5,6 ), qSW5 (grain width 35 ) and OsC1 (leaf sheath colour and apiculus colour 32 ), were among the 55 loci detected in the full population (Fig. 3).…”

“…To perform GWAS in O. rufipogon, we used the k-nearest neighbour algorithm for data imputation (Supplementary Table 6), and phenotyped the O. rufipogon population for two traits, leaf sheath colour and tiller angle. The strongest associations for sheath colour and tiller angle were found to be just around the known loci OsC1, for colouration 32 , and PROG1, for prostrate growth 7,8 (Fig. 1d and Supplementary Figs 7-9).…”

“…The differences between O. sativa and O. rufipogon are reflected in a wide range of morphological and physiological traits [5][6][7][8][9] . Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated.…”

Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation

“…Modification of plant architecture to create new elite cultivars is considered as a viable approach to increasing grain yield [1]. So far, numerous QTLs or genes controlling plant architecture have been cloned [2][3][4][5]. In the case of the 'Green Revolution', grain yields have been significantly increased by growing lodging-resistant semi-dwarf varieties of wheat and rice [6,7].…”