Os07g0211500

Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa) and it encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp).

characteristic

Different colors, such as purple, brown, red and white, occur in the pericarp of rice. Here, two genes affecting proanthocyanidin synthesis in red- and brown-colored rice were elucidated, one of the gene is Rc.)

Mutation

picture1. Length mutation (from reference ).

Grain color has been the target of selection in domesticated Asian rice (as well as other domesticated grains), and the vast majority of O. sativa varieties have white (nonpigmented) grains, compared to the dark red grains that characterize the wild relative and other wild species. The genetic basis of white grains in O. sativa has been pinpointed to loss-of-function mutations in the Rc gene, a regulatory protein in the proanthocyanidin synthesis pathway; these loss-of-function mutations prevent the development of a pigmented pericarp layer. A survey of 337 white pericarp rice cultivars showed that the majority (>97%) have a 14-bp deletion in exon 7 of the gene, resulting in a premature stop codon and a non-functional allele referred to as rc. Our findings for the pericarp color gene, Rc, indicate that remarkably similar genetic mechanisms can be at play. We find that two of the three white pericarp O. glaberrima varieties in our sample harbor a unique point mutation that is predicted to result in a premature stop codon in exon 7 of the Rc gene. Instead, two samples contained a novel point mutation predicted to result in a premature stop-codon in exon 7, hereafter referred to as allele rc-g1 . This mutation is 146 bp upstream of the Rc-s point mutation and 201 bp upstream of the initiation of the 14-bp rc deletion. The third white pericarp O. glaberrima contained no identifiable insertions, deletions, or premature stop-codons, nor does it differ from the red-pericarp O. glaberrima sequences for any predicted amino-acid changes. Comparison of this sample to the most closely related red-pericarp sample showed that they were identical for the sequenced region upstream of the start codon (>1.5 kb) and for the first intron; both of these regions are potentially important as cis-regulatory regions in plants. This study also shows that white pericarps might be achieved by mutations in cis-regulatory regions of Rc or potentially mutations in other genes, a pattern that was not observed in an extensive survey of O. sativa cultivars.(from reference ) Crop domestication can serve as a model of plant evolutionary processes. It involves a series of selection events from standing natural variation and newly occurring mutations and combinations of mutations as a result of natural crossings in populations during local adaptation and propagation of plant lines to other cultivation areas.) To determine the subpopulation origin of the Rc mutations,we examined ancestral haplotypes across the Rc coding sequence and promoter region in 103 genetically diverse, redgrained rices. Four rice insertion/deletion polymorphism (RID) and two rice microsatellite (RM) polymorphisms were used to construct haplotypes across the 6.5-kb region containing the Rc gene.)

Function

Rc alleles from the temperate ecotype of weedy lines LD and C9541 could represent the functional alleles most distant to those in group I (Figure 4). All the donor lines of weedy and cultivated rice in both groups were identified as dormant genotypes, or dormancy was associated with the Rc locus in our previous or present research. Thus, phylogenetic and dormancy data suggest that Rc alleles functional for pericarp color most likely also function for seed dormancy.)

Expression

RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties.We anticipated that similar expression levels of Rc would be detected in red and white seeds. Our results confirmed this expectation and further demonstrated that the RNA transcript from cv Jefferson contained the 14-bp deletion predicted from the sequence information.(from reference )

Nucleotide Polymorphisms

Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.(from reference )

Allele Distribution

Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein.(from reference )

Recombination

The rg7.1 locus was originally mapped to a 7.2-Mb region that included the centromere on rice chromosome 7. Given the low frequency of recombination across this region, it was not clear whether positional cloning would be feasible. This study demonstrates that even in regions that are recombinationally repressed, map-based gene isolation offers a viable approach.(from reference )

Evolution

Repeated phenotypic evolution can occur at the interspecific level, where it is manifest as the appearance of the same trait in multiple domesticated species, and at the intraspecific level, where the same trait arises multiple times within a single crop. In rice, the opportunity exists to examine the genetic basis of repeated trait evolution at both the interspecific and intraspecific level. At the intraspecific level, repeated phenotypic evolution during domestication can be explored in two contexts; one is the repeated evolution of a trait in varieties resulting from a single domestication event, the other is repeated evolution of a trait in varieties that result from multiple, independent domestication events within the same species.(from reference )

Labs working on this gene

• Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
• Plant Science Department, South Dakota State University, Brookings, South Dakota 57007, †Biosciences Research Laboratory, U.S.
• Department of Agriculture–Agricultural Research Service, Fargo, North Dakota 58105, ‡Northern Crop Science Laboratory, U.S.
• Department of Agriculture–Agricultural Research Service, Fargo, North Dakota 58102, §National Institute of Agrobiologica
• Sciences, Tsukuba, Ibaraki 305-8602, Japan
• Agricultural College, Yangzhou University, Yangzhou 225008, China
• Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14953-1901
• Department of Plant Biology, Cornell University, Ithaca, New York 14853
• Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
• International Rice Research Institute, Los Ban˜ os, Philippines*
• Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor, Indonesia
• Department of Agronomy, Chungbuk National University, Chongju, Republic of Korea
• National Institute of Agricultural Biotechnology, Suwon, Republic of Korea
• Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
• Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
• QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
• Genetic Diversity Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
• Department of Biological Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
• Research Institute for Biresources, Okayama University, Kurashiki, Okayama 710-0046, Japan
• National Agricultural Research Center for Kyushu Okinawa Region, National Agriculture and Bio-oriented Research Organization, Nishigoshi, Kikuchi, Kumamoto 861-1192, Japan
• National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
• Plant Breeding Laboratory, Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan