Genetic and Evolutionary Analysis of Purple Leaf Sheath in Rice

Abstract

BackgroundAnthocyanin accumulates in many plant tissues or organs, in rice for example leading to red, purple red and purple phenotypes for protection from damage by biotic and abiotic stresses and for reproduction. Purple leaf, leaf sheath, stigma, pericarp, and apiculus are common in wild rice and landraces and occasionally found in modern cultivars. No gene directly conferring anthocyanin deposited in a purple leaf sheath has yet been isolated by using natural variants. An F2 population derived from ssp. japonica cv. Tainung 72 (TNG72) with purple leaf sheath (PSH) crossed with ssp. indica cv. Taichung Sen 17 (TCS17) with green leaf sheath (GSH) was utilized to isolate a gene conferring leaf sheath color.ResultsBy positional cloning, 10-and 3-bp deletions in the R2R3 Myb domain of OsC1 were uncovered in GSH varieties TCS17 and Nipponbare, respectively. Allelic diversity, rather than gene expression levels of OsC1, might be responsible for anthocyanin accumulation. Parsimony-based analysis of genetic diversity in 50 accessions, including cultivars, landraces, and A-genome wild rice, suggests that independent mutation occurred in Asian, African, South American, and Australian species, while O. meridionalis had a divergent sequence. OsC1 was thought of as a domestication related gene, with up to 90 % reduction of genetic diversity in GSH; however, no values from three tests showed significant differences from neutral expectations, implying that OsC1 had not been subjected to recent selection. Haplotype network analysis revealed that species from different continents formed unique haplotypes with no gene flow. Two major groups of haplotypes corresponding to 10-bp deletion and other sequences were formed in Asian rice, including O. rufipogon, O. nivara and O. sativa. Introgressions of OsC1 between subspecies through natural and artificial hybridization were not rare. Because artificial and natural selection imposed admixture on rice germplasm in Taiwan, the genealogy of OsC1 might not be congruent with the current distribution of alleles through lineage diversification.ConclusionOsC1 is responsible for purple leaf sheath, and much new information about OsC1 is provided e.g., new alleles, non-domestication syndrome, and incongruence of genealogy with geographic distribution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0080-y) contains supplementary material, which is available to authorized users.

Identification of candidate genes for gelatinization temperature, gel consistency and pericarp color by GWAS in rice based on SLAF-sequencing

“…Oikawa et al (2015) [50] identified Kala4 gene controlling anthocyanin biosynthesis, identical to OSB2 gene confirmed by Sakamoto et al (2001) [65] in rice. Chin et al(2016) [66] have showed that the OsC1 gene of chromosome 6 is related to the purple sheath in rice, encoding a MYB transcription factor. In this study, for the whole panel, a pericarp color-related QTL was detected, where the most significant SNP Chr1_22408336 was adjacent to the Rd [49] participating in the proanthocyanidins biosynthesis.…”

Determining factors, regulation system, and domestication of anthocyanin biosynthesis in rice leaves

“…Five putative anthocyanin biosynthesis regulators, including four bHLH genes Ra1 / OsB1 , Rb , Ra2 and OsB2 , and the R2R3‐MYB gene OsC1 , were isolated from rice through comparative mapping between rice and maize or according to the nucleotide sequence homology of known maize orthologues (Hu et al ., , ; Reddy et al ., ; Sakamoto et al ., ; Saitoh et al ., ). Genetic analysis demonstrated that OsC1 is the determinant factor of anthocyanin biosynthesis in leaf sheath and apiculus (Fan et al ., ; Chin et al ., ), and also a domestication‐related gene for the loss of anthocyanin accumulation in cultivated rice (Huang et al ., ). Rc , a bHLH gene, is the determinant factor for pro‐anthocyanidin biosynthesis in the pericarp (Sweeney et al ., ), and also a domestication‐related gene for the loss of pro‐anthocyanidin accumulation in cultivated rice (Sweeney et al ., ).…”

Senescence‐related translocation of nonstructural carbohydrate in rice leaf sheaths under different nitrogen supply

“…However, conflicting reports were also obtained by other researchers (Nagata, Yoshinaga, Takanashi, & Terao, ; Pan et al., ) who concluded that the amount of NSC accumulation in leaf sheaths at heading was not significantly affected by N application, despite a high increase in dry weight under heavy N application. According to Chin, Wu, Hour, Hong, and Lin (), the amount of NSC accumulation in leaf sheaths peaked around the heading date and then decreased gradually along with grain development. Under water deficient conditions, the translocation efficiency of NSC from leaf sheaths to grains markedly increased, but this occurrence was commonly accompanied by a shortened grain‐filling period as well as an accelerated senescence of functional leaves (Yang et al., , ).…”