The genetic constitutions of complementary genes Pp and Pb determine the purple color variation in pericarps with cyanidin-3-O-glucoside depositions in black rice

The purple pericarp color in rice was controlled by two dominant complementary genes, Pb and Pp. Crossing black rice ‘Heugnambyeo’ variants with three varieties of white pericarp rice gave a segregation ratio of 9 purple: 3 brown: 4 white. The Pp genes were segregated by homozygous PpPp alleles for the dark purple pericarps, heterozygous Pppp alleles for the medium and mixed purple pericarps, and homozygous pppp alleles for either brown or white pericarps with a 1 PpPp: 2 Pppp: 1 pppp segregation ratio, indicating that the Pp allele in rice is incompletely dominant to the recessive pp allele. Among the purple seeds, the amount of cyanidin-3-O-glucoside was higher in the dark purple seeds (Pb_PpPp) than in the medium purple seeds (Pb_Pppp). Moreover, no cyanidin-3-glucoside was detected in brown (Pb_pppp) or white pericarp seeds (pbpbpppp). These findings indicated that the level of cyanidin-3-glucoside was determined by the copy number of the Pp allele. Further genotype investigation of the F₃ progeny demonstrated that the dominant Pb allele was present in either purple or brown pericarp. A 2-bp (GT) deletion from the DNA sequences of the dominant and functional Pb was found in the same DNA sequences of the recessive and non-functional pb allele. These findings suggested that the presence of at least a dominant Pb allele was an essential factor for color development in rice pericarps. In conclusion, the Pp allele in rice is incompletely dominant to the recessive pp allele; thus, the number of dominant Pp alleles determines the concentration of cyanidin-3-O-glucoside in black rice.     

The Rc and Rd genes are involved in proanthocyanidin synthesis in rice pericarp

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. Genetic segregation analysis suggested that the Rd and A loci are identical, and both encode dihydroflavonol-4-reductase (DFR). The introduction of the DFR gene into an Rcrd mutant resulted in red-colored rice, which was brown in the original mutant, demonstrating that the Rd locus encodes the DFR protein. Accumulation of proanthocyanidins was observed in the transformants by the introduction of the Rd gene into the rice Rcrd line. Protein blot analysis showed that the DFR gene was translated in seeds with alternative translation initiation. A search for the Rc gene, which encodes a transacting regulatory factor, was conducted using available DNA markers and the Rice Genome Automated Annotation System program. Three candidate genes were identified and cloned from a rice RcRd line and subsequently introduced into a rice rcrd line. Brown-colored seeds were obtained from transgenic plants by the introduction of a gene containing the basic helix-loop-helix (bHLH) motif, demonstrating that the Rc gene encodes a bHLH protein. Comparison of the Rc locus among rice accessions showed that a 14-bp deletion occurred only in the rc locus.     

Global dissemination of a single mutation conferring white pericarp in rice

Here we report that the change from the red seeds of wild rice to the white seeds of cultivated rice (Oryza sativa) resulted from the strong selective sweep of a single mutation, a frame-shift deletion within the Rc gene that is found in 97.9% of white rice varieties today. A second mutation, also within Rc, is present in less than 3% of white accessions surveyed. Haplotype analysis revealed that the predominant mutation originated in the japonica subspecies and crossed both geographic and sterility barriers to move into the indica subspecies. A little less than one Mb of japonica DNA hitchhiked with the rc allele into most indica varieties, suggesting that other linked domestication alleles may have been transferred from japonica to indica along with white pericarp color. Our finding provides evidence of active cultural exchange among ancient farmers over the course of rice domestication coupled with very strong, positive selection for a single white allele in both subspecies of O. sativa.     

Prebreeding selection of rice with colored pericarp based on genotyping <Emphasis Type="Italic">Rc</Emphasis> and <Emphasis Type="Italic">Pb</Emphasis> genes

The research was aimed at developing prebreeding resources of Kazakhstan rice varieties with colored pericarp for breeding. During the study, hybrid analysis of inheritance of the trait “colored pericarp” in breeding material used for the work was performed. Rice genotypes with colored pericarp, as well as white rice varieties possessing important breeding traits and maturing under conditions of the republic, were selected from the collection of the Institute of Plant Biology and Biotechnology, Republic of Kazakhstan. Identification of allelic status of Rc (red pericarp) and Pb (anthocyanin pericarp) genes was performed for selected samples using the PCR method. When selecting parental forms for crossing, foreign rice varieties with colored pericarp (Rubin, Mavr, Black rice, etc.) were used as recipient forms. As donors, we used local white rice varieties of Kazakhstan breeding adapted to the soil and climate conditions of rice growing regions (Madina, Marzhan, Bakanasskiy, PakLi) as well as foreign varieties. The ability to set hybrid caryopses and the percentage of sterility were determined in obtained F1 rice hybrids. As a result, the most promising prebreeding material was selected, which will be used for breeding Kazakhstan rice varieties with colored pericarp.     

Transposon-induced inversions activate gene expression in the maize pericarp

Chromosomal inversions can have considerable biological and agronomic impacts including disrupted gene function, change in gene expression, and inhibited recombination. Here, we describe the molecular structure and functional impact of six inversions caused by Alternative Transpositions between p1 and p2 genes responsible for floral pigmentation in maize. In maize line p1-wwB54, the p1 gene is null and the p2 gene is expressed in anther and silk but not in pericarp, making the kernels white. By screening for kernels with red pericarp, we identified inversions in this region caused by transposition of Ac and fractured Ac (fAc) transposable elements. We hypothesize that these inversions place the p2 gene promoter near a p1 gene enhancer, thereby activating p2 expression in kernel pericarp. To our knowledge, this is the first report of multiple recurrent inversions that change the position of a gene promoter relative to an enhancer to induce ectopic expression in a eukaryote.     

Expression of BrD1, a plant defensin from Brassica rapa, confers resistance against brown planthopper (Nilaparvata lugens) in transgenic rices

Plant defensins are small (5-10 kDa) basic peptides thought to be an important component of the defense pathway against fungal and/or bacterial pathogens. To understand the role of plant defensins in protecting plants against the brown planthopper, a type of insect herbivore, we isolated the Brassica rapa Defensin 1 (BrD1) gene and introduced it into rice (Oryza sativa L.) to produce stable transgenic plants. The BrD1 protein is homologous to other plant defensins and contains both an N-terminal endoplasmic reticulum signal sequence and a defensin domain, which are highly conserved in all plant defensins. Based on a phylogenetic analysis of the defensin domain of various plant defensins, we established that BrD1 belongs to a distinct subgroup of plant defensins. Relative to the wild type, transgenic rices expressing BrD1 exhibit strong resistance to brown planthopper nymphs and female adults. These results suggest that BrD1 exhibits insecticidal activity, and might be useful for developing cereal crop plants resistant to sap-sucking insects, such as the brown planthopper.     

不同类型特种稻种质营养及功能性成分含量的差异

本研究以具有有色种皮、巨胚、甜味、香味、糯性等单一特殊性状或2个以上特殊性状聚合于一体的新创制特种稻种质39份和1份白米种质(对照)为试验材料,进行了黑米、黑褐米、红米、香糯米、黑巨胚糯米、红巨胚糯米、巨胚糯米、黑甜米、红甜米、白甜米等不同类型特种稻种质的营养及功能性成分含量的差异评价。结果表明,供试特种稻类型在大部分氨基酸含量和矿质元素含量上与白米差异不显著,只在个别氨基酸和矿质元素含量上与白米呈显著或极显著差异。黑褐米、红米、黑巨胚糯米、红巨胚糯米、巨胚糯米、红甜米和白甜米等7种类型的赖氨酸含量显著或极显著高于白米,高2.91%~24.68%;黑米、黑褐米、红米、香糯米、黑巨胚糯米和红甜米等6种类型的铁含量显著或极显著高于白米,高17.62%~68.09%;黑褐米、红米、黑巨胚糯米、红巨胚糯米、黑甜米、红甜米、白甜米等7种类型的钙含量显著或极显著高于白米,高23.56%~49.46%;黑米、黑褐米、红米、黑甜米、红甜米、白甜米等6种类型的锌含量显著或极显著高于白米,高12.21%~55.87%。由此表明,具有有色种皮、巨胚、甜味、香味、糯性等单一特殊性状或2~3个特殊性状的聚合对赖氨酸含量与铁、钙和锌含量的提高方面具有一定的增加效应,认为在今后以赖氨酸、铁、钙和锌含量为目标性状的功能性水稻育种中,多个特殊性状的聚合将是增加上述功能性成分含量的有效途径之一。通过鉴定评价,从创新种质中还筛选出一些功能性成分含量相对较高的优异种质,白甜米1553和红巨胚糯米1476的赖氨酸含量较高,比白米分别高29.37%和23.42%;红米1439和红米1440的铁含量较高,比白米分别高99.05%和80.00%;黑甜米1511和黑甜米1515的硒含量较高,比白米分别高194.14%和136.48%;白甜米1551和香糯米1446的γ-氨基丁酸含量较高,比白米分别高14.56%和11.83%;黑巨胚糯米1464和黑米1432的花色苷含量较高,比供试18份有色稻米的平均值分别高253.23%和248.83%。这些新创制的功能性成分含量较高的水稻种质有待于今后在育种、生态适应性鉴定与产业化中进一步得到利用。     

Effect of amylose content on the lipids of mature rice grain

Most of the nonstarch lipids in brown rice (Oryza sativa) of three rices differing in amylose content were contributed by bran, germ, polish and subaleurone layer. Nonstarch lipids consisted of 82–91% neutral lipids (of which 73–82% were triglycerides), 7–10% phospholipids and 2–8% glycolipids. Linoleic, oleic and palmitic acids were the major fatty acids. Nonwaxy (24 and 29% amylose) milled rice had proportionally more starch lipids and less nonstarch lipids than waxy (2% amylose) milled rice. Starch lipids were mainly lysophosphatidyl choline, lysophosphatidyl ethanolamine and free fatty acids. The major fatty acids were palmitic and linoleic acids, followed by oleic acid.     

Association mapping of grain color,phenolic content,flavonoid content and antioxidant capacity in dehulled rice

Phytochemicals such as phenolics and flavonoids in rice grain are antioxidants that are associated with reduced risk of developing chronic diseases including cardiovascular disease, type-2 diabetes and some cancers. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. Association mapping based on linkage disequilibrium has emerged as a powerful strategy for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, genome-wide association mapping using models controlling both population structure (Q) and relative kinship (K) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of grain color and nutritional quality traits in 416 rice germplasm accessions including red and black rice. A total of 41 marker loci were identified for all the traits, and it was confirmed that Ra (i.e., Prp-b for purple pericarp) and Rc (brown pericarp and seed coat) genes were main-effect loci for rice grain color and nutritional quality traits. RM228, RM339, fgr (fragrance gene) and RM316 were important markers associated with most of the traits. Association mapping for the traits of the 361 white or non-pigmented rice accessions (i.e., excluding the red and black rice) revealed a total of 11 markers for four color parameters, and one marker (RM346) for phenolic content. Among them, Wx gene locus was identified for the color parameters of lightness (L*), redness (a*) and hue angle (H ^o). Our study suggested that the markers identified in this study can feasibly be used to improve nutritional quality or health benefit properties of rice by marker-assisted selection if the co-segregations of the marker–trait associations are validated in segregating populations.     

Overexpression of the Arabidopsis AtEm6 gene enhances salt tolerance in transgenic rice cell lines

The Arabidopsis thaliana late embryogenesis abundant gene AtEm6 is required for normal seed development and for buffering the rate of dehydration during the latter stages of seed maturation. However, its function in salt stress tolerance is not fully understood. In this investigation, cell suspension cultures of three plant species rice (Oryza sativa L.), cotton (Gossypium hirsutum L.), and white pine (Pinus strobes L.) were transformed using Agrobacterium tumefaciens strain LBA4404 harboring pBI-AtEm6. Integration of the AtEm6 gene into the genome of rice, cotton, and white pine has been confirmed by polymerase chain reaction, Southern blotting, and northern blotting analyses. Three transgenic cell lines from each of O. sativa, G. hirsutum, and P. strobus were used to analyze salt stress tolerance conferred by the overexpression of the AtEm6 gene. Our results demonstrated that expression of the AtEm6 gene enhanced salt tolerance in transgenic cell lines. A decrease in lipid peroxidation and an increment in antioxidant enzymes ascorbate peroxidase, glutathione reductase and superoxide dismutase activities were observed in the transgenic cell lines, compared to the non- transgenic control. In rice, AtEM6 increased expression of Ca²⁺-dependent protein kinase genes OsCPK6, OsCPK9, OsCPK10, OsCPK19, OsCPK25, and OsCPK26 under treatment of salt. These results suggested that overexpression of the AtEM6 gene in transgenic cell lines improved salt stress tolerance by regulating expression of Ca²⁺-dependent protein kinase genes. Overexpression of the AtEM6 gene could be an alternative choice for engineering plant abiotic stress tolerance.     

紫米基因与RFLP标记的连锁分析

选用种皮呈紫黑色的水稻体细胞无性系变异体黑珍米和其种皮呈无色的原始亲本Ｂａｓｍａｔｉ３７０配制组合,同时应用１２１个ＤＮＡ探针检测了黑珍米与Ｂａｓｍａｔｉ３７０之间的ＲＦＬＰ。应用Ｆ２和Ｆ３群体研究了紫色种皮的遗传控制。结果表明,有一个显性主效基因控制着黑珍米和Ｂａｓｍａｔｉ３７０在种皮颜色上的差异。通过多态性ＤＮＡ探针与种皮颜色的共分离分析,发现该基因与水稻第四染色体上的ＤＮＡ标记ＲＧ３２９和ＲＧ２１４连锁,与ＲＧ３２９和ＲＧ２１４的遗传图距分别为１８．９ｃＭ和２６．３ｃＭ。     

Agrobacterium-mediated co-transformation of rice using two selectable marker genes derived from rice genome components

A method for Agrobacterium-mediated co-transformation of rice (Oryza sativa L.) was developed using rice-derived selection markers. Two T-DNAs were efficiently introduced into separate loci using selectable marker gene cassettes consisting of the mutated acetolactate synthase gene (mALS) under the control of the callus-specific promoter (CSP) (CSP:mALS) and the ferredoxin nitrite reductase gene (NiR) under the control of its own promoter (NiR P:NiR). The CSP:mALS gene cassette confers sulfonylurea herbicide resistance to transgenic rice callus. The NiR P:NiR construct complements NiR-deficient mutant cultivars such as ‘Koshihikari’, which are defective in the regulation of nitrogen metabolism. In the present study, the CaMV35S:GUS and CaMV35S:GFP gene cassettes were co-introduced into the ‘Koshihikari’ genome using our system. Approximately 5–10 independent transgenic lines expressing both the GUS and GFP reporters were obtained from 100 Agrobacterium co-inoculated calli. Furthermore, transgenic ‘Koshihikari’ rice lines with reduced content of two major seed allergen proteins, the 33 and 14–16?kDa allergens, were generated by this co-transformation system. The present results indicate that the generation of selectable antibiotic resistance marker gene-free transgenic rice is possible using our rice-derived selection marker co-transformation system. Key message An improved rice transformation method was developed based on Agrobacterium-mediated co-transformation using two rice genome-derived selectable marker gene cassettes.     

CRISPR/Cas9‐mediated functional recovery of the recessive rc allele to develop red rice

Red rice contains high levels of proanthocyanidins and anthocyanins, which have been recognized as health‐promoting nutrients. The red coloration of rice grains is controlled by two complementary genes, Rc and Rd. The RcRd genotype produces red pericarp in wild species Oryza rufipogon, whereas most cultivated rice varieties produce white grains resulted from a 14‐bp frame‐shift deletion in the seventh exon of the Rc gene. In the present study, we developed a CRISPR/Cas9‐mediated method to functionally restore the recessive rc allele through reverting the 14‐bp frame‐shift deletion to in‐frame mutations in which the deletions were in multiples of three bases, and successfully converted three elite white pericarp rice varieties into red ones. Rice seeds from T₁ in‐frame Rc lines were measured for proanthocyanidins and anthocyanidins, and high accumulation levels of proanthocyanidins and anthocyanidins were observed in red grains from the mutants. Moreover, there was no significant difference between wild‐type and in‐frame Rc mutants in major agronomic traits, indicating that restoration of Rc function had no negative effect on important agronomic traits in rice. Given that most white pericarp rice varieties are resulted from the 14‐bp deletion in Rc, it is conceivable that our method could be applied to most white pericarp rice varieties and would greatly accelerate the breeding of new red rice varieties with elite agronomic traits. In addition, our study demonstrates an effective approach to restore recessive frame‐shift alleles for crop improvement.     

Development of transgenic rice pure lines with enhanced resistance to rice brown planthopper

Summary Mature seed-derived callus from an elite Chinese japonica rice cv. Ewan 5 was cotransformed with two plasmids, pWRG1515 and pRSSGNAl, containing the selectable marker hygromycin phosphotransferase gene (hpt), the reporter β-glucuronidase gene (gusA) and the snowdrop (Galanthus nivalis) lectin gene (gna) via particle bombardment. Thirty-five independent transgenic rice plants were regenerated from 177 bombarded calluses. Eighty-three percent of the transgenic plants contained all three genes, as revealed by Southern blot analysis. Western blot analysis revealed that 23 out of 29 gna-containing transgenic plants expressed Galanthus nivalis agglutinin (GNA) (79%) at various levels, with the highest expression being approximately 0.5% of total soluble protein. Genetic analysis confirmed Mendelian segregation of all three transgenes (gna, hpt and gusA) in the R2 progeny. Amongst the R2 generation two independent homozygous lines were identified that expressed all three transgenes. Insect bioassay and feeding tests showed that these homozygous lines had significant inhibition to rice brown planthopper (Nilaparvata lugens, BPH) by decreasing the survival, overall fecundity of BPH, retarding development, and decreasing the feeding of BPH. These BPH-resistant lines have been incorporated into a rice insect resistance breeding program. This is the first report that homozygous transgenic rice lines expressing GNA, developed by genetic transformation and through genetic analysis-based selection, conferred enhanced resistance to BPH.     

Anthocyanin pathway in rice (Oryza sativa L): identification of a mutant showing dominant inhibition of anthocyanins in leaf and accumulation of proanthocyanidins in pericarp

The present study has surveyed a collection of indica rice (Oryza sativa) lines for tissue-specific anthocyanin pigmentation pattern, which has also been used for a genetically meaningful classification. This classification helped predict probable genotypes of rice lines and, in the process, a leaf blade-specific dominant inhibitor of pigmentation (Ilb) was predicted and its presence later confirmed in two lines. We ascribe most tissue-specific accumulation of anthocyanins to the presence of a different set of Pl alleles. Cyanidin, as a major pigment, and peonidin, as a minor pigment, were detected in purple-pigmented tissues. Further, the floral organ-derived tissues always contained a higher level of anthocyanins and, correspondingly, a relatively increased proportion of peonidin. One line, N22B, with a brown pericarp was identified and shown to accumulate proanthocyanidins, but with no anthocyanins, in the pericarp. We propose that the accumulation of proanthocyanidins is due to a block in the anthocyanin biosynthetic pathway in rice at the anthocyanidin synthase-mediated conversion of leucoanthocyanidin to anthocyanidin.