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

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

Rice is an important cereal in the world. The study of the genetic basis of important agronomic traits in rice landraces and identification of genes will facilitate the breed improvement. Gelatinization temperature (GT), gel consistency (GC) and pericarp color (PC) are important indices of rice cooking and eating quality evaluation and potential nutritional importance, which attract wide attentions in the application of genetic and breeding. To dissect the genetic basis of GT, GC and PC, a total of 419 rice landraces core germplasm collections consisting of 330 indica lines, 78 japonica lines and 11 uncertain varieties were planted, collected, then GT, GC, PC were measured for two years, and sequenced using specific-locus amplified fragment sequencing (SLAF-seq) technology. In this study, 261,385,070 clean reads and 56,768 polymorphic SLAF tags were obtained, which a total of 211,818 single nucleotide polymorphisms (SNPs) were discovered. With 208,993 SNPs meeting the criterion of minor allele frequency (MAF) > 0.05 and integrity> 0.5, the phylogenetic tree and population structure analysis were performed for all 419 rice landraces, and the whole panel mainly separated into six subpopulations based on population structure analysis. Genome-wide association study (GWAS) was carried out for the whole panel, indica subpanel and japonica subpanel with subset SNPs respectively. One quantitative trait locus (QTL) on chromosome 6 for GT was detected in the whole panel and indica subpanel, and one QTL associated with GC was located on chromosome 6 in the whole panel and indica subpanel. For the PC trait, 8 QTLs were detected in the whole panel on chromosome 1, 3, 4, 7, 8, 10 and 11, and 7 QTLs in the indica subpanel on chromosome 3, 4, 7, 8, 10 and 11. For the three traits, no QTL was detected in japonica subpanel, probably because of the polymorphism repartition between the subpanel, or small population size of japonica subpanel. This paper provides new gene resources and insights into the molecular mechanisms of important agricultural trait of rice phenotypic variation and genetic improvement of rice quality variety breeding.

Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.

Anthocyanin Composition and Content in Rye Plants with Different Grain Color

The color of grain in cereals is determined mainly by anthocyanin pigments. A large level of genetic diversity for anthocyanin content and composition in the grain of different species was observed. In rye, recessive mutations in six genes (vi1...vi6) lead to the absence of anthocyanins in all parts of the plant. Moreover, dominant genes of anthocyanin synthesis in aleurone (gene C) and pericarp (gene Vs) also affect the color of the grain. Reverse phase high-performance liquid chromatography and mass spectrometry were used to study anthocyanins in 24 rye samples. A lack of anthocyanins in the lines with yellow and brown grain was determined. Delphinidin rutinoside and cyanidin rutinoside were found in the green-seeded lines. Six samples with violet grains significantly varied in terms of anthocyanin composition and content. However, the main aglycone was cyanidin or peonidin in all of them. Monosaccharide glucose and disaccharide rutinose served as the glycoside units. Violet-seeded accession forms differ in the ratio of the main anthocyanins and the range of their acylated derivatives. The acyl groups were presented mainly by radicals of malonic and sinapic acids. For the colored forms, a profile of the revealed anthocyanins with the indication of their contents was given. The obtained results are discussed in connection to similar data in rice, barley, and wheat, which will provide a perspective for future investigations.

The C-S-A gene system regulates hull pigmentation and reveals evolution of anthocyanin biosynthesis pathway in rice

Floral organs in rice (Oryza sativa) can be purple, brown, or red in color due to the accumulation of flavonoids, but the molecular mechanism underlying specific organ pigmentation is not clear. Here, we propose a C-S-A gene model for rice hull pigmentation and characterize it through genetic, molecular, and metabolomic approaches. Furthermore, we conducted phylogenetic studies to reveal the evolution of rice color. In this gene system, C1 encodes a R2R3-MYB transcription factor and acts as a color-producing gene, and S1 encodes a bHLH protein that functions in a tissue-specific manner. C1 interacts with S1 and activates expression of A1, which encodes a dihydroflavonol reductase. As a consequence, the hull is purple where functional A1 participation leads to high accumulation of cyanidin 3-O-glucoside. Loss of function of A1 leads to a brown hull color due to accumulation of flavonoids such as hesperetin 5-O-glucoside, rutin, and delphinidin 3-O-rutinoside. This shows a different evolutionary pathway of rice color in japonica and indica, supporting independent origin of cultivars in each subspecies. Our findings provide a complete perspective on the gene regulation network of rice color formation and supply the theoretical basis for extended application of this beneficial trait.

Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

Anthocyanins are involved in many diverse functions in rice, but their benefits have yet to be clearly demonstrated. Our objective in this study was to identify anthocyanin-related genes in black rice plants. We identified anthocyanin-related genes in black rice plants using a combination of whole-genome resequencing, RNA-sequencing (RNA-seq), microarray experiments, and reverse-transcriptase polymerase chain reaction (RT-PCR). Using multi-layer screening from 30 rice accessions, we identified 172,922 single-nucleotide polymorphisms (SNPs) and 1276 differentially expressed genes that appear to be related to anthocyanin biosynthesis. We identified 18 putative genes from 172,922 SNPs using intensive selective sweeps. The 18 candidate genes identified from SNPs were not significantly correlated with the RNA-seq expression pattern or other well-known anthocyanin biosynthesis/metabolism genes. We also identified nine putative genes from 1276 differentially expressed genes using RNA-seq transcriptome analysis. In addition, we identified four phylogenetic groups from these nine candidate genes and 51 pathway-network genes. Finally, we verified nine anthocyanin-related genes using a newly designed microarray and semi-quantitative RT-PCR. We suggest that these nine identified genes appear to be related to the regulation of anthocyanin biosynthesis and/or metabolism.

TRANSPARENT TESTA GLABRA 1-Dependent Regulation of Flavonoid Biosynthesis

The flavonoid composition of various tissues throughout plant development is of biological relevance and particular interest for breeding. Arabidopsis thaliana TRANSPARENT TESTA GLABRA 1 (AtTTG1) is an essential regulator of late structural genes in flavonoid biosynthesis. Here, we provide a review of the regulation of the pathway's core enzymes through AtTTG1-containing R2R3-MYELOBLASTOSIS-basic HELIX-LOOP-HELIX-WD40 repeat (MBW(AtTTG1)) complexes embedded in an evolutionary context. We present a comprehensive collection of A. thalianattg1 mutants and AtTTG1 orthologs. A plethora of MBW(AtTTG1) mechanisms in regulating the five major TTG1-dependent traits is highlighted.

Differential effects of rice bran cultivars to limit Salmonella Typhimurium in chicken cecal in vitro incubations and impact on the cecal microbiome and metabolome

In this study, rice brans from different cultivars (Calrose, Jasmine, and Red Wells) were assessed for their ability to inhibit Salmonella enterica serovar Typhimurium using an in vitro mixed anaerobic culture system containing cecal microbiota obtained from broilers of different ages. Salmonella Typhimurium was added to controls (feed only, cecal only, and feed + cecal material) and treatments (feed + cecal + different rice brans) and S. Typhimurium populations were enumerated at 0, 24, and 48 h. Two experimental conditions were applied 1) unadapted condition in which S. Typhimurium was added at the beginning of the culture incubation and 2) adapted condition in which S. Typhimurium was added after a 24 hour pre-incubation of the cecal bacteria with the feed and/or rice bran. Among the three rice brans, only Calrose exhibited a rapid inhibition of S. Typhimurium, which decreased to undetectable levels after 24 h under the adapted incubation. Changes in microbiological composition and metabolites by addition of Calrose bran were also investigated with an Illumina MiSeq platform and gas chromatography-mass spectrometry, respectively. Addition of Calrose bran resulted in significant changes including decreased Firmicutes phylum abundance and an increased number of metabolites associated with fatty acid metabolism. In summary, it appears that rice bran from specific rice cultivars may be effective as a means to reduce Salmonella in the chicken ceca. In addition, Calrose rice bran inclusion leads to changes in cecal microbiological composition and metabolite profile.

Construction of rice chromosome segment substitution lines harboring Oryza barthii genome and evaluation of yield-related traits

Rice (Oryza sativa L.) is one of the most important staple food in the world. To meet the increasing demand for food, a strategy for improving rice yield is needed. Alleles of wild relatives are useful because they confer adaptation to plants under diverse harsh environments and have the potential to improve rice. O. barthii is a wild rice species endemic to Africa and the known progenitor of the African cultivated rice, O. glaberrima. To explore the genetic potential of the O. barthii as a genetic resource, 40 chromosome segment substitution lines (CSSL) of O. barthii in the background of the elite japonica cultivar Koshihikari were developed and evaluated to identify QTLs associated with 10 traits related to flag leaf morphology, grain yield and other agronomic traits. More than 90% of the entire genome of the donor parent was represented in contiguous or overlapping chromosome segments in the CSSLs. Evaluation of the CSSLs for several agriculturally important traits identified candidate chromosome segments that harbors QTLs associated with yield and yield-related traits. These results suggest that alleles from O. barthii might be used as a novel genetic resource for improving the yield-related traits in cultivars of O. sativa.

Functional properties of an alternative, tissue-specific promoter for rice NADPH-dependent dihydroflavonol reductase

NADPH-dependent dihydroflavonol reductase (DFR) plays an important role in both anthocyanin biosynthesis and proanthocyanidin synthesis in plants. A specific and quantitative RT-PCR assay for transcription from the DFR promoter detected high expression with limited variability in rice tissues. A 440 bp minimal promoter region was identified by transfection of β-glucuronidase (GUS) reporter constructs into Jeokjinju variety. Alignment of the region with orthologous promoters revealed three conserved segments containing both bHLH (-386 to -381) and Myb (-368 to -362) binding sites. Transfection of β-glucuronidase constructs with targeted point mutations in the minimal promoter defined two sites important for promoter function to the transcription factor binding consensus sequences. The expression study showed that the bHLH binding domain (-386 to -381) is essential for DFR expression, and that a Myb binding domain (-368 to -362) is also required for full expression of the DFR gene, while the two bHLH binding domains (-104 to -99 and -27 to -22) nearest to the transcriptional start site are not necessary for DFR expression.

Toward Identification of Black Lemma and Pericarp Gene Blp1 in Barley Combining Bulked Segregant Analysis and Specific-Locus Amplified Fragment Sequencing

Black barley is caused by phytomelanin synthesized in lemma and/or pericarp and the trait is controlled by one dominant gene Blp1. The gene is mapped on chromosome 1H by molecular markers, but it is yet to be isolated. Specific-locus amplified fragment sequencing (SLAF-seq) is an effective method for large-scale de novo single nucleotide polymorphism (SNP) discovery and genotyping. In the present study, SLAF-seq with bulked segregant analysis (BSA) was employed to obtain sufficient markers to fine mapping Blp1 gene in an F2 population derived from Hatiexi No.1 × Zhe5819. Based on SNP screening criteria, a total of 77,542 polymorphic SNPs met the requirements for association analysis. Combining two association analysis methods, the overlapped region with a size of 32.41 Mb on chromosome 1H was obtained as the candidate region of Blp1 gene. According to SLAF-seq data, markers were developed in the target region and were used for mapping the Blp1 gene. Linkage analysis showed that Blp1 co-segregated with HZSNP34 and HZSNP36, and was delimited by two markers (HZSNP35 and HZSNP39) spanning 8.1 cM in 172 homozygous yellow grain F2 plants of Hatiexi No.1 × Zhe5819. More polymorphic markers were screened in the reduced target region and were used to genotype the population. As a result, Blp1 was delimited within a 1.66 Mb on chromosome 1H by the upstream marker HZSNP63 and the downstream marker HZSNP59. Our results demonstrated the utility of SLAF-seq-BSA approach to identify the candidate region and discover polymorphic markers at the specific targeted genomic region.

Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice (Oryza sativa L.)

Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa) was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL) for SD were identified in one primary and two advanced backcross (BC) populations derived from a temperate ecotype of weedy rice (34.3°N Lat.). Nine (75%) of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.). The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time) could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM) strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.

Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.

Identification and validation of QTLs for seedling salinity tolerance in introgression lines of a salt tolerant rice landrace 'Pokkali'

Salinity is a major threat to rice production worldwide. Several studies have been conducted to elucidate the molecular basis of salinity tolerance in rice. However, the genetic information such as quantitative trait loci (QTLs) and molecular markers, emanating from these studies, were rarely exploited for marker-assisted breeding. To better understand salinity tolerance and to validate previously reported QTLs at seedling stage, a set of introgression lines (ILs) of a salt tolerant donor line ‘Pokkali’ developed in a susceptible high yielding rice cultivar ‘Bengal’ background was evaluated for several morphological and physiological traits under salt stress. Both SSR and genotyping-by-sequencing (GBS) derived SNP markers were utilized to characterize the ILs and identify QTLs for traits related to salinity tolerance. A total of eighteen and thirty-two QTLs were detected using SSR and SNP markers, respectively. At least fourteen QTLs detected in the RIL population developed from the same cross were validated in IL population. Analysis of phenotypic responses, genomic composition, and QTLs present in the tolerant ILs suggested that the mechanisms of tolerance could be Na⁺ dilution in leaves, vacuolar Na⁺ compartmentation, and possibly synthesis of compatible solutes. Our results emphasize the use of salt injury score (SIS) QTLs in marker-assisted breeding to improve salinity tolerance. The tolerant lines identified in this study will serve as improved breeding materials for transferring salinity tolerance without the undesirable traits of Pokkali. Additionally, the lines will be useful for fine mapping and map-based cloning of genes responsible for salinity tolerance.

Identification of candidate genes for the seed coat colour change in a Brachypodium distachyon mutant induced by gamma radiation using whole-genome re-sequencing

Brachypodium distachyon has been proposed as a model plant for agriculturally important cereal crops such as wheat and barley. Seed coat colour change from brown-red to yellow was observed in a mutant line (142-3) of B. distachyon, which was induced by chronic gamma radiation. In addition, dwarf phenotypes were observed in each of the lines 142-3, 421-2, and 1376-1. To identify causal mutations for the seed coat colour change, the three mutant lines and the wild type were subjected to whole-genome re-sequencing. After removing natural variations, 906, 1057, and 978 DNA polymorphisms were detected in 142-3, 421-2, and 1376-1, respectively. A total of 13 high-risk DNA polymorphisms were identified in mutant 142-3. Based on a comparison with DNA polymorphisms in 421-2 and 1376-1, candidate causal mutations for the seed coat colour change in 142-3 were selected. In the two independent Arabidopsis thaliana lines carrying T-DNA insertions in the AtCHI, seed colour change was observed. We propose a frameshift mutation in BdCHI1 as a causal mutation responsible for seed colour change in 142-3. The DNA polymorphism information for these mutant lines can be utilized for functional genomics in B. distachyon and cereal crops.

Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches

BACKGROUND

Rice breeding program needs to focus on development of nutrient dense rice for value addition and helping in reducing malnutrition. Mineral and vitamin deficiency related problems are common in the majority of the population and more specific to developing countries as their staple food is rice.

RESULTS

Genes and QTLs are recently known for the nutritional quality of rice. By comprehensive literature survey and public domain database, we provided a critical review on nutritional aspects like grain protein and amino acid content, vitamins and minerals, glycemic index value, phenolic and flavonoid compounds, phytic acid, zinc and iron content along with QTLs linked to these traits. In addition, achievements through transgenic and advanced genomic approaches have been discussed. The information available on genes and/or QTLs involved in enhancement of micronutrient element and amino acids are summarized with graphical representation.

CONCLUSION

Compatible QTLs/genes may be combined together to design a desirable genotype with superior in multiple grain quality traits. The comprehensive review will be helpful to develop nutrient dense rice cultivars by integrating molecular markers and transgenic assisted breeding approaches with classical breeding.

Molecular and Biochemical Analysis of Two Rice Flavonoid 3'-Hydroxylase to Evaluate Their Roles in Flavonoid Biosynthesis in Rice Grain

Anthocyanins and proanthocyanidins, the major flavonoids in black and red rice grains, respectively, are mainly derived from 3',4'-dihydroxylated leucocyanidin. 3'-Hydroxylation of flavonoids in rice is catalyzed by flavonoid 3'-hydroxylase (F3'H: EC 1.14.13.21). We isolated cDNA clones of the two rice F3'H genes (CYP75B3 and CYP75B4) from Korean varieties of white, black, and red rice. Sequence analysis revealed allelic variants of each gene containing one or two amino acid substitutions. Heterologous expression in yeast demonstrated that CYP75B3 preferred kaempferol to other substrates, and had a low preference for dihydrokaempferol. CYP75B4 exhibited a higher preference for apigenin than for other substrates. CYP75B3 from black rice showed an approximately two-fold increase in catalytic efficiencies for naringenin and dihydrokaempferol compared to CYP75B3s from white and red rice. The F3'H activity of CYP75B3 was much higher than that of CYP75B4. Gene expression analysis showed that CYP75B3, CYP75B4, and most other flavonoid pathway genes were predominantly expressed in the developing seeds of black rice, but not in those of white and red rice, which is consistent with the pigmentation patterns of the seeds. The expression levels of CYP75B4 were relatively higher than those of CYP75B3 in the developing seeds, leaves, and roots of white rice.

De Novo Transcriptome Assembly and Annotation of the Leaves and Callus of Cyclocarya Paliurus (Bata1) Iljinskaja

Cyclocarya Paliurus (Bata1) Iljinskaja contains various bioactive secondary metabolites especially in leaves, such as triterpenes, flavonoids, polysaccharides and alkaloids, and its leaves are widely used as an hyperglycemic tea in China. In the present paper, we sequenced the transcriptome of the leaves and callus of Cyclocarya Paliurus using Illumina Hiseq 4000 platform. After sequencing and de novo assembly, a total of 65,654 unigenes were generated with an N50 length of 1,244bp. Among them, 35,041 (53.37%) unigenes were annotated in NCBI Non-Redundant database, 19,453 (29.63%) unigenes were classified into Gene Ontology (GO) database, and 7,259 (11.06%) unigenes were assigned to Clusters of Orthologous Group (COG) categories. Furthermore, 11,697 (17.81%) unigenes were mapped onto 335 pathways in Kyoto Encyclopedia of Genes and Genomes (KEGG), among which 1,312 unigenes were identified to be involved in biosynthesis of secondary metabolites. In addition, a total of 11,247 putative simple sequence repeats (SSRs) were detected. This transcriptome dataset provides a comprehensive sequence resource for gene expression profiling, genetic diversity, evolution and further molecular genetics research on Cyclocarya Paliurus.

The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice (Oryza sativa L.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5× and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SNPs in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.

Genome-wide Association Mapping of Polyphenol Contents and Antioxidant Capacity in Whole-Grain Rice

Whole grains contain various bioactive phytochemicals including phenolic acids, and consumption of whole grains may provide desirable health benefits and reduce the risks of chronic diseases due to their antioxidant activities. In this study, we qualified and quantified 9 bound phenolic compounds in 32 red and 88 white pericarp accessions of rice. A genome-wide association study (GWAS) was conducted for free (FP) and bound (BP) phenolic compounds and their antioxidant capacities with high-quality single-nucleotide polymorphisms (SNPs) in two colored grain panels and the whole panel. Rc was detected for all FP and antioxidant capacities in the whole panel. Three loci (chr.1:30970095, chr.6:24392269, and chr.9:6670223) for more than five phenolic-related traits, two loci (chr.4:34120529 and chr.11:28947480) for more than two FP-related traits, and one locus (chr.11:23220681) for ferulic acid detected in two panels were potentially new genes that are valuable for further gene cloning. Overall, this study increases our understanding on the genetics of phenolic acid biosynthesis in the phenylpropanoid pathway.

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea

The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea.

Genome re-sequencing and bioinformatics analysis of a nutraceutical rice

The genomes of two rice cultivars, Nipponbare and 93-11, have been well studied. However, there is little available genetic information about nutraceutical rice cultivars. To remedy this situation, the present study aimed to provide a basic genetic landscape of nutraceutical rice. The genome of Black-1, a black pericarp rice containing higher levels of anthocyanins, flavonoids, and a more potent antioxidant capacity, was sequenced at ≥30 × coverage using Solexa sequencing technology. The complete sequences of Black-1 genome shared more consensus sequences with indica cultivar 93-11 than with Nipponbare. With reference to the 93-11 genome, Black-1 contained 675,207 single-nucleotide polymorphisms, 43,130 insertions and deletions (1-5 bp), 1,770 copy number variations, and 10,911 presence/absence variations. These variations were observed to reside preferentially in Myb domains, NB-ARC domains and kinase domains, providing clues to the diversity of biological functions or secondary metabolisms in this cultivar. Intriguingly, 496 unique genes were identified by comparing it with the genomes of these two rice varieties; among the genes, 119 genes participate in the biosynthesis of secondary metabolites. Furthermore, several unique genes were predicted to be involved in the anthocyanins synthesis pathway. The genome-wide landscape of Black-1 uncovered by this study represents a valuable resource for further studies and for breeding nutraceutical rice varieties.

Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm

Identifying natural variation of health-promoting compounds in staple crops and characterizing its genetic basis can help improve human nutrition through crop biofortification. Some varieties of sorghum, a staple cereal crop grown worldwide, have high concentrations of proanthocyanidins and 3-deoxyanthocyanidins, polyphenols with antioxidant and anti-inflammatory properties. We quantified total phenols, proanthocyanidins, and 3-deoxyanthocyanidins in a global sorghum diversity panel (n = 381) using near-infrared spectroscopy (NIRS), and characterized the patterns of variation with respect to geographic origin and botanical race. A genome-wide association study (GWAS) with 404,628 SNP markers identified novel quantitative trait loci for sorghum polyphenols, some of which colocalized with homologues of flavonoid pathway genes from other plants, including an orthologue of maize (Zea mays) Pr1 and a homologue of Arabidopsis (Arabidopsis thaliana) TT16. This survey of grain polyphenol variation in sorghum germplasm and catalog of flavonoid pathway loci may be useful to guide future enhancement of cereal polyphenols.

Red pericarp introgression lines derived from interspecific crosses of rice: physicochemical characteristics, antioxidative properties and phenolic content

BACKGROUND

Antioxidative properties and physicochemical characteristics of introgression lines (ILs) and their recurrent parents were analyzed. In addition, catalase (CAT) and superoxide dismutase (SOD) activities and free radical-scavenging capacity were evaluated, since these are important antioxidative properties for developing nutraceutical and functional foods.

RESULTS

Comparative analysis of the brown and milled rice fractions of ILs with their respective recurrent parents revealed 2.26- and 1.22-fold increase in total phenolics, 1.95- and 2.09-fold increase in flavonoids, 8.38- and 6.80-fold increase in proanthocyanidins and 1.55- and 1.20-fold increase in tannins in brown and milled rice fractions respectively. Higher CAT (1.36- and 1.89-fold) and SOD (1.71- and 2.02-fold) activities and Trolox equivalent antioxidant capacity (TEAC, 7.13- and 1.98-fold) were observed in brown and milled rice fractions respectively of ILs compared with their respective recurrent parents. A high and positive correlation was obtained between TEAC and total phenols (0.73, P ≤ 0.01), flavonoids (0.66, P ≤ 0.05) and proanthocyanidins (0.69, P ≤ 0.05). The yield parameters and physicochemical characteristics of the grains, in general, were comparable in the ILs and their respective recurrent parents.

CONCLUSION

The ILs of rice reported in the present study exhibited significant positive differences in the content of phenolic constituents and antioxidant properties with good grain quality characteristics over their recurrent parents, indicating their potential as a natural source of phytochemicals for nutraceutical and functional food development.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

BACKGROUND

Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL.

RESULTS

In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL.

CONCLUSIONS

NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the "arms race" with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Analysis of genotype × environment interactions for polyphenols and antioxidant capacity of rice by association mapping

Uncovering the genetic basis of polyphenol content and antioxidant activity traits in rice accessions is important to improve the nutritional quality of whole grain rice and to ameliorate the increasing nutrition problem of the rice-eating population. In this study, 20 diverse rice accessions were planted in Hainan province, China, for 2 years to investigate the effects of genotype, environment, and their interactions on total phenolic (TPC), flavonoid (TFC), proanthocyanidins content (TPAC), ABTS, and DPPH radical scavenging activity by association mapping. Analyses of variance (ANOVA) showed that TPC, TFC, TPAC, ABTS, and DPPH were mainly affected by genetic variance, accounting for >94% of the total variance. The interaction between genotype × environment (G × E) was also highly significant (P < 0.001). Red-pericarp rice accumulates proanthocyanidins, which had significantly higher TPC, TFC, ABTS, and DPPH than white-pericarp rice. The correlation coefficient among these parameters were highly significant (r > 0.96; P < 0.001). Twenty-three putative unique loci were identified by association mapping. Five loci were close to previously identified genes or quantitative trait loci (QTLs). Among them, qPAC7-3 identified for TPAC in 2011 was near to the brown pericarp and seed coat (Rc) gene, and the locus at the qPC4/qFC4/qPAC4/qACA4/qACD4 cluster on chromosome 4 detected in two environments was near to a transcriptional activator A (Ra) gene. Some loci were identified in only one environment, indicating that these QTLs were sensitive to environment. This study provides a primary SNP-resource for further identification of genes responsible for polyhenol contents and antioxidant activity in rice whole grains.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome

Background

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia.

Results

We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58Mbp region on chromosome 5, which suggests that some of the ‘polymorphism deserts’ in this and other parts of the rice genome may have originated prior to domestication due to natural selection.

Conclusions

Analysis of genes in the ‘polymorphism deserts’ indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Genetic dissection of black grain rice by the development of a near isogenic line

Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. 'Koshihikari', which is a leading variety in Japan. We used Oryza sativa L. 'Hong Xie Nuo' as the donor parent and backcrossed with 'Koshihikari' four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F2 plants derived from a cross between the black rice NIL and 'Koshihikari' was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of 'Okunomurasaki', an existing black rice variety. The isogenicity of the black rice NIL to 'Koshihikari' was very high.

Genome-wide analysis of radiation-induced mutations in rice (Oryza sativa L. ssp. indica)

Radiation has been efficiently used for rice germplasm innovation. However, the molecular mechanisms by which radiation induces mutations are still unclear. In this study, we performed whole genome sequencing to reveal the comprehensive mutations in rice treated with radiation. Red-1 (a rice rich in beneficial ingredients for human health) was derived from rice 9311 after γ-radiation. Solexa sequencing technology was applied to uncover the mutations. Compared with the 9311 genome, 9.19% of genome sequences were altered in the Red-1 genome. Among these alterations, there were 381,403 SNPs, 50,116 1-5 bp Indels, 1279 copy number variations, and 10,026 presence/absence variations. These alterations were located in 14,493 genes, the majority of which contained a kinase domain, leucine rich repeats, or Cyt_P450. Point mutations were the main type of variation in the Red-1 genome. Gene ontology clustering revealed that genes that are associated with cell components, binding function, catalytic activity and metabolic processes were susceptible to γ-radiation. It was also predicted that 8 mutated genes were involved in the biosynthetic pathways of beneficial products or pigment accumulation. We conclude that genome-wide analysis of mutations provides novel insights into the mechanisms by which radiation improves the beneficial ingredients in rice Red-1.

Evolution of crop species: genetics of domestication and diversification

Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

Physiological factors affecting transcription of genes involved in the flavonoid biosynthetic pathway in different rice varieties

Flavonoids play an important role in the grain color and flavor of rice. Since their characterization in maize, the flavonoid biosynthetic genes have been extensively studied in grape, Arabidopsis, and Petunia. However, we are still a long way from understanding the molecular features and mechanisms underlying the flavonoid biosynthetic pathway. The present study was undertaken to understand the physiological factors affecting the transcription and regulation of these genes. We report that the expression of CHI, CHS, DFR, LAR, and ANS, the 5 flavonoid biosynthetic genes in different rice varieties, differ dramatically with respect to the stage of development, white light, and sugar concentrations. We further demonstrate that white light could induce the transcription of the entire flavonoid biosynthetic gene pathway; however, differences were observed in the degrees of sensitivity and the required illumination time. Our study provides valuable insights into understanding the regulation of the flavonoid biosynthetic pathway.

Molecular mechanisms involved in convergent crop domestication

Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions.

Regulation, evolution, and functionality of flavonoids in cereal crops

Flavonoids are plant secondary metabolites that contribute to the adaptation of plants to environmental stresses, including resistance to abiotic and biotic stress. Flavonoids are also beneficial for human health and depress the progression of some chronic diseases. The biosynthesis of flavonoids, which belong to a large family of phenolic compounds, is a complex metabolic process with many pathways that produce different metabolites, controlled by key enzymes. There is limited knowledge about the composition, biosynthesis and regulation of flavonoids in cereals. Improved understanding of the accumulation of flavonoids in cereal grains would help to improve human nutrition through these staple foods. The biosynthesis of flavonoids, scope for altering the flavonoid composition in cereal crops and benefits for human nutrition are reviewed here.

Quantitative trait locus and haplotype analyses of wild and crop-mimic traits in U.S. weedy rice

Conspecific weeds retained characteristics from wild ancestors and also developed crop mimicries for adaptation and competitiveness. This research was conducted to identify quantitative trait loci (QTL) associated with the wild and crop-mimic traits and to determine haplotype variants for QTL-rich regions in U.S. weedy rice. An F2 population from the cross between a cultivated (EM93-1) and a U.S. weedy (US1) rice line was evaluated for six wild and eight crop-mimic traits in a greenhouse to identify the QTL. A core collection of 27 U.S. weedy red rice lines and 14 AA-genome wild rice lines were determined for the haplotype variants. A total of 49 QTL were identified, with 45 collocated as clusters on 14 genomic segments. The number of haplotypes across the 14 segments was lower in the weedy (6.1 ± 2.4) than in the wild (7.5 ± 1.8) rice sample. Both samples shared ~50% haplotypes (wild-like). The EM93-1-like haplotypes accounted for a greater proportion (30 ± 26%) of the haplotypes in the weedy than in the wild (7 ± 10%) rice. Based on haplotype patterns for the 14 QTL cluster regions, 26 of the 28 red rice lines were clustered into two groups corresponding to the black-hull awned and straw-hull awnless morphological types, respectively. The QTL analysis demonstrated that conspecific weed-crop differentiation involved many genomic segments with multiple loci regulating natural variation for adaptation and competitiveness. The haplotype analysis revealed that U.S. weedy rice retained large blocks of linkage disequilibrium for the multiple loci from the wild relatives and also incorporated haplotypes from cultivars.

Understanding rice domestication and implications for cultivar improvement

Considerable insights were recently gained into the history and process of rice domestication. It becomes increasingly clear that artificial and natural selections coupled with extensive introgression have shaped the genomes of cultivated rice. The interplay of these evolutionary forces gave rise to the cultivated species, Oryza sativa, with divergent genomic backgrounds from two wild species, O. rufipogon and O. nivara, governed by a set of domestication alleles which had originated primarily at one location of initial cultivation. The mechanistic understanding of domestication suggests that the combination of quantitative trait locus mapping, genome-wide association study, and genome scan will be effective means for discovering potentially valuable alleles from the cultivated and wild species. The accumulation and appropriate sampling of germplasm collections for these analyses should effectively grow the useful allele pool, which combined with molecular breeding may get to a point literally triggering the re-domestication of rice varieties for sustainable food production.

Mapping and characterization of quantitative trait loci for mesocotyl elongation in rice (Oryza sativa L.)

Mesocotyl elongation is an important trait for seedling emergence in direct-seeding cultivation in rice. In this study, a backcross inbred line (BIL) population from a cross between Kasalath and Nipponbare was employed to map quantitative trait loci (QTLs) for mesocotyl elongation. A total of 5 QTLs for mesocotyl length were identified on chromosomes 1, 3, 7, 9, and 12 in 2 independent experiments. At all QTL, the Kasalath alleles contributed to an increase in mesocotyl length. Two QTLs (qMel-1 and qMel-3) on chromosomes 1 and 3 were consistently detected in both experiments. To fine map the QTLs, a cross was made between 2 chromosome segment substitution lines (CSSL-6 and CSSL-15), each harboring the Kasalath allele across the qMel-1 and qMel-3 regions, and an F2:3 population was developed. A two-way ANOVA indicated that no epistatic interaction was detected between the 2 QTLs in the F2 population (P = 0.31). Moreover, analysis of two F3 near-isogenic lines (NILs) derived from the same cross, indicated that the 2 QTLs act additively in distinct or complementary pathways in controlling mesocotyl elongation. Substitution mapping indicated that the qMel-1 QTL was located between the 2 SSR markers RM5448 and RM5310, which are 3,799-kb apart, and that the qMel-3 QTL was located between the 2 SSR markers RM3513 and RM1238, which are 6,964-kb apart. To our knowledge, this is the first report to fine-map QTLs for mesocotyl elongation and to analyze their interaction.

A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa

Yellow seed is a desirable quality trait of the Brassica oilseed species. Previously, several seed coat color genes have been mapped in the Brassica species, but the molecular mechanism is still unknown. In the present investigation, map-based cloning method was used to identify a seed coat color gene, located on A9 in B. rapa. Blast analysis with the Arabidopsis genome showed that there were 22 Arabidopsis genes in this region including at4g09820 to at4g10620. Functional complementation test exhibited a phenotype reversion in the Arabidopsis thaliana tt8-1 mutant and yellow-seeded plant. These results suggested that the candidate gene was a homolog of TRANSPARENT TESTA8 (TT8) locus. BrTT8 regulated the accumulation of proanthocyanidins (PAs) in the seed coat. Sequence analysis of two alleles revealed a large insertion of a new class of transposable elements, Helitron in yellow sarson. In addition, no mRNA expression of BrTT8 was detected in the yellow-seeded line. It indicated that the natural transposon might have caused the loss in function of BrTT8. BrTT8 encodes a basic/helix-loop-helix (bHLH) protein that shares a high degree of similarity with other bHLH proteins in the Brassica. Further expression analysis also revealed that BrTT8 was involved in controlling the late biosynthetic genes (LBGs) of the flavonoid pathway. Our present findings provided with further studies could assist in understanding the molecular mechanism involved in seed coat color formation in Brassica species, which is an important oil yielding quality trait.