Pericarp Color Research Articles

Comparative study of phenolic compounds in different Brazilian rice ( Oryza sativa L.) genotypes

This study was conducted to evaluate the natural variability of total, extractable and non-extractable phenolics in pigmented and non-pigmented rice genotypes ( Oryza sativa L.) and to estimate whether the contents and distribution of these compounds are typical for genotypes from indica and japonica subspecies. Twenty-one samples of commercial as well as new genotypes of brown rice, including seven pigmented genotypes were obtained from two Agronomic Institutes in South Brazil. Free and conjugated phenolics were extracted with ethanol, while bound phenolics were released by alkaline hydrolysis. Total phenolics were estimated in both fractions by the Folin–Ciocalteau method. Genotypes from japonica and indica non-pigmented subspecies were not statistically distinguishable from each other, but differences in phenolic contents were associated with pericarp color. Despite individual differences, total phenolics were four times higher in pigmented than in non-pigmented genotypes (4246 and 1073 mg ferulic acid equiv. kg −1, respectively). These high amounts were mostly due to the presence of extractable (free and conjugated) phenolics, which comprised up to 81% of total phenolics for pigmented genotypes. Non-extractable (bound) phenolics comprised 40% of total phenolics of non-pigmented rice genotypes while pigmented genotypes presented greater absolute amounts, but their contribution on total phenolics was small.

Inference of the japonica Rice Domestication Process from the Distribution of Six Functional Nucleotide Polymorphisms of Domestication-Related Genes in Various Landraces and Modern Cultivars

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. Our earlier identification of three functional nucleotide polymorphisms (FNPs) of distinct genes involved in the rice domestication process led us to propose a model of the japonica rice domestication process. Here, we examined three more FNPs in two domestication-related genes involved in pigment synthesis during the development of seed pericarp color (Rc and Rd) in 91 landraces (and some modern cultivars) of japonica rice collected from throughout the area of distribution of rice. These polymorphisms were assigned by using genome-wide patterns of restriction fragment length polymorphisms (RFLPs) and the local origins of the landraces. The results led us to infer the process of japonica rice domestication in more detail and propose a more refined model of the japonica domestication process. In this model, the critical role of the Rc FNP at an early step of the domestication process was highlighted. Independent artificial selections of two defective Rd alleles were found, suggesting a role for Rd other than in pigment synthesis during rice domestication.

A Mutator transposon insertion is associated with ectopic expression of a tandemly repeated multicopy Myb gene pericarp color1 of maize.

The molecular basis of tissue-specific pigmentation of maize carrying a tandemly repeated multicopy allele of pericarp color1 (p1) was examined using Mutator (Mu) transposon-mediated mutagenesis. The P1-wr allele conditions a white or colorless pericarp and a red cob glumes phenotype. However, a Mu-insertion allele, designated as P1-wr-mum6, displayed an altered phenotype that was first noted as occasional red stripes on pericarp tissue. This gain-of-pericarp-pigmentation phenotype was heritable, yielding families that displayed variable penetrance and expressivity. In one fully penetrant family, deep red pericarp pigmentation was observed. Several reports on Mu suppressible alleles have shown that Mu transposons can affect gene expression by mechanisms that depend on transposase activity. Conversely, the P1-wr-mum6 phenotype is not affected by transposase activity. The increased pigmentation was associated with elevated mRNA expression of P1-wr-mum6 copy (or copies) that was uninterrupted by the transposons. Genomic bisulfite sequencing analysis showed that the elevated expression was associated with hypomethylation of a floral-specific enhancer that is approximately 4.7 kb upstream of the Mu1 insertion site and may be proximal to an adjacent repeated copy. We propose that the Mu1 insertion interferes with the DNA methylation and related chromatin packaging of P1-wr, thereby inducing expression from gene copy (or copies) that is otherwise suppressed.

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.

The Complex History of the Domestication of Rice

BackgroundRice has been found in archaeological sites dating to 8000 bc, although the date of rice domestication is a matter of continuing debate. Two species of domesticated rice, Oryza sativa (Asian) and Oryza glaberrima (African) are grown globally. Numerous traits separate wild and domesticated rices including changes in: pericarp colour, dormancy, shattering, panicle architecture, tiller number, mating type and number and size of seeds.ScopeGenetic studies using diverse methodologies have uncovered a deep population structure within domesticated rice. Two main groups, the indica and japonica subspecies, have been identified with several subpopulations existing within each group. The antiquity of the divide has been estimated at more than 100 000 years ago. This date far precedes domestication, supporting independent domestications of indica and japonica from pre-differentiated pools of the wild ancestor. Crosses between subspecies display sterility and segregate for domestication traits, indicating that different populations are fixed for different networks of alleles conditioning these traits. Numerous domestication QTLs have been identified in crosses between the subspecies and in crosses between wild and domesticated accessions of rice. Many of the QTLs cluster in the same genomic regions, suggesting that a single gene with pleiotropic effects or that closely linked clusters of genes underlie these QTL. Recently, several domestication loci have been cloned from rice, including the gene controlling pericarp colour and two loci for shattering. The distribution and evolutionary history of these genes gives insight into the domestication process and the relationship between the subspecies.ConclusionsThe evolutionary history of rice is complex, but recent work has shed light on the genetics of the transition from wild (O. rufipogon and O. nivara) to domesticated (O. sativa) rice. The types of genes involved and the geographic and genetic distribution of alleles will allow scientists to better understand our ancestors and breed better rice for our descendents.

Phenolic Compounds Accumulate Specifically in Maternally‐Derived Tissues of Developing Maize Kernels

ABSTRACTPhenolic compounds function in natural resistance of plants to insects, pathogens, and abiotic stresses. We investigated the flavonoid and phenolic acid content in developing maize kernels from 8 to 28 days after pollination and found a complex and developmentally dynamic mixture of compounds. LC‐MS analysis showed no detectable levels of the flavonoid maysin in any of the kernel tissue tested. Accumulation of the three most abundant analytes was developmentally and spatially regulated and independent of the regulatory transcription factor pericarp color 1 (P1). Major analytes have UV characteristics similar to hydroxycinnamic acids. LC‐MS indicates molecular weights of 410, 440, and 862 mass units, representing coumaroylferuloylputrescine (CFP), diferuloylputrescine (DFP), and a novel compound, respectively. There are large differences in the abundance of these compounds between genetic backgrounds, and accumulation increases with age. We dissected and analyzed various tissue types and demonstrated that the majority of these compounds are present in pedicels, with lesser amounts in pericarp and placento‐chalazal regions. These data indicate that complex phenolic acids and amides rather than flavonoids are the major phenolic constituents in developing kernels, and accumulation of these compounds is developmentally and spatially regulated, with the greatest abundance in maternal tissues surrounding the kernel.

Differential effects of abscisic acid and ethylene on the fruit maturation of Litchi chinensis Sonn.

Two litchi cultivars, a well-coloured ‘Nuomici’ and a poorly coloured ‘Feizixiao’, were used to investigate changes in endogenous abscisic acid (ABA) concentration and ethylene production during fruit maturation and to test the effects of exogenous growth regulators on litchi fruit maturation. Abscisic acid concentration in both the aril and pericarp increased with fruit maturation. Transfusion of ABA into the fruit 3 weeks before harvest accelerated, whereas transfusion of 6-benzyl aminopurine (6-BA) retarded sugar accumulation and pigmentation. The effect of 6-BA was assumed to link with the resultant decrease in ABA. In contrast, 1-aminocyclopropane-1-carboxylic acid (ACC) concentration and ACC oxidase (ACO) activities in the aril remained relatively constant during sugar accumulation. Transfusion of aminooxyacetic acid (AOA) significantly decreased ACC concentration but had no effect on sugar accumulation in the aril. These results suggested that endogenous ABA, but not ethylene, was critical for the sugar accumulation. However, the roles of ABA and ethylene in pericarp pigmentation were rather complicated. Application of exogenous ABA promoted anthocyanin synthesis significantly, but had very little effect on chlorophyll degradation. Ethylene production in litchi fruit decreased with development, but a transient increase of endogenous ethylene production was detected just around the colour break in ‘Nuomici’. Enhanced ACO activity in the pericarp was detected during pigmentation. Ethrel at 400 mg l−1 showed no effect on pericarp coloration, but accelerated chlorophyll degradation and anthocyanin synthesis at a much higher concentration (800 mg l−1). Fruit dipped in ABA solution alone yielded no effect on chlorophyll degradation, but the combined use of ABA and Ethrel at 400 mg l−1 enhanced both chlorophyll degradation and anthocyanin synthesis. These results indicated the possible synergistic action of ethylene and ABA during litchi fruit colouration. ABA is suggested to play a more crucial role in anthocyanin synthesis, while ethylene is more important in chlorophyll degradation. ABA can increase the sensitivity of pericarp tissue to ethylene.

Quantitative trait loci for maysin synthesis in maize (Zea mays L.) lines selected for high silk maysin content

Maysin is a naturally occurring C-glycosyl flavone found in maize (Zea mays L.) silk tissue that confers resistance to corn earworm (Helicoverpa zea, Boddie). Recently, two new maize populations were derived for high silk maysin. The two populations were named the exotic populations of maize (EPM) and the southern inbreds of maize (SIM). Quantitative trait locus (QTL) analysis was employed to determine which loci were responsible for elevated maysin levels in inbred lines derived from the EPM and SIM populations. The candidate genes consistent with QTL position included the p (pericarp color), c2 (colorless2), whp1 (white pollen1) and in1 (intensifier1) loci. The role of these loci in controlling high maysin levels in silks was tested by expression analysis and use of the loci as genetic markers onto the QTL populations. These studies support p, c2 and whp1, but not in1, as loci controlling maysin. Through this study, we determined that the p locus regulates whp1 transcription and that increased maysin in these inbred lines was primarily due to alleles at both structural and regulatory loci promoting increased flux through the flavone pathway by increasing chalcone synthase activity.

Epigenetic Modifications of Distinct Sequences of thep1Regulatory Gene Specify Tissue-Specific Expression Patterns in Maize

Tandemly repeated endogenous genes are common in plants, but their transcriptional regulation is not well characterized. In maize, the P1-wr allele of pericarp color1 is composed of multiple copies arranged in a head-to-tail fashion. P1-wr confers a white kernel pericarp and red cob glume pigment phenotype that is stably inherited over generations. To understand the molecular mechanisms that regulate tissue-specific expression of P1-wr, we have characterized P1-wr*, a spontaneous loss-of-function epimutation that shows a white kernel pericarp and white cob glume phenotype. As compared to its progenitor P1-wr, the P1-wr* is hypermethylated in exon 1 and intron 2 regions. In the presence of the epigenetic modifier Ufo1 (Unstable factor for orange1), P1-wr* plants exhibit a range of cob glume pigmentation whereas pericarps remain colorless. In these plants, the level of cob pigmentation directly correlates with the degree of DNA demethylation in the intron 2 region of p1. Further, genomic bisulfite sequencing indicates that a 168-bp region of intron 2 is significantly hypomethylated in both CG and CNG context in P1-wr* Ufo1 plants. Interestingly, P1-wr* Ufo1 plants did not show any methylation change in a distal enhancer region that has previously been implicated in Ufo1-induced gain of pericarp pigmentation of the P1-wr allele. These results suggest that distinct regulatory sequences in the P1-wr promoter and intron 2 regions can undergo independent epigenetic modifications to generate tissue-specific expression patterns.

Gene Conversion Between Direct Noncoding Repeats Promotes Genetic and Phenotypic Diversity at a Regulatory Locus of Zea mays (L.)

While evolution of coding sequences has been intensively studied, diversification of noncoding regulatory regions remains poorly understood. In this study, we investigated the molecular evolution of an enhancer region located 5 kb upstream of the transcription start site of the maize pericarp color1 (p1) gene. The p1 gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in maize floral organs. Distinct p1 alleles exhibit organ-specific expression patterns on kernel pericarp and cob glumes. A cob glume-specific regulatory region has been identified in the distal enhancer. Further characterization of 6 single-copy p1 alleles, including P1-rr (red pericarp/red cob) and P1-rw (red pericarp and white cob), reveals 3 distinct enhancer types. Sequence variations in the enhancer are correlated with the p1 gene expression patterns in cob glume. Structural comparisons and phylogenetic analyses suggest that evolution of the enhancer region is likely driven by gene conversion between long direct noncoding repeats (approximately 6 kb in length). Given that tandem and segmental duplications are common in both animal and plant genomes, our studies suggest that recombination between noncoding duplicated sequences could play an important role in creating genetic and phenotypic variations.

Characterization of Fusarium-induced expression of flavonoids and PR genes in maize

In maize, Fusarium ear rots lead to contamination of grains with mycotoxins and loss of yield. We tested if induced expression of 3-deoxyanthocyanidins and related 3-deoxyflavonoid (flavan-4-ols) compounds in maize silks and kernels impart resistance to Fusarium ear rot. In maize, condensed flavan-4-ols (phlobaphenes) accumulate in floral organs including silks and kernel pericarps and their biosynthesis is regulated by Pericarp color1 ( P1) and a linked paralog P2. Three maize lines differing for allelic constitution at the P locus were compared for their response to Fusarium verticillioides and F. graminearum. The moderately resistant maize line P1-rr4B2 carrying both the P1 and the P2 gene showed enhanced accumulation of 3-deoxyanthocyanidins in inoculated silks. The line 4Co63 carrying only the P2 gene exhibited highest resistance to F. verticillioides. Expression data revealed that flavonoid pathway genes were active during the early stages of silk development. In kernels, however, induction of the flavonoid pathway genes was later than that in silks, and higher transcriptional induction was observed in line carrying both P1 and P2 genes. Among the PR genes tested, PR-4 and PR-5 showed developmental as well as fungus-induced expression. Field based ear rot incidence could be correlated with the presence of functional P locus as well as genetic background of the tested maize lines.

Association of Plant Color and Pericarp Color with Colonization of Grain by Members of Fusarium and Alternaria in Near-Isogenic Sorghum Lines.

White sorghum (Sorghum bicolor) grain from tan plants is more desirable for human or animal consumption. Colonization by Fusarium and Alternaria spp. was assessed for near-isogenic lines differing in wound response (purple or tan) and pericarp color (red or white) in field-grown grain and in greenhouse-grown plants. Seeds were screened on a semi-selective medium for Alternaria and Fusarium. Significantly fewer fungal colonies were obtained from tan plants with white seed, and fewer numbers of Alternaria colonies were obtained from white seed, regardless of plant color, from an irrigated field, while there were no differences in fungal composition of seeds grown at a nonirrigated field. Screening of seed from the nonirrigated field on Fusarium semi-selective medium yielded fewer Fusarium isolations from seed grown on purple plants compared with seed from tan plants. When inoculated with Alternaria sp. and F. moniliforme, there can be no differences in lesion lengths on tan/white plants when compared with purple/red plants in most assays; in one assay, tan/white plants had smaller lesion lengths following inoculation with F. moniliforme. These results suggest that plants with white seeds were as resistant as plants with the red pericarp trait to colonization by Alternaria and Fusarium spp. However, the results also suggest that under appropriate environmental conditions seed from tan plants may be more susceptible to Fusarium spp. than seed from purple plants.

Desenvolvimento do fruto da lichieira (Litchi chinensis Sonn.) 'Bengal'

Estudou-se o desenvolvimento do fruto da lichieira (Litchi chinensis Sonn.) 'Bengal'. Realizaram-se amostragens semanais, com início aos 35 dias após a antese e término no início da senescência dos frutos. A partir do 77º dia após a antese, os frutos foram decompostos em pericarpo, semente e arilo. A antese ocorreu na primeira semana de setembro. Foram ajustados modelos sigmoidais simples para acúmulo de matéria seca, comprimento e diâmetro. Para o acúmulo de matéria seca, uma fase inicial, de crescimento lento, prolongou-se até o 63º dia após a antese e coincidiu com um período de intensa queda natural de frutos. Do 63º ao 98º dia após a antese, houve uma fase de rápido acúmulo de matéria seca. Até o 77º dia, pericarpo e semente foram os principais responsáveis pelo acúmulo de matéria seca. Oitenta e oito por cento do comprimento e 65% do diâmetro máximos foram atingidos nesse período. Do 84º ao 98º dia após a antese, o desenvolvimento do fruto foi determinado basicamente pelo arilo. As dimensões e a matéria seca do fruto estabilizaram-se a partir do 98º dia após a antese. O ponto de colheita comercial dos frutos, caracterizado pela coloração avermelhada do pericarpo, ocorreu a partir do 112º dia após a antese. Verificou-se um quadro senescente nos frutos a partir do 119º dia após a antese.

Evaluation of the integrated application of two types of modified atmosphere packaging and hot water treatments on quality retention in the litchi cultivar ‘McLean’s Red’

SummaryThe efficacy of modified atmosphere packaging (MAP), Xtend® (XF) or biorientated polypropylene (BOPP), and hot water dip treatments on quality retention in the litchi cultivar ‘McLean’s Red’ was evaluated as an alternative to SO2-fumigation. Fruits were dipped in hot water at different temperatures and time regimes [50°C 2 min; 55°C 1 min; or 60°C 1 s] and packed in XF or in BOPP. The XF bags were closed with rubber bands, while the BOPP bags were heat-sealed to modify the atmosphere around the fruit. Packed fruits were placed in commercial cardboard cartons and stored at 2°C and 95% RH for 34 d to simulate commercial export conditions. Commercial SO2-fumigation, and fruit without any hot water dip treatment packed in XF or BOPP were included as controls. Weight loss, firmness, pericarp browning, severity of decay, Hunter colour values, titratable acidity, fruit pH and soluble solids concentrations were determined after storage. Sensory analysis was carried out to determine colour retention of the pericarp and aril, flavour qualities, taste, odour, juiciness and overall consumer acceptability. Fruit packed in BOPP showed reduced weight loss, colour deterioration and decay, and retained excellent eating quality during long-term storage due to the high RH and higher O2 concentrations (17%) around the fruit. Hot water dip treatments at 50°C for 2 min, or at 55°C for 1 min, caused deleterious effects on pericarp colour, surface structure and quality parameters.

Phenotypic Selection for Dormancy Introduced a Set of Adaptive Haplotypes From Weedy Into Cultivated Rice

Association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting. A phenotypic selection and recurrent backcrossing technique was used to introduce dormancy genes from a wild-like weedy rice to a breeding line to determine their effects and linkage with the other traits. Five generations of phenotypic selection alone for low germination extremes simultaneously retained dormancy alleles at five independent QTL, including qSD12 (R(2) > 50%), as determined by genome-wide scanning for their main and/or epistatic effects in two BC(4)F(2) populations. Four dormancy loci with moderate to small effects colocated with QTL/genes for one to three of the associated traits. Multilocus response to the selection suggests that these dormancy genes are cumulative in effect, as well as networked by epistases, and that the network may have played a "sheltering" role in maintaining intact adaptive haplotypes during the evolution of weeds. Tight linkage may prevent the dormancy genes from being used in breeding programs. The major effect of qSD12 makes it an ideal target for map-based cloning and the best candidate for imparting resistance to preharvest sprouting.

Isolation of three dormancy QTLs as Mendelian factors in rice

Seed dormancy is a key adaptive trait under polygenic control in many plants. We introduced the chromosomal regions containing the dormancy QTLs qSD1, qSD7-1, and qSD12 from an accession of weedy rice into a nondormant genetic background to examine component genetic effects and their interactions with time of afterripening (DAR). A BC4F2 plant, which was heterozygous for the three loci, was selected to develop the BC4F3 population. Single point analysis detected only qSD7-1 and qSD12 (R2 = 38-72%) at 10, 30, and 50 DAR in the population. However, multiple linear regression analysis detected genetic effects of the three QTLs and their trigenic epistasis, an environmental effect of DAR (E), and interactions of E with qSD12 and with the qSD1 x qSD7-1 and qSD7-1 x qSD12 epistases. The linear model demonstrates that QTL main effects varied with DAR, and that some epistasis or epistasis-by-DAR interactions partially counteract the main effects. The three QTLs were isolated as single Mendelian factors from the BC4F3 population and estimated for component genic effects based on the BC4F4 populations. Isolation improved estimation of the qSD1 effect and confirmed the major effect of qSD12. The qSD1 and qSD12 loci displayed a gene-additive effect. The qSD7-1, which was further narrowed to a chromosomal region encompassing the red pericarp color gene Rc, displayed gene additive and dominant effects.

Identification of QTLs for domestication‐related and agronomic traits in an Oryza sativa×O. rufipogon BC1F7 population

AbstractAsian cultivated rice was domesticated from the wild rice, Oryza rufipogon and throughout the domestication process, a wide range of morphological and physiological changes altered the ancestral form. This study was conducted to identify the genetic basis of changes associated with the domestication process. An recombinant Inbred line (RIL) population consisting of 120 lines was developed from a cross between the Juponica cultivar.‘Hwayeongbyeo’and a presumed wild progenitor. O. rufipogon Griff. Acc.01944. The population was genotyped with 124 simple sequence length repeat (SSR) markers, providing an average interval size of 15 cM, and also evaluated for 20 traits related to domestication and agricultural performance. A total of 63 quantitative trait locus (QTLs) and one locus associated with qualitative variation for pericarp coloration were identified using single point and composite interval analysis. The number of QTLs per trait ranged from one to seven. Phenotypic variation associated with each QTL ranged from 3.7 to 40.4%. with an average of 15.3%. The results indicated that most domestication‐related traits clustered in chromosomal blocks, and the positions of many of these clusters were consistent with those reported in previous studies and with skewed segregation ratios in these BC1,F7 RILs. For 13 (20.6%) of the QTLs identified in this study. the O. rufipogan ‐derived allele contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favourable alleles from O. rufipogan were detected for panicle length, spikelets per panicle, days to heading and leaf discoloration associated with cold stress. When compared with previous studies involving interspecific crosses, it can be concluded that O. rufipogon is useful as a source of valuable alleles for rice improvement and that many of the introgressed regions contain genes that have a favourable impact on phenotype in different genetic backgrounds and different environments.

Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks

Two compounds, the C-glycosyl flavone maysin and the phenylpropanoid product chlorogenic acid (CGA), have been implicated in corn earworm (Helicoverpa zea Boddie) resistance in maize (Zea mays L.). Previous quantitative trait locus (QTL) analyses identified the pericarp color (p) locus, which encodes a transcription factor, as the major QTL for maysin and CGA. QTL analysis has also implicated the dihydroflavanol reductase (DFR; E.C. no. 1.1.1.219) locus anthocyaninless1 (a1) and the duplicate chalcone synthase (CHS; E.C. no. 2.3.1.74) loci colorless2 (c2) and white pollen1 (whp1) as genes underlying QTL for maysin and/or CGA synthesis. Epistatic interactions between p and a1 and between p and c2 were also defined. CHS catalyzes the first step in the flavonoid pathway and represents one of the first enzyme steps following the branch off the general phenylpropanoid pathway towards CGA synthesis. In maize, the reduction of dihydroflavanol to leucoanthocyanin by DFR immediately follows the pathway branch leading to C-glycosyl flavone production. The detection of QTLs for maysin and CGA concentration at loci encoding enzyme steps following the pathway branch points implicates alterations in the flow of biochemical intermediates as the biological basis of the QTL effects. To examine if sequence variation among alleles of a1, c2, and whp1 affect maysin and CGA synthesis in maize silks, we performed an association analysis. Because the p locus has often been a major QTL for maysin and CGA and has exhibited epistatic interactions with a1, c2, and whp1, association analysis was conditioned on the p genotype. A highly significant association of two sequence polymorphisms in the promoter of a1 with maysin synthesis was demonstrated. Additional conditioning on the genotype of the significant a1 polymorphism allowed the detection of a significant polymorphism within the whp1 promoter. Our analyses demonstrate that conditioning for epistatic factors greatly increases the power of association testing.

Genetic analysis of adaptive syndromes interrelated with seed dormancy in weedy rice (Oryza sativa)

Seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. A cross between the weedy strain SS18-2 and the breeding line EM93-1 was developed to investigate the genetic basis and adaptive significance of these interrelationships. These characteristics or their components differed in average degree of dominance from -0.8 to 1.5, in heritability from 0.5 to 0.96, and in their contribution to phenotypic or genotypic variation in dormancy by up to 25%. Five dormancy, four shattering, and three awn-length quantitative trait loci (QTLs) were detected in the BC1 population replicated in 2 years. Two QTLs for hull color were identified, and the SS18-2-derived and EM93-1-derived alleles increased the intensity of black, and red or yellow pigmentations, respectively. The only QTL for pericarp color co-located with the red pericarp gene Rc, with the SS18-2-derived allele increasing the intensity of black and red pigmentations. Four of the five dormancy QTLs were flanked or bracketed by one to four QTLs for the interrelated characteristics. The QTL organization pattern indicates the central role of seed dormancy in adaptive syndromes for non-domesticated plants, implies that the elimination of dormancy from cultivars could arise from the selections against multiple interrelated characteristics, and challenges the use of dormancy genes at these loci in breeding varieties for resistance to pre-harvest sprouting (PHS). However, another QTL (qSD12) provides candidate gene(s) for PHS resistance because it has a large effect in the population and it is independent of the loci for interrelated characteristics.

Comparisons of Maize pericarp color1 Alleles Reveal Paralogous Gene Recombination and an Organ-Specific Enhancer Region

The maize (Zea mays) p1 (for pericarp color1) gene encodes an R2R3 Myb-like transcription factor that regulates the flavonoid biosynthetic pathway in floral organs, most notably kernel pericarp and cob. Alleles of the p1 gene condition distinct tissue-specific pigmentation patterns; to elucidate the molecular basis of these allele-specific expression patterns, we characterized two novel P1-rw (for red pericarp/white cob) alleles, P1-rw1077 and P1-rw751Ac. Structural analysis of P1-rw1077 indicated that this allele was generated by recombination between p1 and the tightly linked paralogous gene, p2. In the resulting gene, the p1 coding sequence was replaced by the p2 coding sequence, whereas the flanking p1 regulatory sequences remained largely preserved. The red pericarp color specified by P1-rw1077 suggests that the p1- and p2-encoded proteins are functionally equivalent as regulatory factors in the flavonoid biosynthesis pathway. Sequence analysis shows that the P1-rw1077 allele lacks a 386-bp sequence in a distal enhancer region 5 kb upstream of the transcription start site. An independently derived P1-rw allele contains an Ac insertion into the same sequence, indicating that this site likely contains cob glume-specific regulatory elements.