Pleiotropic effects of red and purple pericarp genes on seed coating patterns, flavonoids, dormancy, and germination in rice.

Seeds are coated with pigments presumably to promote plant adaptation. To understand the adaptive mechanisms of seed pigment traits, allelic variants of the red (Rc/rc) and purple (Pb/pb) pericarp color genes were assembled into the same genetic background to identify the trait development patterns and pleiotropies of the loci on seed flavonoids, dormancy, and germination in rice (Oryza sativa). Nonallelic recombination and epistasis of the loci dictated 4 patterns of the trait development from 5 to 40 d post-anthesis.

Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice.

Seed dormancy (SD) and longevity (SL) may share developmental and genetic mechanisms, as both traits are developed in the same maternal environment and evolved to coordinate the timing of germination and the life span of seedbanks. To test the hypothesis, allelic variants at the SD1-2, 7-1, 7-2, and 12 loci from weedy and cultivated rice (Oryza sativa) were assembled into the same genetic background, and 16 homozygous lines selected as a tetragenic system. These lines were evaluated for SD measured by germination at 7, 21, 35, and 150 days of after-ripening (DAR), and for SL measured by the seed decay rate and survivability in the soil of a rice field for 7 months.

Two Contrasting Patterns and Underlying Genes for Coadaptation of Seed Dormancy and Flowering Time in Rice.

Association between seed dormancy (SD) and flowering time (FT) may generate a synergy in plant adaptation. This research aimed to identify patterns and underlying genes of the association in rice (Oryza sativa). Four F and two BCF populations from crosses of weedy/cultivated rice, and two families of progeny lines from backcrosses were evaluated for variations in time to flowering and germination ability.

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

Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice () 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.

Map-Based Cloning of Seed Dormancy1-2 Identified a Gibberellin Synthesis Gene Regulating the Development of Endosperm-Imposed Dormancy in Rice.

Natural variation in seed dormancy is controlled by multiple genes mapped as quantitative trait loci in major crop or model plants. This research aimed to clone and characterize the Seed Dormancy1-2 (qSD1-2) locus associated with endosperm-imposed dormancy and plant height in rice (Oryza sativa). qSD1-2 was delimited to a 20-kb region, which contains OsGA20ox2 and had an additive effect on germination.

Genotyping of endosperms to determine seed dormancy genes regulating germination through embryonic, endospermic, or maternal tissues in rice.

Seed dormancy is imposed by one or more of the embryo, endosperm, and maternal tissues that belong to two generations and represent two ploidy levels. Many quantitative trait loci (QTL) have been identified for seed dormancy as measured by gross effects on reduced germination rate or delayed germination in crop or model plants. This research developed an endosperm genotype-based genetic approach to determine specific tissues through which a mapped QTL regulates germination using rice as a model.

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.

Genetic and physiological characterization of two clusters of quantitative trait Loci associated with seed dormancy and plant height in rice.

Seed dormancy and plant height have been well-studied in plant genetics, but their relatedness and shared regulatory mechanisms in natural variants remain unclear. The introgression of chromosomal segments from weedy into cultivated rice (Oryza sativa) prompted the detection of two clusters (qSD1-2/qPH1 and qSD7-2/qPH7) of quantitative trait loci both associated with seed dormancy and plant height. Together, these two clusters accounted for >96% of the variances for plant height and ~71% of the variances for germination rate in an isogenic background across two environments.

Association between seed dormancy and pericarp color is controlled by a pleiotropic gene that regulates abscisic acid and flavonoid synthesis in weedy red rice.

Seed dormancy has been associated with red grain color in cereal crops for a century. The association was linked to qSD7-1/qPC7, a cluster of quantitative trait loci for seed dormancy/pericarp color in weedy red rice. This research delimited qSD7-1/qPC7 to the Os07g11020 or Rc locus encoding a basic helix-loop-helix family transcription factor by intragenic recombinants and provided unambiguous evidence that the association arises from pleiotropy.

The qSD12 underlying gene promotes abscisic acid accumulation in early developing seeds to induce primary dormancy in rice.

Seeds acquire primary dormancy during their development and the phytohormone abscisic acid (ABA) is known to play a role in inducing the dormancy. qSD12 is a major seed dormancy quantitative trait locus (QTL) identified from weedy rice. This research was conducted to identify qSD12 candidate genes, isolate the candidates from weedy rice, and determine the relation of the dormancy gene to ABA.

The qSD12 locus controls offspring tissue-imposed seed dormancy in rice.

Seed component structures were grouped into maternal and offspring (embryo and endosperm) tissues to characterize a dormancy quantitative trait locus (QTL) for tissue-specific function using a marker-assisted genetic approach. The approach was devised to test if genotypic/allelic frequencies of a marker tightly linked to the QTL deviate from Mendelian expectations in germinated and nongerminated subpopulations derived from a segregation population of partially after-ripened seeds and was applied to the dormancy QTL qSD12 and qSD7-1 in a nearly isogenic background of rice. Experimental results unambiguously demonstrated that qSD12 functions in the offspring tissue(s) and suggested that qSD7-1 may control dormancy through the maternal tissues.

Epistatic interactions of three loci regulate flowering time under short and long daylengths in a backcross population of rice.

The short-day plant rice varies greatly in photoperiod sensitivity (PS) for flowering. The hybrid F(1) from a cross between the day-neutral pure line EM93-1 and the weedy rice accession SS18-2 had stronger PS than SS18-2. Some BC(1) (EM93-1/F(1)) segregates were even more sensitive to photoperiod than the F(1), as indicated by later flowering or no flowering after 250 days under a 14-h long daylength.

Posttranslational regulation of pyruvate, orthophosphate dikinase in developing rice (Oryza sativa) seeds.

Pyruvate, orthophosphate dikinase (PPDK; E.C.2.

Dormancy genes from weedy rice respond divergently to seed development environments.

Genes interacting with seed developmental environments control primary dormancy. To understand how a multigenic system evolved to adapt to the changing environments in weedy rice, we evaluated genetic components of three dormancy QTL in a synchronized nondormant genetic background. Two genetically identical populations segregating for qSD1, qSD7-1, and qSD12 were grown under greenhouse and natural conditions differing in temperature, relative humidity, and light intensity during seed development.

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.

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.

A set of three genes regulates photoperiodic responses of flowering in rice (Oryza sativa).

Differentiation in photoperiodic response of flowering has been key to the evolution and wide geographic distribution of rice, an essentially short-day plant. Crosses were made such that the hybrid F1 plants flower later than the late-flowering parents to investigate the genetic basis underlying this differentiation. From initial experiments, three major genes for flowering time were identified from four naturally occurring variants under natural long-day conditions.

Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa).

Weedy rice has much stronger seed dormancy than cultivated rice. A wild-like weedy strain SS18-2 was selected to investigate the genetic architecture underlying seed dormancy, a critical adaptive trait in plants. A framework genetic map covering the rice genome was constructed on the basis of 156 BC(1) [EM93-1 (nondormant breeding line)//EM93-1/SS18-2] individuals.