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 pleiotropic gene expressed in early developing seeds promoted expression of key genes for biosynthesis of abscisic acid (ABA), resulting in an increase in accumulation of the dormancy-inducing hormone; activated a conserved network of eight genes for flavonoid biosynthesis to produce the pigments in the lower epidermal cells of the pericarp tissue; and enhanced seed weight. Thus, the pleiotropic locus most likely controls the dormancy and pigment traits by regulating ABA and flavonoid biosynthetic pathways, respectively. The dormancy effect could be eliminated by a heat treatment, but could not be completely overcome by gibberellic acid or physical removal of the seed maternal tissues. The dormancy-enhancing alleles differentiated into two groups basically associated with tropical and temperate ecotypes of weedy rice. Of the pleiotropic effects, seed dormancy could contribute most to the weed adaptation. Pleiotropy prevents the use of the dormancy gene to improve resistance of white pericarp cultivars against pre-harvest sprouting through conventional breeding approaches. SEEDS acquire primary dormancy during development to enhance adaptation of wild species to diverse environments by distributing germination over time and space. Domestication tends to reduce dormancy by selection for rapid, uniform germination (Harlan et al. 1973). Differentiation in seed dormancy between cereal crops and wild relatives has been associated with seed morphologies (Nilsson-Ehle 1914;Johnson 1935) and quantitative trait loci (QTL). Cloning of validated dormancy loci provides in-depth insights into regulatory mechanisms underlying natural variation in this adaptive or domestication-related trait (Bentsink et al. 2006;Sugimoto et al. 2010).Weedy rice refers to Oryza spp., which competes with cultivated rice (Oryza sativa L. and O. glaberrima Steud.) from tropical to temperate areas (Oka 1988;Delouche et al. 2007). The most persistent type of weedy rice is red rice, which is characterized by a red pericarp color. Red rice has strong seed dormancy (Cohn and Hughes 1981;Noldin et al. 2006). Genetic analysis has associated pericarp color with seed dormancy in red rice (Gu et al. 2005a).This association was first reported for wheat (Triticum aestivum L.), where red grain genotypes were more dormant than the white ones, and this morphology has been used to select cultivars for resistance to pre-harvest sprouting (NilssonEhle 1914;Flintham 2000). However, it remains unknown if the association in rice, wheat, and other crops arises from a tight linkage between genes for these two trai...

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The inheritance of resistance to sunflower downy mildew (SDM) derived from HA-R5 conferring resistance to nine races of the pathogen has been determined and the new source has been designated as Pl ( 13 ) . The F(2) individuals and F(3) families of the cross HA-R5 (resistant) x HA 821 (susceptible) were screened against the four predominant SDM races 300, 700, 730, and 770 in separate tests which indicated dominant control by a single locus or a cluster of tightly linked genes. Bulked segregant analysis (BSA) was carried out on 116 F(2) individuals with 500 SSR primer pairs that resulted in the identification of 10 SSR markers of linkage groups 1 (9 markers) and 10 (1 marker) of the genetic map (Tang et al. in Theor Appl Genet 105:1124-1136, 2002) that distinguished the bulks. Of these, the SSR marker ORS 1008 of linkage group 10 was tightly linked (0.9 cM) to the Pl (13) gene. Genotyping the F(2) population and linkage analysis with 20 polymorphic primer pairs located on linkage group 10 failed to show linkage of the markers with downy mildew resistance and the ORS 1008 marker. Nevertheless, validation of polymorphic SSR markers of linkage group 1 along with six RFLP-based STS markers of linkage group 12 of the RFLP map of Jan et al. (Theor Appl Genet 96:15-22, 1998) corresponding to linkage group 1 of the SSR map, mapped seven SSR markers (ORS 965-1, ORS 965-2, ORS 959, ORS 371, ORS 716, and ORS 605) including ORS 1008 and one STS marker (STS10D6) to linkage group 1 covering a genetic distance of 65.0 cM. The Pl (13) gene, as a different source with its location on linkage group 1, was flanked by ORS 1008 on one side at a distance of 0.9 cM and ORS 965-1 on another side at a distance of 5.8 cM. These closely linked markers to the Pl (13) gene provide a valuable basis for marker-assisted selection in sunflower breeding programs.

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. A fine mapping experiment, followed by marker-assisted progeny testing for selected recombinants, narrowed down qSD12 to a genomic region of \75 kb, where there are nine predicted genes including a cluster of six transposon/retrotransposon protein genes and three putative (a PIL5, a hypothetic protein, and a bHLH transcription factor) genes based on the annotated Nipponbare genome sequence. The PIL5 and bHLH genes are more likely to be the QTL candidate genes. A bacterial artificial chromosome (BAC) library equivalent to 8-9 times of the haploid genome size was constructed for the weedy rice. One of the two BAC contigs developed from the library covers the PIL5 to bHLH interval. A pair of lines different only in the QTL-containing region of \200 kb was developed as isogenic lines for the qSD12 dormancy and non-dormancy alleles. The dormant line accumulated much higher ABA in 10-day developing seeds than the non-dormant line. In the QTL-containing region there is no predicted gene that has been assigned to ABA biosynthetic or metabolic pathways. Thus, it is concluded that the qSD12 underlying gene promotes ABA accumulation in early developing seeds to induce primary seed dormancy.

Cytoplasmic male sterility (CMS) and its fertility restoration (Rf) genes are critical tools for hybrid seed production to utilize heterosis. In sunflower, CMS PET1 and the associated Rf gene Rf (1) is the only source extensively used in commercial hybrid production. The objective of this research was to develop new sources of CMS and fertility restorers to broaden the genetic diversity of hybrid seed production. We identified a new type of CMS, named as CMS GIG2, from an interspecific cross between Helianthus giganteus accession1934 and H. annuus cv. HA 89. Based on reactions to a set of standard Rf testers, CMS GIG2 is different from all previously reported CMS types, including the CMS GIG1 from another H. giganteus accession. We also identified an Rf gene for CMS GIG2 from wild species H. maximiliani accession 1631. The CMS GIG2 and its restoration gene were introduced into HA 89 background through recurrent backcross and single plant selection techniques. Genetic analysis revealed that the CMS GIG2-Rf system is controlled by a completely dominant gene, named as Rf (4), and the gene additive and dominance effects were estimated as 39.9 and 42.2%, respectively, in the HA 89 background. The gene Rf (4) was mapped onto linkage group 3 with simple sequence repeat (SSR) markers and RFLP-derived STS-marker, and is about 0.9 cM away from the SSR marker ORS1114 based on a segregation population of 933 individuals. The CMS GIG2-Rf (4) system tagged by molecular markers provides an alternative genetic source for hybrid breeding in the sunflower crop.