Population structure of a red rice collection from Mississippi Co., Ark., thought to have resulted from a recent cross between rice and red rice. Groupings of genotypes were based on four possible genetic backgrounds ( k 1-4) using model-based clustering analysis. Rice cultivars: KBNT, Kaybonnet; L161, CL 161; and CL 121. Red rice standards: 11D_RR, AR awned red rice; StgS, Stuttgart awnless red rice; redrice_8, AR awned red rice #8; and TX4std, TX awned red rice. Mississippi Co. red rice types: MS-1 to MS-15. 

Contexts in source publication

Context 1

... k 5) with the commercial rice, STBN (Starbonnet; no longer grown). There also was no evidence of significantly shared genetic backgrounds between these red rice accessions and a group of cultivars historically grown in the southern U.S., such as long-grains (‘Rexoro’, ‘Newbonnet’, ‘Lemont’, ‘LaGrue’, ‘Gulfmont’, ‘Drew’, ‘Dawn’, ‘Cypress’, ‘Bluebonnet’, and ‘Carolina Gold’), medium-grains (‘Zenith’, ‘Saturn’, ‘Nato’, ‘Mars’, and ‘Bengal’), as well as several japonica cultivars (‘M-204’ and ‘Koshihikari’) (Lu et al., 2005; data not shown). However, the red rice groups appeared to share common alleles with indica rice germplasm (e.g., ‘TeQing’, data not shown). It is possible that the unusual red rice phenotypes that were tested in these studies may have arisen from preexisting genetic diversity within the red rice populations. It is also possible that rice alleles, which may have been transferred to red rice plants through intercrossing, were subsequently lost from these populations due to selection pressure. Analysis of numerous additional markers, including those specifically associated with commercial rice cultivars (e.g., markers for the SD-1 semidwarfing gene), may be more informative than the markers used in this test, and are being investigated. Using the clustering diagrams with k = 4, the subpopulations identified by STR largely corresponded to pools originating from commercial rice ( k = 1 and 2), black - hull awned red rice standards such as TX4 and redrice_8 ( k = 3), and the awnless red rice standard StgS ( k = 4) (Fig. 2). However, all of the red rice standards, particularly 11D_RR, shared subpopulations to some degree with the commercial rice standards. As would be expected in a segregating population derived from a red rice x rice cross, some red rice accessions were composed of subpopulations more indicative of rice (e.g., MS-12, 13, and 14), others were more indicative of red rice (e.g., MS-8, 9, 10, and 11), and others were indicative of both rice and red rice (e.g., MS-2, 6, and 7). Thus, STR analysis in combination with physical traits suggests that these Mississippi Co. plants had been derived from a cross between long-grain rice and an awned red rice similar to 11D_RR, TX4std, or redrice_8 (Fig. 2). More than one initial cross or involvement of an awnless red rice similar to StgS is also possible. These results have confirmed the effectiveness and efficiency of STR analysis in the evaluation and interpretation of DNA markers for the purpose of identification and subsequent management of rice x red rice crosses in farm fields. Results from these analyses suggest that, in combination with physical traits, STR could be highly useful in monitoring outcrossing and gene flow dynamics between red rice and rice. STR revealed little evidence of the presence of rice DNA markers in red rice accessions that were hypothesized to have been derived from outcrossing events far in the past. This suggests either that the accessions in question were not actually crosses, or that a large portion of the rice DNA originally present in the cross had been lost over time so that it was not easily detected by the small number of markers ...

Context 2

... k 5) with the commercial rice, STBN (Starbonnet; no longer grown). There also was no evidence of significantly shared genetic backgrounds between these red rice accessions and a group of cultivars historically grown in the southern U.S., such as long-grains (‘Rexoro’, ‘Newbonnet’, ‘Lemont’, ‘LaGrue’, ‘Gulfmont’, ‘Drew’, ‘Dawn’, ‘Cypress’, ‘Bluebonnet’, and ‘Carolina Gold’), medium-grains (‘Zenith’, ‘Saturn’, ‘Nato’, ‘Mars’, and ‘Bengal’), as well as several japonica cultivars (‘M-204’ and ‘Koshihikari’) (Lu et al., 2005; data not shown). However, the red rice groups appeared to share common alleles with indica rice germplasm (e.g., ‘TeQing’, data not shown). It is possible that the unusual red rice phenotypes that were tested in these studies may have arisen from preexisting genetic diversity within the red rice populations. It is also possible that rice alleles, which may have been transferred to red rice plants through intercrossing, were subsequently lost from these populations due to selection pressure. Analysis of numerous additional markers, including those specifically associated with commercial rice cultivars (e.g., markers for the SD-1 semidwarfing gene), may be more informative than the markers used in this test, and are being investigated. Using the clustering diagrams with k = 4, the subpopulations identified by STR largely corresponded to pools originating from commercial rice ( k = 1 and 2), black - hull awned red rice standards such as TX4 and redrice_8 ( k = 3), and the awnless red rice standard StgS ( k = 4) (Fig. 2). However, all of the red rice standards, particularly 11D_RR, shared subpopulations to some degree with the commercial rice standards. As would be expected in a segregating population derived from a red rice x rice cross, some red rice accessions were composed of subpopulations more indicative of rice (e.g., MS-12, 13, and 14), others were more indicative of red rice (e.g., MS-8, 9, 10, and 11), and others were indicative of both rice and red rice (e.g., MS-2, 6, and 7). Thus, STR analysis in combination with physical traits suggests that these Mississippi Co. plants had been derived from a cross between long-grain rice and an awned red rice similar to 11D_RR, TX4std, or redrice_8 (Fig. 2). More than one initial cross or involvement of an awnless red rice similar to StgS is also possible. These results have confirmed the effectiveness and efficiency of STR analysis in the evaluation and interpretation of DNA markers for the purpose of identification and subsequent management of rice x red rice crosses in farm fields. Results from these analyses suggest that, in combination with physical traits, STR could be highly useful in monitoring outcrossing and gene flow dynamics between red rice and rice. STR revealed little evidence of the presence of rice DNA markers in red rice accessions that were hypothesized to have been derived from outcrossing events far in the past. This suggests either that the accessions in question were not actually crosses, or that a large portion of the rice DNA originally present in the cross had been lost over time so that it was not easily detected by the small number of markers ...