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Comparative Study
. 2005 Oct;171(2):695-704.
doi: 10.1534/genetics.105.043612. Epub 2005 Jun 21.

Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice

Xing-You Gu  1 , Shahryar F Kianian, Michael E Foley
Affiliations
Comparative Study

Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice

Xing-You Gu et al. Genetics. 2005 Oct.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Breeding scheme for introducing dormancy genes from weedy to cultivated rice. SS18-2, CO39, and EM93-1 are a weedy accession, cultivar, and breeding line, respectively. Plants in parentheses were dormant genotypes selected to develop the next generation.
Figure 2.
Figure 2.
Distribution of percentage of germination for the five populations (see Figure 1). (A) F1 (EM93-1/F2 no. 14a,b,r) (20 DAR). (B) BC1F1 (EM93-1/F1 no. 38) (10 DAR). (C) BC2F1 (EM93-1/BC1F1 no. 60) (10 DAR). (D) BC3F1 (EM93-1/BC2F1 no. 42) (10 DAR). (E) BC4F1 (EM93-1/BC3F1 no. 81) (7 DAR). The open and solid arrows indicate germination levels for the recipient parent EM93-1 and the plant selected as the parent to develop the next generation, respectively. Superscripts indicate if the selected plant had awn (a), black hull color (b), and/or red pericarp/testa color (r) characteristics. N is the population size, and rr,g, ra,g, and rb,g are correlation coefficients between the characteristics red pericarp color (r), awn (a), and black hull color (b) and the percentage of germination evaluated at the specified days of after-ripening (DAR), respectively; the superscripts indicate the correlations were nonsignificant (ns) or significant at the 0.05 (*), 0.01 (**), and <0.0001 (***) probability levels.
Figure 3.
Figure 3.
Graphic genotypes for the BC4F1 plants 132 (A) and 44 (B). Open or solid bars stand for the EM93-1- or SS18-2-derived chromosomes or chromosomal segments, which were determined by the rice microsatellite (RM) markers at the tick mark positions on the framework linkage map (Gu et al. 2004); the chromosomes not shown were identical to EM93-1. Intermarker distances (centimorgans) and QTL for seed dormancy (qSD), shattering (qSH), awn length (qAL), and hull color (qHC), which were estimated on the basis of the BC4F2 populations, are placed to the left of the segments. Dotted lines indicate a digenic epistasis detected between two QTL.
Figure 4.
Figure 4.
Distribution of percentage of germination for the BC4F2 132 (N = 160) (A) and 44 (N = 230) (B) populations. Mean and standard deviation for germination evaluated at 10 (solid circles), 20 or 25 (open columns), and 30 or 45 (open circles) days of after-ripening (DAR) are shown in parentheses.
Figure 5.
Figure 5.
Digenic epistases detected in the BC4F2 (132) qSD1 × qSD7-1 (A) and (44) qSD1 × qSD8 (B) populations. The dormancy loci qSD1, qSD7-1, and qSD8 are represented by their linked markers RM220, RM5672, and RM531, respectively. Marker genotypes are indicated by combinations of alleles from the parents EM93-1 (E) or SS18-2 (S). Lines with open circles (EE), closed circles (SS), and triangles (ES) stand for the three genotypes for RM220. A circle or triangle and vertical bars indicate the mean and standard error for a digenic genotype in arc-sine-transformed percentage of germination (x) evaluated at 20 or 45 days of after-ripening (DAR). R2 and P-values are the proportion of phenotypic variance accounted for by the component epistatic effect and its F-test probability, respectively.
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