HETEROSIS, a term to describe the superiority of

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1 Copyright Ó 2008 y the Genetics Society of Americ DOI: /genetics Dominnce, Overdominnce nd Epistsis Condition the Heterosis in Two Heterotic Rice Hyrids Lnzhi Li,* Kiyng Lu, Zhoming Chen,* Tongmin Mu, Zhongli Hu*,,1 nd Xinqi Li *Key L of the Ministry of Eduction for Plnt Developmentl Biology, College of Life Science, Wuhn University, Wuhn , Chin, Ntionl Key Lortory of Crop Genetic Improvement, Huzhong Agriculturl University, Wuhn , Chin nd Deprtment of Breeding, Chin Ntionl Hyrid Rice Reserch nd Development Center, Chngsh , Chin Mnuscript received My 26, 2008 Accepted for puliction Septemer 10, 2008 ABSTRACT Two recominnt inred (RI) popultions hving 194 nd 222 lines ech, derived, respectively, from highly heterotic inter- (IJ ) nd intrsuspecific (II ) hyrid, were ckcrossed to their respective prents. The RI nd two ckcross popultions long with F 1 nd its two prents of ech hyrid were evluted for nine importnt trits, including grin yield nd eight other yield-relted trits. A totl of 76 quntittive trit loci (QTL) for the IJ hyrid nd 41 QTL for the II hyrid were detected in the RI popultion, midprent heterosis of two ckcross popultions, nd two independent sets of dt y summtion (L 1 1 L 2 ) nd y sutrction (L 1 L 2 ) of two ckcross popultions (L 1 nd L 2 ). The vrince explined y ech QTL rnged from 2.6 to 58.3%. In the IJ hyrid, 42% (32) of the QTL showed n dditive effect, 32% (24) prtil-tocomplete dominnt effect, nd 26% (20) n overdominnt effect. In the II hyrid, 32% (13) of the QTL demonstrted n dditive effect, 29% (12) prtil-to-complete dominnt effect, nd 39% (16) n overdominnt effect. There were 195 digenic interctions detected in the IJ hyrid nd 328 in the II hyrid. The vrince explined y ech digenic interction rnged from 2.0 to 14.9%. These results suggest tht the heterosis in these two hyrids is ttriutle to the orchestrted outcome of prtil-to-complete dominnce, overdominnce, nd epistsis. HETEROSIS, term to descrie the superiority of heterozygous genotypes over their corresponding prentl genotypes (Shull 1908), hs een under investigtion for 100 yers, ut no consensus exists out the genetic sis underlying this very importnt phenomenon. Two contending hypotheses, the dominnce hypothesis nd the overdominnce hypothesis, were proposed to explin this phenomenon out one century go. The dominnce hypothesis ttriutes heterosis to cnceling of deleterious or inferior recessive lleles contriuted y one prent, y eneficil or superior dominnt lleles contriuted y the other prent in the heterozygous genotypes t different loci (Dvenport 1908; Bruce 1910; Jones 1917). The overdominnce hypothesis ttriutes heterosis to the superior fitness of heterozygous genotypes over homozygous genotypes t single locus (Est 1908; Shull 1908). Moleculr mrkers nd their linkge mps hve gretly fcilitted the identifiction of individul loci conditioning heterosis nd the estimtion of gene ction of underlying loci. Quntittive trit locus (QTL) mpping studies iming t understnding the genetic sis of heterosis hve een conducted in rice nd other crops (Xio et l. 1995; Li et l. 1997, 2001; Yu et l. 1997; Luo 1 Corresponding uthor: Key L of the Ministry of Eduction for Plnt Developmentl Biology, College of Life Science, Wuhn University, Wuhn , Chin. E-mil: huzhongli@whu.edu.cn et l. 2001; Hu et l. 2002, 2003; Semel et l. 2006; Frscroli et l. 2007; Melchinger et l. 2007,). Evidence from such studies suggests tht heterosis my e ttriutle to dominnce (Xio et l. 1995; Cockerhm nd Zeng 1996), overdominnce (Stuer et l. 1992; Li et l. 2001; Luo et l. 2001), pseudooverdominnce due to tightly linked loci with eneficil or superior dominnt lleles in repulsion phse (Crow 2000; Lippmn nd Zmir 2007), or epistsis (Schnell nd Cockerhm 1992; Li et l. 2001; Luo et l. 2001). Heterosis is the se of the gret success in hyrid rice. Currently, hyrid rice ccounts for 55% of the totl plnting crege of pddy rice in Chin nd the nnul incresed rice production resulting from plnting hyrid rice mounts to 20 million metric tones, which cn provide min stple food for.70 million people (Lu et l. 2002). Hyrid rice vrieties hve yield dvntge of 10 20% over the est conventionl inred vrieties using similr cultivtion conditions (Lu et l. 2002). Besides the lrge plnting in Chin, hyrid rice vrieties re lso widely plnted in.20 countries round the world. Previous studies indicted the genetic sis of heterosis in rice is very complicted nd vrious, depending on study mterils nd nlysis pproches (Xio et l. 1995; Yu et l. 1997; Li et l. 2001; Hu et l. 2002, 2003). The ojective of this study ws to identify the min-effect QTL nd digenic episttic loci underlying heterosis of Genetics 180: (Novemer 2008)

2 1726 L. Li et l. nine importnt gronomic nd economic trits of rice nd estimte the gene ction of ech QTL nd interction using triple-testcross cross (TTC) design to shed light on the understnding of the genetic sis of heterosis in two diverse nd highly heterotic rice hyrids. MATERIALS AND METHODS Popultions: Two highly heterotic rice hyrids, one intersuspecific etween 9024 (indic) nd LH422 ( jponic) nd one intrsuspecific etween Zhenshn97 (indic) nd Minghui63 (indic), were employed in this study. From the F 1 of the intersuspecific hyrid (designted s IJ hyrid herefter), 194 F 7 lines were developed y single-seed descent. From the F 1 of the intrsuspecific hyrid (designted s II hyrid herefter), 222 F 12 lines were developed through 11 consecutive selfing genertions. Ech of these F 7 nd F 12 lines ws derived from different F 2 plnt. No positive or negtive selection ws performed during ech of the selfing genertions. A single plnt from ech of these 194 F 7 lines nd 222 F 12 lines ws chosen rndomly nd ckcrossed to ech of its two respective prents to produce ckcross progeny nd selfed to generte F 8 or F 13 lines. Phenotypic vrition: For the IJ hyrid, two ckcross popultions hving 194 lines ech, 194 F 8 recominnt inred lines (RILs), long with the two prentl lines nd their F 1, were rrnged in field in rndomized complete lock design with two replictions for phenotypic evlution in the summer seson of 1992 t the Chin Ntionl Hyrid Rice Reserch nd Development Center, Chngsh, Hunn, Chin. Twenty-seven plnts (three rows 3 9 plnts per row) were plnted t density of 300,000 plnts per hectre in ech of 1170 plots. The middle 5 plnts in the centrl row of ech plot were used for phenotypic trit evlution nd dt collection. For the II hyrid, the two ckcross popultions with 222 lines ech, the corresponding 222 F 13 RILs, long with two prentl lines nd their F 1, were lid out in field in rndomized complete lock design with two replictions for phenotypic evlution in the summer seson of 2006 t the experimentl frm of the Huzhong Agriculturl University, Wuhn, Huei, Chin. Twenty-one-dy-old seedlings were trnsplnted into three-row plots with ech plot consisting of single row of RIL nd two rows of ckcross (BC) hyrids. There were seven plnts in ech row, with 16.7 cm etween plnts within ech row nd 26.7 cm etween rows. The middle five plnts in ech row were used for phenotypic trit evlution nd dt collection. Nine quntittive trits of gronomic nd economic importnce evluted were heding dte (HD) (in dys), plnt height (PH) (in centimeters), tillers per plnt (TP), pnicle length (PL) (in centimeters), filled grins per pnicle (FGPP), percentge of seed set (SS), grin density (GD) (in grin numers per centimeter of pnicle length), 1000-grin weight (KGW) (in grms), nd grin yield (YD) (in tons/hectre). Mens over replictions, for ech trit, for the RIL nd ech of two ckcross popultions, were used for QTL nd other nlyses. Anlysis of field dt nd of heterosis: For ech hyrid, dt of recominnt inred (RI) nd BC popultions were nlyzed seprtely. SAS PROC GLM (SAS Institute 1996) ws used to test the differences mong RILs nd the corresponding BC hyrids. Heterosis ws evluted in BC popultions y midprentl heterosis (Hmp). Hmp ¼ F 1 (RIL 1 recurrent prent)/2. F 1 s re men trit vlues of individul BC hyrids while RIL is the corresponding RIL prent for ech of the BC hyrids, nd recurrent prent is 9024 or LH422 in the IJ hyrid nd Zhenshn 97 or Minghui 63 in the II hyrid. To distinguish one from nother, the RIL is designted s RILij in the IJ hyrid nd s RILii in the II hyrid. Following Kersey et l. (2003) nd Frscroli et l. (2007), the crosses of the n RILs to the two recurrent prents re referred s L 1i nd L 2i (i ¼ 1 n), respectively. The two independent sets of dt y summtion (L 1i 1 L 2i )ndy sutrction (L 2i L 1i ) of the two BC popultions vlues herefter re referred to s the SUM dt set nd the DIFF dt set, respectively. Vrition within the SUM dt set is due to dditive effects nd vrition within the DIFF dt set is due to dominnce effects when comined over two BC popultions. In this study, for the IJ hyrid, L 1i nd L 2i represent the n ¼ 194 RILs to 9024 nd LH422, respectively; while for the II hyrid, L 1i nd L 2i represent the n ¼ 222 RILs to Zhenshn97 nd Minghui63, respectively. To distinguish one from nother, the two dt sets SUM nd DIFF in the IJ hyrid re referred s SUMij nd DIFFij nd those in the II hyrid s SUMii nd DIFFii. NCIII nd TTC nlysis: ANOVA ws used to test for dditive (L 1i 1 L 2i ) nd dominnce (L 2i L 1i ) vrition y following the stndrd North Crolin design III (NCIII) nd for episttic vrition (L 1i 1 L 2i P) y following the extended TTC design s descried y Kersey nd Jinks (1968), with P indicted s the RI popultion in this study. Additive (V A ) nd dominnce (V D ) components of genetic vrince were estimted nd used to clculte the verge degree of dominnce [s O(2V D /V A )], which is weighted men of the level of dominnce over ll segregting loci (Kersey nd Pooni 1996). Genetic linkge mps: For the IJ hyrid, suset of 141 polymorphic RFLP mrkers ws selected from the rice highdensity moleculr mp (Cusse et l. 1994) to construct the linkge mp of the RI popultion y Xio et l. (1995). For the II hyrid, linkge mp ws constructed y Xing et l. (2002), which consisted of 221 mrker loci nd covered totl of 1796 cm. QTL mpping nd detection of dominnce degree of mineffect QTL nd episttic-effect QTL: QTL mpping: QTL nlysis ws performed seprtely for the RI, the midprentl heterosis (Hmp) of two ckcross popultions, nd two independent dt sets SUM nd DIFF in the IJ hyrid nd the II hyrid. In the sence of epistsis, the nlysis of RIL nd SUM dt sets identifies QTL with n dditive effect (), wheres the nlysis of Hmp nd DIFF dt sets detects QTL with dominnce effect (d) (Frscroli et l. 2007). Anlysis of min-effect QTL (M-QTL) ws conducted in ech mpping popultion y composite-intervl mpping, using WinQTLcrt (Zeng 1994). A LOD score of 2.0 ws selected s the threshold for the presence of min-effect QTL sed on the totl mp distnce nd the verge distnce etween mrkers. QTL detected in different popultions or for different trits were considered s common if their estimted mp position ws within 20-cM distnce (Groh et l. 1998),which is common pproch in comprtive mpping. Following Frscroli et l. (2007), in the sence of epistsis, the expecttion of genetic effects in RIL, SUM, Hmp, nd DIFF dt ws,, d/2,ndd. Anlysis of digenic interction ws conducted in ech mpping popultion y the mixed liner pproch nd y the use of the computer softwre QTLMAPPER ver. 1.0 (Wng et l. 1999). The nlysis ws first conducted without considering epistsis to confirm the QTL detected with the method previously descried nd then with epistsis considered in the model. A threshold of LOD $ 3.0 (P, 0.001) ws used for declring the presence of puttive pir of episttic QTL. Genetic nlysis methods for estimting QTL dominnce degree: NorthCrolindesignIII(NCIII)wsputforwrdyComstock nd Roinson (1952). In NCIII design, mle progeny from

3 Genetic Bsis of Heterosis in Rice 1727 TABLE 1 Genetic expecttion of regression coefficients of L 1 1 L 2 nd L 1 L 2 when the se popultion ws the DH popultion L 1 1 L 2 L 1 L 2 j(l 1 L 2 )/(L 1 1 L 2 )j 9 I (1 2r 1 ) 1 (1 2r 1 )d 1 d 1 / 1 9 II (1 2r 1 )(1 2r 2 )i 1 2 (1 2r 1 )(1 2r 2 )l d1 d 2 l d1d2/i 12 hq i h 9 3 III m¼1 ð1 2r mþ i 123 ð 1Þ Q i 3 3 m¼1 ð1 2r mþ l d1d2d3 l d1d2d3/i 123 hq i h 9 K K m¼1 ð1 2r mþ i 1...K ð 1Þ Q i K K m¼1 ð1 2r mþ l d1...dk l d1...dk /i 1...K 9 i (i ¼ 1 K, where K is the totl numer of mrkers in linkge mp) is indicted s regression coefficient. i (i ¼ 1 K) nd d i (i ¼ 1 K) re denoted s the dditive effect nd the dominnt effect, respectively; i 1 2 is the dditive 3 dditive episttic effect, i is the dditive 3 dditive 3 dditive episttic effect, etc. l d1 d 2 is the dominnce 3 dominnce episttic effect, l d1 d 2 d 3 is the dominnce 3 dominnce 3 dominnce episttic effect, etc. r m denotes the recominnt vlue. For the RI popultion, the expecttions were similr to those in the DH popultion except for r m, which ws replced y 2r9 m /(1 1 2r9 m ) nd 4r$ m /(1 1 6r$ m ), respectively. The r9 m nd r$ m were recominnt vlues for two RI popultions (selfing popultion nd si-mting popultion), respectively (Hu et l. 2002). d 1 / 1 is indicted s the dominnt degree of min-effect QTL, l d1 d 2 /i 1 2 s the epistsis dominnce degree (EDD), nd l d1 d 2 d 3 /i s the epistsis dominnce degree mong three mrkers, etc. genertion 2 (F 2, which were treted s se popultion) of two inred strins re ckcrossed to their grndmothers (mrked s L 1 nd L 2 ), nd their progeny re rrnged in completely rndomized lock design (Comstock nd Roinson 1952). In 1968, n NCIII design ws developed y Kersey nd Jinks. In their theory, the F 3,F 4,...,F n, doule hploid (DH), nd RIL lso cn e treted s se popultions. Following Kersey, the se popultion ws crossed to the two prents (P 1 nd P 2 ) indicted s L 1 nd L 2.WiththedtofL 1 1 L 2 nd L 1 L 2,the genetic prmeters of QTL such s dditive effect, dominnt effect, nd the degree of dominnce could e estimted. On the sis of the correltion nlysis of detected M-QTL nd digenic interction proposed y Hu et l. (1995, 2002), regression nd vrince nlysis of two dt L 1 1 L 2 nd L 1 L 2 when the se popultion ws the DH popultion could e deduced s follows (Tles 1 nd 2). On the sis of the methodology proposed, we developed softwre QTLIII (not pulished yet), which is suitle for nlyzing the dditive effect, dominnt effect, nd dominnce degree of QTL (including one-fctor, two-fctor, nd threefctor ANOVA, see Tles 1 nd 2). In this study, it ws used to estimte dominnce degree of min-effect nd episttic-effect QTL. The degree of dominnce of M-QTL ws estimted s jd/j. For this purpose, for ll QTL declred s significnt within ny dt set, dominnt nd dditive effects were estimted in SUM nd DIFF dt sets y QTLIII with ANOVA nlysis. These estimtes were used to clculte jd/j nd clssify the QTL s dditive (A) (jd/j, 0.2), prtil dominnce (PD) (0.2 # jd/j, 0.8), dominnce (D) (0.8 # jd/j, 1.2), nd overdominnce (OD) (jd/j $ 1.2) ccording to Stuer et l. (1987). Genetic expecttions of the prmeters estimted in the episttic models differ on the sis of genetic composition of dt sets nlyzed. For the SUM dt set, the estimted interction is expected to e predominntly dditive 3 dditive (), wheres for the DIFF dt set it is expected to e predominntly dominnce 3 dominnce (dd). In this study, jdd/j, defined s epistsis dominnce degree (EDD), ws estimted y the softwre QTLIII with ANOVA nlysis. These estimtes were used to clculte jdd/j to clssify the episttic QTL s A (jdd/j, 0.2), PD (0.2 # jdd/j, 0.8), D (0.8 # jdd/j, 1.2), nd OD (jdd/j $ 1.2). Reltionship etween genomewide or chromosomewide moleculr mrker heterozygosity nd phenotypic trit performnce nd heterosis: GGT (Vn 1999) ws used to clculte genome rtios (percentge of totl genome originted from one prentl genome) for ech line in the RI popultion, initilly for the whole genome nd then for ech chromosome. Reltionship etween moleculr mrker heterozygosity nd phenotypic performnce ws tested y regressing phenotypic performnce on whole-genome heterozygosity in two ckcross popultions in oth IJ nd II hyrids. Menwhile, to elucidte the reltionship etween oserved heterosis nd heterozygosity, (i) the Hmp nd DIFF vlues were respectively regressed ginst heterozygosity cross the whole genome using liner regression (when the DIFF dt set ws used s dependent vrile, genome heterozygosity of ech ckcross popultion ws the independent vrile), nd (ii) the Hmp vlues were regressed ginst heterozygosity on individul chromosomes y multiple regression. RESULTS F 1 heterosis: In the IJ hyrid, LH422 showed significnt higher men trit vlues thn 9024 (Tle 3). All nine trits except heding dte in F 1 hd higher vlue thn oth prents. For midprentl heterosis, yield showed the strongest significnt heterosis (25.58%), followed y 1000-grin weight (15.82%), plnt height (15.34%), pnicle length (9.42%), tillers per plnt (8.00%), seed set (4.06%), nd heding dte (1.74%). However, the F 1 hyrid hd lower trit vlue for filled grins per pnicle nd grin density thn the prentl lines, with negtive heterosis of 2.08 nd 10.17%, respectively. In the II hyrid, the prent Minghui63 hd significntly higher phenotypic vlue thn Zhenshn97 for ll nine trits investigted (Tle 3). The F 1 hyrid hd 91 dys to heding, similr to Minghui63, which took more dys to heding thn Zhenshn97. The vlues of the other trits were significntly higher in F 1 thn in

4 1728 L. Li et l. TABLE 2 Genetic expecttion of vrince components of L 1 1 L 2 nd L 1 L 2 when the se popultion ws the DH popultion qffiffiffiffiffiffiffiffiffiffiffiffi L ANOVA L 1 1 L 2 L 1 L 1 L 2 2 One wy s 2 1 ¼ (1 2r 1) s 2 1 ¼ (1 2r 1) 2 d 2 1 d 1 / 1 Two wy s 2 ¼ (1 2r 1 1) 2 ( 1 1 j 1d2) 2 s 2 ¼ (1 2r 1 1) 2 (d 1 1 j d12) 2 s 2 ¼ (1 2r 2 2) 2 ( 2 1 j d12) 2 s 2 ¼ (1 2r 2 2) 2 (d 2 1 j 1d2) 2 s 2 ¼ (1 2r 12 1) 2 (1 2r 2 ) 2 i 2 12 s 2 ¼ (1 2r 12 1) 2 (1 2r 2 ) 2 l 2 d1d2 l d1d2/i 12 Three wy s 2 ¼ (1 2r 1 1) 2 ( 1 1 j 1d2 1 j 1d3 1 j 1d2d3) 2 s 2 ¼ (1 2r 1 1) 2 (d 1 1 j d12 1 j d13 1 j d123) 2 s 2 ¼ (1 2r 2 2) 2 ( 2 1 j d12 1 j 2d3 1 j d12d3) 2 s 2 ¼ (1 2r 2 2) 2 (d 2 1 j 1d2 1 j d23 1 j 1d23) 2 s 2 ¼ (1 2r 3 3) 2 ( 3 1 j d13 1 j d23 1 j d1d23) 2 s 2 ¼ (1 2r 3 3) 2 (d 3 1 j 1d3 1 j 2d3 1 j 12d3) 2 s 2 ¼ (1 2r 12 1) 2 (1 2r 2 ) 2 (i 12 1 j 12d3) 2 s 2 ¼ (1 2r 12 1) 2 (1 2r 2 ) 2 (l d1d2 1 j d1d23) 2 s 2 ¼ (1 2r 13 1) 2 (1 2r 3 ) 2 (i 13 1 j 1d23) 2 s 2 ¼ (1 2r 13 1) 2 (1 2r 3 ) 2 (l d1d3 1 j d123) 2 s 2 ¼ (1 2r 23 2) 2 (1 2r 3 ) 2 (i 23 1 j d123) 2 s 2 ¼ (1 2r 23 2) 2 (1 2r 3 ) 2 (l d2d3 1 j 1d2d3) 2 s 2 ¼ (1 2r 123 1) 2 (1 2r 2 ) 2 (1 2r 3 ) 2 i s 2 ¼ (1 2r 123 1) 2 (1 2r 2 ) 2 (1 2r 3 ) 2 l 2 d1d2d3 l d1d2d3/i 123 s 2 i (i ¼ 1 K), s 2 ij (i, j, i ¼ 1 K, j ¼ 2 K), nd s 2 ijl (i, j, l, i ¼ 1 K, j ¼ 2 K, l ¼ 3 K) re denoted s vrince components of single mrker, two mrkers, nd three mrkers. The other prmeters re the sme s in Tle 1. L 1 1 L 2 oth prents. The midprentl heterosis of the F 1 plnts ws strongest for yield (83.09%), followed y filled grins per pnicle (29.13%), plnt height (21.94%), heding dte (17.46%), seed set (16.68%), grin density (13.86%), pnicle length (13.42%), tillers per plnt (11.09%), nd 1000-grin weight (8.21%). Heterosis in RI nd BC popultions: RIL nd prentl inred men vlues (Tle 3) were not significntly different for ny trit in oth IJ nd II hyrids. Significnt heterosis for yield ws oserved in II hyrid BC popultions, ut not in IJ hyrid BC popultions. Most of the other trits did not show significnt heterosis in BC popultions of oth IJ nd II hyrids. For the IJ hyrid, the men vlues of the 9024BC nd LH422BC popultions were nd for heding dte, nd for plnt height, nd 9.55 for tillers per plnt, nd for pnicle length, nd for filled grins per pnicle, nd for seed set, 5.60 nd 6.25 for grin density, nd for 1000-grin weight, nd 6.14 nd 6.18 for yield. The heterosis ws (29.5%) nd 3.12 (7.0%) for heding dte, 6.45 (6.4%) nd 5.10 (4.6%) for plnt height, 0.30 ( 2.8%) nd 0.28 (3.0%) for tillers per plnt, 1.65 (7.2%) nd 1.36 (5.5%) for pnicle length, 5.90 ( 6.6%) nd 1.56 ( 1.8%) for filled grins per pnicle, 7.39 ( 10.9%) nd 4.62 (6.9%) for seed set, 0.62 (12.5%) nd 0.97 (20.8%) for grin density, 2.19 (9.1%) nd 1.58 (5.9%) for 1000-grin weight, nd 0.16 ( 2.5%) nd 0.14 (2.3%) for yield, in the 9024BC nd LH422BC popultions, respectively. TABLE 3 Men vlues of nine importnt gronomic trits of P 1,P 2,F 1, RIL, nd their two ckcross popultions in two rice elite hyrids HD PH TP PL FGPP SS GD KGW YD IJ hyrid LH F Heterosis (%) RIL BC LH422BC II hyrid Zhenshn Minghui F Heterosis (%) RIL Zhenshn97BC Minghui63BC For description of gronomic trits see mterils nd methods.

5 Genetic Bsis of Heterosis in Rice 1729 TABLE 4 NCIII nd TTC nlyses of the two rice hyrids Prmeter HD PH TP PL FGPP SS GD KGW YD IJ hyrid V A V D d.d [] *** *** *** *** *** *** *** *** *** [d], [dd] *** *** *** *** *** *** *** *** *** II hyrid V A V D d.d [] *** *** *** *** *** *** *** *** *** [d], [dd] *** *** NS * *** *** ** *** ** *P # 0.05, **P # 0.01, ***P # Estimtes of dditive (V A ) nd dominnce (V D ) vrince, verge degree of dominnce (.d.d.), nd tests for dditive 3 dditive ([]) nd dditive 3 dominnce nd dominnce 3 dominnce ([], [dd]) epistsis. V A ws highly significnt (P # 0.005) for ll trits; V D ws highly significnt for ll trits, except TP (significnt t P # 0.05) in the II hyrid. For the II hyrid, the men vlues of the Zhenshn97BC nd Minghui63BC popultions were nd for heding dte, nd for plnt height, nd for tillers per plnt, nd for pnicle length, nd for filled grins per pnicle, nd for seed set, 5.22 nd 5.09 for grin density, nd for 1000-grin weight, nd 6.73 nd 7.56 for yield. The heterosis vlues were ( 15.9%) nd 1.53 ( 1.8%) for heding dte, 1.72 (1.7%) nd 2.11 (1.9%) for plnt height, 0.59 (1.1%) nd 0.59 (0.9%) for tillers per plnt, 0.75 ( 3.5%) nd 0.74 (3.1%) for pnicle length, 4.7 (4.5%) nd 9.04 (7.7%) for filled grins per pnicle, 4.89 (10.7%) nd 8.75 (13.6%) for seed set, 0.34 (7.1%) nd 0.21 (4.3%) for grin density, 1.64 ( 0.64%) nd 0.16 ( 0.6%) for 1000-grin weight, nd 1.82 (36.9%) nd 1.04 (15.9%) for yield in the Zhenshn97BC nd Minghui63BC popultions, respectively. NCIII nd TTC nlysis: TTC nlysis llows us to test nonllelic interctions. Significnt dditive 3 dditive ([]) epistsis ws detected for ll trits in oth IJ nd II hyrids (Tle 4). The epistsis due to dditive 3 dominnce or dominnce 3 dominnce ([d] nd [dd]) ws significnt for ll trits in the IJ hyrid nd ll the trits except tillers per plnt in the II hyrid. In this study, NCIII nlysis led to the estimtes of V A (dditive vrince) nd V D (dominnce vrince), which were lwys highly significnt (P, 0.005) in oth hyrids, except for the V D of tillers per plnt in the II hyrid, which ws significnt t P, 0.05 (Tle 4). M-QTL: QTL detected in RIL, SUM, two Hmp, nd DIFF dt sets in IJ nd II hyrids re shown in Tles 5 nd 6, respectively. In totl, 76 nd 41 QTL were reveled in five dt sets of IJ nd II hyrids, respectively. Most of these QTL explined,10% of vrition individully. Five QTL (6.76%) in the IJ hyrid nd 4 (9.76%) in the II hyrid ccounted for.20% of phenotypic vrition individully. HD: In the IJ hyrid, 10 QTL were detected. Three showed n dditive effect, 4 prtil-to-complete dominnt effect, nd 3 n overdominnt effect. Six of the 9 QTL showing dominnt effect identified in Hmp nd DIFFij were negtive, with lleles from 9024 incresing the trit vlue. In the II hyrid, 8 QTL were found. Three exhiited n dditive effect nd 5 prtil-tocomplete dominnt effect. Four of the 5 QTL displying dominnt effect reveled in Hmp nd DIFFii were positive, with lleles from Minghui63 incresing the trit vlue. PH: In the IJ hyrid, 12 QTL were found. Six were clssified s dditive, 3 s prtil-to-complete dominnce, nd 4 s overdominnce. In the II hyrid, 4 QTL were detected. Three were found to e dditive nd 1 in Zhenshn97Hmp to e overdominnt. No QTL ws identified in SUMii. TP: In the IJ hyrid, four QTL were identified with two showing n dditive effect, one n overdominnt effect, nd one prtil dominnt effect. No QTL ws found in the LH422Hmp nd DIFFij dt sets. In the II hyrid, five QTL were detected with two exhiiting n dditive effect, one dominnt effect, nd two n overdominnt effect. PL: In the IJ hyrid, 11 QTL were found with 5 clssified s n dditive effect, 4 s n overdominnt effect, nd 2 s prtil-to-complete dominnt effect. In the II hyrid, 2 QTL in RIL nd 1 QTL in SUMii were detected, displying n dditive effect nd with lleles from Minghui63 incresing the trit vlue.

6 1730 L. Li et l. TABLE 5 Min-effect QTL resolved in the IJ hyrid RILij SUMij 9024Hmp LH422Hmp DIFFij Trit Chr-In Intervl A R 2 (%) A R 2 (%) D R 2 (%) D R 2 (%) D R 2 (%) d/ c HD 1-17 RG811-RG A 2-8 RG544-RZ A 3-6 XNPB249-RZ OD 3-8 RZ993-CDO PD 5-1 RZ390-RZ A 6-16 RZ682-RG OD 6-17 RG653-RZ OD 7-6 RG711-XNPB PD 8-1 RG333-RZ PD 11-2 CDO534-XNPB PD PH 1-11 RZ776-RG A 1-17 RG811-RG A 2-8 RG544-RZ PD 3-3 RG558-RG OD 3-5 XNPB232-XNPB PD 3-8 RZ993-CDO A 5-7 RZ70-RG A 6-10 RZ667-RG OD 6-16 RZ682-RG D 7-6 RG711-XNPB OD 7-9 CDO533-RG A 8-1 RG333-RZ A TP 3-1 RG1356-CDO A 4-5 RG214-CDO A 5-11 CDO1160-CDO OD 9-9 XNPB295-RZ PD PL 1-9 RG233-XNPB OD 2-4 CDO1091-CDO A 3-8 RZ993-CDO A 4-13 RZ602-CDO OD 5-4 RZ296-RG PD 5-11 CDO1160-CDO D 6-10 RZ667-RG OD 7-9 CDO533-RG A 9-10 RZ404-RG A 10-4 RZ400-RZ OD 12-4 RZ670-XNPB A FGPP 3-8 RZ993-CDO A 4-2 RG143-RZ A 4-5 RG214-CDO A 5-2 RZ556-RG PD 5-3 RG360-RZ PD 8-1 RG333-RZ OD SS 2-9 RZ599-RG A 3-8 RZ993-CDO PD 4-9 RZ565-XNPB A 5-3 RG360-RZ A 6-17 RG653-RZ PD 7-9 CDO533-RG PD 7-10 RG528-RG PD 8-1 RG333-RZ OD 11-3 XNPB179-XNPB A 12-8 RZ816-XNPB OD (continued )

7 Genetic Bsis of Heterosis in Rice 1731 TABLE 5 (Continued) RILij SUMij 9024Hmp LH422Hmp DIFFij Trit Chr-In Intervl A R 2 (%) A R 2 (%) D R 2 (%) D R 2 (%) D R 2 (%) d/ c GD 3-8 RZ993-CDO A 4-3 RZ590-RZ D 4-4 RZ262-RG PD 6-11 RG1028-RG OD 6-12 RG162-CDO OD 8-2 RZ562-RZ OD 10-3 RZ561-RZ A KGW 1-3 RG350-RZ PD 1-4 RZ739-XNPB A 1-5 XNPB370-RG A 2-4 CDO1091-CDO A 3-7 RG417-RG PD 3-8 RG333-RZ PD 4-10 XNPB271-RG OD 6-9 RZ144-RZ A 7-9 CDO533-RG A 8-1 RG333-RZ OD YD 3-8 RZ993-CDO A 5-2 RZ556-RG A 6-4 XNPB317-RZ D 7-6 RG711-XNPB D 7-7 XNPB20-RZ D 8-1 RG333-RZ OD Effects estimted in 9024Hmp nd LH422Hmp were multiplied y 2, nd the vlues estimted in LH422Hmp nd the DIFF were multiplied y ( 1). Chromosome numer intervl of the QTL detected in the study. A nd D represent dditive effect nd dominnce effect of M-QTL. c The degree of dominnce for ll M-QTL declred s significnt in ny dt set ws determined fter estimting their dditive nd dominnce effects, respectively, in SUM nd DIFF dt sets. QTL were clssified ccording to their jd/j rtio s dditive (A) (jd/j, 0.2), prtil dominnce (PD) (0.2 # jd/j, 0.8), dominnce (D) (0.8 # jd/j, 1.2), nd overdominnce (OD) (jd/j $ 1.2) (Stuer et l. 1987). FGPP: In the IJ hyrid, six QTL were found with three ehving like n dditive effect, two like prtildominnt effect, nd one like n overdominnt effect. In the II hyrid, two QTL were detected with one ppering to e n overdominnt effect nd one prtildominnt effect. No QTL ws reveled in Hmp nd DIFFii. SS: In the IJ hyrid, 10 QTL were found with 4 displying n dditive effect, 4 prtil-dominnt effect, nd 2 n overdominnt effect. In the II hyrid, only 1 QTL ws detected in DIFFii dt, showing overdominnt effect, nd the lleles from Zhenshn97 incresed the trit vlue. GD: In the IJ hyrid, seven QTL were identified with two exhiiting n dditive effect, two prtil-tocomplete dominnt effect, nd three n overdominnt effect. No QTL ws detected in 9024Hmp. In the II hyrid, four QTL were reveled with two showing n dditive effect, one prtil-dominnt effect, nd one n overdominnt effect. No QTL ws found in Minghui63Hmp nd DIFFii dt sets. KGW: In the IJ hyrid, 10 QTL were reveled with 5 displying n dditive effect, 3 prtil-dominnt effect, nd 2 n overdominnt effect. No QTL ws found in 9024Hmp. In the II hyrid, 8 QTL were detected with 2 showing n dditive effect, 3 prtil-to-complete dominnt effect, nd 3 n overdominnt effect. YD: In the IJ hyrid, six QTL were identified with two exhiiting n dditive effect, three dominnt effect, nd one n overdominnt effect. No QTL ws found in SUMij nd LH422Hmp. In the II hyrid, six QTL were detected with one showing n dditive effect nd five n overdominnt effect. No QTL ws found in Zhenshn97Hmp nd SUMii dt sets. Digenic interction: Tle 7 shows the digenic interctions detected in DIFFij dt in the IJ hyrid. A totl of 46 digenic interctions were found in DIFFij dt. No significnt interction ws found for yield. The vrition explined y individul interction rnges from 2.0 to 10.1%. The proportion of totl vrition explined y ll digenic interction ws 30% in most trits. The highest vlue of totl vrition ws oserved for pnicle length in

8 1732 L. Li et l. TABLE 6 Min-effect QTL resolved in the II hyrid RILii SUMii Zhenshn97Hmp Minghui63Hmp DIFFii Trit Chr-In Intervl A R 2 (%) A R 2 (%) D R 2 (%) D R 2 (%) D R 2 (%) d/ c HD 1-6 RM243-RG PD 2-7 R712-RZ PD 2-16 RM208-RM A 6-24 R2549-C A 7-9 RM234-R D 8-2 C1121-RG PD RG118-C D 12-4 C996-G A PH 2-4 R1738-RM A 3-15 RM227-R A 6-15 RM204-R PD RG561-R A TP 2-5 RM53-RZ OD 3-3 C63-RM OD 7-9 RM234-R PD 10-5 C148-RM A RG118-C A PL 5-2 R3166-RG A 6-27 RG653-G A 8-1 R902-C A FGPP 3-4 RM232-G PD 6-16 R1014-RZ OD SS 12-6 R887-G OD GD 3-4 RM232-G PD 6-16 R1014-RZ A 9-7 RG667-RM A RM228-C OD KGW 3-1 C1176-C D 3-7 C1087-RZ PD 3-9 R19-C D 6-1 C764-RM A 6-15 RM204-R A 8-13 L363A-RZ OD CDO127-R OD R2918-C OD YD 2-2 RM211-RG OD 7-8 R1245-RM OD 7-9 RM234-R OD C104-RM OD CDO534-RM OD G389-G A Effects otined in Zhenshn97Hmp nd Minghui63Hmp were multiplied y 2, nd the vlues otined in LH422Hmp nd the DIFF were lso multiplied y ( 1). Chromosome numer intervl of the QTL detected in the study. A nd D represent dditive effect nd dominnce effect of M-QTL. c The degree of dominnce for ll M-QTL declred s significnt in ny dt set ws determined fter estimting their dditive nd dominnce effects, respectively, in SUM nd DIFF dt sets. QTL were clssified ccording to their jd/j rtio s dditive (A) (jd/j, 0.2), prtil dominnce (PD) (0.2 # jd/j, 0.8), dominnce (D) (0.8 # jd/j, 1.2), nd overdominnce (OD) (jd/j $ 1.2) (Stuer et l. 1987).

9 Genetic Bsis of Heterosis in Rice 1733 TABLE 7 Digenic interctions in the DIFFij dt set in the IJ hyrid Trit Chr i Intervl Chr j Intervl LOD A i A j AA ij R 2 (AA ij ) (%) c dd/ d HD 1 RG233-XNPB302 2 XNPB132-RG *** 6.20 A HD 2 CDO1091-CDO395 4 RZ590-RZ ** 2.90 OD HD 2 RG152-RG634 5 RZ390-RZ ** 0.61** 4.16 OD HD 4 CDO244-RG864 9 RZ12-RG *** 7.96 A HD 4 XNPB271-RG449 5 RZ70-RG ** 3.08 PD HD 5 RZ495-RZ70 6 RG653-RZ ** 2.65 D HD 6 XNPB317-RZ CDO127-RZ ** 3.21 OD HD 10 RZ561-RZ RG9-RZ ** 4.47 OD PH 1 RG406-RG462 5 RG697-CDO ** 6.24 PD PH 1 MK16-RG RZ536-CDO *** 8.33 OD PH 6 XNPB317-RZ247 9 XNPB103-XNPB *** 7.03 OD PH 11 RZ536-CDO RZ638-CDO *** 7.09 OD TP 3 XNPB249-RZ16 11 XNPB320-RG *** 6.88 PD TP 5 RG480-RG697 6 RG1028-RG *** 7.39 A TP 6 RG213-RZ RG901-RZ *** 6.18 PD TP 7 CDO405-RG146 9 RZ927-RZ ** 8.10 A TP 9 RZ927-RZ12 12 RG901-RZ ** 7.27 PD PL 2 RG634-RZ825 9 XNPB385-RZ *** 6.36 PD PL 4 RZ569-RG143 5 RG480-RG ** 5.02 A PL 5 RG360-RZ CDO534-XNPB *** 8.18 PD PL 5 RZ70-RG RG9-RZ *** 5.89 PD PL 6 RG653-RZ828 7 XNPB20-RZ *** 5.25 PD PL 7 CDO497-RZ CDO127-RZ * 0.48** 4.28 A PL 9 RZ404-RG RZ892-RZ *** PD FGPP 1 RZ776-RG RZ76-RG *** 5.61 A FGPP 2 RZ987-XNPB132 3 CDO87-RG ** 5.59 PD FGPP 2 CDO395-RZ987 4 RZ569-RG * 5.29** 4.73 A FGPP 3 XNPB249-RZ16 11 RZ536-CDO ** 5.13 D FGPP 6 XNPB317-RZ247 9 XNPB103-XNPB * 5.33** 4.80 PD SS 1 XNPB370-RG541 9 RZ404-RG ** 8.80 PD SS 1 RG406-RG462 5 RZ390-RZ * 2.04 PD SS 1 RG233-XNPB302 3 XNPB232-XNPB *** 6.50 A SS 1 RG462-RG233 6 RZ247-RZ ** 2.68 A SS 1 CDO962-RG RG121-RG ** 2.98 OD SS 5 CDO1083-CDO RG901-RZ ** 5.90 A GD 1 RG233-XNPB302 5 RZ296-RG *** 5.92 D GD 1 XNPB302-RZ776 7 XNPB20-RZ *** 5.78 A GD 1 RG233-XNPB302 9 RG662-XNPB *** 6.43 A GD 1 RG375-CDO RZ583-RZ * 0.30*** 4.62 A GD 2 RG555-TW500 8 RZ562-RZ * 0.36*** 6.50 A GD 5 RZ495-RZ70 10 RG257-RZ *** 7.30 A GD 5 RG480-RG697 6 RG213-RZ ** 5.19 A KGW 2 RZ123-RZ913 4 RZ569-RG *** 5.92 PD KGW 3 RG1356-CDO87 4 XNPB271-RG *** 8.50 PD KGW 4 RZ569-RG RZ561-RZ ** 4.71 PD KGW 7 CDO497-RZ626 9 RZ927-RZ *** 9.14 A *P # 0.05, **P # 0.01, ***P # Chr i nd Chr j represent the chromosomes tht loci i nd loci j re locted on, respectively. A i nd A j re the min effects of loci i nd loci j, nd AA ij is the episttic effect etween loci i nd j. c Percentge of the totl vrition explined y AA ij. d The epistsis dominnce degree (EDD) of digenic interction. Digenic interctions were clssified ccording to their jdd/j rtio s dditive (A) (jdd/j, 0.2), prtil dominnce (PD) (0.2 # jdd/j, 0.8), dominnce (D) (0.8 # jdd/j, 1.2), nd overdominnce (OD) (jdd/j $ 1.2).

10 1734 L. Li et l. TABLE 8 Digenic interctions in the DIFFii dt set in the II hyrid Trit Chr i Intervl Chr j Intervl LOD A i A j AA ij R 2 (AA ij ) (%) c dd/ d HD 1 G359-RG532 1 RM243-RG *** 8.83 A HD 1 C904-R RM258-RG *** 6.27 OD HD 1 R2201-RM RM222-R ** 4.22 A HD 2 R1738-RM53 11 C104-RM ** 3.45 OD HD 2 RZ386-G C794-RG ** 4.91 D HD 4 RZ467-C P-R *** 3.97 OD HD 4 C107-RG620 8 C1121-RG ** 2.02 OD HD 6 C688-R R2147-G * 1.38** 2.70 A HD 8 C483-C R2625-RM *** 4.35 D HD 9 RM215-R C996-G *** 3.05 A PH 1 RM259-RM G4001-RM *** 1.74** 3.48 PD PH 1 RM243-RG173 7 R1440-RG *** 4.08 D PH 2 R1738-RM53 4 RM255-G ** 2.83 A PH 3 C316-C63 6 C226-RZ *** 4.64 OD PH 3 RM200-RM227 4 R78-C *** 4.19 A PH 4 RZ467-C C472-R *** 3.30 PD PH 6 C226-RZ G1314-R * 1.53** 2.68 PD PH 7 R1245-RM234 8 R902-C *** 1.87*** 3.99 PD PH 8 R1394-G CDO127-R *** 3.45 PD PH 8 G1149-R C153B-C ** 1.84 OD PH 10 C1633-C677 4 C56-C *** 7.46 D TP 1 RM259-RM243 1 C2340-C ** 3.39 OD TP 2 RM53-RZ599 2 RZ386-G * 0.52** 4.11 OD TP 5 C734-RZ RG118-C *** 5.92 D TP 5 RM26-C RM222-R *** OD TP 6 RM204-R C472-R ** 3.78 OD TP 6 RZ667-RG424 7 RM70-R ** 2.88 OD TP 7 RG528-RG CDO127-R ** 2.46 OD TP 7 RG528-RG G1128-R ** 0.40** 2.42 OD TP 8 RZ66-G C1633-C *** 5.80 OD TP 10 C909A-C RM20-R * 0.43** 2.78 OD TP 10 C405-C R496-C909B ** 2.48 OD TP 11 G257-RM R543-RZ *** 5.62 OD PL 1 C161-R C104-RM *** 6.15 OD PL 1 C567-C C732-R ** 2.48 D PL 5 RM26-C R1962-C *** 5.91 D PL 6 R2549-C C153A-RM *** 3.05 OD PL 7 RZ471-RM70 4 C56-C *** 7.48 OD PL 11 RM224-MP12 11 RZ536-TEL * 1.13** A FGPP 1 G359-RG532 5 RM26-C *** 4.02 D FGPP 1 G1128-C904 2 RM53-RZ ** 4.94 A FGPP 1 G393-R C624-C *** 5.05 A FGPP 3 C1176-C316 6 RZ667-RG *** 5.05 OD FGPP 4 C107-RG620 6 RG424-R *** 4.40 OD FGPP 5 C734-RZ649 9 R1952-RZ ** 4.36 OD FGPP 6 R1962-C764 6 R2549-C *** 5.31 A FGPP 6 R2549-C R2174-C909A *** 5.12 D FGPP 7 RZ471-RM70 4 C56-C ** 5.29 OD FGPP 8 RM223-L363A 9 RM242-RG ** 3.08 OD FGPP 9 RM257-RM C732-R *** 4.69 D SS 2 RZ386-G RG653-G * 3.44 OD SS 3 C1087-RZ C153A-RM *** 8.34 OD SS 4 G102-RM255 5 RZ649-C *** 5.09 OD (continued )

11 Genetic Bsis of Heterosis in Rice 1735 TABLE 8 (Continued) Trit Chr i Intervl Chr j Intervl LOD A i A j AA ij R 2 (AA ij ) (%) c dd/ d SS 4 C1016-C107 7 C1023-R *** 4.46 OD SS 6 RM204-R C56-C ** 3.42 OD SS 6 RG424-R C820-C ** 3.56 OD SS 7 RG128-C G1314-R ** 3.89 D SS 8 C347-RG978 9 C1232-R *** 3.59 OD SS 8 RZ66-G C87-R *** 4.74 OD SS 9 RM201-C472 9 RG667-RM *** 9.08 OD SS 10 R2174-C909A 12 R887-G ** 3.12 OD GD 1 G393-R C624-C *** 6.64 OD GD 1 G393-R C794-RG ** 3.80 PD GD 1 RG236-C112 9 C472-R *** 6.26 OD GD 2 RZ599-R712 5 RM26-C ** 4.86 D GD 2 R712-RZ324 3 C1087-RZ *** 5.41 OD GD 3 RM232-G C794-RG ** 4.08 PD GD 6 P-R C153B-C *** 4.45 PD GD 6 R2549-C962 9 C153B-C ** 3.84 OD GD 7 RG528-RG C405-C * 0.10** 2.31 OD KGW 2 RZ324-RM29 5 R830-R *** 7.14 A KGW 2 RM213-RM208 5 R830-R ** 4.64 D KGW 5 C1447-RM31 6 C952-Wxy *** 5.55 PD KGW 8 R727-RM R3203-CDO *** 8.71 OD YD 1 RG236-C RZ536-TEL ** 3.62 OD YD 2 RM48-RG520 6 C474-R ** 4.07 OD YD 3 C63-RM232 4 G102-RM *** OD YD 4 C2807-RM241 6 R1962-C ** 4.35 PD YD 4 C2807-RM241 9 C477-C *** 8.24 OD YD 7 RG128-C R3203-CDO *** 6.61 OD YD 9 RG570-RG R543-RZ ** 3.65 OD *P # 0.05, **P # 0.01, ***P # Chr i nd Chr j represent the chromosomes tht loci i nd loci j re locted on, respectively. A i nd A j re the min effects of loci i nd loci j, nd AA ij is the episttic effect etween loci i nd j. c Percentge of the totl vrition explined y AA ij. d The epistsis dominnce degree (EDD) of digenic interction. Digenic interctions were clssified ccording to their jdd/j rtio s dditive (A) (jdd/j, 0.2), prtil dominnce (PD) (0.2 # jdd/j, 0.8), dominnce (D) (0.8 # jdd/j, 1.2), nd overdominnce (OD) (jdd/j $ 1.2). the DIFFij dt set (45.1%), which minly reflected the dominnce 3 dominnce digenic interctions. Tle 8 shows the digenic interction identified in DIFFii dt in the II hyrid. In totl, 81 digenic interctions were reveled. Ech interction generlly showed modest R 2, 10% for ll significnt interctions except one interction with 18.1%. However, in the IJ hyrid, the totl vrition explined y ll digenic interctions ws.40% for most of the trits. The highest vlue of totl R 2 ws oserved for SS in the DIFFii dt set (52.7%). Tle 9 summrizes the digenic interction detected in RIL, SUM, Hmp, nd DIFF dt sets of IJ nd II hyrids. Most of the detected interctions involved QTL without significnt min effect nd ech interction showed modest R 2, 10% for ll trits. However, it should e noted tht n interction occurred etween two significnt M-QTL in Minghui63Hmp for grin weight, which explined 43.4% of phenotypic vrition (dt not shown here). In the IJ hyrid, the numer of digenic interctions detected for ech trit vries from none to 10 in the RILij popultion with n verge of 3.22, nd the vrince explined (R 2 ) y ech pir ws up to 39.1% with n verge of 16.4%. The numer of digenic interctions detected in the SUMij dt set vries from two to 7 with n verge 3.44, nd the R 2 of ech pir vries from 10.9 to 44.7% with n verge of 21.8%. For digenic interction of dominnce 3 dominnce, on verge, 1.11, 1.11, nd 2.00 QTL pirs with n dditive effect were detected in 9024Hmp, LH422Hmp, nd DIFFij nd hd contriution rte of 6.0, 6.4, nd 12.2%, respectively;

12 1736 L. Li et l. TABLE 9 Summries of digenic interction in five dt sets of the two hyrids Hmp (1) Hmp (2) DIFF Prtil-to-complete dominnce Overdominnce Additive Prtil-to-complete dominnce Overdominnce Additive Prtil-to-complete dominnce Overdominnce RIL SUM Additive Trit No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 No. R 2 IJ hyrid HD PH TP PL FGPP SS GD KGW YD Men II hyrid HD PH TP PL FGPP SS GD KGW YD Men In the IJ hyrid, Hmp (1) nd Hmp (2) represent 9024Hmp nd LH422Hmp, respectively; while in the II hyrid, Hmp (1) nd Hmp (2) represent Zhenshn97Hmp nd Minghui63Hmp, respectively. The totl vrition explined y ech trit (%).

13 Genetic Bsis of Heterosis in Rice , 2.44, nd 2.22 QTL pirs with prtil-to-complete dominnce were detected in 9024Hmp, LH422Hmp, nd DIFFij nd hd contriution rte of 14.7, 15.2, nd 13.3%, respectively; nd 1.67, 1.33, nd 0.89 QTL pirs with overdominnce were detected in 9024Hmp, LH422Hmp, nd DIFFij nd hd contriution rte of 10.6, 8.4, nd 4.5%, respectively. For the II hyrid, the numer of digenic interctions identified for ech trit vries from none to 12 in the RILii popultion with n verge of 8.11 nd hd contriution rte (R 2 ) up to 87.0%, with n verge of 47.9%. The numer of digenic interctions detected in the SUMii dt set vries from none to 14 with n verge of 7.44, nd ech pir hd n R 2 up to 59.4% with n verge of 40.4%. For digenic interction of dominnce 3 dominnce, on verge, 1.44, 0.11, nd 1.22 QTL pirs with dditive effect were detected in Zhenshn97Hmp, Minghui63Hmp, nd DIFFii nd hd contriution rte of 7.0, 0.7, nd 7.4%, respectively; 5.44, 1.56, nd 2.44 QTL pirs with prtil-to-complete dominnce were detected in Zhensh97Hmp, Minghui63Hmp, nd DIFFii nd hd contriution rte of 27.7, 13.8, nd 11.8%, respectively; nd 2.44, 0.89, nd 5.33 QTL pirs with overdominnce were detected in Zhenshn97Hmp, Minghui63Hmp, nd DIFFii nd hd contriution rte of 12.2, 5.3, nd 25.3%, respectively. Reltionship etween trit performnce nd genomewide or chromosomewide mrker heterozygosity: The correltion coefficients (Tle 10) etween level of genomewide heterozygosity nd performnce per se of the two ckcross popultions were not significnt for most of the trits in oth IJ nd II hyrids (except plnt height in 9024BC nd 1000-grin weight in Minghui63BC). The nlysis of the reltionship etween level of heterozygosity nd level of heterosis (s evluted in Hmp nd DIFF) showed tht correltion coefficients, for severl trits, were slightly higher thn those previously shown, ut still not significnt for most trits. The significnt correltion coefficients were found for plnt height, heding dte, nd 1000-grin weight in the IJ hyrid nd for tillers per plnt in the II hyrid. In this study, the Hmp vlue ws regressed ginst heterozygosity on individul chromosomes using multiple liner regression (Tle 11). The hyrid performnce ws lso poorly ssocited with mrker heterozygosity in most chromosomes. There were 8, 6, 8, nd 5 significnt regressions etween trit vlue nd mrker heterozygosity in individul chromosomes resolved in 9024Hmp, LH422Hmp, Zhenshn97Hmp, nd Minghui63Hmp, respectively. Nineteen of these 27 (70.3%) significnt regressions were ssocited with one or two M-QTL nd/ or digenic interction. In the IJ hyrid, the F-test vlue ws significnt for pnicle length nd grin density in 9024Hmp nd for plnt height nd heding dte in LH422Hmp. While in the II hyrid, the F-test vlue ws significnt for plnt height in Zhenshn97Hmp nd for TABLE 10 Correltion coefficients etween genomewide moleculr mrker heterozygosity nd phenotypic vlues IJ hyrid II hyrid Performnce per se Heterosis Performnce per se Heterosis Trit 9024BC LH422BC 9024Hmp LH422Hmp DIFF (1) DIFF (2) Minghui63BC Zhenshn97BC Minghui63Hmp Zhenshn97Hmp DIFF (3) DIFF (4) HD ** PH 0.209** ** 0.228** 0.289** TP * PL FGPP SS GD KGW ** ** 0.177* 0.166* YD *P # 0.05, **P # DIFF (1) nd DIFF (2) represent tht, in the IJ hyrid, when the DIFF dt set ws used s dependent vrile, genome heterozygosity of the 9024BC nd LH422BC hyrids ws the independent vrile, respectively. While in the IJ hyrid, DIFF (3) nd DIFF (4) represent tht when the DIFF dt set ws used s dependent vrile, genome heterozygosity of the Zhenshn97BC nd Minghui63BC hyrids ws the independent vrile, respectively.

14 1738 L. Li et l. TABLE 11 Significnt regression coefficients of midprent vlues of ckcross popultions on individul chromosome mrker heterozygosity for the indicted trits Popultion Trit Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12 F r 2 IJ hyrid 9024Hmp HD 0.044* Hmp PH 0.032* Hmp TP 0.004* Hmp PL 0.005* 1.821* Hmp FGPP Hmp SS Hmp GD 0.004* 0.004* 1.821* Hmp KGW 0.007* Hmp YD 3.039* LH422Hmp HD 0.023*** 0.012* 4.000*** 0.21 LH422Hmp PH 0.045** 2.117** 0.12 LH422Hmp TP LH422Hmp PL 0.008* 0.007* LH422Hmp FGPP LH422Hmp SS LH422Hmp GD 0.005* LH422Hmp KGW LH422Hmp YD II hyrid Zhenshn97Hmp HD 0.055* Zhenshn97Hmp PH 0.211** 2.292** 0.12 Zhenshn97Hmp TP 0.017* Zhenshn97Hmp PL Zhenshn97Hmp FGPP Zhenshn97Hmp SS 0.107* Zhenshn97Hmp GD 0.006* 0.005** Zhenshn97Hmp KGW 0.017* 0.016** Zhenshn97Hmp YD Minghui63Hmp HD 0.062* Minghui63Hmp PH Minghui63Hmp TP 0.017* Minghui63Hmp PL 0.019* Minghui63Hmp FGPP Minghui63Hmp SS Minghui63Hmp GD Minghui63Hmp KGW Minghui63Hmp YD 0.095** 0.080** 1.954* 0.10 *P # 0.05, **P # 0.01, ***P # Itlics indicte the presence of QTL on prticulr chromosome. F-test vlue. Determintion coefficients.