Quantitative Trait Loci for Agronomic Traits

4.3.2. Quantitative Trait Loci for Agronomic Traits

There were 93 SSR markers genotyped in backcross mapping population and 74 markers in F 2 mapping population Appendix 7. The markers are expected to segregate according to Mendelian law. However, ten markers 10.75 in backcross population and 29 markers 39.73 in F 2 mapping population had skewed distribution Appendix 11. In the backcross mapping population six markers skewed towards IR64. Interestingly markers namely RM508, RM204, RM276, RM7193, RM3827 were all on chromosome 6 while RM248 was on chromosome 7 skewed. Other markers such as RM1869 on chromosome 4, RM5432 and RM332 on chromosome 8 and RM288 on chromosome 10 were skewed towards heterozygous constitution. On the other hand F 2 population had even more segregation distortion as 27 markers or 39.73 of total SSR markers used in the population. Among them 11 SSR markers skewed to Joryeongbyeo. These are RM493 and RM449 on chromosome 1, RM174 and RM526 on chromosome 2, RM1869 on chromosome 4, RM289 on chromosome 5, RM38 on chromosome 8, RM3769 and RM242 on chromosome 9, RM184 on chromosome 10, and RM8216 on chromosome 12. A set of 14 SSR markers skewed to IR64 namely RM259 and RM3627 on chromosome 1, RM6023 on chromosome 2, RM1230 on chromosome 3, RM6454 and RM6473 on chromosome 4, RM6872, RM11 and RM7351 on chromosome 7, RM223 on chromosome 8, RM3700 on chromosome 9, and RM101, RM3739 and RM17 on chromosome 12. Two markers namely RM570 on chromosome 3 and RM6054 of chromosome 5 were skewed to heterozygotes. Segregation distortion is of wide occurrence and was reported in some crosses such as BC 2 F 2 of IR64O rufipogon Septiningsih et al. 2003, BC 2 F 2 of JeffersonO rufipogon Thomson et al. 2003, Doubled Haploid DH population of IR64Azucena Huang, et al. 1997, NipponbareKasalath Harushima et al. 1996, F 2 population of Taichung 65O glaberrima Doi et al. 1998 and RIL of LH4229024 Xiao et al. 1998. Skewness might be due to the sterility genes that affect the viability of gamete. However it has little effect on the outcome of QTL mapping Kearsey and Pooni 1996. 36 Quantitative Trait Loci for various agronomic traits are summarized in Table 11 and Table 12 for backcross and F 2 mapping population, respectively. The tentative name, the location, closest Marker, donor of superior allele, LOD value and coefficient of determination were calculated. In the backcross population we detected 11 putative QTLs henceforth termed as QTL controlling eight agronomic traits as summarized in Table 11. One or two QTLs were detected for each of the traits. In the F 2 mapping population we detected 17 QTLs Table 12 controlling seven agronomic traits. The number of QTLs detected in F 2 mapping population were relatively higher than those detected using backcross population. It may be related to the amount of variation generated in these populations. Various algorithms such as Single Marker Regression SMR, Simple Interval Mapping SIM, and Composite Interval Mapping CIM were used to locate QTLs. However more emphasis was given to CIM approach since it locates QTLs more precisely and take care of the background effects of neighboring markers. QTLs with a LOD value of greater than 2 are reported in this study and are listed for various traits for both populations in Appendix 12 using SMR, SIM and CIM approaches, Quantitative Trait Loci for Heading Date A QTL named hd-vb12.1 Table 11 controlling heading dates was detected at 16 cM between RM8216 and RM3472 on chromosome 12 in BC mapping population. It accounts for 12.6 of variation and the superior allele was come contributed by IR64 with additive value of -3.811 day. Another QTL hd-vs3.1; Table 12 controlling heading date lied at 158 cM RM570 on chromosome 3. It accounts for 22 of variation contributed by IR64 allele with additive value of -6.03 day and dominant effect of -1.55 day. The QTLs controlling heading date in both populations were not similar. It indicated that the heading date was controlled not by the same genes in these 2 populations. Moncada et al. 2001 reported four QTLs controlling heading date, located at chromosome 2, 3, and 7 explaining 6 to 14 of variation. On the other hand, Septiningsih et al. 2003 reported six QTLs controlling heading date, located at chromosome 2, 7, 11, and 12 explaining 4 to 12 of variation. Linh et al. 2006 37 reported two QTLs controlling heading date located on chromosome 6 and 9 explaining a total of 43.2 of variation. Cui et al. 2004 reported six QTLs controlling heading date located in chromosome 6, 7, 10, and 11 explaining 59.69 of variation. Apparently there are many QTLs controlling heading dates and the ones detected in our study may be similar to those reported earlier. Table 11. Quantitative TraitLoci Detected for Several Agronomic Traits in Backcross Mapping Population No Trait QTL Name Chr Pos Marker Donor Additive LOD R 2 1 HD hd-vb12.1 12 16 RM8216-RM3472 IR64 -3.811 3.362 0.126 2 FLW fll-vb4.1 4 104 RM317-RM3836 IR75862- 1.632 7.489 0.259 3 PH ph-vb4.1 4 128 RM3333 IR75862- 4.296 3.413 0.128 4 PL pl-vb11.1 11 48 RM3701-RM3428 IR64 -13.615 3.073 0.116 5 PL pl-vb12.1 12 62 RM101-RM1246 IR75862- 15.794 3.528 0.132 6 PW pw-vb4.1 4 104 RM317-RM3836 IR75862- 0.39 3.321 0.125 7 SS ss-vb6.1 6 34 RM276 IR64 -0.105 9.944 0.328 8 SS ss-vb6.2 6 68 RM8226-RM7193 IR64 -0.073 4.195 0.155 9 Wt100 wt100-vb2.1 2 108 RM5430-RM526 IR75862- 0.141 5.24 0.189 10 Wt100 wt100-vb3.1 3 68 RM1324-RM6931 IR64 -0.142 5.36 0.193 11 Wt wt-vb11.1 11 62 RM3428-RM5349 IR64 -9.884 4.005 0.148 Note: The code of the traits followed the note at Table 7. LOD threshold were decided by 1000 times permutation, means the LOD is above 5 of LOD threshold, means the LOD is above 1 of LOD threshold Table 12. Quantitative Trait Loci Detected for Several Agronomic Traits in F 2 Mapping Population No Trait QTL Chr Pos Marker Donor Add Dom LOD R2 1 HD hd-vs3.1 3 158 RM570 IR64 -6.03 -1.55 5.774 0.22 2 FLW flw-vs4.1 4 108 RM317-RM6473 Joryeongbyeo 1.369 0.635 3.337 0.134 3 FLW flw-vs6.1 6 116 RM6811 IR64 -0.895 0.83 3.714 0.148 4 PH ph-vs6.1 6 116 RM6811 IR64 -7.83 5 5.264 0.20 5 PH ph-vs8.1 8 44 RM5432-RM331 IR64 -9.91 1 3.14 0.13 6 PH ph-vs8.2 8 64 RM331-RM223 IR64 -15.97 15 3.21 0.13 7 PL pl-vs5.1 5 68 RM6024 IR64 -13.11 4.63 3.24 0.13 8 PL pl-vs6.1 6 88 RM549-RM6811 IR64 -29.78 23.49 4.115 0.16 9 PL pl-vs6.2 6 116 RM6811 IR64 -18.19 7.31 5.509 0.21 10 PL pl-vs8.1 8 44 RM5432-RM331 IR64 -28.89 -0.37 3.943 0.16 11 PL pl-vs8.2 8 62 RM331-RM223 IR64 -36.25 41.39 3.824 0.15 12 PW pw-vs1.1 1 28 RM8145-RM259 IR64 -0.54 -0.29 3.37 0.14 13 PW pw-vs6.1 6 116 RM6811 IR64 -0.46 0.46 3.58 0.14 14 TG tg-vs5.1 5 0 ..-RM405 IR64 -62.29 16.436 3.929 0.156 15 wt100 wt100-vs1.1 1 66 RM493-RM449 IR64 -0.09 0.16 4.272 0.17 16 wt100 wt100-vs2.1 2 132 RM525-RM240 Joryeongbyeo 0.18 0.07 3.801 0.15 17 wt100 wt100-vs9.1 9 36 RM3769 IR64 -0.09 0.12 3.12 0.13 Note: see note of Table 11. 38 Quantitative Trait Loci for Flag Leaf Width One QTL for flag leaf width was detected in backcross mapping population, i.e. fll-vb4.1 Table 11. It is located chromosome 4 at 104 cM RM317-RM3836 explaining 25.9 of variation. The additive allele value was 1.632 mm and contributed by IR75862-206-2-8-3-B-B-B. In the F 2 mapping population we detected two QTLs controlling flag leaf width trait, i.e. flw-vs4.1 and flw-vs6.1. Quantitative Trait Loci of flw-vs4.1 lied at chromosome 4 of 112 cM between RM317 and RM6473. It could explain 13.4 of the total variation. It was contributed by Joryeongbyeo with the additive value of 1.369 mm and dominant effect of 0.635 mm. From the chromosomal location of these QTLs it is evident that in both populations the same QTL was detected. It seems that IR64 seems to have inferior allele. Quantitative Trait Loci of flw-vs6.1 Table 12 located at 116 cM on chromosome 6 close to RM6811. It explained 14.8 of total variation, contributed by IR64 with the additive effect of -0.895 mm and dominant effect of 0.83 mm. It means that IR64 had another allele for reducing leaf width. Flag leaf provides photosynthesis for the filling grain. Jun et al. 2006 reported that flag leaf width of top three leaves was positively correlated with number of spikelets, filled grains, single panicle weight, and grain yield. Kobayashi et al. 2003 and Mei et al. 2003 reported some QTLs controlling flag leaf width. Finding QTLs controlling flag leaf width in this study indicating that it is prospective to develop variety having optimum flag leaf size that optimally support the final grain yield. Quantitative Trait Loci for Plant Height Quantitative Trait Loci of ph-vb4.1 Table 11 controlling plant height was detected in backcross mapping population at 128 cM on chromosome 4, close to RM3333. It explained 12.8 of variation contributed by IR75862-206-2-8-3-B- B-B with the value of additive effect of 4.296 cm. There were three QTLs detected in F 2 mapping population Table 12 controlling plant height, i.e. ph-vs6.1, ph-vs8.1, and ph-vs8.2. The ph-vs6.1 located at 116 cM on chromosome 6, linked to RM6811 was contributed by IR64 with the additive effect of -7.83 cm and dominant effect of 5 cm. It explained 39 20 of variation. The ph-vs8.1 located at 44 cM between RM5432 and RM331 on chromosome 8 contributing 13 of variation and was contributed by IR64. It had additive affect of -9.91 cm and 1 cm of dominant effect. Another QTL namely ph-vs8.2 was also detected at 64 cM between RM331 and RM223 of chromosome 8. It was contributed by IR64 with the value of additive effect as -15.97 cm and 15 cm for dominant effect. It explained 13 of variation. Moncada et al. 2001 reported six QTLs controlling plant height located at chromosome 1, 2, 4, and 5 explaining 6 – 21 of variation. On the other hand, Septiningsih et al. 2003 reported five QTLs controlling plant height located at chromosome 1, 4, 6, 10, and 11 explaining 6 – 55 of variation. Cui et al. 2004 reported four QTLs controlling plant height at maturity located in chromosome 3, 4, and 6 explaining total of 39.76 of variation. You et al. 2006 reported 17 QTLs controlling plant height located spread in the 12 rice chromosome explaining 5 to 23 of variation. Again there are many QTLs controlling plant have been reported by many workers and the ones detected in our study may be similar to those reported earlier. Quantitative Trait Loci for Panicle Length Two QTLs controlling panicle length in the backcross mapping population, i.e. pl-vb11.1 and pl-vb12.1 were detected. The pl-vb11.1 lied at 48 cM on chromosome 11 linked to RM3333 contributing 11.6 of variation. The donor for the unfavorable allele was IR64 with the additive value of -13.62 cm. Another QTL named pl-vb12.1 located at 62 cM on chromosome 12 between RM101 and RM1246 markers. It was contributed by IR75862-206-2-8-3-B-B-B with the value of additive effect 15.79 cm. Both parent contributed to the length of panicle in different direction. In F 2 mapping population we detected 5 QTLs controlling panicle length, i.e. pl-vs5.1, pl-vs6.1, pl-vs6.2, pl-vs8.1, and pl-vs8.2. The allele with negative effect was detected for five QTLs. The pl-vs5.1 lied at 68 cM on chromosome 5 linked to RM6024. It represented 13 of variation with additive affect of -13.11 mm and dominant effect of 4.63 mm. The pl-vs6.1 located at 88 cM on chromosome 6 between RM549 and RM6811 markers explained 16 of variation with additive effect f -29.78 mm and dominant effect of 23.49 mm. Also on 40 chromosome 6, pl-vs6.2 located at 116 cM linked to RM6811 explained 21 of variation with additive value of -18.19 mm and dominant effect of 7.31 mm. A QTL named pl-vs8.1 located at 44 cM on chromosome 8 between RM5432 and RM331 explained 16 of variation with additive effect of -28.89 mm and dominant effect of -0.37 mm. Another QTL on chromosome 8 pl-vs8.2 located at 62 cM between RM331 and RM223 explained 15 of variation with additive effect of -36.25 mm and dominant effect of 41.39 mm. Many QTLs controlling panicle length detected in both populations. It indicats that there are many loci controlling panicle length with the presence of additive and dominant effects. However, combining all the QTLs may not have synergistic effect. Septiningsih et al. 2003 reported five QTLs controlling panicle length located at chromosome 1, 3, 9, and 10 explaining 5 to 25 of variation. The QTLs detected in this study seem to be different to those earlier reported QTLs. Apparently genetic control of panicle length is rather complex. Quantitative Trait Loci for Panicle Weight A QTL, pw-vb4.1, for panicle weight was detected in the backcross mapping population. It was located at 104 cM on chromosome 4 between RM317 and RM3836. It explained 12.5 of variation with additive value of 0.39 g contributed by IR75862-206-2-8-3-B-B-B. Two QTLs controlling panicle weight were detected in F 2 mapping population, i.e. pw-vs1.2 and pw-vs6.1. Both were contributed by IR64 each explain 14 of variation. The first one was having additive effect of -0.54 g and dominant effect of -0.29 g. The second one had additive effect of -0.46 g and dominant effect of 0.46 g. Panicle weight has become main measurement for high yielding variety development. It correlated strongly with plant type, yield, and cultivation measures Jun et al. 2006. Finding QTLs controlling heavy panicle weight would support the development of high yielding variety. Quantitative Trait Loci for Number of Total Grains per Panicle In F 2 mapping population one QTL controlling total number of grain per panicle was detected. The QTL named tg-vs5.1 was located at the tip of 41 chromosome 5 close to RM405. It explained 15.6 of variation with additive effect of -62.29 grains and dominant effect of 16.44 grains. The donor of the favorable allele was IR64. Septiningsih et al. 2003 reported one QTL controlling total number of grain per panicle located in Chromosome 3 explaining 6 of variation. Apparently QTL detected in our study has larger effect. Quantitative Trait Loci for Seed Set Quantitative Trait Loci for seed set were detected only in the backcross mapping population. These are tg-vb6.1 and tg-vb6.2, both located on chromosome 6 and both having IR64 as donor possessing favorable allele. The first QTL was located at 34 cM linked to RM276 and explained 32.8 of variation with additive effect of -0.1. The second was located at 68 cM between RM8226 and RM7193 explaining 15.5 of variation with additive effect of -0.07. Moncada et al. 2001 reported two QTLs controlling the level of sterility located at chromosome 10 explaining around 13 of variation. It was contributed by O rufipogon increasing the level of sterility. Septinigsih et al. 2003 reported three QTLs located on chromosome 1, 2, and 11 explaining 6 to 10 of variation. Apparently, QTLs detected in this study are different to those reported in the above studies. Quantitative Trait Loci for Weight of 100 Grains A total of 5 QTLs were detected controlling grain weight. Two of these were detected in backcross mapping population while the remaining three were observed in F 2 mapping population. Two QTLs detected in backcross mapping population were wt100-vb2.1 and wt100-vb3.1. The first one was contributed by IR75862-206-2-8-3-B-B-B located at 108 cM on chromosome 2 between RM5430 and RM 526 having additive effect of 0.14 g and explained 18.9 of variation. The second one was contributed by IR64 located at 68 cM on chromosome 3 between RM1324 and RM6931. It explained 19.3 of variation with the additive effect of -0.142 g. Three QTLs detected in the F 2 mapping population were wt100-vs1.1, wt100-vs2.1, and wt100-vs9.1. The wt100-vs1.1 was located at 66 cM on chromosome 1 between RM492 and RM449 contributed by IR64 with additive effect of -0.09 g and dominant effect of 0.16 g. It explained 17 of variation. 42 The QTL of wt100-vs2.1 was located in chromosome 2 at 132 cM between RM525 and RM240 contributed by Joryeongbyeo with additive effect of 0.18 g and dominant effect of 0.07 g. It explained 15 of variation. The QTL of wt100- vs9.1 was located at 36 cM on chromosome 9 contributed by IR64 with additive effect of -0.09 g and dominant effect of 0.12 g. It explained 13 of variation. Moncada et al. 2001 reported five QTLs associated with 1000-grain weight all derived from O rufipogon located at chromosome 1, 3, and 11 explaining 5 – 22 of variation. Septiningsih et al. 2003 reported five QTLs controlling grain weight located at chromosome 1, 2, 3, and 7 explaining 4 to 11 of variation. One of the QTLs on chromosome 1 might be close to the QTL found in this study wt100-vs1.1 at 66 cM. Quantitative Trait Loci for Grain Weight per Plant In the backcross mapping population we could detect a QTL for grain weight per plant, i.e. wt-vb11.1 which was located at 62 cM on chromosome 11 between RM3428 and RM5349 contributed by IR64 with additive effect of - 9.884 g. It explained 14.8 of variation. Moncada et al. 2001 reported two QTLs associated with yield per plant located at chromosome 1 and 11 both contributed by O rufipogon for increasing the yield that explained 7 – 14 of variation. Quantitative Trait Loci detected in this study is located on chromosome 11 as well. On the other hand, Septiningsih et al . 2003 reported three QTLs controlling 3 – 6 of variation.

4.3.3. Quantitative Trait Loci for Iron and Zinc Content in Polished Rice Grain