Construction Of SSR Linkage Maps Between Four Sequenced Rice Varieties And Mapping Of Quantitative Trait Loci

Most of crop traits are quantitative in nature, which are controlled by polygene. It's very important for crop improvement to map quantitative trait loci (QTLs). Specially, it's very useful to clone QTL using the materials which genomic full-sequence has been known. This research constructed six F2 mapping populations which derived from the cross between the indica variety 93-11, GuangLuAi-4 (ab. GLA), the japonica variety Nipponbare (ab. NIPP) and the light-temperature sensitive sterility lines PA64S, then 14 types of agronomic QTLs were mapped on the six linkage maps. The main results are as follows:1. The level of polymorphism between the four parents using our synthesized 756 pairs of SSR primers is 33.07% (NIPP-9311), 30.56% (NIPP-GLA), 23.81% (NIPP-PA64S),19.44% (PA64S-9311), 18.52% (PA64S-GLA), 11.24% (9311 -GLA), respectively. The results indicate that the relationship is closer; the frequency of polymorphism is lower.2. There are 90 pairs of new RP# primers mapped on the six linkage maps; the number of mapped RP# markers on the 6 populations (PA64S/9311-F2, PA64S/NIPP-F2, PA64S/GLA-F2, NIPP/9311-F2, NIPP/GLA-F2 and 9311/GLA-F2) is 22, 44, 19, 41, 46 and 4, respectively.3. The number of mapped markers, the length of chromosome covering (cM) and the average mapping distance (cM/marker) on the 6 populations (PA64S/9311-F2 , PA64S/NIPP-F2, PA64S/GLA-F2, NIPP/9311-F2, NIPP/GLA-F2 and 9311/GLA-F2) are 74, 1204, 18.27; 89, 1400.4, 15.73; 89, 1331.9, 14.87; 117, 1670.7, 14.28; 108, 1224.6, 11.34; 53, 1130.6, 21.33, respectively.4. The number of detected QTLs in the six populations (PA64S/9311 -F2, PA64S/NIPP-F2, PA64S/GLA-F2, NIPP/9311-F2, NIPP/GLA-F2 and 9311/GLA-F2) with the method of QTL Interval-mapping is16,23,17,38,25,11, respectively. The major QTLs mapped in those 6 populations are 7 ( qph1, 31.6%; qph2, 29.4%; qpl1, 31.4%; qfl1, 22.7%; qfl2, 21.8%; qtn2, 21.6%; qtn3, 35.5%) ; 8 (qetn2, 31.3%; qpn3, 34.4%; qfl2, 48.7%; qfl3, 53%; qfl4, 66.8%; qss1, 51.8%; qkw2, 29.5%; qph1,32%) ; 4(qpt1, 72.5%; qpt2, 72.9%; qphl, 20.5%; qph5, 32.6%); 18 qptl, 63.1%; qpt3, 64.6%;qpt4, 29%;qphl, 41.5%; qph3, 20.3%; qph4, 26.7%; qmpl3, 27.7%; qmpl4, 24.3%; qhdl, 25%; qhd2, 27.9%;qpl4, 20.6%; 4/77, 22.8%; g/72, 21.4%; qfl4, 29.1%; 2/75 , 25.4%; qpn4 , 22.1%); 8 (qtn2,21.9%; qetn2,21.5%; qpt3,70.2%; qphl,2%.1%;qph2A0.8%;qph3,20%; qpn1,273%;qpn2,23%) and 4 ( qetnl,54.9%; qptl,573%; qph3,23A%; qpl1,20.4%), respectively.5. The analysis of QTL comparative mapping in this research indicated that there were many QTLs of difference traits detected within a same marker interval in all six populations; and , there were 14 QTLs which controlled the traits of Dh, Tn, Etn, PI, Fl, Mpl and Ph respectively, mapped in difference populations.6. The bioinformatic analysis of 20 QTLs which QTL POS=0 indicate that, in the population of PA64S/9311-F2, the linkage QTLs of marker RM547, RM583 and RM263 maybe have the function of increasing flag leaf length (qfl.), reducing plant height (qph) and increasing plant height (qph), respectively; in the population of PA64S/NIPP-F2, the linkage QTLs of marker RP145 and RP395 maybe have the function of increasing panicle length (qpl.) and increasing kilo-grains weight (qkw), respectively, the linkage QTL of marker ORS28 maybe have the function of reducing spikelets per panicle (qspp.) and/or decreasing the density of panicle (qdp.}; in the population of PA64S/GLA-F2, the linkage QTLs of marker RM204 and RP14 maybe have the function of reducing plant height (qph) and shorting flag leaf length (qfl.), respectively; in the population of NIPP/9311-F2, the linkage QTL of marker RP207 maybe have the function of increasing the number of tillering (qtn.) and/or increasing panicle number (qpn.); the linkage QTLs of marker RP164 and RM10 maybe play a role in advancing the heading date (qhd.) and increasing the number of panicle(qpn), respectively;...