Identification Of Tolerance Or Resistance Genes (QTLs)and Utilization For Breeding Based On Chromosome Single Segment Substitution Lines In Rice(Oryza Sativa L.)

In this research, we have generated92SSSLs using the two sequenced rice varieties (indica rice cultivar9311and japonica rice cultivar Nipponbare) as recurrent and donor parents, respectively. On this basis, cold tolerance and drought tolerance of rice, rice blast and false smut disease resistance were analyzed, and we identified several resistance genes (QTLs), and studied the application of those materials in rice breeding.The main results were as follows:1. We treated SSSLs and parents in the condition of4℃and13℃/7℃(day/night) at plumule and seedling stages respectively, and took Survival Seedling Rate (SSR%) and Normal Leaves Rate (NLR%) as the indexes for cold tolerance evaluation. As a result, the cold tolerance of Nipponbare was highly significant better than9311at both plumule stage and seedling stage, and the cold tolerance of different SSSLs was significantly different. The SSSLs, including X709, X712, X686, and X729, had a strong cold tolerance at the plumule stage, and the SSR>70.00%. The SSSLs (X404, X634, X649, X732, X733, and X738) had a strong cold tolerance at seedling stage, and the NLR>60.00%. Therefore, the introgression of japonica segments into those SSSLs could enhance its cold tolerance. X724and X733, which had a superior cold tolerance at both plumule stage and seedling stage, maintained the9311elite agronomic traits, meanwhile, have higher GCA of yield trait than9311. In this research, we totally identified17QTLs with cold tolerance at the plumule stage, and5QTLs with cold tolerance at the seedling stage, which were located on20segments distributed on12chromosomes. Among these, we detected a cold tolerance QTL at plumule stages and seedling stages simultaneously between RM519and RM17on chromosomes12; the QTLs with cold tolerance at the plumule stage (qCTP9, qCTP11.2, qCTP12.1) and the QTLs with cold tolerance at the seedling stage (qCTS1.1and qCTS1.2) had a significant additive effect, and the corresponding substitution lines had a strong cold tolerance at9311background.2. We evaluated the drought tolerance of the SSSLs and parents in field, and found that the plant height, grain number, effective panicle number, seed setting rate, grain weight and yield per plant of the SSSLs and parents were significantly decreased under the condition of drought stress, but the significantly differences for drought tolerance was found among different SSSLs. Taking the seed setting rate and yield per plant as drought tolerance evaluation indexes, we identified25SSSLs which had stronger drought tolerance than the parent9311. Among these, under the condition of drought stress, X705and X707had a>80%seed setting rate; the yield per plant of X633and X707reached more than14gram. Compared with normal irrigation, X707, X632, X630, X699and X666had a few yield losses under the condition of drought stress. Comparing to the CK9311, drought-resistant lines (X699, X705and X707) had elite agronomic performance and the GCA of yield-related traits, which could be used to breed drought-resistant hybrid rice.47QTLs related plant height, heading date, grain number, effective panicle number, seed setting rate and yield-related had been detected through t-test (P<0.001) between the SSSLs and recipient.31QTLs related drought tolerance were located at30regions on rice12chromosomes. Among these QTLs,13QTLs related plant height all had positive effects except qPH5.2and qRPH5,59QTLs related heading date, grain number, effective panicle number, seed setting rate and yield-related all had negative effect except for qDH10, qSN4, qRPN1.1, qRGY1. In addition, some segments contain multiple QTL loci affecting different traits, such as the region of RM16792-RM185on chromosome4, the region of RM421-RM31on chromosome5, the region of RM141on chromosome6, the region of RM410-RM201on chromosome9, the region of RM1261-RM519on chromosome12. These multiple QTLs in the same area, maybe have the pleiotropic effects or closely linked genes effect.3. We evaluated the disease resistance of the SSSLs and parents using "natural field induced" identification methods for the rice blast and false smut in Sichuan Province. The results showed that both the rice blast and false smut resistance of the donor parent Nipponbare were better than the receptor9311. The rice blast and false smut resistance varied between different substitution lines,37lines had strong rice blast resistance at Ya’an point, and the average disease spike rate was from3.17%to17.50%. X648, X565and X646had strong rice blast resistance at Pujiang point, and the average disease spike rate was from8.89%to15.65%, the identification results of the same material had a relative consistency in two points (r=0.325**). Substitution lines X411, X560, X496, X495, X509, X704and X441had a strong false smut resistance (disease spike rates all were0). The different resistance genes derived from Nipponbare caused different disease resistance although the substitution lines had the same background. Blast-resistance line X565had excellent agronomic traits with moderate plant height and heading date, longer spike and more grains, grain weight higher, higher seed setting rate and higher yield than the CK9311, additionally, all the GCA of grain number, seed setting rate and yield were higher than that of9311. Blast-resistance lines X656, X437, X697, X671and X701had excellent agronomic traits, with moderate heading date and plant height (the X701slightly higher), strong tillering (PN>4), large grain density (SN>200), high seed setting rate (SSR>90%), large grain weight (TGW>30g), and yield was higher than9311; X679, X723, X704, X705, X701, X656and X717had a strong yield-related combining ability, which could be used as materials to breed blast-resistant hybrid rice. Taking the disease spike rate as the value of the resistance phenotype,11QTLs for rice blast resistance and8QTLs for false smut resistance were detected, which were located on6,9,10,11chromosomes. Among these,17QTLs had negative effects, which corresponding introgression segments enhanced the resistance of substitution lines, and2QTLs had positive effects, which introgression segments decreased the resistance of substitution lines. Blast-resistance locus qBR1.3and qBR5were detected at two points, additive effects were-11.15,-30.74,-8.53,-27.41, respectively. False smut resistance QTL qFSR2and rice blast resistance QTL qBR2.1were located at the same substitution segment of the same substitution line, and both QTLs had negative effects, the blast and false smut disease spikes rate of corresponding substitution line X560were14.59%and0respectively, and were significantly decreased comparing to9311, qFSR9.1and qBR9also existed at the same substitution segment of the same substitution line, but the effect was adverse, the additive effect was2.82and-13.25respectively. Compared with9311, the false smut disease spike rate of substitution lines was increased by150.94%, the rice blast disease spike rate of substitution lines was reduced by89.32%.