Li Zhikang

Genetic Background and Environmental Effects on QTLs for Sheath Blight Resistance Revealed by Reciprocal Introgression Lines in Rice

Abstract To detect quantitative trait loci (QTLs) for resistance to rice sheath blight (SB) that expressed stably in different genetic backgrounds and environments, the reciprocal introgression line populations derived from the cross of Lemont and Teqing (LT-ILs and TQ-ILs) were planted in the field in 2006–2007 and inoculated with isolate RH-9 of Rhizoctonia solani . Lemont was highly susceptible, whereas Teqing was moderately resistant to RH-9. The relative lesion height (a ratio of lesion height to plant height) of TQ-ILs was normally distributed, whereas that of LT-ILs was apparently inclined to the susceptible parent Lemont. A total of 10 main-effect QTLs (M-QTLs) and 13 epistatic QTLs (E-QTLs) conferring sheath blight resistance (SBR) were mapped using data obtained from different years and genetic backgrounds. Among them, 6 M-QTLs detected in 2006 were verified in 2007, suggesting that these M-QTLs had reliable performance across years. QRlh4 was the only M-QTL expressed under the reciprocal backgrounds. On chromosome 10, QRlh10a between RM216 and RM311 detected in TQ-ILs and QRlh10b between RM222 and RM216 detected in LT-ILs were regarded as different genes because their directions of additive effect were opposite. Most QTLs identified in TQ-ILs were not expressed in LT-ILs, indicating the presence of a significant effect of genetic background. By comparative mapping, 8 M-QTLs detected in this study were located in the same or near regions that were associated with SBR identified in the previous studies. These M-QTLs have great potential to be applied in rice breeding for SBR by marker-assisted selection (MAS), and M-QTLs expressed stably in different backgrounds are favorable for gene pyramiding in SBR improvement in rice.

Genetic Analysis of Cold Tolerance at Seedling Stage and Heat Tolerance at Anthesis in Rice (Oryza sativa L.)

A set of 240 introgression lines derived from the advanced backcross population of a cross between a japonica cultivar, Xiushui 09, and an indica breeding line, IR2061, was developed to dissect QTLs affecting cold tolerance (CT) at seedling stage and heat tolerance (HT) at anthesis. Survival rate of seedlings (SRS) and spikelet fertility (SF), the index traits of CT and HT, showed significant differences between the two parents under stresses. A total of four QTLs (qSRS1, qSRS7, qSRS11a and qSRS11b) for CT were identified on chromosomes 1, 7, 11, and the Xiushui 09 alleles increased SRS at all loci except qSRS7. Four QTLs for SF were identified on chromosomes 4, 5, 6, and 11. These QTLs could be classified into two major types based on their behaviors under normal and stress conditions. The first was QTL expressed only under normal condition; and the second QTL was apparently stress induced and only expressed under stress. Among them, two QTLs (qSF4 and qSF6) which reduced the trait difference between heat stress and normal conditions must have contributed to HT because of their obvious contribution to trait stability, and the IR2061 allele at the qSF6 and the Xiushui 09 allele at the qSF4 improved HT, respectively. No similar QTL was found between CT at seedling stage and HT at anthesis. Therefore, it is possible to breed a new variety with CT and HT by pyramiding the favorable CT- and HT-improved alleles at above loci from Xiushui 09 and IR2061, respectively, through marker-assisted selection (MAS).

QTL mining for sheath blight resistance using the backcross selected introgression lines for grain quality in rice.

QTLs for disease scale(DS),relative lesion height(RH) and plant height(PH) were mapped using the four introgression lines selected against grain quality from the four introgression populations between two elite varieties,IR64 and Teqing as recurrent parents and two tall varieties,Tarom Molaii and Binam with high grain quality and sheath blight resistance(SBR) as donors.DS had high significant positive correlation with RH,and both of them were significantly negatively correlated with PH.DS,RH and PH presented wide segregations even in the relative small(28-60) introgression populations,including some semid-warf plants segregated with overparent SBR.Ten,eight,eight,and six QTLs for the three traits were identified in IR64/Tarom Molaii,Teqing/Tarom molaii,IR64/Binam and Teqing/Binam,respectively by one way ANOVA analysis.The two donor alleles at most QTLs reduced DS and RH as well as increased PH.No any a common QTL for each of the three traits was detected in the populations of the same donor in the two different backgrounds,indicating there was a obvious genetic background effect on ex-pression of SBR-and PH-QTLs.QTLs linked to the same marker loci between PH and DS,and PH and RH accounted for 38% and 52% of total QTLs for the two traits,respectively,indicating SBR had tight relationship with PH and both of them shared some linked loci.As compared with the previous QTL mapping results of grain quality in the same populations,most QTLs for grain quality and SBR distributed in different chromosome regions and independently inherited.Efficiency,influencing factors and its application in breeding of QTL mapping for non-target traits using introgression lines selected against the target trait were deeply discussed,and importance of selective introgression lines in QTL mining and breeding use was also emphasized.

Advanced Backcross QTL Analysis for the Whole Plant Growth Duration Salt Tolerance in Rice (Oryza sativa L.)

Salinity is a major factor limiting rice yield in coastal areas of Asia. To facilitate breeding salt tolerant rice varieties, the whole-plant growth duration salt tolerance (ST) was genetically dissected by phenotyping two sets of BC2F5 introgression lines (ILs) for four yield traits under severe natural salt stress and non-stress filed conditions using SSR markers and the methods of advanced backcross QTL (AB-QTL) analysis and selective introgression. Many QTLs affecting four yield traits under salt stress and non-stress conditions were identified, most (>90%) of which were clustered in 13 genomic regions of the rice genome and involved in complex epistasis. Most QTLs affecting yield traits were differentially expressed under salt stress and non-stress conditions. Our results suggested that genetics complementarily provides an adequate explanation for the hidden genetic diversity for ST observed in both IL populations. Some promising Huanghuazhan (HHZ) ILs with favorable donor alleles at multiple QTLs and significantly improved yield traits under salt stress and non-stress conditions were identified, providing excellent materials and relevant genetic information for improving rice ST by marker-assisted selection (MAS) or genome selection.

Effect of Genetic Background on QTLs for Heading Date and Plant Height and Interactions Between QTL and Environment Using Reciprocal Introgression Lines in Rice

Expression of quantitative trait locus (QTL) is affected by genetic background (GB) and environment. The GB effect on QTL mapping and QTL by environment interaction for heading date (HD) and plant height (PH) were studied in Beijing and Hainan environments using a large set of reciprocal introgression lines (ILs) derived from a japonica rice (Oryza sativa L.) variety Lemont and an indica variety Teqing. In both environments, the 2 IL populations showed transgressive segregation for HD and PH traits. A total of 16 and 17 main-effect QTLs (M-QTLs) were identified for HD and PH, respectively. Among them, only 5 M-QTLs were detected under the 2 GBs, indicating that the expressions of most M-QTLs are specific to GB. Under both GBs, significant interactions between QTLs and environment responsible for HD were observed at 3 M-QTLs, of which QHd8a antedated heading for 2–3 d in Hainan but delayed heading for 2–3 d in Beijing. Therefore, QHd8a could be considered as an important M-QTL for HD. By comparing with the previous results on QTL mapping using another 7 populations derived from the same parents, a few M-QTLs were found to express stably under different GBs in various environments, such as QHd3, QHd8a, QPh3, and QPh4. These QTLs show applicable potential in marker-assisted breeding for HD and PH in rice.

Differential Expressions of Two-Component Element Genes in Rice Under Drought Stress

Abstract The objectives of this study were to gain insight into the temporal and spatial expression patterns of two-component system (TCS) genes in rice (Oryza sativa L.) under drought stress and to understand the relationship between TCS gene expression and drought resistance. Using a whole rice genome microarray, the expression profiles of TCS genes of rice lines with different drought resistance were analyzed at various growth stages. The TCS genes showed greatly difference of expression pattern in various organs but in similar patterns in the same tissues at different stages. Genes for type-A response regulator (RR), a negative regulator of cytokinin (CK) signaling, were mostly repressed by drought stress, whereas, genes for type-B RR with an opposite role to type-A RR were mostly induced by drought stress. These changes were supposed to be related to the enhancement of CK signaling under drought stress. This supposition was confirmed by the down regulation of ethylene receptor genes and the cross-talk of hormones under drought condition. The His kinase genes (HK5 and HK3) that are homologous to CK receptor genes (AHK2, AHK3, and CRE1) in Arabidopsis were induced by drought stress. However, HK6 homologous to AHK5 (CK-independent 2, CKI2) was repressed when exposed to drought stress. These results provided further confirmations of the above supposition. In drought resistant introgression lines and IR64, no significant differences of TCS gene expression profiles were observed under drought stress. This result indicates that the TCS genes are probably in relation to drought responsiveness.

Construction of the Primary Physical Map of Rice Chromosome 12

A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite markers on chromosome 12 by colony hybridization and polymerase chain reaction (PCR) amplification. A total of 59 contigs consisting of 419 BAC clones including 5 single-clones were physically aligned on rice chromosome 12 with the largest BAC contig covering 855 kb. The whole physical map had a size of ∼16 Mb and covered about 52% of rice chromosome 12. This physical map will be certainly helpful for map-based gene cloning of agronomically and biological important genes and understanding the genome structure of the chromosome.