Identification of quantitative trait loci affecting hemicellulose characteristics based on cell wall composition in a wild and cultivated rice species.

Cell wall hemicellulosic polysaccharides are structurally complex and diverse. Knowledge about the synthesis of cell wall hemicelluloses and their biological roles is limited. Quantitative trait loci (QTL) mapping is a helpful tool for the dissection of complex phenotypes for gene identification. In this study, we exploited the natural variation in cell wall monosaccharide levels between a common wild rice, Yuanj, and an elite indica cultivar, Teqing, and performed QTL mapping with their introgression lines (ILs). Chemical analyses conducted on the culms of Yuanj and Teqing showed that the major alterations are found in glucose and xylose levels, which are correlated with specific hemicellulosic polymers. Glycosidic linkage examination revealed that, in Yuanj, an increase in glucose content results from a higher level of mixed linkage ß-glucan (MLG), whereas a reduction in xylose content reflects a low level of xylan backbone and a varied arabinoxylan (AX) structure. Seventeen QTLs for monosaccharides have been identified through composition analysis of the culm residues of 95 core ILs. Four major QTLs affecting xylose and glucose levels are responsible for 19 and 21% of the phenotypic variance, respectively. This study provides a unique resource for the genetic dissection of rice cell wall formation and remodeling in the vegetative organs.

Identification of quantitative trait loci controlling drought tolerance at seedling stage in Chinese Dongxiang common wild rice (Oryza rufipogon Griff.).

Common wild rice (Oryza rufipogon Griff.) is the ancestor of cultivated rice (O. sativa L.), which has a greater genetic diversity and important traits that remain to be employed in cultivated rice. In this study, a set of introgression lines (BC4F5 and/or BC4F6) carrying various introgressed segments from common wild rice, collected from Dongxiang county, Jiangxi Province, China, in the background of an Indica (O. sativa L. ssp. indica) cultivar, Guichao 2, was used. A total of 12 drought-related quantitative trait loci (QTL) were identified by investigating drought tolerance of introgression lines under 30% PEG treatment at the young seedlings stage. Of these QTLs, the alleles of 4 QTLs on chromosome 2, 6 and 12 from Dongxiang common wild rice were responsible for increased drought tolerance of the introgression lines. In particular, a QTL qSDT12-2, near RM17 on chromosome 12, was consistently detected in different replications, and expressed stably under PEG stress throughout the study. It was also found that the QTLs located on different chromosomes might express at different stages.

Fine mapping of a quantitative trait locus for grain number per panicle from wild rice (Oryza rufipogon Griff.).

SIL040, an introgression line (IL) developed by introgressing chromosomal segments from an accession of Oryza rufipogon into an indica cultivar Guichao 2, showed significantly less grains per panicle than the recurrent parent Guichao 2. Quantitative trait locus (QTL) analysis in F2 and F3 generations derived from the cross between SIL040 and Guichao 2 revealed that gpa7, a QTL located on the short arm of chromosome 7, was responsible of this variation. Alleles from O. rufipogon decreased grains per panicle. To fine mapping of gpa7, a high-resolution map with 1,966 F2 plants derived from the cross between SIL040 and Guichao 2 using markers flanking gpa7 was constructed, and detailed quantitative evaluation of the structure of main panicle of each of F3 families derived from recombinants screened was performed. By two-step substitution mapping, gpa7 was finally narrowed down to a 35-kb region that contains five predicted genes in cultivated rice. The fact that QTLs for five panicle traits (length of panicle, primary branches per panicle, secondary branches per panicle, grains on primary branches and grains on secondary branches) were all mapped in the same interval as that for gpa7 suggested that this locus was associated with panicle structure, showing pleiotropic effects. The characterizing of panicle structure of IL SIL040 further revealed that, during the domestication from common wild allele to cultivated rice one at gpa7, not only the number of branches and grains per panicle increased significantly, more importantly, but also the ratio of secondary branches per panicle to total branches per panicle and the ratio of grains on secondary branches per panicle to total grains per panicle increased significantly. All these results reinforced the idea that gpa7 might play an important role in the regulation of grain number per panicle and the ratio of secondary branches per panicle during the domestication of rice panicle.

Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits.

Introgression lines (ILs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action or interaction in theoretical studies. A set of 159 ILs carrying variant introgressed segments from Chinese common wild rice (Oryza rufipogon Griff.), collected from Dongxiang county, Jiangxi Province, in the background of Indica cultivar (Oryza sativa L.), Guichao 2, was developed using 126 polymorphic simple sequence repeats (SSR) loci. The 159 ILs represented 67.5% of the genome of O. rufipogon. All the ILs have the proportions of the recurrent parent ranging from 92.4 to 99.9%, with an average of 97.4%. The average proportion of the donor genome for the BC(4)F(4) population was about 2.2%. The mean numbers of homozygous and heterozygous donor segments were 2 (ranging 0-8) and 1 (ranging 0-7), respectively, and the majority of these segments had sizes less than 10 cM. QTL analysis was conducted based on evaluation of yield-related traits of the 159 ILs at two sites, in Beijing and Hainan. For 6 out of 17 QTLs identified at two sites corresponding to three traits (panicles per plant, grains per panicle and filled grains per plant, respectively), the QTLs derived from O. rufipogon were usually associated with an improvement of the target trait, although the overall phenotypic characters of O. rufipogon were inferior to that of the recurrent parent. Of the 17 QTLs, 5 specific QTLs strongly associated with more than one trait were observed. Further analysis of the high-yielding and low-yielding ILs revealed that the high-yielding ILs contained relatively less introgressed segments than the low-yielding ILs, and that the yield increase or decrease was mainly due to the number of grain. On the other hand, low-yielding ILs contained more negative QTLs or disharmonious interactions between QTLs which masked trait-enchancing QTLs. These ILs will be useful in identifying the traits of yield, tolerance to low temperature and drought stress, and detecting favorable genes of common wild rice.

[Isolation and analysis of a novel MYC gene from rice].

A MYC (Myelocytomatosis) transcription factor gene, OsMYC, was cloned in rice (Oryza sativa L.). The putative protein of the OsMYC gene has a typical DNA binding domain: basic/helix-loop-helix (bHLH) motif at the C-terminus. Its nucleocide sequnce has 78%, 48%, 46% identity with that of the AtMYC2, MYC7E and PG1 genes, respectively. The identity of deduced amino acid between OsMYC and AtMYC2, MYG7E and PG1 is 95%, 84%, and 77% in the bHLH domain, and that is 81%, 54% and 52% in the N-terminus conserved region. The identity is 100% in the nuclear localization signal between them. Phylogenetic comparisons revealed that the OsMYC protein was related to the Arabidopsis AtMYC2, Zea MYC7E and Phaseolus vulgaris PG1. OsMYC gene was expressed at high level in stem, but low level in leaf and root and can be induced by ABA and Fe3+, which is similar to the expression pattern of MYC7E and RAP1 genes. Thus, this gene is a new member of the rice MYC family.

[Mapping QTLs controlling vascular bundle and panicle-related traits from Yuanjiang common wild rice (Oryza rufipogon Griff.)].

An advanced backcross population (BC3F2), derived from the cross between Yuanjiang common wild rice as the donor parent and Teqing as recurrent parent, was used to map QTLs controlling the number of vascular bundle and panicle-related traits from Yuanjiang common wild rice. Seven QTLs controlling the number of large vascular bundles in peduncle were detected on chromosome 1, 2, 3, 4, 7 and 10. Five QTLs for the number of small vascular bundles in peduncle were mapped on chromosome 1, 2, 3, 4 and 8. A total of 15 QTLs for the number of primary and secondary rachis branches and spikelets per panicle were identified on all chromosomes except chromosome 11 and 12. Most of alleles derived from O. rufipogon Griff. showed negative effect that reduced significantly vascular bundle, rachis branches and spikelets per panicle, suggesting that during the evolution from common wild rice to cultivated rice, favorable alleles were retained while removed undesirable ones. Most of QTLs controlling vascular bundle, rachis branches and spikelets per panicle showed cluster form or close linkage on chromosomes. The directions of their additive effects were consistent, which explained the genetic basis of significant correlation of their phenotypic characters. All the information suggested parallel evolution relationship among these traits.

[Identification of quantitative trait loci controlling plant height and days to heading from Yuanjiang common wild rice (Oryza rufipogon Griff.)].

An advanced backcross strategy was used to identify quantitative trait loci (QTLs) associated with plant height and days to heading in the BC3F2 population derived from an accession of common wild rice (Oryza rufipogon Griff.) from Yuanjiang in Yunnan Province of China, as the donor, and an elite Indica cultivar "Teqing", as the recipient. Based on analyses of 116 SSR markers distributed throughout the rice genome and by using single-point analysis, four putative QTLs derived from O. rufipogon were detected for plant height on chromosome 1, and 6 QTLs for days to heading on chromosome 1, 3, 7, 8 and 11. All Alleles of QTLs for plant height from O. rufipogon could increase plant height of the backcross population. One QTL near RM104 on chromosome 1, explaining 27% and 28% of phenotypic variance and additive value reached 26.24 cm and 26.28 cm respectively in Beijing and Hefei, was detected. The location of this QTL is corresponding to sd-1. One QTL near the marker RM25 on chromosome 1, explaining 13% and 15% of phenotypic variance was identified. The additive value of this QTL reached 4.60 days and 3.65 days respectively in Beijing and Hefei, and the allele from O. rufipogon could delay the backcross population's days to heading.

[Pyramiding of senescence-inhibition IPT gene and Xa23 for resistance to bacterial blight in rice (Oryza sativa L.)].

Transgenic lines (GC-1) carrying a senescence-inhibition cheimeric gene, IPT (isopentenyl transferase) gene, CBB23, a isogenic lines carrying Xa23 gene for resistance to bacterial blight, and Hexi15, a commercial cultivar showing high resistance to blast disease, were used as donors to pyramid IPT gene and Xa23 by marker-assisted selection (MAS). Seventeen BC1F1 plants pyramiding Xa23 gene and IPT genes were obtained from three multi-cross combinations. Then, the plants carrying Xa23 and IPT genes were crossed with parental lines of two-line hybrid rice, such as 9311, E32, Pei' ai 64S and W9834S. The progenies were backcrossed the acceptor parents. A total of 17 plants carrying Xa23 and IPT genes were detected by PCR, disease resistance identification and analysis of CTK contents of in the four combinations of "(9311///Hexi15/CBB23// GC-1) x 9311", "(E32///Hexi15/CBB23//GC-1) x E32", "(Pei'ai 64S///Hexi15/CBB23//GC-1) x Pei' ai 64S" and "(GC-1/CBB23//W9834S/Hexi15) x W9834S". These plants showed resistance to blast disease by inoculating test using 21 the lines of Pyricularia grisea from Northern China. Six plants of BC2F1 pyramiding Xa23 and IPT genes were further obtained in the combinations of "[(9311///Hexi15/CBB23//GC-1) x 9311] x 9311", "[(E32///Hexi15/CBB23//GC-1) x E32] x E32". After backcrossed and self-crossed 1 approximately 2nd, the plants pyramiding Xa23 and IPT genes can be used in the program of hybrid rice breeding.