Tao Chen

QTL Mapping for Grain Size Traits Based on Extra-Large Grain Rice Line TD70

Abstract Grain size traits, including grain length, grain width and grain thickness, are controlled by quantitative trait loci (QTLs). Many QTLs relating to rice grain size traits had been reported, but their control mechanisms have not yet been elucidated. A recombinant inbred line (RIL) population of 240 lines, deriving from a cross between TD70, an extra-large grain size japonica line with 80 g of 1000-grain weight, and Kasalath, a small grain size indica variety, were constructed and used to map grain size QTLs to a linkage map by using 141 SSR markers in 2010 and 2011. Five QTLs for grain length, six for grain width and seven for grain thickness were detected distributing over chromosomes 2, 3, 5, 7, 9 and 12. Seven QTLs, namely qGL3.1 , qGW2 , qGW2.2, qGW5.1 , qGW5.2 , qGT2.3 and qGT3.1 , were detected in either of the two years and explained for 56.19%, 4.42%, 29.41%, 10.37%, 7.61%, 21.19% and 17.06% of the observed phenotypic variances on average, respectively. The marker interval RM1347–RM5699 on chromosome 2 was found common for grain length, grain width and grain thickness; qGL3.1 and qGT3.1 were mapped to the same interval RM6080–RM6832 on chromosome 3. All 18 QTL alleles were derived from the large grain parent TD70. Most of the QTLs mapped in the present study were found the same as the genes previously cloned ( GW2 , GS3 or qGL3 , GW5 and GS5 ), and several were the same as the QTLs ( GS7 and qGL-7 ) previously mapped. Three QTLs, qGL2.2 on chromosome 2, qGW9 and qGT9 on chromosome 9, were first detected. These results laid a foundation for further fine mapping or cloning of these QTLs.

Transferring Translucent Endosperm Mutant Gene Wx-mq and Rice Stripe Disease Resistance Gene Stv-bi by Marker-Assisted Selection in Rice (Oryza sativa)

A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-bi and a translucent endosperm mutant gene Wx-mq. From F2 generations, a sequence characterized amplified region (SCAR) marker tightly linked with Stv-bi and a cleaved amplified polymorphic sequence (CAPS) marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.

Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (Oryza sativa)

Abstract Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelin-content gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.

Development of New InDel Marker to Detect Genotypes of Rf-1a Conferring Fertility Restoration of BT-Type Cytoplasmic Male Sterility in Rice

Restorer line breeding is an important approach to enhance the heterosis and improve the yields of japonica hybrid rice. To improve the selection efficiency of restorer lines for BT-type cytoplasmic male sterility (CMS) in japonica rice, a functional marker InDel-Rf-1a based on the difference of nucleotide sequence in Rf-1a locus between BT-type CMS lines and restorer lines was developed to detect the genotypes of different rice materials. Conventional indica rice varieties, restorer and maintainer lines without 574 bp deletion could restore the fertility for BT-type CMS in japonica rice. By contrast, most conventional japonica rice varieties except Aichi 106 and Yijing 12, with genotype of rf-1arf-1a showed the 574 bp deletion maintained sterility for BT-type CMS lines. To further verify the effect of genotyping detection in Rf-1a locus, this marker was also used to amplify the genomic DNA in different japonica rice restorer lines, CMS lines, hybrids and F2 segregation population, and three genotypes in Rf-1a locus could be distinguished distinctly. Therefore, the marker InDel-Rf-1a could be widely used for genetic identification and marker-assisted selection (MAS) in breeding japonica restorer lines.

Detection of QTL for Cold Tolerance at Bud Bursting Stage Using Chromosome Segment Substitution Lines in Rice (Oryza sativa)

The cold tolerance at the bud bursting stage (CTB) was evaluated at 5°C by using a set of 95 chromosome segment substitution lines (CSSLs) derived from an indica rice 9311 and a japonica rice Nipponbare with a genetic background of 9311. The result showed that six CSSLs had slightly stronger effect on CTB than 9311. Total four quantitative trait loci (QTLs) for CTB were preliminary mapped on chromosomes 5 and 7 by substitution mapping. qCTB-5-1, qCTB-5-2 and qCTB-5-3 were mapped in the region of RM267–RM1237, RM2422–RM6054 and RM3321–RM1054, which were 21.3 cM, 27.4 cM and 12.7 cM in genetic distance on rice chromosome 5, respectively. qCTB-7 was mapped in a 6.8-cM region of RM11–RM2752 on rice chromosome 7.

A novel semidwarf mutant 02428ha in rice is caused by reduced gibberellin sensitivity

The rice (Oryza sativa L.) elongated uppermost internode (eui) gene effectively results in a recessive tall plant type. In eui background, we found a mutant 02428ha that exhibited a semidwarf phenotype. Because semidwarf varieties possess high yield potential, this mutant may be useful for hybrid rice breeding. The present study aimed to characterize the dwarfing mechanism in the mutant. Microscopic observation revealed that the cell length in the uppermost internode was reduced compared to the wild type. The mutant showed a decreased sensitivity to exogenous gibberellin A3 (GA3) and gibberellin (GA) biosynthesis inhibitor, uniconazole. Meanwhile, it contained a high level of endogenous gibberellin A1 (GA1). These results indicated that the semidwarf phenotype of 02428ha was caused by impairment of GA signal transduction rather than by block in GA biosynthesis. Furthermore, expression analysis of genes involved in the GA signaling pathway showed that transcript of GIBBERELLIN INSENSITIVE DWARF2 (GID2) was down-regulated in the mutant. Sequence analysis also revealed a 15-base pair (bp) insertion between base 594 and 595 in the coding region of GID2. Consequently, the reason for down-regulation expression of GID2 or sequence variation of GID2 might play roles in the phenotype of 02428ha.

Research progress on the breeding of japonica super rice varieties in Jiangsu Province, China

Abstract In this study we report the results of a decade-long breeding program for japonica super rice made by Nanjing Branch of Chinese National Center for Rice Improvement in Jiangsu Academy of Agricultural Sciences. We concluded that selection of parents with good comprehensive traits and complementary advantages and disadvantages of both parents in the hybrid combination, and early selection of high heritability traits in earlier segregating generations could significantly improve the breeding efficiency. The use of closely-linked functional markers in pyramiding of multiple genes could greatly increase breeding efficiency, avoiding time-consuming and laborious steps that were used in traditional breeding program. It is also important to coordinate the yield components with variety characteristics such as yield stability, wide adaptability, lodging resistance, and an attractive grain appearance during late growth stage of rice.

Substitution mapping of QTL for panicle exertion using CSSL in rice (Oryza sativa L.)

Panicle exertion, the distance between the leaf cushion of flag and the neck-panicle node, is an important morphological trait, which has significant impact on hybrid seed production of rice. In this study, 94 chromosome segment substitution lines (CSSL), derived from 9311/Nipponbare with 9311 as the recurrent parent, were used to analyze quantitative trait loci (QTL) controlling the panicle exertion. The results showed that 17 CSSL contained QTL for the panicle exertion. Using substitution mapping, 8 QTLs were mapped on rice chromosomes 2, 3, 7, 8, 9, and 11, respectively. The QTL additive effect ranged from 0.10 to 3.20, and the additive effects of qPE-9 and qPE-11 were 3.15 and 2.95, respectively, showing the feature of a major gene. In addition, qPE-2-2, qPE-3-1, qPE-3-2, qPE-7, and qPE-8 were mapped in a marker interval less than 10.0 cM. Mapping of the QTL has laid a foundation for improving the panicle exertion with marker-assisted selection and cloning of the QTL in rice.

Genetic Analysis and Mapping of glup-t Gene for 57H Mutant in Rice: Genetic Analysis and Mapping of glup-t Gene for 57H Mutant in Rice

谷蛋白是水稻胚乳中主要的贮藏蛋白，约占总蛋白的80%。谷蛋白最初在粗糙内质网表面以57 kD前体的形式合成，这些前体经加工转运等过程，最终沉积在第二类蛋白体PB-II中，裂解为成熟的酸碱性亚基。任一谷蛋白转运步骤的缺陷都有可能导致谷蛋白57 kD前体的积累，形成谷蛋白前体增加突变体，即57H突变体。细老鼠牙是一个57H自然突变体，其57 kD谷蛋白前体增加而相应的37~39 kD酸性和22~23 kD碱性亚基减少，此外，该突变体还表现为13 kD醇溶蛋白大大增加。本研究以细老鼠牙与武运粳7号、02428杂交获得的F 2 群体为材料，对57H突变体进行遗传分析和基因定位，结果表明，细老鼠牙的57H突变性状受1对隐性核基因控制，暂命名为 glup-t 。利用简单重复序列(simple sequence repeat, SSR)、插入缺失(insertion deletion, Indel)和酶切扩增多态性序列(cleaved amplified polymorphic sequence, CAPS)等分子标记的方法，将该突变基因 glup-t 定位在水稻第4染色体长臂上的CAPS4-3与Indel4-7、Indel4-8之间，遗传距离均为0.26 cM。