Shukun Jiang

Identification and Fine Mapping of qCTH4, a Quantitative Trait Loci Controlling the Chlorophyll Content from Tillering to Heading in Rice(Oryza sativa L.)

The chlorophyll content is one of the most important traits selected by breeders, and it is controlled by quantitative trait loci (QTLs) derived from natural variations in rice. We analyzed the QTL controlling chlorophyll content by using 94 RILs derived from a cross between 2 japonica rice cultivars, Lijiangxintuanheigu (LTH) and Shennong265 (SN265). Twenty-two QTLs controlling chlorophyll content at tillering stage, heading stage, and maturity stage were detected, respectively. Among them, Rice cv. LTH had a positive allele only at 1 locus (qCTH4) on chromosome 4. Further analysis indicated that the genetic effect of qCTH4 was the net effects within the period from tillering to heading. The QTL qCTH4 controlling chlorophyll content from tillering to heading locates between RM255 and RM349 on chromosome 4 with a LOD score 19.41, and the QTL qCTH4 explains 61.42% of phenotypic variation. In order to eliminate the influence of other QTLs, 1 single residual heterozygous plant, RH-qCTH4, was selected based on the genotypes of 114 Simple Sequence Repeat (SSR) markers. Using the segregating population derived from RH-qCTH4 by self-crossing, this region was narrowed down to an interval between RM3276 and RM17494 in an approximately 771kb target region. These results are useful for map-based cloning of qCTH4 and for marker-assisted selection of high photosynthetic efficiency variety.

Fine mapping of the quantitative trait locus qFLL9 controlling flag leaf length in rice

The morphological traits of leaves, such as size and shape, are major determinants of plant architecture and strongly affect high yield performance. To understand the molecular mechanism governing flag leaf length, we analyzed quantitative trait loci (QTLs) affecting flag leaf length by employing 176 F2 individuals derived from a cross between two japonica rice cultivars: Shennong265 (SN265) and Lijiangxintuanheigu (LTH). We identified qFLL3, qFLL6 and qFLL9 from this F2 population. Flag leaf length was increased by SN265 alleles at qFLL3 and qFLL6, but by LTH allele at qFLL9. In order to eliminate the influence of qFLL3 and qFLL6, one single residual heterozygous plant for qFLL9 region, RH-qFLL9, was selected based on the genotypes of 114 simple sequence repeat (SSR) markers and used as the parent of a segregating population. Using this segregating population of 889 plants, this region was narrowed down to an interval between RM24423 and RM24434. According to the rice annotation project database, there are 17 predicted genes in the 198-kb target region.

Development of a highly informative microsatellite (SSR) marker framework for rice (Oryza sativa L.) genotyping.

Abstract To select highly informative microsatellite markers (SSRs) and establish a useful genetic SSR framework for rice genotyping, 15 rice (Oryza sativa L.) cultivars including six indica varieties and nine japonica varieties were used to analyze the polymorphism information content (PIC) value of 489 SSR markers. A total of 1 296 alleles were detected by 405 polymorphic markers with an average of 3.2 per locus. The PIC value of each chromosome was ranged from 0.4039 (chromosome 2) to 0.5840 (chromosome 11). Among the two rice subspecies, indica (0.3685-0.4952) gave a higher PIC value than japonica (0.1326-0.3164) and displayed a higher genetic diversity. Genetic diversity of indica was high on chromosome 12 (0.4952) and low on chromosome 8 (0.3685), while that for japonica was high on chromosome 11 (0.3164) and low on chromosome 2 (0.1326). A SSR framework including 141 highly informative markers for genotyping was selected from 199 SSR markers (PIC > 0.50). Ninety-three SSR markers distributed on 12 chromosomes were found to be related to indica-japonica differentiation. Of these 93 pairs of SSR primers, 17 pairs were considered as core primers (all the japonica varieties have the same specific alleles, while the indica varieties have another specific alleles), 48 pairs as the second classic primers (all the japonica or indica varieties have the same specific alleles, while the indica or japanica varieties have two or more other specific alleles) and 28 pairs as the third classic primers (all the japonica and indica varieties have two or more alleles, but the specific alleles are different between japonica and indica). Thirty-two SSR markers were selected to be highly informative and useful for genetic diversity analysis of japonica varieties. This work provides a lot of useful information of SSR markers for rice breeding programs, especially for genotyping, diversity analysis and genetic mapping.

Comparison Between QTLs for Chlorophyll Content and Genes Controlling Chlorophyll Biosynthesis and Degradation in Japonica Rice

Abstract The objectives of this study were to understand the expression patterns of chlorophyll content-related genes at different growth stages of rice ( Oryza sativa L.) and to disclose the genetic mechanism of stay-green at later stage. Quantitative trait loci (QTLs) controlling chlorophyll content at tillering, heading, and maturity stages were located using 126 recombinant inbred lines (RILs) derived from a cross between 2 japonica rice cultivars, Shennong 265 and Lijiang Xintuanheigu. A total of 22 QTLs for chlorophyll content were identified, of which 5 loci were expressed at tillering stage, 7 at heading stage, and 10 at maturity stage. These QTLs were located on all the rice chromosomes except chromosome 5. According to the comparison between the locations of these QTLs and genes underlying the key enzymes of chlorophyll biosynthesis and degradation, relatively rich QTLs for chlorophyll biosynthesis and degradation at earlier stage were located in the regions harboring the loci for chlorophyll content. With the process of plant growth, more QTLs were detected but only a few of them were involved in chlorophyll biosynthesis and degradation. These results suggest that the expression levels of most genes/QTLs for chlorophyll biosynthesis or degradation were not different at earlier stage but the expression levels of specific key genes were increased at later stage. Therefore, the genetic basis for stay-green is proposed in 2 pathways: increase of transcripts for chlorophyll biosynthesis-related genes and decrease of expression for chlorophyll degradation genes.

Analysis of QTLs for Mesocotyl Length in Rice (Oryza sativa L.)

Abstract The objective of this study was to understand the genetic basis underlying the relationship between mesocotyl elongation and plant hormone gibberellin (GA) in rice (Oryza sativa L.). Using a recombinant inbred line (RIL) population derived from a cross between 2 japonica rice cultivars, Shennong 265 (long mesocotyl) and Lijiang Xintuan Heigu (short mesocotyl), quantitative trait loci (QTLs) for mesocotyl length were detected under both water and GA germination conditions. The treatment of 1.50 μmol L−1 of GA dramatically stimulated the mesocotyl elongation of rice. A total of 5 QTLs for mesocotyl length were identified on chromosomes 1, 2, 3, 6, and 11 under water and GA germination conditions, which accounted for 7–33% of the phenotypic variance, respectively. The LOD value of each QTL ranged from 3.65 to 15.52. Among the 5 QTLs, qML3, qML6, and qML11 were common in both germination conditions, whereas qML1 and qML2 were detected only under water germination condition. qML3 was usually detected in several experiments using different populations, indicating that it might be a major QTL for mesocotyl elongation of rice.

Optimization of a Reaction System of Sequence Related Amplified Polymorphism and Segregation of Polymorphic Loci in an F2 Population of Rice

An effective PCR protocol for detecting the sequence related amplified polymorphism (SRAP) in rice was developed. One hundred and ten pairs of SRAP primers were used for segregation analysis in an F2 population derived from a cross between Shennong 606 and Lijiangxintuanheigu. Among the 110 primer pairs, 35 pairs generated 143 polymorphic bands with an average of 4.09 polymorphic bands per primer pair, and 24 pairs (16.78%) showed the genetic distortion (P<0.05). Of the 24 primer pairs, 12 pairs deviated toward the male parent Shennong 606 and 11 pairs toward the female parent Lijiangxintuanheigu, only one toward heterozygote. It was found that the segregation distortion might be caused by the joint gametic and zygotic effects.

Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield

Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China.