Changdeng Yang

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid (DH) population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus (QTL) for three related traits of panicle-layer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniformity in two locations: Hangzhou (HZ) and Hainan (HN). A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH-4 and qTPH-8 were co-located with the QTLs for qLPH-4 and qLPH-8, which were only significant in the HZ environment, whereas the qTPH-6 and qLPH-6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD-10-1 and qPLD-10-2, were closely linked to qTPH-10, and they might have been at the same locus. One QTL, qPLD-3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD-3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD-3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.

Responses of Rice Genotypes Carrying Different Dwarf Genes to Fusarium moniliforme and Gibberellic Acid

Abstract A total of 32 rice genotypes carrying different dwarf or semi-dwarf genes were inoculated with the fungus Fusarium moniliforme Sheldon or treated with 50 mg l-1 GA3 in order to select resources resistant to rice bakanae disease from the dwarf materials. The length of the elongated seedlings was measured, and the percentage of death of the seedlings after transplanting to field was also counted. A significant correlation was found between the length of the seedling treated with GA3 and disease injury by bakanae fungus. Rice materials carrying dwarf gene such as sd1 were not only sensitivity to GA3 but also susceptive to rice bakanae disease. Materials carrying dwarf gene d1 were insensitive to GA3 but susceptive to bakanae. On the other hand, all materials carrying d29, sd6 or sdq(t) genes showed resistance to bakanae. The present study indicated that dwarf and semi-dwarf rice materials might be useful resources for improvement of bakanae resistance in rice breeding programs.

Mapping QTLs for heading synchrony in a doubled haploid population of rice in two environments.

Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid (DH) population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus (QTL) for heading synchrony related traits, i.e., early heading date (EHD), late heading date (LHD), heading asynchrony (HAS), and tiller number (PN). A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.

Comparison of physiological and yield traits between purple- and white-pericarp rice using SLs

Five physiological and eleven yield traits of two pairs of sister lines generated from a high generation with similar genetic background (SLs) for purple pericarp were investigated to explore the reasons behind low-yield production of colored rice. Of the five physiological traits examined, except grain anthocyanin content, there were generally similar trends between the P (purple-pericarp) lines and the corresponding W (white-pericarp) lines over two seasons (in the year 2009 and 2010 separately). The results demonstrated that the chlorophyll content of flag leaves, the net photosynthetic rate of flag leaves, and the grain anthocyanin content could be easily influenced by the environment. The physiological functions of the traits for the P lines were more active than those of the corresponding W lines in the year 2010. The grain anthocyanin content of the P lines was much greater in the year 2010 than in the year 2009 during the growth period. The investigation of yield traits revealed that the P lines had reduced 1000-grain weight, yield per plot and grain/brown rice thickness compared to the W lines. A difference comparison of these traits and a source-sink and transportation relationship analysis for these SLs suggested that small sink size was a key reason behind yield reduction of purple pericarp rice.

Pyramiding blast, bacterial blight and brown planthopper resistance genes in rice restorer lines

Abstract Rice blast, bacterial blight (BB) and brown planthopper (BPH) are the three main pests of rice. This study investigated pyramiding genes resistant to blast, BB and BPH to develop restorer lines. Ten new lines with blast, BB and/or BPH resistance genes were developed using marker-assisted selection (MAS) technique and agronomic trait selection (ATS) method. Only HR13 with resistance genes to blast, BB and BPH was obtained. In addition to blast and BB resistance, four lines (HR39, HR41, HR42, HR43) demonstrated moderate resistance to BPH, but MAS for BPH resistance genes were not conducted in developing these four lines. These data suggested that there were unknown elite BPH resistance genes in the Zhongzu 14 donor parent. A more effective defense was demonstrated in the lines with Pi1 and Pi2 genes although the weather in 2012 was favorable to disease incidence. Blast resistance of the lines with a single resistance gene, Pita, was easily influenced by the weather. Overall, the information obtained through pyramiding multiple resistance genes on developing the restorer lines is helpful for rice resistance breeding.

The way to a more precise sheath blight resistance QTL in rice

Rice sheath blight (ShB), caused by Rhizoctonia solani, leads to severe yield losses in many rice production areas worldwide. Resistance to rice ShB is a typical quantitative trait controlled by quantitative trait loci (QTLs). To identify the QTLs responsible for ShB resistance, phenotypes for ShB resistance have been surveyed in different individuals/lines in various mapping populations. The 0–9 rating system, based on the percentage of plant height (PH) above the water line with ShB symptoms, is extensively used in the evaluation of ShB in rice communities. By reviewing previous ShB-QTL-mapping studies, we found that the ShB disease score attained using the 0–9 system was inevitably affected by PH and resulted in the colocalization of QTLs for PH and ShB resistance, i.e., some of the PH-QTLs were mistaken as “ShB-QTLs” and had pleiotropic effects. These colocalizing “ShB-QTLs” are irrelevant to physiological ShB resistance and should not be targeted for utilization. We analyzed the ways in which PH affects ShB resistance through the 0–9 rating system and suggest solutions for improving the accuracy of QTL mapping for rice ShB resistance. We also developed the first physical map of the ShB-QTLs and PH-QTLs detected since 1995. This map will be useful in the marker-assisted selection of ShB-resistant QTLs. Under current circumstances, we believe that conventional breeding remains an effective approach for developing ShB-resistant varieties.

Fine mapping and candidate gene analysis of LM3 , a novel lesion mimic gene in rice

A rice lesion mimic mutant, lm3, was obtained by the mutagenesis of an indica cultivar, 93-11, using γ-ray radiation. Brownish lesions appeared on the leaves of lm3 at the young seedling stage and persisted until the ripening stage. The lm3 mutant was characterised by a shorter plant height and delayed heading compared with the wild-type 93-11. A genetic analysis indicated that the lesion mimic phenotype was controlled by a single recessive gene. Using simple sequence repeat (SSR) markers, the target gene LM3 was first located between marker RM5748 and RM14906 on chromosome 3. We then developed Insertion-Deletion (InDel) markers to fine-map LM3, and the locus was localised to a 29 kb region defined by two InDel markers, In12571 and In12600. Five ORFs were predicted in the candidate region, and DNA sequencing detected a single-nucleotide polymorphism (SNP) in the coding region of LOC Os03g21900. The SNP in the fourth exon (C in 93-11; T in lm3) of LOC_Os03g21900 results in the substitution of a proline (P) with a serine (S) at the 140th amino acid of the deduced uroporphyrinogen decarboxylase protein. We did not detect polymorphisms in the other predicted ORF regions between lm3 and 93-11. These results suggest that LOC_Os03g21900 is the most likely candidate gene for LM3.

Mapping resistant QTLs for rice sheath blight disease with a doubled haploid population

Abstract Sheath blight (SB) disease, caused by Rhizoctonia solani Kuhn, is one of the most serious diseases causing rice (Oryza sativa L.) yield loss worldwide. A doubled haploid (DH) population was constructed from a cross between a japonica variety CJ06 and an indica variety TN1, and to analyze the quantitative trait loci (QTLs) for SB resistance under three different environments (environments 1–3). Two traits were recorded to evaluate the SB resistance, namely lesion height (LH) and disease rating (DR). Based on field evaluation of SB resistance and a genetic map constructed with 214 markers, a total of eight QTLs were identified for LH and eight QTLs for DR under three environments, respectively. The QTLs for LH were anchored on chromosomes 1, 3, 4, 5, 6, and 8, and explained 4.35–17.53% of the phenotypic variation. The SB resistance allele of qHNLH4 from TN1 decreased LH by 3.08 cm, and contributed to 17.53% of the variation at environment 1. The QTL for LH (qHZaLH8) detected on chromosome 8 in environment 2 explained 16.71% of the variation, and the resistance allele from CJ06 reduced LH by 4.4 cm. Eight QTLs for DR were identified on chromosomes 1, 5, 6, 8, 9, 11, and 12 under three conditions with the explained variation from 2.0 to 11.27%. The QTL for DR (qHZaDR8), which explained variation of 11.27%, was located in the same interval as that of qHZaLH8, both QTLs were detected in environment 2. A total of six pairs of digenic epistatic loci for DR were detected in three conditions, but no epistatic locus was observed for LH. In addition, we detected 12 QTLs for plant height (PH) in three environments. None of the PH-QTLs were co-located with the SB-QTLs. The results facilitate our understanding of the genetic basis for SB resistance in rice.

Application of a simplified marker-assisted backcross technique for hybrid breeding in rice

Hybrid rice has contributed greatly to the self-sufficiency of the food supply in China. However, bacterial blight is a major disease that limits hybrid rice production in China. The study was conducted to develop an efficient breeding technique to improve the bacterial blight resistance in hybrid rice. A marker-assisted backcross breeding technique was adopted to improve HN189, an elite restorer line containing the Pi1 gene. This breeding technique was simplified to foreground selection with only one generation of backcrossing and background selection based on phenotypic selection. A novel bacterial blight resistance gene, Xa23, was introgressed into HN189. Two improved restorer lines, HBH145 (with one generation of backcrossing) and HBH146 (with two generations of backcrossing), were obtained that had a significant bacterial blight resistance advantage over HN189. The corresponding hybrid combination Tianyou H145 (Tianfeng A / HBH145) was certified one year earlier than Qianyou H146 (Qianjiang 1A / HBH146). The use of the marker-assisted backcross breeding technique with one generation of backcrossing and without background selection in rice breeding programs shortened the breeding period of the rice.

Combination of Eight Alleles at Four Quantitative Trait Loci Determines Grain Length in Rice.

Grain length is an important quantitative trait in rice (Oryza sativa L.) that influences both grain yield and exterior quality. Although many quantitative trait loci (QTLs) for grain length have been identified, it is still unclear how different alleles from different QTLs regulate grain length coordinately. To explore the mechanisms of QTL combination in the determination of grain length, five mapping populations, including two F2 populations, an F3 population, an F7 recombinant inbred line (RIL) population, and an F8 RIL population, were developed from the cross between the U.S. tropical japonica variety ‘Lemont’ and the Chinese indica variety ‘Yangdao 4’ and grown under different environmental conditions. Four QTLs (qGL-3-1, qGL-3-2, qGL-4, and qGL-7) for grain length were detected using both composite interval mapping and multiple interval mapping methods in the mapping populations. In each locus, there was an allele from one parent that increased grain length and another allele from another parent that decreased it. The eight alleles in the four QTLs were analyzed to determine whether these alleles act additively across loci, and lead to a linear relationship between the predicted breeding value of QTLs and phenotype. Linear regression analysis suggested that the combination of eight alleles determined grain length. Plants carrying more grain length-increasing alleles had longer grain length than those carrying more grain length-decreasing alleles. This trend was consistent in all five mapping populations and demonstrated the regulation of grain length by the four QTLs. Thus, these QTLs are ideal resources for modifying grain length in rice.