Genetic dissection of grain nitrogen use efficiency and grain yield and their relationship in rice

Breeding for improved grain yield (GY) and grain nitrogen use efficiency (NUE) is an important objective of many rice breeding programs. A better understanding of the genetics of these two complex traits and their genetic relationship is required for more efficient breeding. This study reports the results of a linkage mapping study conducted for these two traits using 127 rice recombinant inbred lines (RILs) derived from the cross of Zhanshan 97/Minghui 63. Phenotypic data were collected under two nitrogen conditions in 2006 and 2007. For NUE, four and six QTLs were identified in 2006 and 2007, respectively. These QTLs were on chromosomes 1, 2, 6, 7 and 11. For GY, nine and five QTLs were detected on chromosomes 1, 2, 7 and 11 in 2006 and 2007, respectively. The phenotypic and genetic correlations between NUE and GY are positive and highly significant. Four genomic regions, including C86-C2340 on chromosome 1, RZ599-R1738 on chromosome 2, RZ471-C1023 on chromosome 7 and R3203-RM20a on chromosome 11, were found to contain QTLs for both NUE and GY. The effects of the co-located QTLs were in the same direction for NUE and GY, providing a genetic basis for the observed positive genetic correlation between the two traits. These genomic regions might be explored for the simultaneous improvement of NUE and GY in breeding.     

Association mapping of grain quality and flowering time in elite japonica rice germplasm

Grain quality traits play an important role in the economic prosperity of commercial rice markets. The objective of our research was to identify candidate molecular markers associated with three grain quality and flowering traits in a collection of elite rice japonica inbred lines evaluated in five U.S. states. Candidate marker effects were associated with the traits mapped within regions reported from previous QTL analyses while several new allelic interactions were also detected. Common markers for each trait were observed across two or more locations, and two-way interactions unique to a single location were also found. Significant genotype × location interactions were detected while broad-sense heritability estimates were low for all characters. All but one selected marker effect was associated with a reduction in apparent amylose content. A reduction in heading date at three locations was observed with one marker as a main effect or as a component of two-way interactions that mapped ∼ 5 cM from the Hd3a flowering locus. The majority of selected effects for head rice were associated with modest to substantial increases in value. Marker loci and their interactions identified in this study highlighted targeted regions for future association studies and marker-assisted breeding efforts of grain quality traits.     

Responses of SUB1 rice introgression lines to submergence in the field: Yield and grain quality

Prolonged submergence is a major constraint to rice production, affecting over 15 million ha in South and Southeast Asia and causing an annual yield loss of over US$ 600 million. This is because all the modern high-yielding rice varieties are sensitive to complete submergence. A major quantitative trait locus (QTL), SUB1, associated with submergence tolerance, was mapped on chromosome 9 and recently bred into popular rainfed lowland rice varieties sensitive of complete submergence, using marker-assisted backcrossing (MABC). Here, we assessed the impact of introgressing SUB1 into three rice varieties popular in farmers’ fields of South and Southeast Asia, Swarna, Sambha Mahsuri, and IR64, under control conditions as well as following submergence in the field. Under control conditions, no differences were observed between Sub1 introgression lines and their recurrent parents in grain yield or quality aspects. Submergence substantially delayed flowering and maturity, and reduced grain yield, shoot biomass, harvest index, and yield components across cultivars. The reduction in yield was more drastic in the sensitive varieties, particularly when submerged for longer duration (17 d). The significant decline in grain yield was mainly attributed to reductions in grain filling, number of grains per panicle, and grain weight. The SUB1 QTL is effective in conferring tolerance of submergence for about 12–17 d, depending on floodwater conditions. Sub1 introgression lines showed a yield advantage of up to 3.8 t ha⁻¹ and slightly better grain quality after submergence compared with their parents. Apparently, the introgression of SUB1 into popular varieties did not have any negative impact on their performance under control conditions but considerably enhanced their yield and grain quality following short-term submergence.     

Variation in rice quality of different cultivars and grain positions as affected by water management

A field experiment was conducted to study the effect of cultivar and grain position on rice quality under different water management treatments. Water treatments significantly affected all quality traits in the study, except alkali digestibility (AD). There were significant interactions of water treatment by grain position and genotype for brown rice rate (BRR), chalky grain rate (CGR) and amylose content (AC), and interactions of grain position by water treatment and cultivar for head milled rice rate (HMRR). The interaction of water treatment by genotype for protein content (PC) was also significant. Of all variance components, water treatment ranked the highest for PC. Similarly grain position was ranked the highest for AC, BRR, CGR and HMRR. In comparison with wet cultivation, plastic-film mulched cultivation had significantly lower BRR, HMRR, CGR and higher PC. There were marked differences in milled quality, appearance and AD among differently positioned grains within a spike. For appearance and PC, the difference between plastic-film mulched cultivation and wet cultivation was greater for upland rice than paddy rice. For milled and cooking–eating quality, the difference between plastic-film mulched cultivation and wet cultivation was greater for the good quality paddy rice than the upland rice and the poor quality paddy rice. In plastic-film mulched cultivation, top grains showed lower milled quality and PC. While in wet cultivation, the opposite result was seen. With the decrease in soil water content, BRR and appearance showed increased and decreased differences among grains within a spike, respectively. The results indicate the possibility of improving rice quality by use of better water management and suitable cultivars.     

Relationship of milled grain percentages and flowering-related traits in rice

The economic value of harvested rice is determined by the grain yield and the percentages of head rice (at least 3/4 the length of a head or kernel) and total milled rice. This study was conducted to determine the effects of flowering-related traits such as duration of flowering, rate of flowering, heading, and duration from heading to maturity on head rice and total milling percentages of rice. Flowering data, gathered for two years from 105 long grain rice genotypes grown in Beaumont, Texas were analyzed for their effects on and relationship with milling traits. A positive linear relationship was obtained for rate of flowering and the duration from heading to maturity but negative for duration of flowering and days to heading. Genotypes with early heading had relatively shorter flowering durations, and genotypes with shorter flowering duration had higher head rice and total milled rice. A faster rate in attaining 100% flowering and more days from heading to maturity were favorable in increasing head rice and total milled grains. The duration from the start of flowering to heading or to 100% flowering can be used in the evaluation and selection for high head rice and total milled rice percentages in rice.     

东乡野生稻苗期抗寒性QTL的初步定位

以9311/东乡野生稻F2群体为材料,用108对SSR标记构建连锁图谱,以苗期分蘖叶片相对电导率为抗寒性鉴定指标,采用完备区间作图法检测抗寒性QTL.结果在第3号和11号染色体上定位到2个与抗寒性相关的QTL qSCR3和qSCR11,其表型贡献率分别为16.3％和19.2％.     

QTL mapping for quality traits of northern-style hand-made Chinese steamed bread

QTLs for quality traits of northern-style hand-made Chinese steamed bread (CSB) were mapped based on recombinant inbred lines (RILs) derived from the cross between two Chinese winter wheat varieties, Chuang 35050 and Shannong 483. We detected eight putative QTLs for eight quality traits on seven chromosomes, 2B, 2D, 4A, 5B, 5D, 6B and 7B. The contributions of QTLs ranged from 9.88 to 64.87%. The additive effects of QTLs for color, elasticity, and stickiness were positive, with Chuan 35050 increasing the effects. Additive effects for volume, specific volume, appearance, smell, and total score were negative, with Shannong 483 increasing the effects. Two co-location QTLs were detected in the marker region Xgwm644–Xgwm193–Xgwm608b on chromosome 6B. The contributions of four QTLs for appearance, stickiness, smell and total score were very high (29.80–64.87%), indicating that these traits are controlled by major gene loci. The contribution of the smell QTL in Xissr25b–Xissr23b–Xwmc308–Xsrap7c on chromosome 4A was the highest (64.87%). We speculate that a major gene related to the smell or taste is located on chromosome 4A.     

Nucleotide polymorphisms in OsAGP genes and their possible association with grain weight of rice

ADP-Glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme participating in starch biosynthesis, which may be responsible for the filling rate and starch accumulation in the developing rice kernel. However, it is still unknown whether the naturally occurring variation in the sequence of ADP-Glucose pyrophosphorylase of rice (OsAGP) is related to the grain weight (GW). In this study, we discovered a total of 38 single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) in the partial sequences of six OsAGP isoform genes from 30 rice accessions with diverse agronomic traits. We then developed ten cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers for genotyping the SNPs and InDels for an association mapping population consisting of 416 rice accessions. Candidate gene association study indicated that an InDel of OsAGPL4 was associated with GW in two environments and an SNP of OsAGPL2 was associated with GW in one environment. Each gene marker only explained 1% of the variation of GW, thus it could be concluded that both genes contributed little to GW of rice. However, the markers identified in this study could be used for tagging other traits of interests and in molecular breeding.     

Grain filling duration,a crucial determinant of genotypic variation of grain yield in field-grown tropical irrigated rice

Grain filling, a crucial determinant of grain yield in cereal crops, is characterized by duration and rate of grain filling. This study aimed to (1) seek genotypic variations in grain filling duration and rate on area basis, (2) compare the contribution of grain filling duration and rate to grain yield and (3) examine the influence of temperature and solar radiation on grain filling duration and rate for effective grain filling period in the field-grown tropical irrigated rice. Six tropical genotypes were used in the 2004 dry season and wet season at the International Rice Research Institute (IRRI), Laguna, Philippines.     

Yield, grain quality and water use efficiency of rice under non-flooded mulching cultivation

Plastic film or straw mulching cultivation under non-flooded condition has been considered as a new water-saving technique in rice production. This study aimed to investigate the yield performance in terms of quality and quantity and water use efficiency (WUE) under such practices. A field experiment across 3 years was conducted with two high-yielding rice cultivars, Zhendao 88 (a japonica cultivar) and Shanyou 63 (an indica hybrid cultivar) and four cultivation treatments imposed from transplanting to maturity: traditional flooding as control (TF), non-flooded plastic film mulching (PM), non-flooded wheat straw mulching (SM), and non-flooded no mulching (NM). Compared with those under the TF, root oxidation activity, photosynthetic rate, and activities of key enzymes in sucrose-to-starch conversion in grains during the grain filling period were significantly increased under the SM, whereas they were significantly reduced under the PM and NM treatments. Grain yield showed some reduction under all the non-flooded cultivations but differed largely among the treatments. The reduction in yield was 7.3–17.5% under the PM, 2.8–6.3% under the SM, and 39–49% under the NM. The difference in grain yield was not significant between TF and SM treatments. WUE for irrigation was increased by 314–367% under the PM, 307–321% under the SM, and 98–138% under the NM. Under the same treatment especially under non-flooded conditions, the indica hybrid cultivar showed a higher grain yield and higher WUE than the japonica cultivar. The SM significantly improved milling, appearance, and cooking qualities, whereas the PM or the NM decreased these qualities. We conclude that both PM and SM could significantly increase WUE, while the SM could also maintain a high grain yield and improve quality of rice. The SM would be a better practice than the PM in areas where water is scarce while temperature is favorable to rice growth, such as in Southeast China.     

Genetic relationship between grain yield and the contents of protein and fat in a recombinant inbred population of rice

To study the genetic relationship between grain yield and the nutrient contents in rice, 209 recombinant inbred lines derived from a cross between indica rice Xieqingzao B and Milyang 46 were used to determine quantitative trait loci (QTLs) affecting the yields and contents of the two major nutritional components in brown rice. Seven traits were analyzed, including brown rice recovery (BRR), protein content (PC), fat content (FC), grain yield (GYD), brown rice yield (BRYD), protein yield (PYD) and fat yield (FYD). The nutrient contents were significantly negatively correlated with BRR, GYD and BRYD, and the variations on nutrient yield were mainly ascribed to GYD. A total of 22 QTLs distributed on 10 regions of eight chromosomes were detected. Two QTL clusters were found on the short arm of chromosome 6 and the long arm of chromosome 10, respectively. The former was responsible for all the seven traits, and the latter for all the traits except BRR and FC. In both regions, the maternal alleles decreased nutrient contents, but they increased the yields of grain, brown rice, protein and fat. Implication of these results for the breeding of rice varieties with enhancing nutritional capacity is discussed.     

QTL analysis of kernel size and shape in two hexaploid wheat mapping populations

Kernel size and shape in wheat are important because of their relationship with yield and milling quality. This paper reports QTL analyses of kernel morphology in two hexaploid wheat mapping populations, grown in NY and CA. Kernel morphology was evaluated through a new and improved method, combining measurements from two orthogonal pictures. Single marker regression showed that several genomic positions, scattered through the genome, were related to kernel size and shape, in both populations. The direction of allele effects was consistent between environments, although the LOD scores varied considerably. Composite interval mapping revealed QTLs on all seven homoeologous groups, considering both populations. For the QTLs detected through this method, the signal and magnitude of additive effects were similar between environments, indicating small QTL × environment interaction. In the population W7984 × Opata 85, the strongest signal was detected on the chromosome 5B, for kernel length. In the population AC Reed × Grandin, the most important QTLs were detected on chromosome 2D, affecting the lateral dimensions of the kernel. This study agreed with previous reports that the genetic control of kernel length and width are largely independent. Additionally, it was shown that QTLs detected on different mapping populations, with identical evaluation methods, can be very distinct.     

水稻粒形QTLs的研究进展

主要介绍了水稻粒形QTL的研究概况,包括水稻粒形性状的遗传特征,粒形QTL的研究进展,讨论了水稻粒形QTL定位与克隆在育种上的意义和前景。     

稻谷储藏时间对稻米品质影响的研究

2000年对储藏了3.5年的陈种与0.5年的新种稻谷米质变化进行了研究。结果表明，11个灿稻品种的陈种，其表观直链淀粉含量、热水不溶性直链淀粉含量基本稳定，但其粘滞性淀粉谱发生了显著变化；所有11个品种的起浆温度从平均的75.8℃增高到84.7℃，增幅为4.0-15.1℃；有10个品种的峰值粘度和崩解值下降，1个品种上升；热浆粘度、冷胶粘度和消碱值有升有降，品种之间存在差异。     

Effects of cultivar resistance and single fungicide application on rice sheath blight, yield, and quality

The increased number of sheath blight (Rhizoctonia solani)-resistant rice (Oryza sativa) cultivars available will allow producers to use less fungicide and avoid significant reductions in grain and milling yields. Among cultivars currently in cultivation in the southern United States, sheath blight resistance levels range from very susceptible to moderately resistant. A study was conducted to determine the response of cultivars, with different levels of susceptibility, to sheath blight inoculations and fungicide application and to determine the impact of sheath blight disease development on rice yield and quality. Sheath blight epidemics in field plots were initiated by inoculation at the panicle differentiation growth stage in 2006 and 2007. Azoxystrobin at 0.17 kg a.i. ha⁻¹ was applied at mid-boot. Inoculation significantly increased sheath blight severity and incidence and caused yield losses of 8% in moderately resistant cv. Jupiter to 40% in very susceptible cv. Trenasse. Milling yields were affected to a lesser extent. Fungicide treatments reduced sheath blight incidence and severity, regardless of cultivar except in Jupiter. Single azoxystrobin applications were effective in minimizing yield loss due to sheath blight in all cultivars.     

香米品质与微量元素含量特征关系的研究

采用“江永香稻”与、香稻80－66”两个香稻品种，在香稻产地与非产地同时进行大田试验，对其稻米、灌溉水与土壤中的11种微量元素含量与稻米品质各项指标进行了分析。结果表明：不同产地同一品种稻米品质与不同品种稻米品质存在明显差异；江永香米的Zn,Mn,Cr含量均比普通稻米及香稻80－66的含量高，香稻80－66香米中Zn含量也较普通稻米高。香米产地香米香味长期不退化，可能与灌溉水中Zn元素含量较高有关。     

QTL analysis of cold tolerance at seedling stage in rice (Oryza sativa L.) using recombination inbred lines

Cold tolerance at seedling stage of rice (Oryza sativa L.) is a favorable trait for the stable establishment in temperate and high-elevation areas. In the present study, 71 recombinant inbred lines (RIL) derived from the cross of Asominori (Japonica) and IR24 (Indica) were used to identify quantitative trait loci (QTL) affecting cold tolerance at seedling stage. The putative QTL was further confirmed using some chromosome segment substitution lines (CSSLs), in which IR24 was used as the donor parent and Asominori as the recurrent parent. The average seedling mortality was used as cold tolerance after cold treatment with 6 °C for 7 days and recovery culture with 25 °C for 4 days at three-leaf seedling stage. Three QTL affecting cold tolerance at seedling stage were detected on chromosomes 1, 5 and 6 with LOD scores ranging from 2.2 to 4.1 using composite interval mapping (CIM). Among them, qSCT-1 located in the region of XNpb87-2-C955 on chromosome 1 was a major QTL which explained 24.51% of total phenotypic variance and favorable allele came from japonica parent, Asominori. In addition, IR24 alleles at the other two loci (qSCT-5 and qSCT-6) increased cold tolerance. And these three QTL were confirmed by four lines from the IR24 CSSLs. Transferring favorable allele from japonica variety to indica background or pyramiding different QTL identified from indica is an effective way to improve cold tolerance of rice.     

Agronomic performance of rice breeding lines selected based on plant traits or grain yield

Selection for yield per se has greatly contributed to yield improvement in many crops. It is expected that selection based on plant traits is more effective in increasing crop yield potential. This study was conducted to compare the effectiveness of trait-based and yield-based selection in increasing rice yield and to determine whether lines with ideotype traits have the potential to express higher yield under optimal crop management conditions. Lines were selected based on plant traits or on grain yield measured in a breeder's replicated yield trial. The main target traits for selection were plant height, leaf and panicle morphology, grain size, total dry weight, and grain-filling percentage. Yield performance of trait-based selection was compared with that of yield-based selection in an agronomic trial with optimum crop management for three seasons. Trait-based selection increased leaf area index and total dry weight but reduced spikelet number per m² and harvest index compared with yield-based selection. Consequently, selection based on plant traits did not increase grain yield compared with selection based on yield per se. In one of the three seasons, yield of trait-based selection was significantly lower than that of yield-based selection. Among all tested breeding lines, maximum yield was produced by yield-based selection and minimum yield came from trait-based selection. These results suggest that lines with ideotype traits did not express higher grain yield than lines selected based on yield per se under optimal crop management conditions, and yield-based selection was as effective in increasing rice grain yield as trait-based selection in the late generations of the breeding cycle.