Investigation and genome-wide association study of grain copper content in Chinese common wheat

Copper is a necessary trace mineral for the human body, and its deficiency threatens human health. Here, a panel of 243 Chinese wheat cultivars from five replications was used to measure the grain copper content (GCC) by atomic absorption spectrometry. Phenotypic analysis results revealed that the averaged GCC of surveyed cultivars ranged from 6.81 to 11.36 mg/kg with an average of 9.23 mg/kg. A genome-wide association study (GWAS) indicated that a total of 489 single-nucleotide polymorphisms (SNPs) were significant, explaining 10.1%–32.6% of the phenotypic variation and were mainly distributed on chromosomes 2A and 5A. Further analysis indicated that GCC_Hap_2A1, GCC_Hap_3B1, and GCC_Hap_5A1 may be important genetic loci that regulate GCC in wheat. Linkage mapping using a bi-parental population detected four QTLs on 1D, 6A, 6B, and 7D, explaining 8.66%, 7.55%, 8.21%, and 4.71% of the phenotypic variation, respectively. Additionally, two of the significant SNPs were located on 1D, as detected by GWAS, and were within the interval of QGCC.hau-1D, suggesting that this locus plays an important role in regulating wheat GCC. This study dissected the genetic mechanism of GCC in wheat and provides useful information for the utilization of high-GCC wheat germplasm by marker-assisted selection in wheat quality breeding.     

Mapping QTLs for milling yield and grain characteristics in a tropical japonica long grain cross

Percent milling yield is an economically important trait of commercial rice because it largely determines the price that farmers receive for their crop. Analyzing 22 trait variables including milling yield, grain dimensions, chemistry and appearance, we identified 43 quantitative trait loci (QTLs) in a long grain japonica by long grain japonica cross. We report one QTL explaining 20% of the variation in brown rice recovery; two QTLs explaining 14% and 13% of the variation in milled rice recovery; and one QTL explaining 14% of the variation in head rice (HR) recovery. QTLs for the proportion of pre-broken brown rice kernels, seed density, amylose content, and kernel whiteness and chalkiness were found in the same region as the HR QTL. QTLs explaining up to 54% of the variation in grain shape measurements were identified and mapped to areas independent from those identified for milling yield. Analyses of grain appearance traits identified two QTLs for chalk in brown rice and one in head rice, and a QTL explaining up to 33% of the variance in green kernel area. Our results confirm previous findings on the multigenically complex nature of milling yield.     

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.     

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.     

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.     

QTL mapping of grain quality traits in rice

Grain quality improvement is one of the most important goals in a rice breeding program. An indica variety with small grain size was crossed to a japonica variety with large grain size to construct a set of recombinant inbred lines (RILs) which was used to identify quantitative trait loci (QTLs) controlling eight grain quality traits. Based on a linkage map of 185 SSR markers, a total of 16 QTLs were mapped on six chromosomes. A pleiotropic main effect QTL (M-QTL) flanked by RM3204 and RM16 on chromosome 3 influences the grain length (GL), length width ratio (LWR) and head rice ratio (HRR), explaining the phenotypic variation of 46.0, 36.1 and 29.7%, respectively. A total of 18 epistatic QTLs were identified for all the traits except MRR, distributed on all the chromosomes except chromosome 10. Two M-QTLs for GL and one M-QTL for GW were involved in epistatic QTL. No significant interaction between M-QTL or epistatic QTL and environment was detected except AC having significant M-QTL by environment interaction with minor effect. GL and LWR have a significant negative relation with HRR which might make it difficult to develop long grain with higher HRR in the rice breeding practice.     

Preliminary study on quality and storability of giant hybrid rice grain

Grain quality is one of the key targets for rice breeding. Two-meter-high giant rice, Xiangju-1, is a new high-quality restorer line of hybrid rice. Here, the grain quality and storability of three varieties Jufeng 5 (JF5), Jufeng 6 (JF6), and Jufeng 8 (JF8) were studied. The grain sizes of three giant hybrid rice varieties (JFs) were larger than that of the control rice Jingliangyou 1212 (1212). With respect to nutritional value, the three JFs varieties had similar protein content (~8%) but much higher fat content (>0.8%) than 1212. In addition, JF6 had better storability than JF8 when assessed by controlled deterioration treatment (CDT). RNA-seq analysis revealed that the heatmaps of differentially expressed genes in JF6 and JF8 were similar after 20 days of CDT when compared with 0 days. Of particular interest were the different mRNA levels of several genes related to the pathways of DNA damage response and abscisic acid biosynthesis in JF6 and JF8 after 20 days of CDT. Taken together, the data suggested that JF6 had better grain quality and storability than the other hybrid varieties, and several candidate genes for seed storability were identified.     

Genetic bases of source-,sink-,and yield-related traits revealed by genome-wide association study in Xian rice

The source-sink relationship determines the ultimate grain yield.We investigated the genetic basis of the relationship between source and sink and yield potential in rice.In two environments,we identified quantitative trait loci(QTL)associated with sink capacity(total spikelet number per panicle and thousand-grain weight),source leaf(flag leaf length,flag leaf width and flag leaf area),source-sink relationship(total spikelet number to flag leaf area ratio)and yield-related traits(filled grain number per panicle,panicle number per plant,grain yield per plant,biomass per plant,and harvest index)by genome-wide association analysis using 272 Xian(indica)accessions.The panel showed substantial variation for all traits in the two environments and revealed complex phenotypic correlations.A total of 70 QTL influencing the 11 traits were identified using 469,377 high-quality SNP markers.Five QTL were detected consistently in four chromosomal regions in both environments.Five QTL clusters simultaneously affected source,sink,source–sink relationship,and grain yield traits,probably explaining the genetic basis of significant correlations of grain yield with source and sink traits.We selected 24 candidate genes in the four consistent QTL regions by identifying linkage disequilibrium(LD)blocks associated with significant SNPs and performing haplotype analysis.The genes included one cloned gene(NOG1)and three newly identified QTL(qHI6,qTGW7,and qFLA8).These results provide a theoretical basis for high-yield rice breeding by increasing and balancing source–sink relationships using marker-assisted selection.     

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.     

Identification of CIMMYT spring bread wheat germplasm maintaining superior grain yield and quality under heat-stress

Unpredictable temperatures and rainfall associated with climate change are expected to affect wheat (Triticum aestivum L.) production in various countries. The development of climate-resilient spring wheat cultivars able to maintain grain yield and quality is essential to food security and economic returns. We tested 54 CIMMYT spring bread wheat genotypes, developed and/or released over a span of 50 years, in the field for two years under optimum sowing dates, as well as using two delayed sowing dates to expose crops to medium and severe heat-stress conditions. The grain yield and yield components were severely affected as the heat-stress increased. Two contrasting groups of 10 lines each were identified to determine the effect of heat-stress on bread-making quality. The first set included entries that produced high yields in optimal conditions and maintained higher yields under heat-stress (superior-yielding lines), while the second set included genotypes that did not perform well in the environment with high temperature (inferior-yielding lines). We identified genotypes exhibiting bread-making quality stability, as well as the quality traits that had higher correlation with the loaf volume in the environment without stress and under heat-stress. Of all the quality traits tested, dough extensibility (AlvL) and grain protein content had a significant influence in heat-stress adaptation. Most of the lines from the superior-yielding group were also able to maintain and even improve quality characteristics under heat-stress and therefore, could be used as parents in breeding to develop high-yielding and stable quality wheat varieties.     

Effect of high water temperature during vegetative growth on rice growth and yield under a cool climate

Global warming is likely to increase spring temperatures in regions with a cool climate. To examine the effects of this change on rice productivity, we exposed rice plants to a higher (by +2.7 to +2.8 °C) water temperature (T_w) during the vegetative growth period (for 35-50 days) under three levels of N fertilization. High T_w during vegetative growth made the heading stage occur 4-7 days earlier for all levels of N fertilization in both years. The crop growth rate during the treatment period was greatly enhanced by high T_w: by 51-82% in 2008 and by 49-62% in 2009. There was no T_w × N fertilizer interaction. This increased growth was associated with increased leaf expansion and increased canopy radiation capture rather than with increased radiation-use efficiency. However, the positive effect decreased during subsequent growth stages under all levels of N fertilization, leading to no significant differences in total biomass at maturity. High T_w during vegetative growth greatly reduced SPAD values during the grain-filling stage compared with SPAD values in the control T_w treatment, for all levels of N fertilization, and decreased leaf photosynthesis during the mid-grain filling stage. Grain yield was not significantly affected by high T_w at any N fertilizer level or in either year.     

不同向日葵品种群体光合生理参数及产量比较研究

以3个向日葵品种为材料,通过两年的田间试验研究向日葵群体的光合生理特征。结果表明,向日葵群体的叶面积指数（LAI）增长极快,出苗后第51d前后即达到最大值（LAImax）3.57～5.64,因品种而异。群体光合势与生物产量和子实产量呈极显著正相关。平均净光合率为5.08～7.02g/m2&;#8226;d,因品种和年份而异。生物产量积累动态趋势为“慢-快-慢”,符合Logistic方程。生物产量在各个器官中的分配比例一般为：茎秆（或子实）>子实（或茎秆）>叶片>葵盘>叶柄,子实所占比例即经济系数两年平均为29.7%和34.4%,因年份而异。早熟品种的经济系数大于中早熟和中熟品种。     

Responses of biomass growth and grain yield of midseason rice to the anticipated warming with FATI facility in East China

Crop model projections and historical data analyses have shown that global warming may cause serious decrease in crop productivity, however, many uncertainities remain on the impact quantification due to the unclear understanding of actual crop response. Therefore, we performed a three-year field warming experiment with free air temperature increase (FATI) facility to investigate the actual response of midseason rice growth in East China. There were four treatments (AW: all-day warming; DW: daytime warming; NW: nighttime warming; CK: ambient control) with three replicates. This FATI facility presented a good simulation of the local air temperature pattern with an increase in the daily mean temperature of about 1.1-2.0 °C during rice whole growth duration compared to the ambient control. Warming shortened the pre-heading phase respectively by 3.3 d, 1.7 d and 2.0 d in the AW, DW and NW plots, while the post-heading phase stayed almost unchanged. During the three years, warming slightly decreased the aboveground biomass by an average of 9.1%, 10.3% and 3.3%, and the grain yield by an average of 0.9%, 6.4% and 6.1% in the AW, DW and NW plots, respectively. Warming tended to decrease rice photosynthesis rate and stimulate the nighttime respiration rate. It also enlarged the flag leaf area and increased its chlorophyll content. No significant difference and interaction in the actual response of rice growth were found between the warming regimes. The above evidences suggest that the expected warming less than 2.0 °C may not cause significant decrease in rice productivity in East China.     

Effect of tolerance to Septoria tritici blotch on grain yield,yield components and grain quality in Argentinean wheat cultivars

Septoria tritici blotch (STB) caused by Zymoseptoria tritici (Mycosphaerella graminicola) is a major disease of wheat worldwide due to significant losses in grain yield and quality. Disease tolerance is the ability to maintain yield performance in the presence of disease symptoms. Therefore, it could be a useful tool in the management of the disease. Although it is known, that there is disease tolerance to STB in some wheat cultivars, this aspect has not been studied among Argentinean cultivars. The aims of this study were to evaluate genotypic differences in tolerance to STB among Argentinean cultivars, considering the relationship between the area under disease progress curve or the green leaf area or the non-green leaf area duration with the grain yield. In addition the effect of the disease on yield, yield components, test weight, grain protein concentration, wet and dry gluten concentration and the influence of tolerance on these traits was investigated. Field experiments were carried out with ten cultivars in a split-split-plot design during 2010 and 2011. Inoculation treatments were the main plots and cultivars, the subplots. STB significantly reduced grain yield, their components, test weight and increase grain protein and gluten concentration. Cultivar Baguette 10 showed major tolerance to STB, indicated by a consistent low regression slope between the green area duration and yield, while Klein Chaja was non-tolerant due to a high regression slope. However, many cultivars such as Buck Brasil, Buck 75 Aniversario, Klein Escorpion and Klein Flecha had considerably similar regression slopes to Baguette 10, provided good levels of tolerance. Other cultivars presented no significant differences. The correlation coefficient between tolerance and grain yield potential was not significant, suggesting that tolerant high-yielding cultivars can be obtained. No relationship was found between quality group or tolerance with the increase in protein and gluten concentration due to STB either.     

Possible alternative utilization of Cynara spp.: I. Biomass, grain yield and chemical composition of grain

Globe artichoke (Cynara scolymus L.) and cultivated cardoon (C. cardunculus L. var. altilis DC.) are horticulturally important crop plants. These species have potential as biomass and oilseed crops. We field tested, for 3 years, two artichoke and two cardoon cultivars and one wild cardoon (C. cardunculus L. var. sylvestris Lam.) population on the Sicilian plain of Catania (37°27′ N, 15°04′ E, 10 m a.s.l.). On a 3-year average, the dry aboveground biomass resulted about 31 t ha⁻¹ in both cultivated cardoons, 18.8 t ha⁻¹ in wild cardoon, 13.7 t ha⁻¹ in globe artichoke ‘3/10 V.S.’ and 9.9 t ha⁻¹ in globe artichoke ‘374’ F₁. The caloric values of aboveground biomass (except for seeds), which was not significantly different among genotypes, ranged between 16 005 and 17 028 KJ kg⁻¹ of dry matter. The cultivated cardoon ‘Gigante di Lucca’ had the greatest grain yield (on 3-year average, 2.6 t ha⁻¹), whereas the two globe artichokes had the lowest yield (on 3-year average, 0.5 t ha⁻¹). Regardless of genotypes and years, the grains contain 20.1% crude protein, 24.4% oil, 18.5% crude fiber and 4.1% ash (dry weight basis). The grains of globe artichokes showed the highest crude protein content (21.6%), whereas those of cardoons the highest oil content (25.2%).     

Effects of yield-related QTLs SPIKE and GPS in two indica rice genetic backgrounds

Recent progress in rice genomics has promoted the identification of quantitative trait loci (QTLs) associated with yield and its related traits. SPIKE, a QTL controlling spikelet number per panicle, and GPS, a QTL controlling leaf photosynthesis rate, were identical to NAL1. To assess the effect of SPIKE/GPS on yield potential, we compared DNA sequences of these alleles and conducted yield experiments in the field of Japan using the near-isogenic lines NIL-SPIKE (allele from Daringan in IR 64 genetic background), NIL-GPS (allele from Koshihikari in Takanari genetic background), and a chromosome segment substitution line, SL2115 (allele from Koshihikari in IR 64 genetic background). Despite the two SNPs in the promoter regions between Koshihikari and Daringan, both alleles were effective to increase the number of spikelets per panicle both in Takanari and IR 64 backgrounds. However, the extent of the increase was smaller and unstable in Takanari background than that in IR 64 background. In addition, SPIKE/GPS improved percentage of filled spikelets only in the IR 64 background. These results suggest that the effects of SPIKE/GPS alleles are similar but are affected by the difference of the genetic backgrounds. Because the increasing effect of spikelets number per panicle was canceled by the decrease of the number of panicles, which seems to be affected by environmental factors, none of NIL-SPIKE, SL2115, or NIL-GPS significantly out-yielded their parental cultivars. These results indicate the importance to consider genetic backgrounds and QTL-environment interaction toward the future use of SPIKE/GPS.     

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.     

磷对大豆不同品种产量和品质的影响

土壤盆栽试验表明,低磷处理下大豆品种的籽粒产量很低,籽粒中蛋白质含量高,脂肪含量低。施磷后大豆的产量极显著增加,但增产效果品种间差异也极显著。施磷大大降低籽粒中蛋白质和氨基酸含量,而增加脂肪含量;对脂肪酸组成中的油酸和亚油酸含量也有影响。     

Extreme nighttime air temperatures in 2010 impact rice chalkiness and milling quality

Research shows that elevated nighttime air temperatures (NTATs) contribute to increased chalk formation and reduced milling quality in rice. Arkansas rice-growing regions experienced exceptionally warm weather conditions during the summer of 2010, providing an opportunity to test this hypothesis under extreme conditions. Data from a previous study, conducted in years 2007-2009 (Ambardekar et al., 2011), was extended to include 2010 data, and analyzed to evaluate the correlations of 95th percentiles of NTAT frequencies (NT₉₅) occurring during reproductive (R) stages of six rice cultivars with chalk and peak head rice yields (pHRYs). Long-grain cultivars produced chalk values that were positively correlated to NT₉₅, and pHRYs that were inversely correlated, during the R5 through R8 stages. Medium-grain cultivars, Bengal and Jupiter, which in the original study showed little or no response to elevated NTATs during all R-stages, showed significant positive correlations between chalk, and negative correlations between pHRY, and NT₉₅, during the R7 and R8 stages. The 2007-2009 analyses indicated quadratic relationships of chalk with NT₉₅ and linear relationships of pHRY with NT₉₅. However, addition of the 2010 data indicated that both of these relationships were quadratic in nature. The extreme temperatures observed in 2010 also verified that while cultivars vary in their level of resistance to NTAT effects, all of the rice cultivars analyzed throughout the four-year study exhibited some degree of susceptibility to extreme NTAT temperatures occurring during critical grain-filling stages.     

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.