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 mapping for crude protein and protein fraction contents in rice (Oryza sativa L.)

Improvement of rice storage proteins is important in rice breeding for high nutritional quality. Seventy-one recombinant inbred lines (RIL) derived from a cross between japonica variety Asominori and indica variety IR24 were used to study the inheritance of crude protein and protein fraction contents in rice. A total of 16 QTL were identified and mapped on eight chromosomes. Several QTL affecting contents of different protein fractions were mapped in the same chromosomal region. In particular, two QTL with a significant contribution were identified to simultaneously affect prolamin and glutelin contents. One QTL denoted as qCP-12 affecting crude protein content (CP) was located in the same region as QTL qGLT-12 affecting glutelin content, in agreement with the positive correlation between glutelin level and protein content. QTL with larger genetic effects were further confirmed using two sets of chromosome segment substitution lines (CSSL), where Asominori and IR24 were used as the recurrent parents. By QTL comparative analysis, two QTL for CP, three for globulin content and one for prolamin content were located in the vicinity of CP QTL previously identified in polished rice. Application of these results in rice breeding is discussed.     

Inheritance of flour paste viscosity is associated with a rice Waxy gene exon 10 SNP marker

Apparent amylose content is a key element for characterizing a rice (Oryza sativa L.) cultivar for cooking quality. However, cultivars with similar apparent amylose content can have widely varying quality attributes, including major parameters of flour paste viscosity. It has been postulated that the presence of a rice Waxy gene single nucleotide polymorphism (SNP) marker is associated with elevated Rapid Visco Analyser (RVA) properties in specific high amylose rice cultivars. A mapping population derived from a cross between two varieties, Cocodrie and Dixiebelle, having similar high apparent amylose contents, but with different paste viscosity properties and Waxy gene markers was analyzed for the genetic segregation of various pasting properties, measured with RVA instrumentation. Marker inheritance analyses revealed that the Waxy exon 10 SNP marker was associated with the proportion of soluble to insoluble apparent amylose and most RVA pasting measurements. Waxy gene markers can be used to efficiently improve the selection of rice with desirable characteristics, particularly for superior parboiling and canning quality.     

Positional variations in phytic acid and protein content within a panicle of japonica rice

Six japonica rice cultivars differing in phytic acid and protein content were used to investigate the effect of grain position in the panicle on grain weight, phytic acid and protein content. There were significant differences in grain weight, albumin, globulin, prolamin, glutelin, and total protein content among the grains within a panicle for all six cultivars, but no differences were found for phytic acid content. An effect of grain position between primary rachises on grain weight and protein content was clearly detected, while that among top, middle and bottom rachis showed a greater change, varying with the cultivar. Albumin and globulin contents tended to be lower in the grains on the primary rachis than in those on the secondary rachis, and glutelin and total protein contents showed the opposite trend in the three cultivars with lower protein content. There was no significant correlation between phytic acid and protein content in the different grain positions within a panicle. The accumulation of phytic acid and protein during grain development appears to be independent.     

Influence of high temperature during filling period on grain phytic acid and its relation to spikelet sterility and grain weight in non-lethal low phytic acid mutations in rice

Low phytic acid (lpa) crop is considered as an effective strategy to improve crop nutrition. However, the inferior agronomic performance of lpa crops and their environmental growth adaptation have not yet been fully understood. Three rice lpa lines and their corresponding wild-types were used to compare their differences in grain phytic acid (PA) in response to high temperature (HT) and its relation to spikelet sterility and grain weight at a controlled temperature at the filling stage. Results showed that HT caused an increase in grain PA and inorganic phosphate contents, with more substantial increase of PA content for lpa lines compared with corresponding wild-types. This increase in PA content in high temperature-ripened grains was not simply attributed to the reduction in grain weight and relatively enhanced proportion of aleurone-layer fraction to whole grains. Significant increase in PA contents was also detected in milled rice. Moreover, spikelet sterility and grain plumpness of lpa lines were more susceptible to HT stress than those of wild-types. Exogenous PA spraying with an appropriate concentration could increase grain PA content, but it had only a slight contribution to the enhancement of heat-tolerance and injury alleviation for rice exposed to stressful HT.     

The difference in amylose content within a panicle as affected by the panicle morphology of rice cultivars

The variation of amylose content (AC) among grains within a panicle and its relation to panicle morphology were investigated using 44 japonica rice cultivars differing in grain density (GD), panicle bending degree (BD) and palatability. Morphological traits of the rice panicle were poorly associated with mean grain AC on the average of the whole panicle, but closely related to AC variation and spatial distribution within a panicle, with the compact-panicle cultivars (GD>6.5 grain/cm and BD< 30°) having greater variation than loose-panicle cultivars (GD<6.0 grain/cm and BD>70°). The extent of AC differences among the rachides within a panicle was also cultivar-dependent, and greater differences were found between middle and top rachides for the compact-panicle cultivars, and between middle and bottom rachides for the loose-panicle cultivars. The difference in spatial distribution of AC variation between Bing110 (a compact-panicle cultivar) and XS11 (a loose-panicle cultivar) indicated that grains with low AC were principally distributed on interior rachis of middle branches for Bing110, but on bottom-rachis for XS11. Such a distribution is basically associated with the difference in the timing procedure of floret initiation and development, and final grain weight.     

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.     

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 analysis and validation of quantitative trait loci associated with reproductive-growth traits and grain yield under drought stress in a doubled haploid line population of rice (Oryza sativa L.)

Drought is a major constraint for rice production and yield stability in rainfed ecosystems, especially when it occurs during the reproductive stage. Combined genetic and physiological analysis of reproductive-growth traits and their effects on yield and yield components under drought stress is important for dissecting the biological bases of drought resistance and for rice yield improvement in water-limited environments. A subset of a doubled haploid (DH) line population of CT9993-5-10-1-M/IR62266-42-6-2 was evaluated for variation in plant water status, phenology, reproductive-growth traits, yield and yield components under reproductive-stage drought stress and irrigated (non-stress) conditions in the field. Since this DH line population was previously used in extensive quantitative trait loci (QTLs) mapping of various drought resistance component traits, we aimed at identifying QTLs for specific reproductive-growth and yield traits and also to validate the consensus QTLs identified earlier in these DH lines using meta-analysis. DH lines showed significant variation for plant water status, reproductive-growth traits, yield and yield components under drought stress. Total dry matter, number of panicles per plant, harvest index, panicle harvest index, panicle fertility, pollen fertility, spikelet fertility and hundred grain weight had significant positive correlations with grain yield under drought stress. A total of 46 QTLs were identified for the various traits under stress and non-stress conditions with phenotypic effect ranging from 9.5 to 35.6% in this study. QTLs for panicle exsertion, peduncle length and pollen fertility, identified for the first time in this study, could be useful in marker-assisted breeding (MAB) for drought resistance in rice. A total of 97 QTLs linked to plant growth, phenology, reproductive-growth traits, yield and its components under non-stress and drought stress, identified in this study as well as from earlier published information, were subjected to meta-analysis. Meta-analysis identified 23 MQTLs linked to plant phenology and production traits under stress conditions. Among them, four MQTLs viz., 1.3 for plant height, 3.1 for days to flowering, 8.1 for days to flowering or delay in flowering and 9.1 for days to flowering are true QTLs. Consensus QTLs for reproductive-growth traits and grain yield under drought stress have been identified on chromosomes 1 and 9 using meta-QTL analysis in these DH lines. These MQTLs associated with reproductive-growth, grain yield and its component traits under drought stress could be useful targets for drought resistance improvement in rice through MAB and/or map-based positional analysis of candidate genes.     

Radiation use efficiency,N accumulation and biomass production of high-yielding rice in aerobic culture

The concept of aerobic culture is to save water resource while maintaining high productivity in irrigated rice ecosystem. This study compared nitrogen (N) accumulation and radiation use efficiency (RUE) in the biomass production of rice crops in aerobic and flooded cultures. The total water input was 800–1300 mm and 1500–3500 mm in aerobic culture and flooded culture, respectively, and four high-yielding rice cultivars were grown with a high rate of N application (180 kg N ha⁻¹) at two sites (Tokyo and Osaka) in Japan in 2007 and 2008. The aboveground biomass and N accumulation at maturity were significantly higher in aerobic culture (17.2–18.5 t ha⁻¹ and 194–233  kg N ha⁻¹, respectively) than in flooded culture (14.7–15.8 t ha⁻¹ and 142–173 kg N ha⁻¹) except in Tokyo in 2007, where the surface soil moisture content frequently declined. The crop maintained higher N uptake in aerobic culture than in flooded culture, because in aerobic culture there was a higher N accumulation rate in the reproductive stage. RUE in aerobic culture was comparable to, or higher than, that in flooded culture (1.27–1.50 g MJ⁻¹ vs. 1.20–1.37 g MJ⁻¹), except in Tokyo in 2007 (1.30 g MJ⁻¹ vs. 1.37 g MJ⁻¹). These results suggest that higher biomass production in aerobic culture was attributable to greater N accumulation, leading to higher N concentration (N%) than in flooded culture. Cultivar differences in response to water regimes were thought to reflect differences in mainly (1) early vigor and RUE under temporary declines in soil moisture in aerobic culture and (2) the ability to maintain high N% in flooded culture.     

Genetic analyses of heading date of Japonica rice cultivars from Northeast China

Northeast regions of China (38–55°N latitude) play an important role in Japonica rice planting. Heading dates of 10 Japonica rice cultivars native to the Northeast of China were investigated and their sensitivities to photoperiod and temperature were analyzed. The results showed that these Japonica rice cultivars were insensitive to photoperiod but strongly sensitive to temperature, i.e. a high temperature can markedly shorten the heading date. Genetic analyses were conducted on these 10 cultivars using a set of heading date tester lines. All these Japonica cultivars carried a dominant early heading gene Ef-1, and most of these cultivars carried the photoperiod insensitivity allele e₁, and two types of alleles were presented at the Se-1 locus, including recessive photoperiod insensitivity gene Se-1^e and dominant strong photoperiod-sensitivity (PS) gene Se-1ⁿ. The PS of these cultivars carrying E₁ or Se-1ⁿ can be repressed or weakened by Ef-1 and the recessive allele hd2 they carried. These results provided a reasonable explanation to the adaptability of Japonica rice to the high latitude environment of the Northeast China, and could be useful for breeding new cultivars well adapted to the high latitude regions and expanding the rice cultivation range.     

Hormonal changes are related to the poor grain filling in the inferior spikelets of rice cultivated under non-flooded and mulched condition

Non-flooded plastic mulching cultivation (PM) of rice can save much irrigation but usually exhibits a poor grain filling and low grain weight when compared to traditional flooding cultivation (TF). This study measured the variations of plant hormones during grain filling and investigated whether they were related to the grain-filling problem under mulching in a field experiment. Hormonal levels in the grains and the grain development of both superior (early flowered) and inferior spikelets (later flowered) were monitored continuously during the grain filling period. The contents of indole-3-acetic acid (IAA), zeatin riboside (ZR) and abscisic acid (ABA) were higher in superior grains than in inferior ones at early grain-filling stage. For individual spikelets, the peaks of IAA and ZR contents appeared just before the peak grain-filling rate but the peak ABA content matched it. The earlier flowered superior spikelets did not show much difference in grain filling characteristics and hormonal changes under the two cultivation treatments. Distinctively with the inferior spikelets in a panicle, PM led to lower grain weight, higher grain-filling rate at early stage and shorter active grain-filling period than the TF. PM also resulted in less IAA and ZR but more ABA contents in the grains than TF at early and middle grain filling stages in these inferior spikelets. Peaks of these hormone contents in the PM inferior grains usually appeared earlier and also disappeared more quickly than those in TF inferior grains. When exogenous IAA was applied to plants at the initial grain-filling stage, IAA and ZR were increased and ABA was reduced in the inferior grains. The treatment prolonged the active grain-filing period and reduced the peak grain-filling rate of inferior grains, similarly as the case with TF. As a result, IAA spraying enhanced the weight of PM inferior grains but reduced that of TF ones. Exogenous ABA spraying led to the opposite effects to those of IAA. The results suggest that the shortened grain-filling period in the inferior grains under PM is related to the increased ABA and reduced IAA and ZR in the grains. Regulation of the ratio of ABA to IAA in grains could potentially increase the weight of inferior grains under the water-saving cultivation with film mulching.     

A set of near-isogenic lines for blast resistance genes with an Indica-type rainfed lowland elite rice (Oryza sativa L.) genetic background

A set of near-isogenic lines for blast resistance genes was developed by using an Indica-type elite rice variety, IR49830-7-1-2-2, suitable for the rainfed lowland conditions in the tropics, as a genetic background. Initially, we revealed that IR49830-7-1-2-2 harbors five blast resistance genes - Pia, Pib, Pik-s, Pita, and Pi11(t) - by using a differential system involving 19 selected standard blast isolates from the Philippines. Based on this result, we developed nine near-isogenic lines (NILs) targeting eight resistance genes - Pik, Pi7(t), Pi3, Pi5, Pita-2, Piz-5, Pish, and Pi9 - by recurrent backcrossing. The introgression of each resistance gene in the NILs was confirmed by reaction patterns to the blast isolates, allelism tests, and DNA marker analysis. In addition, a genome-wide DNA marker survey revealed that most of the chromosome regions in each NIL were of the IR49830-7-1-2-2 type. The agricultural characteristics of most of the developed NILs were almost the same as those of IR49830-7-1-2-2. Moreover, with one exception, they showed submergence tolerance similar to IR49830-7-1-2-2. The developed NILs could be used as a multiline variety suitable for the rainfed lowland in the tropics.     

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.     

Analysis of sample size for variables related to plant,soil, and soil microbial respiration in a paddy rice field

Pre-samplings for sample size determination are strongly recommended to assure the reliability of collected data. However, there is a certain dearth of references about sample size determination in field experiments. Seldom if ever, differences in sample size were identified under different management conditions, plant traits, varieties grown and crop age. In order to analyze any differences in sample size for some of the variables measurable in rice field experiments, the visual jackknife method was applied to pre-samples collected in a paddy rice field in Northern Italy, where a management typical for European rice was conducted. Sample sizes for 14 variables describing plant features (plant density, spikelet sterility, biomass, carbon and nitrogen concentration for the different plant organs and for the whole plant) and for 12 variables describing physical and chemical soil features (texture, pH, water holding capacity, soil organic matter, total carbon and nitrogen concentration, mineral nitrogen concentration) and soil microbial activity were estimated. The elementary units of observation were a 3-plant sample and an aggregate sample of four 125 cm³ sub-samples respectively for plant- and soil-related variables. Sample sizes ranged between 15 and 27 for plant-related variables and between 5 and 6 for soil variables. Relating to plant features, remarkable differences in sample size were observed in carbon concentration values of different plant organs, probably due to maintenance respiration. Homogeneity among sample sizes for soil variables could be explained by the capability of aggregate samples in capturing a big part of the total variance. This study underlines importance of carrying out pre-samplings aiming at sample size determination for different variables describing the cropping system.     

Identification of a GDSL-motif carboxylester hydrolase from rice bran (Oryza sativa L.)

A major esterase (designated OsEST1) showing high activity using 1-naphthyl acetate as a substrate was identified from rice bran and purified approximately 239-fold to near-homogeniety. The purified enzyme migrated as a single polypeptide band on native and SDS-polyacrylamide gels and had a molecular mass of 25 kDa under denaturing conditions. Analysis of its tryptic peptides by MALDI-TOF-MS and subsequent data mining identified a corresponding cDNA OsEST1 consisting of 714 nucleotides and encoding a 238 amino acid protein. Analysis of its primary sequence indicated that OsEST1 is a GDSL-motif carboxylester hydrolase belonging to the SGNH protein subfamily in containing the putative catalytic triad of Ser¹¹, Asp¹⁸⁷, and His¹⁹⁰. OsEST1 showed the highest catalytic activity at approximately pH 8.0–8.5 and at 45 °C with K_m and V_max values for 1-naphthyl acetate of 172 μM and 63.7 μmol/min/mg protein, respectively. However, OsEST1 showed no activity with triacylglycerol. Alignment of the primary sequence of OsEST1 and other rice GDSL-motif esterases/lipases showed that OsEST1 aligns with a specific family of plant SGNH esterases involved in response to dehydration and cuticle formation. These results suggest that OsEST1 is not a lipase but an esterase activity which has some other function in rice, especially during seed development.     

Grain quality characteristics of rice in Madagascar retail markets

A survey of rice in retail markets of Madagascar with emphasis on the surplus regions of Marovoay and Lac Alaotra and the deficient area, Antananarivo City showed rices of Madagascar to be predominantly medium-long, medium-shaped, with high apparent amylose content, low gelatinization temperature, and soft, hard or medium gel consistency. Mean protein content was 7.5%. Percent white grains among red and white grains ranged from 0 to 100% (mean 56%), head rice 0–94%, translucency 6–66% and Kett whiteness 12–48%.     

Investigating early vigour in upland rice (Oryza sativa L.): Part II. Identification of QTLs controlling early vigour under greenhouse and field conditions

Early vigour is an important characteristic for direct-seeded rice systems. The genetic control of early vigour was studied using a population of 129 backcross lines derived from a cross between Vandana, an improved indica, and Moroberekan, a traditional japonica. Screening was conducted under controlled conditions in greenhouse and field conditions, and indicators of early vigour, including shoot length, shoot biomass, leaf area, number of roots, root biomass, partitioning coefficients, and growth rates, were measured. Phenotypic correlations suggested that traits that were related and combined could be used to define early vigour. Broad-sense heritability ranged from moderate to high. Many regions were identified containing more than one QTL, suggesting that these traits were controlled by pleiotropic and/or closely linked QTLs. Many QTLs were specific to one environment but G × E interaction analysis showed that the main effects of the environment were large. Differences in temperature between experiments resulted in large differences in seedling age when expressed in thermal time. Different genes (QTLs) may be expected to control growth at different time intervals and thus may partly explain the limited agreement between experiments. However, several regions showed co-location of QTLs from more than one experiment. Comparisons with published studies revealed that these regions were previously identified in different genetic backgrounds and could potentially be used as introgression targets in a marker-assisted breeding program to improve germplasm for direct-seeded environments.     

Identification of deletion mutants with improved performance under water-limited environments in rice (Oryza sativa L.)

Rice (Oryza sativa L.) is a semi-aquatic member of the grass family that is poorly adapted to dry environments and has greater sensitivity to water-deficits than other important cereals in this family. To increase productivity in aerobic or water-limited environments rice must overcome its adaptations to flooded environments. Deletion mutants offer an alternative genetic resource for improving drought tolerance. Almost 3500 IR64 deletion mutants were screened under vegetative and reproductive stage drought stress in the field and evaluated for leaf drying and/or grain yield. Seven novel conditional mutants of rice which showed gain of function through continued growth as drought stress developed compared to the wild type were identified. Mutant recovery rate was 0.1%. Further evaluation of putative drought mutants revealed that their average shoot biomass at maturity and grain yield per plant under stress exceeded those of the wild type by two-fold. Studies under controlled conditions confirmed mutants to have continued growth of both roots and shoots as drought developed compared to the wild type, and a tendency for greater water extraction. We propose that deletions in these mutants have affected a regulator of the highly conservative growth response common to irrigated lowland rice cultivars. Our results suggest that screening deletion mutants for performance under managed drought stress in the field could be a highly effective way to identify valuable genetic resources for improved drought response and aerobic adaptation in rice.     

Waxy gene haplotypes: Associations with pasting properties in an international rice germplasm collection

Associations between RVA pasting properties and three single nucleotide polymorphism (SNP) sites in the Waxy gene intron 1, exon 6, and exon 10 were determined using rice genotypes of diverse geographic origin. A total of four SNP-haplotypes (combination of SNP alleles) were identified that explained high proportions of the variation in RVA pasting properties (R² = 0.574–0.704). A haplotype containing DNA sequence variation in exon 10 (exon 10 cytosine nucleotide) was exclusively found in high-apparent amylose content (AAC) genotypes with a higher RVA viscosity profile compared to the high AAC genotypes with a different haplotype. The exon 10 SNP explained variances in coolpaste and setback (coolpaste–hotpaste) to 0.642 and 0.499, respectively. Across three haplotypes, which contained exon 10 adenine nucleotide, AAC was correlated with peak, hotpaste, breakdown and setback (coolpaste–hotpaste) at r = −0.85, −0.75, −0.79, and 0.49, respectively. Therefore, the exon 10 SNP differentiates high AAC types with a strong RVA profile and thus can be used by molecular breeding programs focused on quality improvement. Additionally, characterizing genotypes by their functional SNPs allowed us to better understand the relationship between the Waxy gene, its chemical product (i.e., AAC) and the functionality created by the product (i.e., pasting properties).