Genetic relationship between grain chalkiness,protein content,and paste viscosity properties in a backcross inbred population of rice

A backcross inbred line population derived from a cross between Koshihikari and Kasalath was used to dissect the genetic relationship among chalkiness, protein content, and paste viscosity properties in rice in three environments. A total of 11 traits (or parameters) were analyzed, including percentage of grains with chalkiness (PGWC), protein content (PC) and protein index (PI), and eight parameters from the viscosity profile. PGWC, PC and PI were significantly correlated with the paste viscosity parameters. We identified 39 QTLs in three environments; ten QTL clusters emerged. Eight QTLs were consistently detected across the three environments and further confirmed using a set of chromosome segment substitution lines (CSSLs) where Kasalath was used as the donor parent and Koshihikari as the recurrent parent. One and two major clusters on chromosome 6 corresponded to the Wx and Alk loci, respectively. The former was responsible for PGWC and most of the viscosity parameters, and the latter for PI and some viscosity parameters. Particularly, QTL qPI-6.1 was linked with both the Wx and Alk loci. The co-locations of QTLs for PGWC and viscosity parameters and the linkage of qPI-6.1 and qBDV-6 at the Wx locus could be largely responsible for the phenotypic correlations between these traits.     

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).     

Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.)

The Waxy (Wx) gene is responsible for the synthesis of amylose, a key determinant of the cooking and processing qualities of rice. Polymorphisms of CT-microsatellite and G–T single-nucleotide polymorphism (SNP) in the Wx gene and their relationship to amylose content (Ac) were explored using 178 non-waxy rice genotypes. Nine Wx microsatellite alleles, namely (CT)10 and 11, and (CT)14–20 were identified and 11 haplotypes were recognised by different combinations of CT-microsatellite and G–T SNP. Amylose content analysed in a random set of 39 genotypes was correlated with different microsatellite alleles/haplotypes. The highest Ac levels (>30%) correlated with (CT)10 and 16, high (26–30%) with (CT)11, 15 and 20, and intermediate (21–25%) with (CT)14, in all cases with G at the G–T SNP. The CT-classes (CT)17 and 18 (mean Ac value of 21%), could be subdivided into low amylose haplotypes (16–20%) for 17T and 18T and intermediate amylose haplotypes (21–25%) for 17G and 18G. The use of haplotypes proved to discriminate between intermediate and low amylose accessions within the same microsatellite class. Analyses of a segregating population of a cross between low and high Ac parents showed that CT-microsatellite may help to classify breeding lines and identify pollen contamination. We suggest that CT-microsatellite together with G–T SNP may be used as molecular marker by breeders to develop varieties with desired amylose levels.     

Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection

Apparent amylose content (AAC), the key determinant of rice end-use quality attributes, is primarily controlled by the Waxy gene which codes for granule bound starch synthase (GBSS). We examined the combination of sequence variation in the Waxy gene and environmental effects, and their associations with AAC using 171 rice accessions originating from 43 countries. The combination of two single-nucleotide-polymorphism (SNP) markers in the Waxy gene allows for the identification of three marker haplotypes in this gene. The first SNP is at the leader intron splice site (In1 SNP), and the second polymorphism is in exon 6. The haplotypes explained 86.7% of the variation in AAC and discriminated the three market classes of low, intermediate and high AAC rice from each other. The environment affected the AAC of all haplotypes. Higher air temperature during grain development associated with a decrease in AAC of low and intermediate AAC-types, but with an increase in AAC of high AAC-type. The association of AAC with several Waxy RM190 microsatellite-(CT_n) alleles in combination with the In1 SNP was also examined. In conclusion, the Waxy haplotypes studied appear to be useful markers for selecting the AAC of breeding lines developed from the world's rice germplasm.     

Genomic regions associated with the degree of red coloration in pericarp of rice (Oryza sativa L.)

The degree of red coloration (DRC) in pericarp of rice depends on the content of flavonoid compounds which have beneficial health effects for humans. In this study, 182 backcross-recombinant inbred lines (BILs) derived from Koshihikari (white pericarp)/Kasalath (red pericarp)//Koshihikari were used to detect the genomic regions associated with DRC through the QTL mapping approach. As a result, a total of four genomic regions were found to associate with DRC on chromosomes 1, 7, 9 and 11, respectively. Interestingly, the two genomic regions having the largest effects corresponded to previously characterized Rc and Rd genes on chromosome 7 and 1, respectively. In addition, two novel genomic regions having minor effects on DRC and located on chromosomes 9 and 11, respectively, are reported here for the first time. These results and the identification of tightly linked molecular markers that flank the genomic regions provide an opportunity for marker-aided improvement of red coloration in pericarp of rice.     

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.     

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.     

Plant characteristics associated with weed competitiveness of rice under upland and lowland conditions in West Africa

Weeds are a major constraint to rice (Oryza spp.) production in West Africa. Superior weed competitive rice genotypes may reduce weed pressure and improve rice productivity. Two upland and two lowland experiments were conducted in southern Benin to examine genotypic variations in weed-suppressive ability and grain yield under weedy conditions, and to identify plant characteristics that could be used as selection criteria for improved weed competitiveness. A total of 19 genotypes, including Oryza sativa and Oryza glaberrima genotypes and interspecific hybrids developed from crossing O. sativa and O. glaberrima, were grown under weed-free and weedy conditions in an upland with supplemental irrigation and in a flooded lowland. In weedy plots, hand weeding was done once or not at all. Mean relative yield loss across all genotypes due to weed competition ranged from almost 0% to 61%. Large genotypic variations in weed biomass and grain yield under weedy conditions were found. Visual growth vigor at 42 and 63 days after sowing (DAS) under weed-free conditions significantly correlated with weed biomass at maturity in both upland and lowland experiments (R² = 0.26–0.48). Where weed pressure was low to moderate, with mean relative yield loss less than 23%, the multiple regression models using grain yield and plant height at maturity or only grain yield measured under weed-free conditions as independent variables could explain 66–88% of the genotypic variation in grain yield under weedy conditions. At higher weed pressure (mean relative yield loss: 61%), as observed in one of the upland experiments, biomass accumulation of rice at 42 days after sowing was associated with higher grain yield under weedy conditions. Biomass accumulation also significantly correlated with visual growth vigor at the same sampling dates. Therefore, we conclude that grain yield, plant height at maturity and visual growth vigor at 42–63 DAS under weed-free conditions appear to be useful selection criteria for developing superior weed competitive rice genotypes.     

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.     

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.     

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.     

Physiological characterization of introgression lines derived from an indica rice cultivar, IR64, adapted to drought and water-saving irrigation

Water scarcity threatens sustainable rice production in many irrigated areas around the world. To cope with the scarcity, aerobic rice culture has been proposed as a promising water-saving technology. The objective was to elucidate the physiological attributes behind the performance of rice introgression lines in water-saving culture. We evaluated yield potential and physiological adaptation traits to water deficit of BC₃-derived lines with the genetic background of an elite indica cultivar, IR64, in the field and in pot experiments. One line, YTH183, had 26% higher yield than IR64 under non-stress conditions (895 vs. 712 g m⁻² on average). This was attributed to enlarged sink capacity due to large grain size, which contributed to more efficient use of assimilates and hence a higher harvest index. YTH183 also showed better dehydration avoidance under intermittent soil drying, due to the adaptive response of deep rooting to water deficiency. The grain yield of YTH183 exceeded that of IR64 by 92-102% under moderate water deficit caused by limited irrigation in aerobic rice culture (143 vs. 72 g m⁻²). Two introgressed segments on chromosomes 5 and 6 might, at least in part, confer the higher yield potential and greater dehydration avoidance in YTH183 simultaneously. Advanced backcross breeding combined with molecular genetics and physiological characterization of introgressed segments would be effective for developing new rice cultivars with high yield potential and drought adaptation traits.     

Quality characteristics and field performance of selectable marker-free transgenic rice with antisense Wx gene and improved quality derived from the elite parents of hybrid indica rice

In rice grains, high amylose content (AC) is correlated with poor grain quality, particularly in indica hybrid rice. To obtain indica hybrid rice with improved cooking and eating qualities, we introduced the antisense Waxy (Wx) gene into 2 elite parental lines of indica hybrid rice by using co-transformation methods. Subsequently, we selected several elite homozygous transgenic lines that did not contain the selectable marker. The expression of the endogenous Wx gene of the selected transgenic lines was significantly downregulated, resulting in low AC in the mature seeds; moreover, the AC in some lines reduced to the level observed in glutinous rice. With the decrease in AC, the gel consistency of the transgenic rice became softer, and the gelatinization temperature tended to be higher than those of the wild types, especially in the case of the Longtefu-derived transformants. We also analyzed the pasting properties of the selected transgenic low-AC lines, and we noted an improvement in the pasting properties of the transgenic rice lines. The results from a field trial indicated that the grain weights of the transgenic lines with lower AC exhibit remarkable reduction compared with those of the wild types.     

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.     

An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.)

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R² = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R² = 11.25%) and trough viscosity (p < 0.01, R² = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.     

The large-effect drought-resistance QTL qtl12.1 increases water uptake in upland rice

Drought stress is the most important abiotic factor limiting upland rice yields. Identification of quantitative trait loci (QTL) conferring improved drought resistance may facilitate breeding progress. We previously mapped a QTL with a large effect on grain yield under severe drought stress (qtl12.1) in the Vandana/Way Rarem population. In the current paper, we present results from a series of experiments investigating the physiological mechanism(s) by which qtl12.1 affects grain yield under drought conditions. We performed detailed plant water status measurements on a subset of lines having similar crop growth duration but contrasting genotypes at qtl12.1 under field (24 genotypes) and greenhouse (14 genotypes) conditions. The Way Rarem-derived allele of qtl12.1 was confirmed to improve grain yield under drought mainly through a slight improvement (7%) in plant water uptake under water-limited conditions. Such an apparently small increase in water uptake associated with this allele could explain the large effect on yield observed under field conditions. Our results suggest that this improvement of plant water uptake is likely associated with improved root architecture.     

Transgressive variants for red pericarp grain with high yield potential derived from Oryza rufipogon × Oryza sativa: Field evaluation, screening for blast disease, QTL validation and background marker analysis for agronomic traits

Five transgressive variants (advanced breeding lines from BC₂F₅ and BC₂F₆ generation) were derived from a cross between the wild relative, O. rufipogon Griff. and O. sativa L. subsp. indica cv. MR219, a popular high yielding Malaysian rice cultivar. The aim of the study was to evaluate the pericarp colour of the grains along with yield potential and to validate quantitative trait loci (QTLs) for agronomic traits. The variants were screened against blast disease. Background marker analysis was also done for the promising variants. The field trials were carried out at a single location (due to containment purposes) over two seasons using randomized complete block design (RCBD) with three replications. A trait-based marker analysis was used to identify QTLs for validation in BC₂F₅ generation. Analysis of variance (ANOVA) showed that the seasonal factors influenced different agronomic traits. Variant G33 produced significantly (p < 0.05) higher yield (5.20 t/ha) than the control, MR219 (4.53 t/ha). Eighteen QTLs for different agronomic traits were identified in BC₂F₂ population in a previous study. Among them 14 QTLs were found in BC₂F₅ population of the present study. The yield of variant G33 was influenced by several QTLs viz. qGPL-1, qSPL-1-2, qSPL-8 and qYLD-4, which were introgressed from the donor parent revealed by background marker analysis using BC₂F₇ generation. Percentage (99%) of red pericarp grain of G33 and G34 in BC₂F₅ and BC₂F₆ generations indicated the stability of pericarp colour which was transferred from the wild relative. Variant G33 showed resistance against two pathotype of blast disease (Magnaporthe oryzae). Among the evaluated variants, G33 could be considered for inclusion in the cultivar development program for red rice with high yield potential and resistance to blast disease. This study demonstrated that the alleles from wild relative could improve the yield and yield related traits through allelic interaction, even though the phenotypic traits were inferior to the recurrent parent.     

Improvement of bacterial blight resistance of hybrid rice in China using the Xa23 gene derived from wild rice (Oryza rufipogon)

A novel bacterial blight (BB) resistance gene, Xa23, identified from Oryza rufipogon was introgressed into three popular restorer lines (Minghui63, YR293 and Y1671) for wild abortive cytoplasmic male sterility by marker-assisted backcross breeding approach in combination with artificial inoculation and stringent phenotypic selections. The three derived BB resistant restorer lines (Minghui63-Xa23, YR293-Xa23 and Y1671-Xa23) and their hybrid combinations with Zhenshan97A (Shanyou63-Xa23), NongfengA (Fengyou293-Xa23) and Zhong9A (Zhongyou1671-Xa23) demonstrated similar BB resistance spectrum as the donor parent, CBB23 (B). The newly developed BB resistant restorers and their derived hybrids were identical to their respective original versions for agronomic traits especially under disease free condition. However, under severe disease condition, the three BB resistant restorer lines exhibited significantly higher grain weight and spikelet fertility as compared to the respective original restorer lines thus further resulting in BB resistant hybrids with significantly higher grain yields than their respective popular original hybrids. The results indicated that the Xa23 gene could completely express its dominant broad spectrum resistance in different backgrounds of both restorer and male sterile lines across different growth stages, suggesting its immense breeding value in BB resistance improvement for hybrid rice. Moreover, a reasonable utilization and deployment of Xa23 gene for efficient control of BB disease in hybrid rice production was recommended.     

Molecular marker assisted selection for improvement of the eating,cooking and sensory quality of rice (Oryza sativa L.)

II-32B is a key maintainer line used for hybrid rice breeding in China. However, it is of poor quality for most Chinese consumers because of its high apparent amylose content (AAC), high gelatinization temperature (GT) and non-fragrance. It is well known that the AAC, GT and fragrance traits are largely controlled by the Wx, starch synthase IIa (SSIIa), and fragrance (fgr) genes, respectively. With the aid of functional markers, we improved the quality of II-32B by introgressing the Wx, SSIIa, and fgr genes from Yixiang B, a fragrant maintainer line that has low AAC and low GT. The microsatellite allele (CT)₁₇ of Wx, the contiguous single nucleotide polymorphism TT allele of SSIIa and the 8-bp deletion allele of fgr were transferred to II-32B by two backcrosses and three selfings. Molecular marker assisted selection was applied in the series to select for individuals carrying Wx-(CT)₁₇, SSIIa-TT, and fgr-deletion alleles. According to the marker genotypes, seventeen homozygous lines for Wx-(CT)₁₇, SSIIa-TT, and fgr gene markers were finally selected. The improved II-32B lines were fragrant with reduced AAC and GT.     

Weed competitiveness of the lowland rice varieties of NERICA in the southern Guinea Savanna

Weed competition is a major constraint to lowland rice production in West Africa. Interspecific rice varieties named New Rice for Africa (NERICA) may have superior weed competitiveness and could as such play an important role in integrated weed management. The NERICA varieties were developed from the wide cross between high-yielding Oryza sativa (L.) and weed competitive and disease resilient Oryza glaberrima (Steud.). In this study weed competitiveness of all 60 lowland varieties of NERICA (NERICA-L) was compared with their most frequently used parents [IR64 (O. sativa) and TOG5681 (O. glaberrima)], the weed competitive variety Jaya (O. sativa) and the O. glaberrima upland NERICA parent CG14. During the 2006 and 2007 rainy seasons these varieties were grown under weed-free and weedy conditions in a lowland farmers’ field with partially controlled irrigation in south-east Benin. Weedy plots included single hand weeding at 28 days after sowing, whereas weed-free plots were weekly weeded.