Moussa Sie

Yield Potential and Physiological and Morphological Characteristics Related to Yield Performance in Oryza glaberrima Steud.

Abstract Oryza glaberrima has mostly been used as a source to improve stress resistance of Oryza sativa. Improvement of this species could be an approach to use its adaptability to local environments in Africa such as multiple resistance to several indigenous constraints. The yield of O. glaberrima was inferior to that of O. sativa under favorable growth conditions but not under unfavorable conditions. Moreover, spikelet number before grain shattering was no less in O. glaberrima than in O. sativa at any fertilizer input levels, suggesting that the yield potential of O. glaberrima is as high as that of O. sativa. Inferior yield of O. glaberrima reported in favorable environments could result from grain shattering enhanced by such growth environments where higher incidence of lodging, which is another undesirable character of O. glaberrima, can occur. Regarding characteristics associated to yield generation, O. glaberrima seemed to possess: higher dry matter production and greater leaf area than O. sativa at least until heading; a lower photosynthetic rate per leaf area but a higher rate against the same leaf nitrogen content in a low content range; higher responsiveness of dry matter, leaf area and leaf photosynthesis to increases in nitrogen inputs; lower water-use efficiency on dry matter accumulation and gas exchange bases; faster progress of leaf senescence during maturity; and faster completion of grain filling during maturity than O. sativa.

Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq

The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97–99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1–89.2% attributable to differences within groups.

Nutrient constraint of rainfed rice production in foot slope soil of Guinea Forest in Côte d’Ivoire

Soil nutrient deficiencies can affect rice yield and grain mineral content wherever they occur, but an understanding of their effect on upland rice production in humid forest zone of West Africa is still limited. Therefore, a nutrient omission trial was conducted on foot slope soil in 2003, 2004 and 2005 in Côte d’Ivoire using rice variety WAB 56–104. The effect on rice grain yield (GY) and nutrient content of complete fertilizer (Fc with nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) and zinc (Zn)) was compared with Fc from which a specific nutrient was excluded (Fc – N, Fc – P, Fc – K, Fc – Ca, Fc – Mg and Fc – Zn). Before the trial, soil K (0.10 cmol kg−1) and Mg (0.20 cmol kg−1) contents were suitable, but available P-Bray I (4.2 mg kg−1) was found to be deficient. In course of the study, K, Mg and P deficiencies were observed. An antagonistic effect was observed between rice GY and grain concentrations in P, Mg and Ca for treatments Fc – Mg, Fc – P and Fc – K, respectively. Therefore, the use of P, K and Mg fertilizers is recommended for successive cropping seasons in order to rich stable and high rice yield while decreasing of grain concentrations in P, Mg and Ca can be observed.

Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs

Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several ‘New Rice for Africa (NERICA)’ improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as ‘Advanced Rice for Africa (ARICA)’. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.

Generation mean analysis to estimate genetic parameters of some traits for riceweed competitiveness

Weeds are the most widespread biotic production constraint of rice in Africa and one of the major factors limiting grain yield. An efficient breeding strategy could be particularly important for improving weed management in sub-Saharan Africa (SSA) because most smallholder rice farmers use few external inputs. To understand rice weed competitiveness, experiments on reciprocal interspecific crosses derived from FKR19 (Oryza sativa) and CG20 (Oryza glaberrima) were carried out to estimate gene effects and heritability of traits: plant height at five leaves, plant height 30 days after transplanting, plant height at maturity, number of tillers at 30 and 60 DAT, number of fertile tillers, width of leaves at 80 DAT and at maturity, and length of leaves at 80 DAT and at maturity for rice–weed competitiveness. Six generations – P1, P2, F1, F2, BC1F1 and BC2F1 – were raised and subjected to generation mean analysis. The lowest heterosis of F1 was obtained in both crosses (CG20/FKR19 and FKR19/CG20), except for plant height at 30 days after transplanting and leaf width at maturity in the CG20/FKR19 cross. The majority of traits displayed higher dominance gene effects (H5_L, H30 and L_80 for CG20/FKR19; W_mat and L_mat for FKR19/CG20) than additive gene effects; the latter were slight and non-significant for the majority of traits. Duplicate epistasis was observed for the number of tillers 30 days after transplanting and leaf length at maturity and plant height at maturity. Additive genetic variance values were higher in CG20/FKR19, revealing that the CG20 variety can be used as a donor parent. Plant height at maturity, length of leaves at 80 DAT and at maturity showed high narrow-sense heritability (hn 2 >0.70), influencing weed competitiveness.