Molecular profiling of interspecific lowland rice populations derived from IR64 (Oryza sativa) and Tog5681 (Oryza glaberrima)

Several lowland NERICAs (New Rice for Africa) were derived from crosses between IR64 (an Oryza sativa subsp. indica variety) and Tog5681 (an Oryza glaberrima variety) that possess useful traitsadapted to lowland conditions in West Africa. The proportion of parental genomic contribution and extent of genetic differences among these sister lines is unknown at the molecular level. The objectivesin this study were therefore to determine, with 60 SSR markers that cover 1162 cM of the rice genome, the frequency and magnitude of deviations from the expected parental contributions among 21 BC2F10,17 BC3 F8 and 10 BC4F8 lines and determine patterns of their genetic relationships. The estimated average O. glaberrima genome coverage was 7.2% (83.5 cM) at BC2F10, 8.5% (99.3 cM) at BC3F8 and 8.1%(93.8 cM) at BC4F8 lines. The O. sativa parent accounted for 73.2% (851.3 cM) at BC2F10, 82.6% (959.5 cM) at BC3F8 and 78.2% (908.6 cM) at BC3F8. Non-parental alleles were detected at all 3 backcross generations but the frequency of such alleles at BC2 (8.8%) was twice that of BC3F8 (3.4%) and nine times that of BC4F8 (0.9%). Both cluster and principal component analyses revealed two major groups irrespective of the level of backcross generations and the proportion of parental genome contribution

Molecular profiling of an interspecific rice population derived from a cross between WAB 56-104 (Oryza sativa) and CG 14 (Oryza glaberrima)

NERICA rices are interspecific inbred progeny derived from crosses between Oryza sativa x O. glaberrima. In this study, we evaluated 70 BC2 interspecific lines, developed by crossing a tropicaljaponica variety (WAB 56-104) as the recurrent parent to an O. glaberrima variety (CG 14) as the donor parent, followed by the use of anther culture to derive doubled haploids (DH) (26 lines) or eightgenerations of inbreeding to fix the lines (44 lines). Seven of these BC2 derived inbred lines have been released as NERICA 1 - NERICA 7. This study examined the relative contribution of each parent and theextent of genetic differences among these 70 sister lines using 130 well-distributed microsatellite markers which cover 1725 cM of the rice genome. The average proportion of O. sativa recurrent parentgenome was 87.4% (1,508 cM), while the observed average proportion of O. glaberrima donor genome was 6.3% (108 cM). Non-parental alleles were detected in 83% of the lines and contributed an average of38 cM per line (~2.2% of genomic DNA). Lines that had undergone eight generations of inbreeding in the field contained significantly more non-parental alleles (av. 2.7%) compared to the DH lines (av. 1.3%)that were developed from BC2 anthers. Using both cluster and principal component analyses, two major groups were detected in these materials. The NERICA varieties (NERICA 1 to 7) clustered in one group while the remaining 63 lines clustered in another group, suggesting that the second group may offer significant opportunities for further selection and variety development

Fine genetic mapping of a gene required for Rice yellow mottle virus cell-to-cell movement

International audienceThe very high resistance to rice yellow mottle virus observed in the two rice varieties Gigante (Oryza sativa) and Tog 5681 (O. glaberrima) is monogenic and recessive. Bulked segregant analysis was carried out to identify AFLP markers linked to the resistance gene. Mapping of PCR-specific markers, CAPS and microsatellite markers on 429 individuals of an IR64 × Gigante F 2 population pinpointed this resistance gene on the long arm of chromosome 4 in a 3.7-cM interval spanned by PCR markers. These markers also flanked the resistance gene of the O. glaberrima accession Tog 5681 and confirmed previous allelism tests. The rarity of this recessive natural resistance was in line with a resistance mechanism model based on point mutations of a host component required for cell-to-cell movement of the virus. Preliminary data on the genetic divergence between the two cultivated rice species in the vicinity of the resistance locus suggested that two different resistance alleles are present in Gigante and Tog 5681. A large set of recombinants is now available to envisage physical mapping and cloning of the gene

Evaluation of rice cultivars for resistance to rice yellow mottle virus

Rice yellow mottle virus (RYMV), which is only found in Africa, threatens rice farming on the continent. A local Oryza sativa cultivar collected from Burkina Faso (named BM24), was evaluated with that of well known highly resistant and tolerant cultivars. Firstly, three RYMV isolates were used to characterise the differential interaction within the cultivars. Secondly, disease kinetics of symptom expression and virus titer on leaves at 21 days after inoculation were assessed using the BF1 isolate. Thirdly, the allelic profile of O. sativa varieties using SSR marker RM101 located on chromosome 12 was also assessed. IR64 showed susceptibility to all isolates; while Tog5681 was resistant to all isolates. Ng122 overcame the resistance of Gigante, with mild leaf symptoms at 42\ua0dpi. Azucena and BM24 had, therefore, different resistance level regarding the three isolates (Ng117b, Ng122 and Ng144). When infected with the isolate, BF1, BM24 and Azucena exhibited same resistance patterns in early growth stages with delayed of symptoms appearance, but BM24 outperformed Azucena at later stages. The virus content in the two accessions, at 14 days post inoculation, was statistically different with BM24, showing less virus compared to Azucena. However, the two accessions depicted an identical allelic profile at RM101 locus.Le virus de la panachure jaune du riz (RYMV) est end\ue9mique seulement en Afrique, et fait des ravages dans les rizi\ue8res du continent. Une vari\ue9t\ue9 de riz local (appel\ue9e BM24), r\ue9sistante au RYMV et collect\ue9e au Burkina Faso a \ue9t\ue9 compar\ue9e avec des cultivars bien connus qui sont r\ue9sistants ou tol\ue9rants au RYMV. Tout d\u2019abord, trois isolats ont \ue9t\ue9 utilis\ue9s pour caract\ue9riser les interactions diff\ue9rentielles au sein des cultivars. Ensuite, la cin\ue9tique de l\u2019expression des sympt\uf4mes de la maladie et le titre en virus sur les feuilles \ue0 21 jours apr\ue8s inoculation ont \ue9t\ue9 \ue9valu\ue9e avec l\u2019isolat BF1. Enfin, le profile all\ue9lique des vari\ue9t\ue9s de Oryza sativa a \ue9t\ue9 \ue9valu\ue9 au marqueur SSR RM101 situ\ue9 sur le chromosome 12. La vari\ue9t\ue9 IR64 s\u2019est av\ue9r\ue9e sensible \ue0 tous les isolats tandis que Tog5681 s\u2019est montr\ue9 r\ue9sistant \ue0 tous les isolats. L\u2019isolat Ng122 a surmont\ue9 la r\ue9sistance de Gigante avec la pr\ue9sence de sympt\uf4mes mod\ue9r\ue9s \ue0 42 jours apr\ue8s inoculation (JAI). Azucena et BM24 par contre ont eu diff\ue9rents niveaux de r\ue9sistance en pr\ue9sence des trois isolats (Ng117b, Ng122 and Ng144). Lorsqu\u2019ils sont infect\ue9s avec l\u2019isolat BF1, BM24 et Azucena expriment le m\ueame niveau de r\ue9sistance avec un retard de l\u2019apparition des sympt\uf4mes dans les premiers moments suivant l\u2019inoculation mais au-del\ue0 de 14 JAI, les sympt\uf4mes apparaissent plus rapidement chez Azucena compar\ue9 \ue0 BM24. A 14 JAI, le titre de virus contenu dans e cultivar Azucena est bien sup\ue9rieur statistiquement \ue0 celui de BM24. Cependant, les deux cultivars ont eu un profile all\ue9lique identique au locus RM101

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

Why NERICA is a successful innovation for African farmers

This paper responds to ‘Funding international agricultural research and the need to be noticed: a case study of NERICA rice’ by Stuart Orr, James Sumberg, Olaf Erenstein and Andreas Oswald, published in this issue of Outlook on Agriculture. In summary, the article by Orr et al, based on an internal WARDA document written in November 2003 and augmented with results from Internet searches, is outdated and does not seem to be fair, objective or useful. We invite the authors to visit WARDA or any of its partners in Sub-Saharan Africa for evidence of the impact of NERICA varieties or the other improved varieties and technologies that have been developed and disseminated by WARDA in recent years

Phytosanitary Interventions for Safe Global Germplasm Exchange and the Prevention of Transboundary Pest Spread: The Role of CGIAR Germplasm Health Units

The inherent ability of seeds (orthodox, intermediate, and recalcitrant seeds and vegetative propagules) to serve as carriers of pests and pathogens (hereafter referred to as pests) and the risk of transboundary spread along with the seed movement present a high-risk factor for international germplasm distribution activities. Quarantine and phytosanitary procedures have been established by many countries around the world to minimize seed-borne pest spread by screening export and import consignments of germplasm. The effectiveness of these time-consuming and cost-intensive procedures depends on the knowledge of pest distribution, availability of diagnostic tools for seed health testing, qualified operators, procedures for inspection, and seed phytosanitation. This review describes a unique multidisciplinary approach used by the CGIAR Germplasm Health Units (GHUs) in ensuring phytosanitary protection for the safe conservation and global movement of germplasm from the 11 CGIAR genebanks and breeding programs that acquire and distribute germplasm to and from all parts of the world for agricultural research and food security. We also present the challenges, lessons learned, and recommendations stemming from the experience of GHUs, which collaborate with the national quarantine systems to export and distribute about 100,000 germplasm samples annually to partners located in about 90 to 100 countries. Furthermore, we describe how GHUs adjust their procedures to stay in alignment with evolving phytosanitary regulations and pest risk scenarios. In conclusion, we state the benefits of globally coordinated phytosanitary networks for the prevention of the intercontinental spread of pests that are transmissible through plant propagation materials