Nourollah Ahmadi

Genetic basis and mapping of the resistance to rice yellow mottle virus. I. QTLs identification and relationship between resistance and plant morphology

Abstractu2002Rice yellow mottle virus (RYMV) resistance QTLs were mapped in a doubled-haploid population of rice, ‘IR64/Azucena’. Disease impact on plant morphology and development, expression of symptoms and virus content were evaluated in field conditions. Virus content was also assessed in a growth chamber. RYMV resistance was found to be under a polygenic determinism, and 15 QTLs were detected on seven chromosomal fragments. For all of the resistance QTLs detected, the favourable allele was provided by the resistant parent ‘Azucena’. Three regions were determined using different resistance parameters and in two environments. On chromosome 12, a QTL of resistance that had already been detected in this population and another indica/japonica population was confirmed both in the field and under controlled conditions. Significant correlations were observed between resistance and tillering ability, as measured on control non-inoculated plants. In addition, the three genomic fragments involved in resistance were also involved in plant architecture and development. In particular, the semi-dwarfing gene sd-1, on chromosome 1, provided by the susceptible parent, ‘IR64’, mapped in a region where resistance QTLs were detected with most of the resistance parameters. In contrast, the QTL of resistance mapped on chromosome 12 was found to be independent of plant morphology.

Genetic basis and mapping of the resistance to Rice yellow mottle virus. III. Analysis of QTL efficiency in introgressed progenies confirmed the hypothesis of complementary epistasis between two resistance QTLs

Abstractu2008u2008Our previous studies have hypothesised that a complementary epistasis between a QTL located on chromosome 12 and a QTL located on chromosome 7 was one of the major genetic factors controlling partial resistance to Rice yellow mottle virus (RYMV). We report research undertaken to verify this hypothesis and to introgress the resistant allele of these two QTLs from an upland resistant japonica variety, Azucena, into a lowland susceptible indica variety IR64. Three cycles of molecular marker-assisted back cross breeding were performed using RFLP and microsatellite markers. Resistance to RYMV was evaluated in F2 and F3 offspring of the BC1 and BC2 generations. Marker-assisted introgression (MAI) was very efficient: in the selected BC3 progeny the proportion of the recipient genome was close to 95% for the ten non-carrier chromosomes, and the length of the donor chromosome segment surrounding the two QTLs was less than 20 cM. The relevancy of the complementary epistasis genetic model proposed previously was confirmed experimentally: in BC1 and BC2 generations only F3 lines having the allele of the resistant parent on QTL12 and QTL7 show partial resistance to RYMV. Comparison of our experimental process of MAI with the recommendations of analytic and simulation studies pointed out the methodological flexibility of MAI. Our results also confirmed the widely admitted, but rarely verified, assumption that QTL-alleles detected in segregating populations could be treated as units of Mendelian inheritance and that the incorporation of these alleles into elite lines would result in an enhanced performance. The next step will be the design of tools for the routine use of molecular markers in breeding for partial resistance to RYMV and the development of material for the analysis of resistance mechanisms and the structure of a virus resistance gene in rice.

A major quantitative trait locus for rice yellow mottle virus resistance maps to a cluster of blast resistance genes on chromosome 12.

ABSTRACT Two doubled-haploid rice populations, IR64/Azucena and IRAT177/ Apura, were used to identify markers linked to rice yellow mottle virus (RYMV) resistance using core restriction fragment length polymorphism (RFLP) maps. Resistance was measured by mechanical inoculation of 19-day-old seedlings followed by assessment of virus content by enzyme-linked immunosorbent assay tests 15 days after inoculation. IR64/Azucena and IRAT177/Apura populations, 72 and 43 lines, respectively, were evaluated, and resistance was found to be polygenic. Resistance was expressed as a slower virus multiplication, low symptom expression, and limited yield loss when assessed at the field level. Bulked segregant analysis using the IR64/Azucena population identified a single random amplified polymorphic DNA marker that mapped on chromosome 12 and corresponded to a major quantitative trait locus (QTL) evidenced by interval mapping. When pooling RFLP data, integrated mapping of this chromosome revealed that the QTL was common to the two populations and corresponded to a small chromosomal segment known to contain a cluster of major blast resistance genes. This region of the genome also reflected the differentiation observed at the RFLP level between the subspecies indica and japonica of Oryza sativa. This is consistent with the observation that most sources of RYMV resistance used in rice breeding are found in upland rice varieties that typically belong to the japonica subspecies.

Unlocking the Oryza glaberrima treasure for rice breeding in Africa.

130 (eds M.C.S. Wopereis et al.) in O. sativa (Second, 1982; Wang et al., 1992; Ishii et al., 2001). The domestication of O. glaberrima occurred much later than that of O. sativa, but prior to the introduction of the latter into Africa (Sweeney and McCouch, 2007). The most recent analysis of diversity, comparing nucleotide variation of 14 independent nuclear loci between O. glaberrima and O. barthii, showed that O. glaberrima has lost 76% of the nucleotide diversity of its wild progenitor (Li et al., 2011a), while O. barthii itself harbours slightly less diversity than O. sativa subsp. indica. The low genetic diversity of O. glaberrima compared to O. sativa is likely to have resulted from a reduction of diversity during the migration of the wild progenitor of African Oryza species into Africa plus a severe genetic bottleneck during its domestication from small initial populations of O. barthii. The ecogeographical diversity seems to be so low that clustering analysis is unable to pinpoint the domestication places and dispersion of O. glaberrima (Li et al., 2011a). Portères’ (1970) hypothesis remains the most probable – that African rice was first domesticated in the inland delta of the upper Niger River and subsequently spread along Sahelian rivers and their tributaries to two Domestication and Genetic Diversity of Oryza glaberrima

Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

Key messageRice breeding programs based on pedigree schemes can use a genomic model trained with data from their working collection to predict performances of progenies produced through rapid generation advancement.AbstractSo far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5–F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r2xa0=xa00.2 at 0.80xa0Mb in RP and at 1.1xa0Mb in PP). Consequently, average marker density above one per 22xa0kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41–0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed.

Evaluation of a collection of rice landraces from Burkina Faso for resistance or tolerance to Rice yellow mottle virus

A collection of accessions of Burkina Faso rice germplasm was evaluated for resistance using four Rice yellow mottle virus (RYMV) isolates: Ng122, Ng144, B27 and BF1. B27, an isolate from Benin was used first, followed by Ng122 and Ng144 (isolates from Niger), and BF1 an aggressive isolate from Burkina Faso was used last to assess the accessions status against RYMV. Fourteen-day-old plantlets were inoculated and symptoms scored fortnightly from 14 to 56 days post inoculation (dpi). Plant height of all accessions was recorded at 49 dpi with isolates Ng122 and Ng144. The Oryza sativa accessions of the collection were highly susceptible except one (BM24), which combined partial resistance and tolerance. Twenty one O. glaberrima accessions out of 48 were found resistant to Ng122 and Ng144. When these 21 accessions were subsequently screened with the aggressive RYMV strain BF1, eight of them displayed a delay in the appearance of RYMV symptoms while two showed resistance. The new sources of resistance identified in this study, could be exploited in breeding to control the spread of RYMV in Africa.

Additional file 3: Table S3. of Association mapping of resistance to rice blast in upland field conditions

Blast disease scores measured on 18 differential lines in Andranomanelatra in 2011 and 2015. (XLSX 9 kb)