Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines

BMC Plant Biology, Jan 2010

Background Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. Results We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiapó). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11. Conclusions Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice.

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Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines

BMC Plant Biology Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa O. glaberrima introgression lines Andrs Gonzalo Gutirrez 0 Silvio James Carabal 0 Olga Ximena Giraldo 0 Csar Pompilio Martnez 0 Fernando Correa 0 1 Gustavo Prado 0 Joe Tohme 0 Mathias Lorieux 0 2 0 Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT) , A.A. 6713, Cali , Colombia 1 Agrobiodiversity and Biotechnology Project, International Center for Tropical Agriculture (CIAT) , A.A. 6713, Cali, Colombia. Current Address: RiceTec , Inc. , PO Box 1305, Alvin, Texas 77512 , USA 2 Institut de Recherche pour le Developpement (IRD), Plant Genome and Development Laboratory, UMR 5096 IRD-CNRS-Perpignan University , 911 Av. Agropolis, 34394 Montpellier Cedex 5 , France. Current address: Agrobiodiversity and Biotechnology Project , CIAT, A.A. 6713, Cali , Colombia Background: Developing new population types based on interspecific introgressions has been suggested by several authors to facilitate the discovery of novel allelic sources for traits of agronomic importance. Chromosome segment substitution lines from interspecific crosses represent a powerful and useful genetic resource for QTL detection and breeding programs. Results: We built a set of 64 chromosome segment substitution lines carrying contiguous chromosomal segments of African rice Oryza glaberrima MG12 (acc. IRGC103544) in the genetic background of Oryza sativa ssp. tropical japonica (cv. Caiap). Well-distributed simple-sequence repeats markers were used to characterize the introgression events. Average size of the substituted chromosomal segments in the substitution lines was about 10 cM and covered the whole donor genome, except for small regions on chromosome 2 and 4. Proportions of recurrent and donor genome in the substitution lines were 87.59% and 7.64%, respectively. The remaining 4.78% corresponded to heterozygotes and missing data. Strong segregation distortion was found on chromosomes 3 and 6, indicating the presence of interspecific sterility genes. To illustrate the advantages and the power of quantitative trait loci (QTL) detection using substitution lines, a QTL detection was performed for scored traits. Transgressive segregation was observed for several traits measured in the population. Fourteen QTLs for plant height, tiller number per plant, panicle length, sterility percentage, 1000-grain weight and grain yield were located on chromosomes 1, 3, 4, 6 and 9. Furthermore, a highly significant QTL controlling resistance to the Rice stripe necrosis virus was located between SSR markers RM202-RM26406 (44.5-44.8 cM) on chromosome 11. Conclusions: Development and phenotyping of CSSL libraries with entire genome coverage represents a useful strategy for QTL discovery. Mapping of the RSNV locus represents the first identification of a genetic factor underlying resistance to this virus. This population is a powerful breeding tool. It also helps in overcoming hybrid sterility barriers between species of rice. - Background Asian rice (Oryza sativa L.) is one of the most important food crops for mankind and is considered to be a model system for molecular genetic research in monocots, due to its small genome size and its synteny with other cereal crops [1,2]. Recent advances in large-scale genomic research has provided extremely useful tools, such as a complete, high-quality genome sequence [3], Bacterial Artificial Chromosome libraries [4], insertional mutant collections [5], and the discovery of new molecular markers [6-8]. Plant breeders and geneticists have taken advantage of these advances by using both cultivated and wild germplasm as new sources of genetic variation to facilitate identification of genes and QTLs of economic importance, contributing to an increased rice production. Although methodologies for mapping genes or QTLs underlying quantitative traits have made considerable progress, the need to develop new population types to facilitate the study of alleles from wild species, has been pointed out. These materials would allow identification and use of new sources of allelic variation that have not been sufficiently exploited yet [9-14]. Different types of segregating populations, like Recombinant Inbred Lines (RIL), Doubled Haploids (DH), Backcross (BC) or F2/F3 populations have been extensively used for QTL mapping. Nevertheless, these populations do not have sufficient power in detecting QTLs with minor effects, at least when standard population sizes of a few hundreds of segregating individuals are used [11,15]. Moreover, in the case of interspecific crosses, hybrid sterility often hampers developing such population types. To circumvent these issues, researchers have developed novel population types, which are all very similar in essence: Introgression Lines (ILs) in tomato [11]Brassica napus [16] and Brassica oleracea [17], Stepped Aligned Inbred Recombinant (...truncated)


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Andrés Gutiérrez, Silvio Carabalí, Olga Giraldo, César Martínez, Fernando Correa, Gustavo Prado, Joe Tohme, Mathias Lorieux. Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa × O. glaberrima introgression lines, BMC Plant Biology, 2010, pp. 6, 10, DOI: 10.1186/1471-2229-10-6