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

Abstract

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.

Figure 1

Graphical representation of the genotypes of 64 BC3DH lines selected from a library of 312 lines. The 12 rice chromosomes are displayed vertically. They are covered by 125 evenly dispersed SSR markers. The genotypes are displayed horizontally. Color legend indicates the allelic status of chromosomes, where "Recurrent" means homozygous for the Caíapo allele and "Donor" means homozygous for the MG12 allele.

Figure 2

Genetic locations of the 15 QTLs for yield components an RSNV resistance (% Healthy plants) detected in this work. On the left, SSR marker positions and distances (cM) based on IR64/TOG5681 genetic linkage map, developed at CIAT in 2007 (our unpublished data). On the right, QTL for yield, yield components and RSNV resistance on chromosomes 1, 3, 4, 6, 9 and 11.

Figure 3

Major QTL for O. glaberrima Acc. MG12 resistance to the Rice Stripe Necrosis Virus (RSNV), located on rice chromosome 11 between SSR markers RM479 and RM5590 (F = 70.63, P ~ 0.0). On the right, solid grey bars indicate the value of percentage of healthy plants for each line. The resistant lines (% of healthy plants > 85) are located within the black frame. The most probable location of the resistance QTL is given by the intersection of the black frame and the positions of the markers RM479 and RM5590, which define a common introgressed region between the resistant lines.

Figure 4

Frequency distribution of yield component traits in 312 BC₃F₁DH lines. Parental values are indicated by arrows. C = Caíapo (O. sativa), M = MG12 (O. glaberrima).

Figure 5

Development scheme of the population of BC3DH lines derived from Caíapo (O. sativa) × MG12 (O. glaberrima) interspecific cross.

Figure 6

Characteristic symptoms of the disease "crinkling" caused for RSNV in rice plants (A) Yellow stripes on leaves or foliar striping and (B) Crinkling or deformation (Courtesy: Gustavo Prado, Rice Pathology Laboratory, CIAT, Cali, Colombia).