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. 2015;35(2):81.
doi: 10.1007/s11032-015-0276-7. Epub 2015 Feb 14.

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga

Juan D Arbelaez  1 , Laura T Moreno  2 , Namrata Singh  1 , Chih-Wei Tung  3 , Lyza G Maron  1 , Yolima Ospina  4 , César P Martinez  4 , Cécile Grenier  5 , Mathias Lorieux  6 , Susan McCouch  1
Affiliations

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga

Juan D Arbelaez et al. Mol Breed. 2015.

Abstract

Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.

Keywords: Allele discovery; Chromosome segment substitution lines (CSSLs); Crop wild relatives; Genotyping by sequencing (GBS); Marker-assisted selection (MAS); Oryza sativa; Rice.

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Figures

Fig. 1
Fig. 1
Graphical genotypes, distribution of target and non-target introgressions, and genotypic statistics for 32 CUR/MER ILs. Graphic representation of the genotypic make-up for the recurrent parent CUR (gray), the donor parent MER (red) in the 32 ILs (MER1-MER32) from the bottom to the top of the graph across each of the 12 chromosomes. The chromosome where the target introgression is located, its base-pair size, number of donor segments and percentage of recurrent and donor genome are listed next to each IL. (Color figure online)
Fig. 2
Fig. 2
Graphical genotypes and distribution of target and non-target introgressions for 40 CUR/RUF ILs. Graphic representation of the genotypic make-up for the recurrent parent CUR (gray), the donor parent RUF (green) in 40 ILs (RUF1-RUF48) from the bottom to the top of the graph across each of the 12 chromosomes. The chromosome where the target introgression is located, its base-pair size, number of donor segments and percentage of recurrent and donor genome are listed next to each IL. (Color figure online)
Fig. 3
Fig. 3
a Polymorphic markers between the recurrent parent CUR and the two donor parents MER and RUF, using SSR markers, and SNP-markers from 6K Infinium platform and GBS platform. b Genotyping-platforms comparison. Illustration of a 12.2 Mbp region in chromosome 1 genotyped in two CUR/MER lines, MER3 (on the left) and MER19 (on the right) using SSR markers, a 6K-SNP Infinium chip and GBS. Respectively for each platform 4, 35 and 4,079 markers segregate. The MER alleles are color-coded red, and the CUR alleles are color-coded blue. Comparisons between platforms are determined by dashed lines. (Color figure online)
Fig. 4
Fig. 4
Chromosome 7 donor introgressions a Chromosome 7 zoom-in. Genotypic introgression of 12 different IL and parents in chromosome 7, the recurrent genome is colored in gray and the donor genome in red. The phenotype of each IL is shown in the right border b PCR products to detect the functional 14-bp indel marker in the Rc locus (Sweeney et al. 2006) from seven colored-pericarp ILs, and four white colored-pericarp, the parents CUR, RUF, MER and two controls lines IR64 and Azucena. c Summary of significant regions associated with pericarp color (LOD > 3.1) using logistic regression (SMA-LR) analysis. (Color figure online)
Fig. 5
Fig. 5
CUR/RUF upland field evaluation Boxplots showing the distribution of CUR/RUF ILs for four phenotypes. In each, the recurrent parent (CUR) is colored red and ILs significantly higher than CUR (p < 0.05) are colored orange, and lower than CUR (p < 0.05) are colored green. a ‘Days to flowering.’ b ‘Average plant height.’ c ‘Number of tillers.’ d ‘Number of panicles’. (Color figure online)
Fig. 6
Fig. 6
Upland field evaluation summary, a GBS SNP coverage across the CUR/RUF ILs population (black lines in chromosome bars), graphic location of SNPs significantly associated with ‘days to flowering’ (green lines) and ‘plant height’ (orange lines), and published QTL regions that co-localize with the associated SNPs from this study (red and blue bars). b Summary of significant regions associated with plant height (LOD > 3.5), and days to flowering (LOD > 5) using a stepwise regression single-marker analysis (SR-SMA) for days to flowering and plant height. (Color figure online)
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