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Research Project: Genomic Approaches and Genetic Resources for Improving Rice Yield and Grain Quality

Location: Dale Bumpers National Rice Research Center

Title: Why develop O. sativa x O. rufipogon chromosome segment substitution line libraries?

Author
item Eizenga, Georgia
item Singh, Namrata - Cornell University - New York
item Shakiba, Ehsan - University Of Arkansas
item Ali, M Liakat - University Of Arkansas
item Kim, Hyunjung - Cornell University - New York
item Declerck, Genevieve - Cornell University - New York
item Wright, Mark - Cornell University - New York
item Ahn, Sang-nag - Chungnam National University
item Mccouch, Susan - Cornell University - New York

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 2/1/2016
Publication Date: 7/2/2017
Citation: Eizenga, G.C., Singh, N., Shakiba, E., Ali, M., Kim, H., Declerck, G.A., Wright, M.H., Ahn, S., Mccouch, S.R. 2017. Why develop O. sativa x O. rufipogon chromosome segment substitution line libraries?. Proc. 36th Rice Technical Working Group Meeting Proceedings. p. 66. 1-4 March 2016. CDROM.

Interpretive Summary:

Technical Abstract: Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield in advanced backcross mapping populations derived from crosses between several adapted O. sativa varieties and a single accession (IRGC105491) of the ancestral parent, O. rufipogon. The phenomena of hybrid vigor, related to transgressive variation, is often observed when the O. sativa subspecies (ssp.) indica is crossed with the japonica subspecies, demonstrating the potential of transgressive variation for increasing yield and food security. The objective of this study was to develop chromosome segment substitution line (CSSL) libraries to further dissect the transgressive variation identified in O. sativa x O. rufipogon mapping populations. To develop the CSSL libraries, two adapted rice varieties, IR64 and Cybonnet, were selected as recurrent parents to represent the subspecies indica and japonica, respectively. Based on previous phylogenetic analyses, one O. rufipogon donor parent (IRGC106148) clustered with O. sativa ssp. indica accessions, one (NIAS W1944) with O. sativa ssp. japonica accessions, and the third (IRGC105567) only clustered with O. rufipogon accessions. Marker assisted backcrossing was used to select individual pre-CSSLs which were advanced each generation based on targeted segments. Initially, two Illumina 384 SNP arrays, one for each recurrent parent, were designed for genotyping and subsequent selections. The second-generation of 384 SNP arrays were redesigned to replace SNPs that performed poorly and to decrease the size of monomorphic regions. Most recently, an Infinium 5,000 SNP array was used for high-resolution genotyping and provided between 1,069 to 1,952 (˜4-5 SNP/MB) polymorphic genome-wide SNPs per library. The CSSL libraries with IRGC106148 and IRGC105567 as donors, have been advanced to the BC4F3 or BC5F3 generation and the two libraries with the W1944 donor, to the BC3F3. Currently, the CSSLs selected for each of the six libraries are being genotyped using genotyping-by-sequencing (GBS) technology. Once complete, each CSSL library will consist of 60-90 lines, with each line having the targeted wild donor segment and less than 5 percent donor DNA in the background, in most cases. Collectively, the complete set of CSSLs for a given library will represent the entire genome of the wild donor parent in the background of either IR64 or Cybonnet. Thus, the six CSSL libraries will provide complete coverage of the three divergent O. rufipogon genomes in either an indica or japonica background, and will be among the most densely genotyped CSSL libraries available to the rice community. To illustrate the usefulness of CSSL libraries for identifying genes underlying agronomically important traits, four to six segregating F2 lines derived from the heterozygous pre-CSSLs containing the specific targeted wild segment, were phenotyped in the greenhouse for several traits including days to 50% heading, plant height, culm color, presence of bent culms (elbows), plant type, number of tillers, lodging, panicle type, presence of awns, hull color and pericarp color. The genotypes of the F2 families were examined to determine if the phenotypic segregation corresponded to the genotypic segregation of the targeted wild segment. In those families where there was correspondence, the CSSLs homozygous for the targeted segment will be used to fine map the particular trait and identify the candidate gene(s) underlying the segregating trait. In the future, we will use these CSSL libraries to understand the genetic basis of transgressive variation especially as it relates to grain yield. The libraries also will be used to identify novel genes, alleles or QTL contributed by the wild donor, characterize genetic interactions between wild donor and divergent elite cultivated backgrounds, and broaden the gene pool of cultivated ric