ARS | Publication request: Analysis of Plant Traits in Rice Sub-populations and O. rufipogon

Submitted to: Rice Technical Working Group Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: December 1, 2007
Publication Date: March 1, 2008
Citation: Eizenga, G.C., Ali, M.L., McCouch, S.R., McClung, A.M. 2008. Analysis of plant traits in rice sub-populations and O. rufipogon. In: Proceedings of the 32nd Rice Technical Working Group Meetings, February 18-21, 2008, San Diego, CA. 2008. CDROM.

Technical Abstract: The main objective of this project is to determine if the sub-population structure in rice is predictive of transgressive variation (the occurrence of progeny displaying phenotypes more extreme than either parent) and begin to characterize the underlying genetic basis of this phenomenon in part by developing chromosome segment substitution lines (CSSLs) between rice (Oryza sativa) and its progenitor, O. rufipogon. At this time, the preliminary data collected on agronomic and seed traits on a diverse collection of O. sativa and O. rufipogon accessions for an association mapping study are reported. The 400 O. sativa accessions included 174 diverse accessions genotyped in previous studies by S.R. McCouch, 165 accessions which are a subset of the USDA-ARS NSGC core collection, 57 accessions from the USDA-ARS O. sativa germplasm collection, and four reference cultivars (Spring, Cocodrie, Cybonnet and 93-11). In 2006, these accessions were grown as space plants in two replications and a single plant selected for purification, evaluation and seed increase in the 2007 growing season with a similar plot design. Also, 100 O. rufipogon accessions were selected from 208 accessions based on genotyping with 36 SSR markers, plant type, seed set, and crossability. The O. rufipogon accessions were purified as single plants selections and are being characterized for most of the same traits as the O. sativa accessions. All accessions are being genotyped with 30-36 SSR markers. These SSR markers overlap significantly with those being used for genotyping on the USDA-ARS NCGC core collection, the standard panel for rice used at Cornell Univ., and those being used for genotyping as part the Generation Challenge Program at the International Rice Research Institute, Philippines. In the field during 2006 and 2007, the O. sativa accessions were characterized for days to heading which ranged from 47-127 days; plant height (62-208 cm), number of panicles per plant (3-104 panicles), and plant type grouped into five categories. In 2006 the plants matured about 9 days earlier and were shorter as compared to data for these traits collected in 2007. The primary panicle was characterized for flag leaf length ranging from 12-85 cm, flag leaf width (0.5-2.3 cm), panicle length (12.8-50.0 cm), number of primary panicle branches per panicle (5-19 branches), florets per panicle (57-404 florets) and seeds per panicle (0-344 seeds). The percent lodging, type of panicle, type of awn, seed shattering, and leaf pubescence also were noted. The seeds are being characterized with the WinSEEDLE Image Analysis system. Preliminary data on paddy rice (with hull) from 167 accessions grown in 2006 included hull color which divided into six categories, seed length ranged from 6.4-12.8 mm, seed width (2.2-3.9 mm), curved seed length (6.5-12.9 mm), curved seed width (2.2-3.9 mm), and seed volume (3.6-17.4 mm3). Subsequently, similar data were collected on dehulled grains including seed color which divided into six categories, grain length (4.6-9.0 mm), grain width (1.8-3.6 mm), curved grain length (4.7-8.2 mm), curved grain width (1.8-3.3 mm), and grain volume (2.7-12.4 mm3). The chemical characteristics of percent amylose, alkali spreading value and grain protein also will be determined. The genotype of the 400 O. sativa accessions is being confirmed with 30 SSR markers. A cluster analysis will group the O. sativa accessions with one of the two rice sub-species, indica or japonica and most accessions should group into one of the five rice sub-populations (indica, tropical japonica, temperate japonica, aromatic or aus). These sub-populations will be an important consideration in the analysis of the phenotypic trait data. Similarly, the 100 O. rufipogon accessions are being evaluated for most of the same traits as the O. sativa accessions in the greenhouse. Preliminary data collected on many of the 208 O. rufipogon accessions determined that the plant height ranged from 30-200 cm, number of tillers per plant from 1-220 tillers, and the plant type grouped into nine categories. Seed traits being measured with the WinSEEDLE Image Analysis included hull color, seed length, seed width, curved seed length, curved seed width, seed surface area, and seed volume. In co-operation with co-PI: Carlos Bustamante (Dept. of Biological Statistics & Computational Biology, Cornell Univ.), these data will be used to conduct an association mapping analysis with the 10,000 SNPs to identify marker-trait associations for the 32 phenotypic traits presently being characterized in the 400 O. sativa and 100 O. rufipogon accessions. This research is supported by the NSF Plant Genome Project grant no. 0606461 entitled “Exploring the Genetic Basis of Transgressive Variation in Rice”.