RiceCAP bioinformatics & data management 2008 progress report and plan

1. RiceCAP bioinformatics & data management2008 progress reportand plan RiceCAP planning meeting DBNRRC April 30, 2008 Clare Nelson Dept. of Plant Pathology Kansas State University

2. Summary • Progress in 2008 (since RTWG, 2.08) • Submitted MY1 MS (Euphytica) • Resumed MY2 analysis (X. Lacaze) • Examined phenotypic data quality • Began QTL mapping • Began SB2 marker analysis (no news) • Work plans for remainder of 2008

3. Objectives and questions relative to MY2 data • Analysis of the high heterozygosity of the RILs as revealed by genotypic data • Test of possible mislabeling of the genotypes under field conditions • Detection of QTL for milling yield

4. 1. Heterozygosity MY2 dataset (Cypress x Lagrue) 108 markers 299 RILs to be used in QTL detection 15% of marker genotypes are heterozygous Question : Is heterozygosity revealed by genotyping really biological, with a genetic basis, or is it due to genotyping artifacts?

5. One wayto test for “biological heterozygosis” Chr X Chr X ? A Hetero B Hetero A B B Hetero A Hetero B A H motif HHH motif

6. Frequency of heterozygosity in MY2 % of RILs with x H motifs Number of singleton heterozygous loci % of RILs with x HHH motifs Number of triplet heterozygous loci

7. Correspondence between H and HHH motifs Chr X Hetero A B ChrX B A Hetero B Hetero A B A Hetero

8. Conclusion and perspectives • Heterozygosity in MY2 is a real biological phenomenonwith uneven distribution across chromosomes. • Strategy for QTL analysis: eliminate RILs and markers with high rate (>30%) of heterozygosity (1 RIL and 4 markers)

9. 2. Possible mislabeling, height nonuniformity Unexpected differences in height between replicates • Hypothesis: possible mislabeling of some or more RILs in AR 2006 • Is there a systematic mislabeling or just a border effect in the field data of MY2?

10. Height data from AR 2007 LaGrue allele 0 < 110 cm Cypress allele 1 > 110 cm R. Fjellstrom pers. comm.

11. Height data from AR 2007 plus sd1 assignment Semidwarf gene R. Fjellstrom pers. comm.

12. Height data from AR 2007, deduced vs. observed allele Good correspondence between phenotypic and genotypic information

13. AR 2006 : mislabeling or a border effect? REP1 REP2

14. In presence of a simulated mislabeling REP 1

15. Conclusion and perspectives Mislabeling of MY2 RILs in field? • There was no mislabeling of the genotypes • There was in AR 2006 a possibleherbicide effect on the borders • Irregularities such as those in height were not observed in phenology or milling traits.

16. 3. QTL detection for milling yield Milling yield in AR, LA 2006, 2007 • % Whole and % Total • Traits showed similar heritability: 0.43 • Heritability of height: 0.93 • SS for GxE (% of total SS) 34%, 38%

17. QTL detection results Quantitative trait: % total “QTL chr1” - additive effect : 0.8 - Cypress > Lagrue

18. QTL detection results for % whole quantitative trait % whole “QTL chr10” - additive effect : 1.1 - Cypress > Lagrue

19. QTL detection results QTL chr1 colocates with QTL of grain filling duration QTL chr10 colocates with QTL of heading date

20. 4. Conclusions and perspectives QTL detection for milling yield • Milling yield is subject to G x E interaction • QTL for milling yield are probably QTL for phenology and grain filling duration and are subject to QTL x E interaction • QTL on chr10 is also a QTL implicated in fissuring • We would like to understand the climatic scenarios (temperature, humidity) that favor losses in milling yield. • For this we plan to incorporate the climatic conditions of each experiment