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Oryza sativa mini-core collection

The Rice Biodiversity Center for Africa has genotyped a total of 5,738 O. sativa accessions with 49,685 SNPs of which 25,904 SNPs were polymorphic. Using the SNP genotype data, we have selected a subset of the most genetically diverse 600 O. sativa accessions to represent a mini-core set, which includes 400 indica and 200 japonica accessions. This mini-core represents 54 countries and 6 rice growing ecologies, with 77.3% of them originating within Africa.

Nearly 99% of the SNPs that were polymorphic across the 5,738 accessions were polymorphic in the mini-core set. Genetic distance between pairs of the 5,738 accessions varied from 0.010 to 0.441 and the overall average was 0.256. In the mini-core set, genetic distance varied from 0.050 to 0.445 with an average of 0.300. The proportion of pairs of accessions with a genetic distance exceeding 0.256 (which is the average in all accession) was just 35.6% in the whole set as compared with 77.9% in the mini-core set.

Type of subset

Selective

Method of selection

DArTseq-based genotyping

Crop

rice

Number of accessions

600

FAO WIEWS Institute

Africa Rice Center

Creation date

2020

Published in Genesys

20 January 2022

Subset metadata

Subset creators

Data curator

Marie-Noelle Ndjiondjop Africa Rice Center

Data collector

Kpeki Sedjro Bienvenu AfricaRice

Data manager

Romeo Jesuskpego Tohoun Africa Rice Center

Data collector

Comlan Arnaud Gouda Africa Rice Center

Data and resources

MCPD passport data

MCPD - 9dbff968-cdf6-4840-a71f-69445fd84662.xlsx

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Accessions

List of accessions included in the subset

1. WAB0000010 • Oryza sativa L. subsp. japonica S.Kato • IAC 164 • Advanced/improved cultivar • BRA

CIV033 • DOI: 10.18730/H85V1

2. WAB0000016 • Oryza sativa L. subsp. japonica S.Kato • ITA 317 • Advanced/improved cultivar • NGA

CIV033 • DOI: 10.18730/H8606

3. WAB0000025 • Oryza sativa L. subsp. japonica S.Kato • IDSA 6 • Advanced/improved cultivar • CIV

CIV033 • DOI: 10.18730/H865B

4. WAB0000054 • Oryza sativa L. subsp. japonica S.Kato • WAB181-18 • Advanced/improved cultivar • CIV

CIV033 • DOI: 10.18730/H86W$

5. WAB0000055 • Oryza sativa L. subsp. indica S.Kato • ITA 333 • Advanced/improved cultivar • NGA

CIV033 • DOI: 10.18730/H86X=

6. WAB0000072 • Oryza sativa L. subsp. indica S.Kato • ITA 325 • Advanced/improved cultivar • NGA

CIV033 • DOI: 10.18730/H87AB

7. WAB0000202 • Oryza sativa L. subsp. japonica S.Kato • IR 74095-AC-64 • Breeding/Research Material • PHL

CIV033 • DOI: 10.18730/H89B2

8. WAB0000221 • Oryza sativa L. subsp. japonica S.Kato • IRAT 104 • Advanced/improved cultivar • CIV

CIV033 • DOI: 10.18730/H89PD

9. WAB0000273 • Oryza sativa L. subsp. indica S.Kato • TOX 3443-65-2-3-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H8AF1

10. WAB0001503 • Oryza sativa L. subsp. indica S.Kato • TOG 6297 • Traditional cultivar/Landrace • LBR

CIV033 • DOI: 10.18730/H8EVY

11. WAB0001599 • Oryza sativa L. subsp. japonica S.Kato • TOG 6397 • Traditional cultivar/Landrace • LBR

CIV033 • DOI: 10.18730/SEA2T

12. WAB0003657 • Oryza sativa L. subsp. indica S.Kato • BG 367-4 • Advanced/improved cultivar • LKA

CIV033 • DOI: 10.18730/H92R1

13. WAB0003661 • Oryza sativa L. subsp. indica S.Kato • BKN 6806-46-60 • Breeding/Research Material • THA

CIV033 • DOI: 10.18730/H92W5

14. WAB0004142 • Oryza sativa L. subsp. indica S.Kato • RD 15 • Traditional cultivar/Landrace • THA

CIV033 • DOI: 10.18730/H979=

15. WAB0004150 • Oryza sativa L. subsp. indica S.Kato • ROK 10 • Advanced/improved cultivar • SLE

CIV033 • DOI: 10.18730/H97E3

16. WAB0004194 • Oryza sativa L. subsp. indica S.Kato • TOX 1941-5-103-202 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H98AZ

17. WAB0004201 • Oryza sativa L. subsp. indica S.Kato • TOX 3095-71-1-3-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H98H1

18. WAB0004211 • Oryza sativa L. subsp. indica S.Kato • TOX 3114-10-1-2-3-3 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H98TA

19. WAB0004217 • Oryza sativa L. subsp. indica S.Kato • TOX 3133-11-1-3-1-1-1-1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H98ZF

20. WAB0004229 • Oryza sativa L. subsp. indica S.Kato • TOX 3380-42-1-4-1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H998R

21. WAB0004298 • Oryza sativa L. subsp. indica S.Kato • AMINA NJAI MANO • Traditional cultivar/Landrace • GMB

CIV033 • DOI: 10.18730/H9AJX

22. WAB0004316 • Oryza sativa L. subsp. indica S.Kato • DANEWOL DIONDORI (WALA LADDE) • Traditional cultivar/Landrace • MLI

CIV033 • DOI: 10.18730/H9B39

23. WAB0004320 • Oryza sativa L. subsp. japonica S.Kato • IET 8580 • Breeding/Research Material • IND

CIV033 • DOI: 10.18730/H9B7D

24. WAB0004341 • Oryza sativa L. subsp. indica S.Kato • ITA 418 • Advanced/improved cultivar • NGA

CIV033 • DOI: 10.18730/H9BMT

25. WAB0004377 • Oryza sativa L. subsp. indica S.Kato • B 7546G-KN-1 • Breeding/Research Material • IDN

CIV033 • DOI: 10.18730/H9CRS

26. WAB0004469 • Oryza sativa L. subsp. indica S.Kato • TOX 3211-14-1-2-2-1B • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9FA~

27. WAB0004545 • Oryza sativa L. subsp. indica S.Kato • ECIA 66-129-1-1-1 • Breeding/Research Material • CUB

CIV033 • DOI: 10.18730/H9HBR

28. WAB0004556 • Oryza sativa L. subsp. indica S.Kato • GIGANTE (TETE) • Traditional cultivar/Landrace • MOZ

CIV033 • DOI: 10.18730/H9HN$

29. WAB0004577 • Oryza sativa L. subsp. indica S.Kato • KAU 166 • Traditional cultivar/Landrace • IND

CIV033 • DOI: 10.18730/H9J9H

30. WAB0004661 • Oryza sativa L. subsp. indica S.Kato • TOX 3211-49-1-2-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9MPM

31. WAB0004692 • Oryza sativa L. subsp. indica S.Kato • CHOKOTO • Traditional cultivar/Landrace • JPN

CIV033 • DOI: 10.18730/H9NKC

32. WAB0004806 • Oryza sativa L. subsp. indica S.Kato • DOM SOFOOD • Traditional cultivar/Landrace • IRN

CIV033 • DOI: 10.18730/H9RZ9

33. WAB0004807 • Oryza sativa L. subsp. indica S.Kato • DR 60 • Breeding/Research Material • PAK

CIV033 • DOI: 10.18730/H9S0A

34. WAB0004810 • Oryza sativa L. subsp. indica S.Kato • FRX 23F3B-13F6BF7 • Breeding/Research Material • MWI

CIV033 • DOI: 10.18730/H9S3D

35. WAB0004811 • Oryza sativa L. subsp. indica S.Kato • FRX 78F3B-12F4BF5 • Breeding/Research Material • MWI

CIV033 • DOI: 10.18730/H9S4E

36. WAB0004846 • Oryza sativa L. subsp. indica S.Kato • CK 4 • Traditional cultivar/Landrace • GIN

CIV033 • DOI: 10.18730/H9SY3

37. WAB0004871 • Oryza sativa L. subsp. indica S.Kato • TOX 3519-45-1-2-1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9TDJ

38. WAB0004873 • Oryza sativa L. subsp. indica S.Kato • TCA 80-4 • Traditional cultivar/Landrace • IND

CIV033 • DOI: 10.18730/H9TFM

39. WAB0004928 • Oryza sativa L. subsp. indica S.Kato • TOX 3441-123-2-3-2-3-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9VHH

40. WAB0004951 • Oryza sativa L. subsp. indica S.Kato • TOX 3413-210-3-2-1-1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9W2$

41. WAB0004963 • Oryza sativa L. subsp. indica S.Kato • WITA 11 • Advanced/improved cultivar • CIV

CIV033 • DOI: 10.18730/H9WB6

42. WAB0004973 • Oryza sativa L. subsp. indica S.Kato • MASS • Traditional cultivar/Landrace • NGA

CIV033 • DOI: 10.18730/H9WJD

43. WAB0004984 • Oryza sativa L. subsp. indica S.Kato • KSHIRA • Traditional cultivar/Landrace • SLE

CIV033 • DOI: 10.18730/H9WTN

44. WAB0005048 • Oryza sativa L. subsp. indica S.Kato • TOX 3913-1-1-1-1-3-3 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/H9YC$

45. WAB0005194 • Oryza sativa L. subsp. indica S.Kato • TOX 3967-31-2-3-3-1-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/HA1EN

46. WAB0005437 • Oryza sativa L. subsp. indica S.Kato • PTB 12 • Traditional cultivar/Landrace • IND

CIV033 • DOI: 10.18730/HA3QM

47. WAB0005479 • Oryza sativa L. subsp. indica S.Kato • TOX 4329-WAT-36-3-3-2-1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/HA4JA

48. WAB0005519 • Oryza sativa L. subsp. indica S.Kato • TOX 4335-WAT-21-2-1-3-2 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/HA5QA

49. WAB0005564 • Oryza sativa L. subsp. indica S.Kato • TOX 4216-WAT-26-3-1-E1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/HA6P4

50. WAB0005598 • Oryza sativa L. subsp. indica S.Kato • TOX 4312-WAT-63-3-2-E1 • Breeding/Research Material • NGA

CIV033 • DOI: 10.18730/HA6YC