View Full Table | Close Full ViewTable 1.

Chenopodium accessions included in the diversity panel. Underscored accessions were used in the genomic reduction experiment for single nucleotide polymorphism (SNP) discovery.

Name Species† Coded name Passport origin Source‡
PI 614881 C. quinoa A1 Jujuy, Argentina USDA-NPGS
PI 614883 C. quinoa A2 Jujuy, Argentina USDA-NPGS
PI 614884 C. quinoa A3 Jujuy, Argentina USDA-NPGS
PI 587173 C. quinoa A4 Jujuy, Argentina USDA-NPGS
Jujuy C. quinoa A_Jujuy Jujuy, Argentina CIP-FAO
PI 614902 C. quinoa B2 Oruro, Bolivia USDA-NPGS
PI 614904 C. quinoa B3 Oruro, Bolivia USDA-NPGS
PI 614905 C. quinoa B4 Oruro, Bolivia USDA-NPGS
PI 614907 C. quinoa B6 Oruro, Bolivia USDA-NPGS
PI 614909 C. quinoa B8 Oruro, Bolivia USDA-NPGS
PI 614910 C. quinoa B9 Oruro, Bolivia USDA-NPGS
PI 614911 C. quinoa B10 Oruro, Bolivia USDA-NPGS
PI 614912 C. quinoa B11 Oruro, Bolivia USDA-NPGS
PI 614915 C. quinoa B13 Oruro, Bolivia USDA-NPGS
PI 614916 C. quinoa B14 Oruro, Bolivia USDA-NPGS
PI 614919 C. quinoa B15 Oruro, Bolivia USDA-NPGS
PI 614920 C. quinoa B16 Oruro, Bolivia USDA-NPGS
PI 614927 C. quinoa B23 La Paz, Bolivia USDA-NPGS
PI 614928 C. quinoa B24 La Paz, Bolivia USDA-NPGS
PI 614929 C. quinoa B25 La Paz, Bolivia USDA-NPGS
PI 614931 C. quinoa B27 Oruro, Bolivia USDA-NPGS
PI 614932 C. quinoa B28 Oruro, Bolivia USDA-NPGS
PI 614933 C. quinoa B29 Oruro, Bolivia USDA-NPGS
PI 614934 C. quinoa B30 Oruro, Bolivia USDA-NPGS
PI 614935 C. quinoa B31 Oruro, Bolivia USDA-NPGS
PI 614936 C. quinoa B32 Oruro, Bolivia USDA-NPGS
PI 614937 C. quinoa B33 Oruro, Bolivia USDA-NPGS
PI 614938 C. quinoa B34 Oruro, Bolivia USDA-NPGS
PI 478415 C. quinoa B35 La Paz, Bolivia USDA-NPGS
PI 478418 C. quinoa B36 Potosi, Bolivia USDA-NPGS
PI 478410 C. quinoa B37 La Paz, Bolivia USDA-NPGS
PI 478414 C. quinoa B38 La Paz, Bolivia USDA-NPGS
PI 614002 C. quinoa B39 Cochabamba, Bolivia USDA-NPGS
Ames 13215 C. quinoa B40 La Paz, Bolivia USDA-NPGS
PI 478408 C. quinoa B41 La Paz, Bolivia USDA-NPGS
Ames 13217 C. quinoa B42 La Paz, Bolivia USDA-NPGS
Ames 13218 C. quinoa B43 La Paz, Bolivia USDA-NPGS
Ames 13219 C. quinoa B44 La Paz, Bolivia USDA-NPGS
Embrapa C. quinoa BRZ_Embrapa Brazil CIP
Chucapaca C. quinoa B_Chucapaca Bolivia PROINPA
Jaccha Grano C. quinoa B_JacchaGrano Bolivia PROINPA
Kamiri C. quinoa B_Kamiri Bolivia CIP
L-26 C. quinoa B_L-26 Bolivia PROINPA
L-P C. quinoa B_LP Bolivia PROINPA
Maniquena C. quinoa B_Maniquena Bolivia PROINPA
Mocko C. quinoa B_Mocko Bolivia PROINPA
Pandela C. quinoa B_Pandela Bolivia PROINPA
Ratuqui C. quinoa B_Ratuqui Bolivia CIP
Real C. quinoa B_Real Oruro, Bolivia CIP
Sayana C. quinoa B_Sayana Bolivia CIP
Surumi C. quinoa B_Surumi Bolivia PROINPA
Ames 22153 C. quinoa C1 Pichilemu, Chile USDA-NPGS
Ames 22154 C. quinoa C2 Cajon, Chile USDA-NPGS
Ames 22155 C. quinoa C3 Pichaman, Chile USDA-NPGS
Ames 22156 C. quinoa C4 Cajon, Chile USDA-NPGS
Ames 22157 C. quinoa C5 Lo Valdivia, Chile USDA-NPGS
Ames 22158 C. quinoa C6 Llico, Chile USDA-NPGS
Ames 22159 C. quinoa C7 Bucalemu, Chile USDA-NPGS
Ames 22160 C. quinoa C8 Iloca, Chile USDA-NPGS
Ames 22161 C. quinoa C9 Llico, Chile USDA-NPGS
PI 614880 C. quinoa C10 Los Lagos, Chile USDA-NPGS
PI 614880 C. quinoa C10b Los Lagos USDA-NPGS
PI 614882 C. quinoa C11 La Araucania, Chile USDA-NPGS
PI 614885 C. quinoa C12 Bio-Bio, Chile USDA-NPGS
PI 614886 C. quinoa C13 Maule, Chile USDA-NPGS
PI 614887 C. quinoa C14 Bio-Bio, Chile USDA-NPGS
PI 614888 C. quinoa C15 Bio-Bio, Chile USDA-NPGS
PI 614889 C. quinoa C16 Bio-Bio, Chile USDA-NPGS
PI 433232 C. quinoa C17 Groben, Chile USDA-NPGS
PI 584524 C. quinoa C18 Chillan, Chile USDA-NPGS
RU-2 C. quinoa CENG_RU-2 England–Chilean origin CIP
NL-6 C. quinoa CHOL_NL6 Holland–Chilean origin CIP
PI 596293 C. quinoa CO1 Colorado, U.S. USDA-NPGS
Narino C. quinoa COL_Narino Columbia CIP
BaerI C. quinoa C_BaerI Chile CIP
G-205-95DK C. quinoa C_G20595DK Denmark–Chilean origin PROINPA
KU-2 C. quinoa C_KU2 Chile CIP
KU-2b§ C. quinoa C_KU2b Chile PROINPA
Ollague C. quinoa C_Ollague Chile CIP
Ames 13228 C. quinoa E1 Otavalo, Equador USDA-NPGS
ECU-420 C. quinoa E_ECU420 Ecuador CIP
Ingapirca C. quinoa E_Ingapirca Ecuador CIP
L-3204 C. quinoa L-3204 Bolivia PROINPA
NSL 86628 C. quinoa MD1 Maryland, U.S. USDA-NPGS
PI 510532 C. quinoa P1 Puno, Peru USDA-NPGS
PI 510533 C. quinoa P2 Puno, Peru USDA-NPGS
PI 510536 C. quinoa P3 Puno, Peru USDA-NPGS
PI 510537 C. quinoa P4 Puno, Peru USDA-NPGS
PI 510543 C. quinoa P5 Puno, Peru USDA-NPGS
PI 510547 C. quinoa P6 Puno, Peru USDA-NPGS
PI 510551 C. quinoa P8 Puno, Peru USDA-NPGS
PI 596498 C. quinoa P9 Cusco, Peru USDA-NPGS
PI 510542 C. quinoa P10 Puno, Peru USDA-NPGS
PI 510540 C. quinoa P11 Puno, Peru USDA-NPGS
PI 510550 C. quinoa P12 Puno, Peru USDA-NPGS
PI 510545 C. quinoa P13 Puno, Peru USDA-NPGS
PI 510548 C. quinoa P14 Puno, Peru USDA-NPGS
Ames 26191 C. quinoa P15 Puno, Peru USDA-NPGS
PI 510546 C. quinoa P16 Puno, Peru USDA-NPGS
0654 C. quinoa P_0654 Puno, Peru PROINPA
03-21-072RM C. quinoa P_0321072RM Puno, Peru CIP
03-21-079BB C. quinoa P_0321079BB Puno, Peru CIP
CICA-17 C. quinoa P_CICA17 Cusco, Peru CIP
CICA-67 C. quinoa P_CICA67 Peru CIP
E-DK-4 C. quinoa P_EDK4 Denmark–Peruvian origin CIP
G-205-95 C. quinoa P_G20595 Peruvian origin CIP
Huariponcho C. quinoa P_Huariponcho Puno, Peru CIP
Illpa C. quinoa P_Illpa Puno, Peru CIP
Kancolla C. quinoa P_Kancolla Puno, Peru CIP
Salcedo C. quinoa P_Salcedo Puno, Peru CIP
NSL 86649 C. quinoa SC1 South Carolina, U.S. USDA-NPGS
Ames 19047 C. quinoa TX1 Texas, U.S. USDA-NPGS
NSL 92331 C. quinoa WA1 Washington, U.S. USDA-NPGS
Ames 29207 C. berlandieri var. macrocalycium Ames 29207 Maine, U.S. USDA-NPGS
BYU 567 C. berlandieri subsp. nuttalliae BYU 567 Mexico ININ-Mexico
Ames 29307 BYU 802 C. berlandieri var. boscianum BYU 802 Louisiana, U.S. USDA-NPGS
BYU 652 C. berlandieri var. zschackei BYU 652 Utah, U.S. BYU
BYU 943 C. ficifolium BYU 943 Czech Republic IEB
BYU 1101 C. hircinum BYU 1101 Argentina UBA
BYU 1102 C. hircinum BYU 1102 Argentina UBA
BYU 839 C. watsonii BYU 839 New Mexico (2X) BYU
Chenopodium ficifolium and C. watsonii are diploid species. All other species are allotetraploids.
Origin information is derived from the Germplasm Resources Information Network for all USDA accessions. BYU, Brigham Young University, Provo, UT; CIP, Internal Potato Center, FAO; IEB, Institute of Experimental Botany, Czech Republic; ININ, National Institute for Nuclear Investigation, Toluca, Mexico; PROINPA, The Foundation for the Promotion and Investigation of Andean Products, La Paz, Bolivia; UBA, University of Buenos Aires, Buenos Aires, Argentina; USDA-NPGS, USDA National Plant Germplasm System, Ames, IA.
§Two different sources for KU-2 were included the genomic reduction (PROINPA and CIP).

View Full Table | Close Full ViewTable 2.

Summary information for single nucleotide polymorphisms (SNPs) identified for each populations.

Population (Pop)† SNPs‡ Unique contigs‡ SNP base coverage Minor allele frequency range
SNP type (%)
20–29% 30–39% 40–49% A/C A/G A/T C/G C/T G/T
Pop1 2885 1514 7.8 817 1072 996 10.2 30.6 12.2 4.5 31.3 11.2
Pop39 3615 1888 8.0 993 1055 874 10.8 30.5 12.7 5.2 29.5 11.3
Pop40 2918 1551 8.0 767 1102 1049 10.9 31.0 11.5 5.7 30.4 10.5
PopM3 2092 995 7.6 599 759 734 10.1 29.5 12.9 5.02 32.2 10.3
PopGO 2668 1359 7.7 739 1055 874 10.3 31.5 11.54 5.25 30.8 10.6
Average 2836 1461 7.8 783 1009 905 10.5 30.6 12.2 5.1 30.8 10.8
Pop1 is KU-2 × 0654; Pop39 is NL-6 × 0654; Pop40 is NL-6 × Chucapaca; PopM3 is L-P × 0654; PopGO × G-205-95 × Ollague.
SNPs were called if coverage at the base was ≥6x, the frequency of the minor allele was ≥20%, and 100% of the alleles called within a parental line were identical.