Development of chromosome 6D-specific markers for α-gliadin

genes and their use in assessing dynamic changes at the Gli-2

loci

Peng-Fei Qi1, 2, Yu-Ming Wei1&, Guo-Yue Chen1, Qian-Tao Jiang1, Ya-Xi Liu1, Wei Li3,

Shou-Fen Dai1, You-Liang Zheng2&

1 Triticeae Research Institute, Sichuan Agricultural University, Yaan, Sichuan 625014,

China

2 Key Laboratory of Southwestern Crop Germplasm Utilization, Ministry of

Agriculture, Sichuan Agricultural University, Ya’an, Sichuan 625014, China

3 Agronomy College, Sichuan Agricultural University, Yaan, Sichuan 625014, China

& Corresponding authors. Y.M. Wei, E-mail: ymwei@sicau.edu.cn; Y.-L Zheng,

E-Mail: ylzheng@sicau.edu.cn; Phone: +86-835-2882007; Fax +86-835-2883153

Submitted to Molecular Breeding

Supplementary files

Supplementary Table 1 Detection of the 11 chromosome 6D-specific PM markers in

21 Sichuan local varieties of T. aestivum. '1' and '0' indicate positive and negative PM

markers, respectively

Supplementary Table 2 Detection of the 11 chromosome 6D-specific PM markers in

47 accessions of T. aestivum subspecies. '1' and '0' indicate positive and negative PM

markers, respectively

Supplementary Table 3 Detection of the 11 chromosome 6D-specific PM markers in

55 accessions of Ae. tauschii. '1' and '0' indicate positive and negative PM marker,

respectively

Supplementary Fig. 1 Bootstrap tested (1000 replicates) neighbor-joining tree for

α-gliadin genes. Accession numbers ended with the letter ‘p’ indicate pseudogenes.

Bold symbols (I, II, III, IV and V) indicate boxed clusters

Species

Accession

Gli-39A

Gli-56T

Gli-135G

Gli-190G

Gli-195T

Gli-268A

Gli-723A

Gli-724G

Gli-734T

Gli-841G

Gli-857C

C

Total

AS1589 1 1 1 1 1 1 1 1 1 1 0 10AS1647 1 1 1 1 1 1 1 1 0 1 0 9AS1588 1 1 1 1 1 1 1 1 1 1 0 10AS1587 1 1 1 1 1 1 1 1 1 1 0 10AS1648 1 1 1 1 1 1 1 1 1 1 0 10AS1649 1 1 1 1 1 1 1 1 1 1 0 10AS1676 1 1 1 1 1 1 1 1 1 1 0 10AS1672 1 1 1 1 1 1 1 1 1 1 0 10AS1652 1 1 1 1 1 1 1 1 1 1 0 10AS1577 1 1 1 1 1 1 1 1 1 1 0 10AS1579 1 1 1 1 1 1 1 1 1 1 0 10AS1582 1 1 1 1 1 1 1 1 1 1 0 10AS1675 1 1 1 1 1 1 1 1 1 1 0 10AS1572 1 1 1 1 1 1 1 1 1 1 0 10AS1625 1 1 1 1 1 1 1 1 1 1 0 10AS1699 1 1 1 1 1 1 1 1 1 1 0 10AS1670 1 1 1 1 1 1 1 1 1 1 0 10AS1592 1 1 1 1 1 1 1 1 1 1 0 10AS1598 1 1 1 1 1 1 1 1 1 1 0 10AS1590 1 1 1 1 1 1 1 1 1 1 0 10AS1641 0 1 0 1 1 1 1 1 0 1 0 7

20 21 20 21 21 21 21 21 19 21 0Total

T. aestivum

(Sichuan local varieties)

FushunZhongjiangFushunLongchangSantai

AnyueZizhongAnyue

GaoxianDianjiang

Tongnan

YibinYilongNanchongPengxian

FengduJiangjinLuxianGaoxian

Origin

SantaiQiuyang

Supplementary Table 1 Detection of the 11 chromosome 6D-specific PM markers in 21 Sichuanlocal varieties of T. aestivum. '1' and '0' indicate positive and negative PM markers, respectively

Species

Accession

Gli-39A

Gli-56T

Gli-135G

Gli-190G

Gli-195T

Gli-268A

Gli-723A

Gli-724G

Gli-734T

Gli-841G

Gli-857C

C

Total

PI352466 1 1 1 1 1 1 1 1 1 1 0 10PI355508 1 1 1 1 1 1 1 1 1 1 1 11PI355510 1 1 1 0 1 1 1 1 0 1 1 9PI355513 0 0 1 0 1 1 1 1 0 1 0 6PI355514 1 1 1 1 1 1 1 1 1 1 0 10PI428146 1 1 1 0 1 1 1 1 1 1 0 9PI428148 1 1 1 0 1 1 1 1 0 1 0 8PI428178 1 1 1 1 1 1 1 1 1 1 0 10PI528179 0 1 1 0 1 1 1 1 1 1 0 8PI572909 0 1 1 0 1 1 1 1 0 1 1 8PI323439 1 1 1 1 1 1 1 1 1 1 0 10CItr8610 1 1 1 1 1 1 1 1 1 1 0 10PI277141 1 1 1 1 1 1 1 1 1 1 0 10PI272580 1 1 1 1 1 1 1 1 1 1 0 10PI272581 1 1 1 1 1 1 1 1 1 1 0 10PI282451 1 1 1 1 1 1 1 1 1 1 0 10PI282452 1 1 1 1 1 1 1 1 1 1 0 10PI352499 1 1 1 1 1 1 1 1 1 1 0 10PI324492 1 1 1 1 1 1 1 1 1 1 0 10PI337997 1 1 1 1 1 1 1 1 1 1 0 10PI115818 1 1 1 1 1 1 1 1 1 1 0 10PI42013 1 1 1 1 1 1 1 1 1 1 0 10PI42014 1 1 1 1 1 1 1 1 1 1 0 10PI 294567 1 1 1 1 1 1 1 1 1 1 0 10PI 486428 1 1 1 1 1 1 1 1 1 1 0 10PI 554120 1 1 1 1 1 1 1 1 1 1 0 10PI 554121 1 1 1 1 1 1 1 1 1 1 0 10PI 565431 1 1 1 1 1 1 1 1 1 1 0 10PI 566594 1 1 1 1 1 1 1 1 1 1 0 10PI 599665 1 1 1 1 1 1 1 1 1 1 0 10PI 606764 1 1 1 1 1 1 1 1 1 1 0 10PI 630983 1 1 1 1 1 1 1 1 1 1 0 10PI 352303 1 1 1 1 1 1 1 1 1 1 0 10PI 357307 1 1 1 1 1 1 1 1 1 1 0 10PI 372151 1 1 1 0 1 1 1 1 1 1 0 9CItr13967 1 1 1 1 1 1 1 1 1 1 0 10CItr14138 1 1 1 1 1 1 1 1 1 1 0 10CItr15071 0 0 1 0 1 1 1 1 1 1 0 7CItr17764 1 1 1 1 1 1 1 1 1 1 0 10PI168682 1 1 1 1 1 1 1 1 1 1 0 10PI190960 1 1 1 1 1 1 1 1 0 1 0 9PI190963 1 1 1 1 1 1 1 1 1 1 1 11PI191100 1 1 1 1 1 1 1 1 1 1 0 10PI191392 1 1 1 1 1 1 1 1 1 1 0 10PI191617 1 1 1 1 1 1 1 1 1 1 0 10PI192717 1 1 1 1 1 1 1 1 1 1 0 10PI221404 0 1 1 1 1 1 1 1 0 1 0 8

42 45 47 39 47 47 47 47 41 47 4

India

IndiaIndia

Former Soviet UnionFormer Soviet UnionFormer Soviet Union

AustraliaGeorgia

IndiaIndia

Yugoslavia Serbia

AustraliaAustralia, Victoria

US, OregonUS, WashingtonUS, WashingtonAustralia

US, Virginia

PolandPortugal

US, OregonUS,OregonUS US, Washington

Spain, ZaragozaSpain, Zaragoza

Germany

UnknownUS, MontanaUS, Ohio

US,Washington

India

IndiaUS,Colorado

Former Soviet Union

IndiaIndiaIndia

SwitzerlandSweden, UppsalaRussian, StavroItaly, LatiumIran, Esfahan

China,Jiangsu

Supplementary Table 2 Detection of the 11 chromosome 6D-specific PM markers in 47accessions of T. aestivum subspecies. '1' and '0' indicate positive and negative PM markers,respectively

Origin

Total

T. aestivum

ssp. macha

T. aestivum

ssp. sphaerocossumT

. aestivum ssp. com

pactum

US,Nebraska

T. aestivum

ssp. spelta

Spain Ethiopia

Accession

Gli-39A

Gli-56T

Gli-135G

Gli-190G

Gli-195T

Gli-268A

Gli-723A

Gli-724G

Gli-734T

Gli-841G

Gli-857C

C

Total

CIae 5 1 1 0 1 0 0 1 1 1 1 0 7CIae 8 0 0 0 1 1 1 1 1 1 1 0 7CIae 10 1 1 1 1 1 1 1 1 1 1 0 10CIae 13 1 1 1 1 1 1 1 1 1 1 0 10CIae 17 1 0 1 0 0 1 0 1 0 1 0 5CIae 19 1 0 0 1 1 1 1 1 1 1 0 8CIae 20 0 0 0 1 1 1 1 1 1 1 0 7PI431599 0 0 1 0 1 0 0 1 1 1 0 5PI431603 0 0 1 1 1 0 0 1 1 1 0 6PI452130 1 1 0 1 0 0 1 1 1 1 1 8PI476874 1 1 1 1 0 0 1 1 1 1 0 8PI486265 1 1 1 1 1 1 1 1 1 0 0 9PI486266 0 0 1 1 1 1 1 1 1 1 0 8PI486267 0 0 1 0 1 1 0 1 0 0 0 4PI486268 1 1 1 1 1 1 0 1 1 0 0 8PI486270 1 1 1 1 1 0 1 1 1 1 0 9PI486271 1 1 1 1 0 1 1 1 1 1 1 10PI486272 1 1 1 1 1 1 1 1 1 1 0 10PI486274 1 1 1 1 1 1 1 1 1 1 0 10PI486275 1 1 0 1 0 1 1 1 1 1 0 8PI486276 1 1 1 1 0 1 1 1 1 1 1 10PI486277 0 0 1 1 0 1 1 1 1 1 0 7PI499262 1 1 1 1 0 0 1 1 1 1 0 8PI499264 1 1 1 1 1 1 1 0 1 1 0 9PI499265 1 0 1 1 0 0 1 1 1 1 0 7PI508261 0 0 1 1 0 0 1 1 1 1 0 6PI508262 1 1 1 1 0 1 1 1 1 1 0 9PI508263 1 1 1 1 0 1 1 1 1 1 0 9PI508264 1 1 1 1 0 1 1 1 1 0 0 8PI511362 0 0 1 1 0 0 0 1 1 1 0 5PI511363 1 1 0 0 0 0 1 1 0 0 0 4PI511365 1 1 1 1 1 0 0 1 1 1 0 8PI511366 0 0 1 1 0 0 1 1 1 1 0 6PI511367 1 1 1 1 0 0 1 1 1 1 0 8PI511368 0 1 1 1 1 1 1 1 1 1 0 9PI511369 1 1 1 1 0 0 1 1 1 1 0 8PI511370 1 1 1 0 1 1 0 1 0 1 0 7PI511375 0 1 1 1 0 0 1 1 0 1 0 6PI560536 0 0 1 1 0 1 0 1 1 1 0 6PI560538 1 1 0 1 0 0 1 1 0 1 0 6PI560754 1 1 1 0 0 0 0 1 1 1 0 6PI560755 0 0 1 1 0 1 0 1 0 0 0 4PI574464 1 1 1 1 0 0 0 0 0 0 0 4PI574465 1 0 1 1 1 1 0 1 0 1 0 7PI574466 1 1 1 1 0 0 1 0 0 1 0 6PI574467 1 1 1 1 0 0 1 1 0 1 0 7PI574468 1 1 1 1 0 1 0 1 0 1 1 8PI574469 1 1 1 1 0 1 1 1 1 1 0 9PI603220 1 1 1 1 0 1 1 1 1 1 0 9PI603221 1 1 1 1 0 0 1 1 1 1 0 8PI603222 1 1 1 1 0 1 1 1 1 1 0 9PI603223 1 1 1 0 1 1 1 1 1 1 0 9PI603224 1 1 1 1 1 0 1 1 1 1 0 9PI603225 1 0 1 1 0 0 1 1 1 1 0 7AS60 Middle East 1 1 0 1 0 1 1 1 1 1 1 9

41 38 46 48 21 31 41 52 43 48 5Total

Iran

IranIranIranIran

AzerbaijanAzerbaijan,NaxcivanChina, HenanAfghanistan

Origin

AfghanistanIran

Supplementary Table 3 Detection of the 11 chromosome 6D-specific PM markers in 55accessions of Ae. tauschii . '1' and '0' indicate positive and negative PM marker, respectively

Turkey, HakkariTurkey, HakkariTurkey, HakkariTurkey, HakkariTurkey, HakkariTurkey, VanTurkey, VanTurkey, KarsTurkey, KarsTurkey, KarsTurkey, KarsChina, XinjiangFranceUnknownChina, XinjiangChina, XinjiangChina, ShaanxiChina, HenanPakistan, BaluchistanAfghanistan, FaryabPakistan, BaluchistanAfghanistan, ZabulAfghanistan, KabulIran, TehranIran, MazandaranIran, MazandaranUnknownTurkey, VanTurkey, Bitlis

Armenia

Iran, Mazandaran

Turkey, HakkariTurkey, HakkariAzerbaijanAzerbaijanGeorgiaRussia, Dagest

Russia, DagestTurkmenistan, Balkan

IndiaWestern AsiaWestern AsiaFormer Soviet Union