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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (10): 1604-1612.doi: 10.3724/SP.J.1006.2019.81091

• RESEARCH NOTES • Previous Articles    

Hexaploid ancestor of cultivated hexaploid oats inferred from high throughput GBS-SNP markers

ZHOU Ping-Ping1,2,YAN Hong-Hai1,2,3,*(),PENG Yuan-Ying2,*()   

  1. 1College of Life Sciences, China West Normal University, Nanchong 637009, Sichuan, China
    2Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
    3Collaboration and Innovation Center of Tissue Repair Material Engineering Technology, China West Normal University, Nanchong 637009, Sichuan, China
  • Received:2018-12-24 Accepted:2019-05-12 Online:2019-10-12 Published:2019-09-10
  • Contact: Hong-Hai YAN,Yuan-Ying PENG E-mail:Honghai_yan@outlook.com;yy.peng@hotmail.com
  • Supported by:
    This study was supported by the National Natural Science Foundation of China(31571739);the Doctoral Scientific Research Foundation of West China Normal University(17E081)

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Abstract:

Cultivated hexaploid oat is one of the most important cereal crops in the word, clearing its hexaploid ancestor would substantially improve the utilization efficiency of the genetic resources of oat, and therefore provide theoretical reference for oat germplasm conservation. In this study, 27 naked oats originated from China were sequenced by using GBS (genotyping by sequencing). SNPs were calling by combining the previously published GBS data of another 66 hexaploid oats including six species using UNEAK pipeline. A total of 8902 SNPs with MAF > 0.5, call rate > 0.95 were obtained. Four taxa with missing value greater than 15% were excluded for further analyses. Finally, 89 oat taxa meeting the requirement were used for PCA, STRUCTURE and UPGMA clustering analyses. All three analyses revealed some consistent results as follows: most wild hexaploid oats with the exception of A. sterilis showed strong genetic differentiations among each other, resulting in a grouping by species. Clustering analysis divided all the taxa into two clusters representing wild species and cultivated species, respectively, indicating some significant genetic differences existed between this two types of hexaploids. Within cultivated hexaploid oats, A. byzantina showed a high degree of genetic homogeneity with A. sativa, while naked oats differed from the others and formed an independent subcluster with close relationships with A. sativa. The taxa from the wild hexaploid species A. sterilis were mainly subdivided into two groups. Notably, these accessions of A. sterilis originated from western Asia (Iran-lraq-Turkey region) were clustered with the cultivated oats A. sativa and A. byzantina, suggesting that A. sativa and A. byzantina might be derived from progenitor germplasm from Iran-lraq-Turkey region. Another wild hexaploid species A. hybrida showed high degree of genetic homogeneity with A. fatua, is better to consider as a subspecies of A. fatua. This research contributes to clarifying the hexaploid origin of cultivated hexaploid oats.

Key words: cultivated hexaploid oat, GBS, domestication, origin, SNPs

Table 1

Materials used in this study including species name, accession number, origin and germplasm type"

种名a
Speciesa		 材料编号b
Accession numberb		 来源地
Origin		 种质类型
Germplasm type
A. byzantina CN 21305 Antalya, Turkey Cultivated material
A. byzantina CN 52992 Alabama, United States Cultivar
A. byzantina CN 53022 Kansas, United States Cultivar
A. byzantina CN 53030 Georgia, United State Cultivar
A. byzantina CN 53046 Georgia, United States Cultivar
A. byzantina CN 53811 Algeria Cultivated material
A. byzantina CN 88661 Colonia, Uruguay Cultivar
A. fatua CN 21269 Iraq Wild species
A. fatua CN 22544 Turkey Wild species
A. fatua CN 24167 Israel Wild species
A. fatua CN 24919 Iran Wild species
A. fatua CN 82124 Gansu, China Wild species
A. fatua PI 545459 South Dakota United States Wild species
A. fatua PI 560776 Van Turkey Wild species
A. fatua PI 544659 South Dakota, United States Wild species
A. hybrida CN 24884 Iran Wild species
A. hybrida CN 24885 Iran Wild species
A. hybrida CN 24926 Iran Wild species
A. hybrida CN 24930 Iran Wild species
A. hybrida CN 25241 Ordu, Turkey Wild species
A. occidentalis CN 23036 Canary Islands, Spain Wild species
A. occidentalis CN 25942 Morocco Wild species
A. occidentalis CN 4541 Canary Islands, Spain Wild species
A. occidentalis CN 4547 Canary Islands, Spain Wild species
A. occidentalis CN 25956 Morocco Wild species
A. occidentalis CN 26226 Canary Islands, Spain Wild species
A. sativa CN 18136 Ontario, Canada Cultivar
A. sativa CN 1954 Transvaal, South Africa Cultivated material
A. sativa CN 22319 Ethiopia Cultivated material
A. sativa CN 24549 Mugla, Turkey Cultivated material
A. sativa CN 2806 Alger, Algeria Cultivar
A. sativa CN 2807 Alabama, United States Cultivar
A. sativa CN 2897 Morocco Cultivated material
A. sativa CN 5220 Texas, United States Cultivar
A. sativa CN 5224 United States Cultivar
A. sativa CN 53006 Montana, United States Cultivar
A. sativa CN 64264 Heves, Hungary Cultivated material
A. sativa CN 21340 Kirsehir, Turkey Cultivated material
A. sativa CN 63538 Uttar Pradesh, India Landrace
A. sativa CN 64364 Gruzinsk, Georgia Landrace
A. sativa CN 64371 Chernivtsi, Ukraine Landrace
A. sativa CN 64377 Irkutsk, Russian Federation Cultivated material
A. sativa CN 64378 Dzavhan, Mongolia Cultivated material
A. sativa CN 64379 Khevsuretiya, Georgia Landrace
A. sativa CN 64399 Ankara, Turkey Landrace
A. sativa PI 40650 Gansu, China Landrace
A. sativa PI 636013 Heves, Hungary Landrace
A. sativa CN 63917 Gonder, Ethiopia Landrace
A. sativa ssp. nuda CN 53975 Illinois, United States Cultivar
种名a
Speciesa		 材料编号b
Accession numberb		 来源地
Origin		 种质类型
Germplasm type
A. sativa ssp. nuda ZY000674 Deqing, Yunnan, China Landrace
A. sativa ssp. nuda ZY000670 Lijiang, Yunnan, China Landrace
A. sativa ssp. nuda ZY000671 Lijiang, Yunnan, China Landrace
A. sativa ssp. nuda ZY000386 Fanshi, Shanxi, China Landrace
A. sativa ssp. nuda ZY000347 Lanxian, Shanxi, China Landrace
A. sativa ssp. nuda ZY000619 Huangzhong, Shanxi, China Landrace
A. sativa ssp. nuda ZY000383 Shenchi, Shanxi, China Landrace
A. sativa ssp. nuda ZY000290 Youyu, Shanxi, China Landrace
A. sativa ssp. nuda ZY000615 Minhe, Qinghai, China Landrace
A. sativa ssp. nuda ZY000607 Xining, Qinghai, China Landrace
A. sativa ssp. nuda ZY000012 Fengning, Hebei, China Landrace
A. sativa ssp. nuda ZY000021 Kangbao, Hebei, China Landrace
A. sativa ssp. nuda ZY000016 Zhuolu, Hebei, China Landrace
A. sativa ssp. nuda ZY000024 Shangyi, Hebei, China Landrace
A. sativa ssp. nuda ZY000232 Ningcheng, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000100 Huhhot, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000064 Jining, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000236 Keqi, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000083 Fengzhen, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000090 Zhuozi, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000241 Zuoqi, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000245 Shangdu, Inner Mongolia, China Landrace
A. sativa ssp. nuda ZY000632 Pingli, Shaanxi, China Landrace
A. sativa ssp. nuda ZY000625 Xunyang, Shaanxi, China Landrace
A. sativa ssp. nuda ZY000635 Ningshan, Shaanxi, China Landrace
A. sativa ssp. nuda ZY000622 Zhenping, Shaanxi, China Landrace
A. sativa ssp. nuda ZY000630 Zhenping, Shaanxi, China Landrace
A. sterilis CN 19783 Esfahan, Iran Wild species
A. sterilis CN 19991 Mazandaran, Iran Wild species
A. sterilis CN 20234 Iraq Wild species
A. sterilis CN 20235 Iraq Wild species
A. sterilis CN 20239 Iraq Wild species
A. sterilis CN 20242 Iraq Wild species
A. sterilis CN 20280 Iraq Wild species
A. sterilis CN 20349 Lebanon Wild species
A. sterilis CN 20625 Israel Wild species
A. sterilis CN 20982 Elazig, Turkey Wild species
A. sterilis CN 23417 Morocco Wild species
A. sterilis CN 24168 Israel Wild species
A. sterilis CN 24842 Siirt, Turkey Wild species
A. sterilis CN 25974 Morocco Wild species
A. sterilis CN 21178 Algeria Wild species
A. sterilis CN 22266 Ethiopia Wild species
A. sterilis CN 75938 Israel Wild species

Fig. 1

Distribution of MAF of obtained GBS markers The number above each bar represents the percentage of distribution of MAF of obtained GBS markers."

Fig. 2

PCA analysis of 89 Avena taxa based on 8902 GBS markers"

Fig. 3

STRUCTURE analysis based on 8902 GBS markers A: the delta K value reaches to the peak with K=4. B: the grouping results at the optimal K(4) value. Each color represents a group. Each vertical bar represents one of Avena taxa."

Fig. 4

Phylogenetic tree was constructed by using UPGMA method"

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